First report of major histocompatibility complex class II loci from the Amazon pink river dolphin (genus Inia)

We report the first major histocompatibility complex (MHC) DQB1 sequences for the two species of pink river dolphins (Inia geoffrensis and Inia boliviensis) inhabiting the Amazon and Orinoco River basins. These sequences were found to be polymorphic within the Inia genus and showed shared homology with cetacean DQB-1 sequences, especially, those of the Monodontidae and Phocoenidae. On the other hand, these sequences were shown to be divergent from those described for other riverine dolphin species, such as Lipotes vexillifer, the Chinese river dolphin. Two main conclusions can be drawn from our results: 1) the Mhc DQB1 sequences seem to evolve more rapidly than other nuclear sequences in cetaceans, and 2) differential positive selective pressures acting on these genes cause concomitant divergent evolutionary histories that derive phylogenetic reconstructions that could be inconsistent with widely accepted intertaxa evolutionary relationships elucidated with other molecular markers subjected to a neutral dynamics.     

Response of melon fly (Diptera: Tephritidae) to weathered SPLAT-Spinosad-Cue-Lure

Studies were conducted in Hawaii to measure attraction of male melon fly, Bactrocera cucurbitae (Coquillett) (Diptera: Tephritidae), to SPLAT-Cue-Lure (C-L) and SPLAT-Melo-Lure (M-L) (raspberry ketone formate). Direct field comparisons of SPLAT-C-L and SPLAT-M-L at low (5%) and high (20%) concentrations indicated few differences in attraction over a 15-wk period. Subsequently, only SPLAT-Spinosad-C-L (5%) was compared with Min-U-Gel C-L with naled (standard used in California) in weathering studies. Treatments were weathered for 1, 2, 4, and 8 wk in Riverside, CA, and shipped to Hawaii for attraction/toxicity tests under field and semifield conditions by using released males of controlled ages, and for feeding tests in the laboratory. In terms of attraction, SPLAT-Spinosad-C-L compared favorably to, or outperformed the current standard of Min-U-Gel-C-L with naled. In terms of toxicity, the cumulative 24-h mortality did not differ between the two insecticide-containing C-L treatments in field cage studies after 8 wk. However, in feeding studies in which individual males were exposed for 5 min to the different C-L treatments after 4 wk of weathering, SPLAT-Spinosad-C-L demonstrated reduced mortality compared with the Min-U-Gel-C-L with naled, suggesting reduced persistence of the spinosad material. Spinosad has low contact toxicity and when mixed with SPLAT and C-L offers a reduced risk alternative for control of B. cucurbitae and related C-L-responding species, without many of the negative effects to humans and nontargets of broad-spectrum contact poisons such as naled.     

Arabidopsis Uracil DNA Glycosylase (UNG) Is Required for Base Excision Repair of Uracil and Increases Plant Sensitivity to 5-Fluorouracil

Uracil in DNA arises by misincorporation of dUMP during replication and by hydrolytic deamination of cytosine. This common lesion is actively removed through a base excision repair (BER) pathway initiated by a uracil DNA glycosylase (UDG) activity that excises the damage as a free base. UDGs are classified into different families differentially distributed across eubacteria, archaea, yeast, and animals, but remain to be unambiguously identified in plants. We report here the molecular characterization of AtUNG (Arabidopsis thaliana uracil DNA glycosylase), a plant member of the Family-1 of UDGs typified by Escherichia coli Ung. AtUNG exhibits the narrow substrate specificity and single-stranded DNA preference that are characteristic of Ung homologues. Cell extracts from atung^−/− mutants are devoid of UDG activity, and lack the capacity to initiate BER on uracil residues. AtUNG-deficient plants do not display any apparent phenotype, but show increased resistance to 5-fluorouracil (5-FU), a cytostatic drug that favors dUMP misincorporation into DNA. The resistance of atung^−/− mutants to 5-FU is accompanied by the accumulation of uracil residues in DNA. These results suggest that AtUNG excises uracil in vivo but generates toxic AP sites when processing abundant U:A pairs in dTTP-depleted cells. Altogether, our findings point to AtUNG as the major UDG activity in Arabidopsis.     

Polychaetes (Annelida: Polychaeta) epibiont on Spondylus americanus (Bivalvia: Spondylidae) from Mochima National Park, Venezuela

The polychaetes epibiontic on the mollusk Spondylus americanus Hermann, 1781 were extracted from mollusks hand-collected at a depth of 10-30 m in Mochima National Park, Venezuela (10 degrees 21'00" N-63 degrees 23'36" W), using scuba diving gear. Forty-three polychaete species were identified on the 32 bivalve specimens analyzed. The Serpulidae included 17 especies, Eunicidae six and Terebellidae four species. The most abundant species were Hydroides dirampha M?rch, 1863, Pileolaria militaris Claparède, 1868 (Serpulidae), and Notaulax nudicollis Kr?yer, 1856 (Sabellidae). Their geographic affinitie were: 51.3% Atlantic, 28.2% widely distributed, 17.9% Amphiamericans, and 2.6% have a disjunct distribution.     

Research on arbuscular mycorrhizae in Mexico: an historical synthesis and future prospects

This review analyzes the historical development and advances of the research on arbuscular mycorrhizal fungi (AMF) in Mexico, as well as the prospects for future research. AMF-research has been focused on studying both diversity and functionality in several ecosystems of Mexico, but mainly in the tropical dry and rainy ecosystems, and the agricultural systems. In Mexico, 95 species of AMF have been recorded, representing 41% of the known species worldwide. The functional effects of AMF colonization have been examined in approximately 10% of the known host plants, but greenhouse studies continue to dominate over those conducted under field conditions. Even though research to date has been at the organismic level, further effort is needed due to the high plant diversity in Mexico. Studies on AMF biomass under field conditions and more taxonomic determination are required based on morphological features, biochemical determinations (fatty acids) and molecular tools. In addition, ecophysiological and ecological in situ studies would help in understanding the relationships among AMF, soil fauna, nutrients, and host plants. The contribution of AMF to ecosystemic processes is a priority line of research that requires an integrated approach (inter- and multidisciplinary) in order to define the role of AM symbioses for biogeochemical models. The creation of a Mexican mycorrhizal research network has and will help to identify the main challenges. Generating similar research protocols, and sharing databases and experience will assist mycorrhizologists working under the diverse financial and ecological contexts that is to be found in Mexico and Latin America.     

Direct and indirect landscape effects on Quercus ilex regeneration in heterogeneous environments

Understanding how plant–animal interactions shape plant regeneration is traditionally examined at local scales. In contrast, landscape ecologists working at regional scales often have to infer the mechanisms underlying vegetation patterns. In this study, we empirically explored how landscape attributes (patch connectivity, size, shape, irradiance, slope, and elevation) influence biotic interactions in 1- and 2-year seedlings and saplings of Quercus ilex. We combined field data and GIS-based information under a set of five connectivity scenarios, presuming low, intermediate, and long-distance seed dispersal. Our study emphasizes that landscape, apart from its direct effects on plants, plays a key, albeit indirect, role in plant demography through its effects on seed dispersers and predators. Moreover, the effects of landscape on recruitment differed between plant life stages. One-year seedlings and saplings appear to depend more on plant–animal interactions, while 2-year seedlings depend more on irradiance. Differences in patch connectivity resulted in direct and indirect effects on biotic interactions, which, in turn, produced contrasting positive and negative effects on regeneration at different stages of the life cycle. While jays and wild boars seem crucial to all life stages and most of the connectivity scenarios, rodents and herbivores affected only 1-year seedlings and saplings, respectively, and only a few of the connectivity scenarios. By simultaneously including an ensemble of explanatory factors, our study emphasizes that regeneration depends on a set of key drivers, both abiotic (i.e. irradiance) and biotic (i.e. jays and wild boars), whose effects are greatly modulated by landscape traits.     

A Simple Strain Typing Assay for Trypanosoma cruzi: Discrimination of Major Evolutionary Lineages from a Single Amplification Product

Background

Trypanosoma cruzi is the causative agent of Chagas'' Disease. The parasite has a complex population structure, with six major evolutionary lineages, some of which have apparently resulted from ancestral hybridization events. Because there are important biological differences between these lineages, strain typing methods are essential to study the T. cruzi species. Currently, there are a number of typing methods available for T. cruzi, each with its own advantages and disadvantages. However, most of these methods are based on the amplification of a variable number of loci.

Methodology/Principal Findings

We present a simple typing assay for T. cruzi, based on the amplification of a single polymorphic locus: the TcSC5D gene. When analyzing sequences from this gene (a putative lathosterol/episterol oxidase) we observed a number of interesting polymorphic sites, including 1 tetra-allelic, and a number of informative tri- and bi-allelic SNPs. Furthermore, some of these SNPs were located within the recognition sequences of two commercially available restriction enzymes. A double digestion with these enzymes generates a unique restriction pattern that allows a simple classification of strains in six major groups, corresponding to DTUs TcI–TcIV, the recently proposed Tcbat lineage, and TcV/TcVI (as a group). Direct sequencing of the amplicon allows the classification of strains into seven groups, including the six currently recognized evolutionary lineages, by analyzing only a few discriminant polymorphic sites.

Conclusions/Significance

Based on these findings we propose a simple typing assay for T. cruzi that requires a single PCR amplification followed either by restriction fragment length polymorphism analysis, or direct sequencing. In the panel of strains tested, the sequencing-based method displays equivalent inter-lineage resolution to recent multi- locus sequence typing assays. Due to their simplicity and low cost, the proposed assays represent a good alternative to rapidly screen strain collections, providing the cornerstone for the development of robust typing strategies.     

The Pleistocene glacial cycles shaped the historical demography and phylogeography of a pine fungal endophyte

The fungal endophyte Lophodermium nitens is an obligate symbiont of soft pines inhabiting only two pine species in Mexico with a broad distribution of geographically isolated populations. A previous study for the hosts indicated a main east–west subdivision with recurrent gene flow within these regions and demographic expansion of populations. We took these patterns as null hypotheses to test for the demography and phylogeographical patterns of the fungus, given the obligatory relationship of the endophyte to the host and its reduced capacity for long-distance dispersal. For this purpose, we employed two nuclear DNA loci, fragments of the actin and chitin synthase I genes. Both loci showed high genetic variation, consisting of private single-copy alleles, as well as few ones at high frequency that were shared among almost all populations. In order to distinguish between shared polymorphism due to incomplete lineage sorting and gene flow posterior to population divergence, we applied the coalescent-based Isolation–Migration (IM) model. We found patterns of gene flow and isolation similar to those of the hosts as well as signs of population expansion. Mean migration time and divergence time estimates fell within the Pleistocene, previous to Last Glacial Maximum. The results presented here for L. nitens emphasize the potential use of endophytic fungi to deepen the knowledge of historical patterns and processes of their host plants.     

Diagnostic Peptide Discovery: Prioritization of Pathogen Diagnostic Markers Using Multiple Features

The availability of complete pathogen genomes has renewed interest in the development of diagnostics for infectious diseases. Synthetic peptide microarrays provide a rapid, high-throughput platform for immunological testing of potential B-cell epitopes. However, their current capacity prevent the experimental screening of complete “peptidomes”. Therefore, computational approaches for prediction and/or prioritization of diagnostically relevant peptides are required. In this work we describe a computational method to assess a defined set of molecular properties for each potential diagnostic target in a reference genome. Properties such as sub-cellular localization or expression level were evaluated for the whole protein. At a higher resolution (short peptides), we assessed a set of local properties, such as repetitive motifs, disorder (structured vs natively unstructured regions), trans-membrane spans, genetic polymorphisms (conserved vs. divergent regions), predicted B-cell epitopes, and sequence similarity against human proteins and other potential cross-reacting species (e.g. other pathogens endemic in overlapping geographical locations). A scoring function based on these different features was developed, and used to rank all peptides from a large eukaryotic pathogen proteome. We applied this method to the identification of candidate diagnostic peptides in the protozoan Trypanosoma cruzi, the causative agent of Chagas disease. We measured the performance of the method by analyzing the enrichment of validated antigens in the high-scoring top of the ranking. Based on this measure, our integrative method outperformed alternative prioritizations based on individual properties (such as B-cell epitope predictors alone). Using this method we ranked 10 million 12-mer overlapping peptides derived from the complete T. cruzi proteome. Experimental screening of 190 high-scoring peptides allowed the identification of 37 novel epitopes with diagnostic potential, while none of the low scoring peptides showed significant reactivity. Many of the metrics employed are dependent on standard bioinformatic tools and data, so the method can be easily extended to other pathogen genomes.