Latitudinal and bathymetric distribution of the most abundant and frequent species in the shrimp bycatch from the Gulf of California, Mexico

The Gulf of California is one of the most mega-diverse regions in the world, for which few fishery information is available. We present here latitudinal and bathymetric distribution of the most abundant and frequent bycatch species from the Gulf of California. The samples were obtained from a total of 111 hauls taken during seven research cruises of the closed shrimp season (2002-2005-2007), and also, from research cruises made at depths up to 90 m. Due to the high variety species in this experimental shrimp bycatch, only those with highest biological value index (BVI) were selected. A total of fifteen species had the highest BVI and represented about 60% of the total abundance. A total of 16 508 organisms were analyzed, representing 243 fish, crustacean, mollusk and echinoderm species. Fish were the most abundant, being the most frequent species: Urobatis halleri, Synodus scituliceps, Diplectrum pacificum, Haemulopsis nitidus and Eucinostomus argenteus. A wide latitudinal distribution of these species along the study area, as well as a bathymetric distribution from 9 to 67 m depth, was observed. Two of these species were found at 325 m depth. Due to the wide bathymetric distribution obtained, total abundances and sizes for each species by depth strata should be determined, and one can assume that deeper than 25 m, the capture of these species decreases, and these areas can be used as natural repopulation areas, for depths where they are mainly captured by the commercial shrimp fishery.     

A unifying framework for assessing changes in life expectancy associated with changes in mortality: the case of violent deaths

For over forty years, demographers have worked intensely to develop methods that assess a gain in life expectancy from a reduction in mortality, either hypothetical or observed. This considerable body of research was motivated by assessing the gains in life expectancy when mortality declined in a particular manner and determining the contribution of a cause of death in observed changes in life expectancy over time. As yet, there has been no framework unifying this important demographic work. In this paper, we provide a unifying framework for assessing the change in life expectancy given a change in age- and cause-specific mortality. We consider both conceptualizations of mortality change—counterfactual assessment of a hypothetical change and a retrospective assessment of an observed change. We apply our methodology to violent deaths, the leading cause of death among young adults, and show that realistic targeted reductions could have important impacts on life expectancy.     

Determination of the amino acid sequence requirements for catalysis by the highly proficient orotidine monophosphate decarboxylase

Orotidine 5'-monophosphate decarboxylase (ODCase) catalyzes the decarboxylation of orotidine 5'-monophosphate to uridine 5'-monophosphate during pyrimidine nucleotide biosynthesis. This enzyme is one of the most proficient known, exhibiting a rate enhancement of over 17 orders of magnitude over the uncatalyzed rate. An interesting question is whether the high proficiency of ODCase is associated with a highly optimized sequence of active site residues. This question was addressed by randomizing 24 residue positions in and around the active site of the E. coli ODCase (pyrF) by site-directed mutagenesis. The libraries of mutants were selected for function from a multicopy plasmid or by single-copy replacement at the pyrF locus on the E. coli chromosome. Stringent sequence requirements for function were found for the mutants expressed from the chromosomal pyrF locus. Six positions were not tolerant of substitutions and several others accepted very limited substitutions. In contrast, all positions could be substituted to some extent when the library mutants were expressed from a multicopy plasmid. For the conserved quartet of charged residues Lys44-Asp71-Lys73-Asp76, a cysteine substitution was found to provide function at positions 71 and 76. A lower pK(a) for both cysteine mutants supports a mechanism whereby the thiolate group of cysteine substitutes for the negatively charged aspartate side chain. The partial function mutants such as D71C and D76C exhibit reduced catalytic efficiency relative to wild type but nevertheless provide a rate enhancement of 15 orders of magnitude over the uncatalyzed rate indicating the catalytic proficiency of the enzyme is robust and tolerant of mutation.     

Effects of a DNA vaccine in an animal model of Alternaria alternata sensitivity

Sensitivity to the fungus Alternaria is associated with asthma persistence and severity. Current therapeutic options for treating Alternaria-induced airway inflammation are limited. In this study, Brown Norway rats are used to study the effectiveness of a DNA-based vaccine delivered to the airway in attenuating the response to a major Alternaria allergen, rAlt a 2. Compared to untreated sensitized animals, or animals receiving an “out-of-frame” DNA-based vaccine, animals treated with “in-frame” DNA vaccine showed an attenuation in specific IgE antibody titers to rAlt a 2, an increase in IgG^2b (a Th1 response), a reduction in spontaneous IL-13 release by peribronchial lymph node cell suspensions, and an attenuation in the decrease in total lung capacity 72 h post-allergen challenge. Further, histopathologic examination of the lung tissues revealed reduced pulmonary inflammation post-allergen challenge in the DNA-vaccine-treated compared to sensitized, untreated animals. We conclude that a DNA-based vaccine delivered to the airway significantly influences the immunologic, pulmonary physiologic, and histological alterations induced by challenge with a major Alternaria allergen, rAlt a 2, in sensitized animals.     

Vagotomy enhances experimental metastases of 4THMpc breast cancer cells and alters substance P level

We have previously demonstrated that inactivation of capsaicin-sensitive sensory neurons enhances lung and heart metastases of breast carcinoma. Because a significant part of sensory innervation of lung tissue is supplied by the vagus nerve, we here examined the effects of unilateral mid-cervical vagotomy in the metastases of 4THMpc breast carcinoma and tissue Substance P (SP) levels. Balb-c mice were injected orthotopically with 4THMpc cells 1 week after vagotomy. Animals were sacrificed 27-30 days after injection of 4THMpc cells and the extent of metastases was determined. Unilateral vagotomy, right or left significantly increased the lung, liver and kidney metastases without altering the growth rate of the primary tumor. Heart metastases were increased only following left vagotomy. The changes in SP levels were somewhat surprising such that vagotomy actually increased while sham-operation decreased SP levels in lung. The effect of sham-operation was reversed by unilateral vagotomy demonstrating that vagal activity decreases total SP levels in the lung. Increased SP levels might be due to decreased degradation of the peptide. Presence of the tumor markedly increased SP level in the lung, which was more prominent in vagotomized animals. These results provide evidence that vagal activity may protect against metastatic disease.     

Protein disulfide isomerase

During the maturation of extracellular proteins, disulfide bonds that chemically cross-link specific cysteines are often added to stabilize a protein or to join it covalently to other proteins. Disulfide formation, which requires a change in the covalent structure of the protein, occurs as the protein folds into its three-dimensional structure. In the eukaryotic endoplasmic reticulum and in the bacterial periplasm, an elaborate system of chaperones and folding catalysts ensure that disulfides connect the proper cysteines and that the folding protein does not make improper interactions. This review focuses specifically on one of these folding assistants, protein disulfide isomerase (PDI), an enzyme that catalyzes disulfide formation and isomerization and a chaperone that inhibits aggregation.     

Qualitative stability and ambiguity in model ecosystems

Qualitative analysis of stability in model ecosystems has previously been limited to determining whether a community matrix is sign stable or not with little analytical means to assess the impact of complexity on system stability. Systems are seen as either unconditionally or conditionally stable with little distinction and therefore much ambiguity in the likelihood of stability. First, we reexamine Hurwitz's principal theorem for stability and propose two "Hurwitz criteria" that address different aspects of instability: positive feedback and insufficient lower-level feedback. Second, we derive two qualitative metrics based on these criteria: weighted feedback (wF(n)) and weighted determinants (wDelta(n)). Third, we test the utility of these qualitative metrics through quantitative simulations in a random and evenly distributed parameter space in models of various sizes and complexities. Taken together they provide a practical means to assess the relative degree to which ambiguity has entered into calculations of stability as a result of system structure and complexity. From these metrics we identify two classes of models that may have significant relevance to system research and management. This work helps to resolve some of the impasse between theoretical and empirical discussions on the complexity and stability of natural communities.