Genomic changes underlying host specialization in the bee gut symbiont Lactobacillus Firm5

Bacteria that engage in long‐standing associations with particular hosts are expected to evolve host‐specific adaptations that limit their capacity to thrive in other environments. Consistent with this, many gut symbionts seem to have a limited host range, based on community profiling and phylogenomics. However, few studies have experimentally investigated host specialization of gut symbionts and the underlying mechanisms have largely remained elusive. Here, we studied host specialization of a dominant gut symbiont of social bees, Lactobacillus Firm5. We show that Firm5 strains isolated from honey bees and bumble bees separate into deep‐branching host‐specific phylogenetic lineages. Despite their divergent evolution, colonization experiments show that bumble bee strains are capable of colonizing the honey bee gut. However, they were less successful than honey bee strains, and competition with honey bee strains completely abolished their colonization. In contrast, honey bee strains of divergent phylogenetic lineages were able to coexist within individual bees. This suggests that both host selection and interbacterial competition play important roles in host specialization. Using comparative genomics of 27 Firm5 isolates, we found that the genomes of honey bee strains harbour more carbohydrate‐related functions than bumble bee strains, possibly providing a competitive advantage in the honey bee gut. Remarkably, most of the genes encoding carbohydrate‐related functions were not conserved among the honey bee strains, which suggests that honey bees can support a metabolically more diverse community of Firm5 strains than bumble bees. These findings advance our understanding of the genomic changes underlying host specialization.     

Genome-wide studies of histone demethylation catalysed by the fission yeast homologues of mammalian LSD1

In order to gain a more global view of the activity of histone demethylases, we report here genome-wide studies of the fission yeast SWIRM and polyamine oxidase (PAO) domain homologues of mammalian LSD1. Consistent with previous work we find that the two S. pombe proteins, which we name Swm1 and Swm2 (after SWIRM1 and SWIRM2), associate together in a complex. However, we find that this complex specifically demethylates lysine 9 in histone H3 (H3K9) and both up- and down-regulates expression of different groups of genes. Using chromatin-immunoprecipitation, to isolate fragments of chromatin containing either H3K4me2 or H3K9me2, and DNA microarray analysis (ChIP-chip), we have studied genome-wide changes in patterns of histone methylation, and their correlation with gene expression, upon deletion of the swm1(+) gene. Using hyper-geometric probability comparisons we uncover genetic links between lysine-specific demethylases, the histone deacetylase Clr6, and the chromatin remodeller Hrp1. The data presented here demonstrate that in fission yeast the SWIRM/PAO domain proteins Swm1 and Swm2 are associated in complexes that can remove methyl groups from lysine 9 methylated histone H3. In vitro, we show that bacterially expressed Swm1 also possesses lysine 9 demethylase activity. In vivo, loss of Swm1 increases the global levels of both H3K9me2 and H3K4me2. A significant accumulation of H3K4me2 is observed at genes that are up-regulated in a swm1 deletion strain. In addition, H3K9me2 accumulates at some genes known to be direct Swm1/2 targets that are down-regulated in the swm1Delta strain. The in vivo data indicate that Swm1 acts in concert with the HDAC Clr6 and the chromatin remodeller Hrp1 to repress gene expression. In addition, our in vitro analyses suggest that the H3K9 demethylase activity requires an unidentified post-translational modification to allow it to act. Thus, our results highlight complex interactions between histone demethylase, deacetylase and chromatin remodelling activities in the regulation of gene expression.     

Eosinophil peroxidase oxidation of thiocyanate. Characterization of major reaction products and a potential sulfhydryl-targeted cytotoxicity system

Although the pseudohalide thiocyanate (SCN(-)) is the preferred substrate for eosinophil peroxidase (EPO) in fluids of physiologic halide composition, the product(s) of this reaction have not been directly identified, and mechanisms underlying their cytotoxic potential are poorly characterized. We used nuclear magnetic resonance spectroscopy (NMR), electrospray ionization mass spectrometry, and quantitative chemical analysis to identify the principal reaction products of both the EPO/SCN(-)/H(2)O(2) system and activated eosinophils as roughly equimolar amounts of OSCN(-) (hypothiocyanite) and OCN(-) (cyanate). Red blood cells exposed to increasing concentrations of OSCN(-)/OCN(-) are first depleted of glutathione, after which glutathione S-transferase and glyceraldehyde-3-phosphate dehydrogenase then ATPases undergo sulfhydryl (SH) reductant-reversible inactivation before lysing. OSCN(-)/OCN(-) inactivates red blood cell membrane ATPases 10-1000 times more potently than do HOCl, HOBr, and H(2)O(2). Exposure of glutathione S-transferase to [(14)C]OSCN(-)/OCN(-) causes SH reductant-reversible disulfide bonding and covalent isotope labeling. We propose that EPO/SCN(-)/H(2)O(2) reaction products comprise a potential SH-targeted cytotoxic system that functions in striking contrast to HOCl, the highly but relatively indiscriminantly reactive product of the neutrophil myeloperoxidase system.     

Box-Jenkins analysis for shark landings in Costa Rica

Sharks are highly vulnerable to intense and prolonged fishery extraction. This article analyzes the data on shark landings from the artisan fishing fleet on Costa Rica's Pacific coast between 1988 and 1997. The data come from an invoicing system administered by the Costa Rican Fisheries Institute (Instituto Costarricense de la Pesca y Acuacultura, INCOPESCA). Pacific coast shark fishing during the period under study represented approximately 20% of the total national fisheries volume. According to data from the invoicing system, the Northern Pacific region was the most productive, reporting 58% of the shark catch nationwide. Within this region, shark fishing in Papagayo Gulf represented 91% and 53% of the landings by fishery region and nationwide, respectively. The mid-sized and advanced (length of boat > 10 meters) artisan fishing fleets reported 96% of the shark catches in the zone. The study of shark fisheries in the Papagayo Gulf zone is crucial for an understanding of fishery dynamics for this resource at the national level. A monthly chronological series was constructed with the landings in the Papagayo Gulf zone, and a Univariate Box-Jenkins (UBJ) Model was estimated for first-order moving averages MA(1) with a seasonal component of the Yt = lamda(t-1) + gammaS12 + a(t) type.     

Effect of a pharmacological activation of PPAR on the expression of RAR and TR in rat liver

It has recently been shown that high-fat diets induce the expression of peroxisome proliferator-activated receptor (PPAR) with a concomitant decrease in expression of retinoic acid (RAR) and triiodothyronine (TR) receptors in rat liver. The authors have suggested that PPAR activation may be responsible for these modifications in nuclear receptor expression. With the aim of gaining further insight into a possible relationship between the patterns of expression of these receptors, we have examined, using a pharmacological model, the effect of a strong and specific PPAR activation induced by bezafibrate, a peroxisome proliferator agent. Activation of PPAR was evaluated by quantifying PPARα mRNA and acyl-CoA oxidase mRNA. The expression of RAR and TR was determined by assaying the binding properties of these nuclear receptors and by quantifying the mRNA level of RARβ and TRα₁,β₁ isoforms. After a 10 day treatment of young rats, induction of PPAR (PPARα mRNA was increased by 40% [P< 0.05 and acyl-CoA oxidase mRNA by 411% [P<0.001]) and a concomitant decrease of RAR and TR expression (Maximal Binding Capacity was decreased by 21 and 26%, respectively [P<0.05]) in the liver was observed. RXRα mRNA expression was unchanged by treatment. Cross-talk between RAR, TR and PPAR signalling pathways may be implicated in the new patterns of nuclear receptor expression observed. The decreased expression of RAR and TR reported here could provide a novel element for the understanding of the link between PPAR and tumorigenesis in rat liver.     

Abundance and morphometry of tuberculosa Anadara and A. similis (Mollusca: Bivalvia) in the Manglar de Purruja, Dulce Gulf, Costa Rica

The density, population, length, yield and sex proportion of the mollusks Anadara tuberculosa and A. similis were studied in Bahía de Golfito, Golfo Dulce, Pacific coast of Costa Rica from February 1998 to February 1999. A. tuberculosa was more abundant (0.9 units m(-2)), than A. similis (0.2 units m(-2)); the highest abundance was found at the canal mouths. The average lengths were 43.3 mm for A. tuberculosa and 42.8 mm for A. similis (both under the Costa Rican legal minimal length for exploitation: 47 mm). Maximum lengths were measured in the middle and upstream Canal Mayor, respectively: 43.0 mm and 43.4 mm. The correlation between length and fresh weight was 0.81 (Pearson). The average total weights were 26.2 g for A. tuberculosa and 19.1 g for A. similis. The condition index (a meat yield measurement) was higher in A. similis (21.2%) than in A. tuberculosa (17.2%). The maximum yield for both species lies in the 31-35 mm range. The male ratio was 43.7%. A species recovery plan is urgent because these results suggest both a decrease in density and illegal exploitation.     

Melting curve analysis of SNPs (McSNP): a gel-free and inexpensive approach for SNP genotyping

High-throughput methods for assaying DNA variation require two important steps: (i) discriminating the variation and (ii) detecting the signal. In this report, we describe a novel SNP genotyping method that we refer to as melting curve analysis of SNPs (McSNP). McSNP combines a classic approach for discriminating alleles, restriction enzyme digestion, with a more recent method for detecting DNA fragments, melting curve analysis. Melting curve analysis is performed by slowly heating DNA fragments in the presence of the dsDNA-specific fluorescent dye SYBR Green I. As the sample is heated, fluorescence rapidly decreases when the melting temperature of a particular fragment is reached. We show that it is possible to determine the composition of simple mixtures of DNA fragments, such as those that result from restriction enzyme digestions of short PCR products. McSNP is well suited for high-throughput genotyping because 96 samples can be analyzed and automatically scored in 20 min. Our results clearly demonstrate that McSNP is a simple, inexpensive, and accurate means of genotyping SNP variation.     

Influence of boron and calcium on the tolerance to salinity of nitrogen-fixing pea plants

The effects of different levels of B (from 9.3 to 93 M B) and Ca (from 0.68 to 5.44 mM Ca) on plant development, nitrogen fixation, and mineral composition of pea (Pisum sativum L. cv. Argona) grown in symbiosis with Rhizobium leguminosarum bv. viciae 3841 and under salt stress, were analysed. The addition of extra B and extra Ca to the nutrient solution prevented the reduction caused by 75 mM NaCl of plant growth and the inhibition of nodulation and nitrogen fixation. The number of nodules recovered by the increase of Ca concentration at any B level, but only nodules developed at high B and high Ca concentrations could fix nitrogen. Addition of extra B and Ca during plant growth restored nodule organogenesis and structure, which was absolutely damaged by high salt. The increase in salt tolerance of symbiotic plants mediated by B and Ca can be co-related with the recovery of the contents of some nutrients. Salinity produced a decrease of B and Ca contents both in shoots and in nodulated roots, being increased by the supplement of both elements in the nutrient solution. Salinity also reduced the content in plants of other nutrients important for plant development and particularly for symbiotic nitrogen fixation, as K and Fe. A balanced nutrition of B and Ca (55.8 M B, 2.72 mM Ca) was able to counter-act the deficiency of these nutrients in salt-stressed plants, leading to a huge increase in salinity tolerance of symbiotic pea plants. The necessity of nutritional studies to successfully cultivate legumes in saline soils is discussed and proposed.     

Relative frequency of Boophilus microplus (Acari: Ixodidae) in bovines (Bos taurus and B. indicus) in 8 ecological zones of Costa Rica

The research on the relative abundancy of Boophilus microplus took place in ten farms, distributed in eight ecological zones (EZ) and two rainfall systems of Costa Rica. Monthly visits were made to pick up ticks larger than 4 mm from the right side of the animals. The total number of ticks was increased by two and divided between the total of sampled bovines per farm. Farm visits were adjusted to animals bath to allow the recovery of the tick population. B. microplus was detected in all sampled farms throughout the year. Media comparison statistic analyses were made and no differences were found among EZ, farms and seasons. On the contrary, there were important statistical differences between rainfall systems. The rainfall system 1, that included rain seasonality, showed larger tick infestations (p = 0.03). An isothermal and low variability regarding relative humidity situations were present in some of the areas included in this research. Bath intensity was lower to other past studies. Even though no differences were found between production systems, it is important to emphasize that bath intensity was higher in european cattle farms, in comparison to others of the same EZ, but of crossbred. A tick manual removable system was recommended in dual-purpose and specialized dairy farms with no more than 30-35 animals, as an alternative feasible system that significantly reduced acaricide use.