Sequence and functional analyses of Haemophilus spp. genomic islands

Background

A major part of horizontal gene transfer that contributes to the diversification and adaptation of bacteria is facilitated by genomic islands. The evolution of these islands is poorly understood. Some progress was made with the identification of a set of phylogenetically related genomic islands among the Proteobacteria, recognized from the investigation of the evolutionary origins of a Haemophilus influenzae antibiotic resistance island, namely ICEHin1056. More clarity comes from this comparative analysis of seven complete sequences of the ICEHin1056 genomic island subfamily.

Results

These genomic islands have core and accessory genes in approximately equal proportion, with none demonstrating recent acquisition from other islands. The number of variable sites within core genes is similar to that found in the host bacteria. Furthermore, the GC content of the core genes is similar to that of the host bacteria (38% to 40%). Most of the core gene content is formed by the syntenic type IV secretion system dependent conjugative module and replicative module. GC content and lack of variable sites indicate that the antibiotic resistance genes were acquired relatively recently. An analysis of conjugation efficiency and antibiotic susceptibility demonstrates that phenotypic expression of genomic island-borne genes differs between different hosts.

Conclusion

Genomic islands of the ICEHin1056 subfamily have a longstanding relationship with H. influenzae and H. parainfluenzae and are co-evolving as semi-autonomous genomes within the 'supragenomes' of their host species. They have promoted bacterial diversity and adaptation through becoming efficient vectors of antibiotic resistance by the recent acquisition of antibiotic resistance transposons.     

Assessing the availability of life cycle assessments in Austria

The International Journal of Life Cycle Assessment - This study aims to present the availability of studies that are related to life cycle assessments (LCA) in Austria since 2000. This study also...     

Desert bighorn sheep habitat selection,group size,and mountain lion predation risk

Bighorn sheep (Ovis canadensis) evolved for thousands of years in the presence of numerous predators, including mountain lions (Puma concolor). Bighorn sheep have presumably developed predator avoidance strategies; however, the effectiveness of these strategies in reducing risk of mountain lion predation is not well understood. These strategies are of increasing interest because mountain lion predation on bighorn sheep has been identified as a leading cause of mortality in some sheep populations. Therefore, we investigated how mountain lions affect both bighorn sheep habitat selection and risk of mortality in Arizona, USA. We used 2 approaches to investigate the predator-prey relationship between mountain lions and bighorn sheep. We fit 103 bighorn sheep (81 females and 22 males) with global positioning system radio-collars in 2 Arizona populations from 2013 to 2017, and used a negative binomial resource selection probability function to evaluate whether bighorn sheep selected for habitat features in accordance with presumed predator avoidance strategies, including terrain ruggedness, slope, topographic position, and horizontal obstruction, in 2 seasons (winter and summer). We then estimated how habitat features such as terrain ruggedness, slope, horizontal obstruction, and group size, influence the risk of mortality due to mountain lion predation using an Andersen-Gill proportional hazards model. Generally, both sexes selected areas with lower horizontal obstruction and intermediate ruggedness and slope, but selection patterns differed between seasons and sexes. The use of more rugged areas and steeper slopes decreased the risk of mortality due to mountain lion predation, consistent with presumed predator avoidance strategies. Increased group size decreased risk of bighorn sheep mortality due to mountain lion predation but this effect became marginal at approximately 10 individuals/group. We did not identify a relationship between horizontal obstruction and bighorn sheep mortality risk. Our findings can be used in habitat and population management decisions such as the prioritization of habitat restoration sites or selection of translocation sites. In addition, we suggest that augmentation of low-density bighorn sheep populations may reduce mountain lion predation risk by increasing group size, and that releasing large groups of bighorn sheep in population augmentation and reintroduction efforts may help to reduce mountain lion predation.     

Effects of twinning, birth size, and postnatal growth on glucose tolerance and hypothalamic-pituitary-adrenal function in postpubertal sheep

Low birth weight is associated with postnatal physiological changes, including impaired glucose tolerance and increased cortisol secretion, that may predispose to disease in adulthood. Twins are born lighter than singletons, but there are conflicting data regarding the association between birth weight and postnatal physiology in twins. We studied glucose tolerance and ACTH and cortisol responses to a combined corticotropin-releasing hormone and arginine vasopressin (CRH + AVP) challenge in postpubertal female twin (n = 7 twin pairs) and singleton (n = 13) sheep from the same flock. There were no differences in glucose tolerance between twins and singletons and no association with birth weight. Twins had a greater ACTH (P < 0.05), but not cortisol, response to CRH + AVP than singletons. ACTH area under the curve was inversely related to birth weight in both singletons [R(2) = 0.31, P = 0.05; -8,311 (SD 3,736) pg.min.ml(-1).kg(-1)] and twins (R(2) = 0.49); in twins, this was due to the within-twin pair rather than the between-twin pair coefficient in the regression analysis [P = 0.02, -26,856 (9,806) vs. P = 0.1, 8,619 (4,950) pg.min.ml(-1).kg(-1)]. We conclude that the reduced fetal growth in twins has postnatal consequences for hypothalamic-pituitary-adrenal function and that this is determined by factors specific to the fetus (within-twin pair) rather than by shared maternal factors (between-twin pair). Studies investigating the associations between fetal growth and postnatal outcomes in twins benefit from an appropriate singleton control group and from analyses evaluating the contribution from both between- and within-pair coefficients in twins.     

Weak self-association in a carbohydrate system

The physiological importance of weak interactions between biological macromolecules (molar dissociation constants >10 microM) is now well recognized, particularly with regard to cell adhesion and immunological phenomena, and many weak interactions have been measured for proteins. The concomitant importance of carbohydrate-carbohydrate interactions has also been identified, although no weak interaction between pure carbohydrate systems has ever been measured. We now demonstrate for the first time to our knowledge using a powerful probe for weak interactions--sedimentation velocity in the analytical ultracentrifuge--that at least some carbohydrates (from the class of polysaccharides known as heteroxylans and demonstrated here to be biologically active) can show well-defined weak self-interactions of the "monomer-dimer" type frequently found in protein systems. The weak interaction between the heteroxylans is shown from a temperature dependence study to be likely to be hydrophobic in nature.     

Inhibition of Agrobacterium-induced cell death by antiapoptotic gene expression leads to very high transformation efficiency of banana

The death of plant cells in culture following exposure to Agrobacterium tumefaciens remains a major obstacle in developing Agrobacterium-mediated transformation into a highly efficient genotype-independent technology. Here, we present evidence that A. tumefaciens exposure induces cell death in banana cell suspensions. More than 90% of embryogenic banana cells died after exposure to A. tumefaciens and cell death was accompanied by a subset of features associated with apoptosis in mammalian cells, including DNA laddering, fragmentation, and formation of apoptotic-like bodies. Importantly, these cellular responses were inhibited in cells expressing the animal antiapoptosis genes Bcl-xL, Bcl-2 3' untranslated region, and CED-9. Inhibition of cell death resulted in up to 90% of cell clumps transformed with Bcl-xL, a 100-fold enhancement over vector controls, approaching the transformation and regeneration of every "transformable" cell. Similar results using sugarcane, a crop plant known for recalcitrance to Agrobacterium transformation, suggest that antiapoptosis genes may inhibit these phenomena and increase the transformation frequency of many recalcitrant plant species, including the major monocot cereal crop plants. Evidence of inhibition of plant cell death by cross-kingdom antiapoptotic genes also contributes to the growing evidence that genes for control of programmed cell death are conserved across wide evolutionary distances, even though these mechanisms are not well understood in plants.     

Genomic investigation of piglet resilience following porcine epidemic diarrhea outbreaks

Porcine epidemic diarrhea virus (PEDV) belongs to the Coronaviridae family and causes malabsorptive watery diarrhea, vomiting, dehydration and imbalanced blood electrolytes in pigs. Since the 1970s, PED outbreaks have become a source of problems in pig producing countries all over the world, causing large economic losses for pig producers. Although the infection in adults is not fatal, in naïve suckling piglets mortality is close to 100%. In this study, we investigated genome‐wide differences between dead and recovered suckling piglets from commercial farms after PED outbreaks. Samples from 262 animals (156 dead and 106 recovered) belonging to several commercial lines were collected from five different farms in three different countries (USA, Canada and Germany) and genotyped with the porcine 80K SNP chip. Mean F_st value was calculated in 1‐Mb non‐overlapping windows between dead and recovered individuals, and the results were normalized to find differences within the comparison. Seven windows with high divergence between dead and recovered were detected—five on chromosome 2, one on chromosome 4 and one on chromosome 15—in total encompassing 152 genes. Several of these genes are either under‐ or overexpressed in many virus infections, including Coronaviridae (such as SARS‐CoV). A total of 32 genes are included in one or more Gene Ontology terms that can be related to PED development, such as Golgi apparatus, as well as mechanisms generally linked to resilience or diarrhea development (cell proliferation, ion transport, ATPase activity). Taken together this information provides a first genomic picture of PEDV resilience in suckling piglets.     

Promoters derived from banana bunchy top virus DNA-1 to −5 direct vascular-associated expression in transgenic banana (Musa spp.)

The intergenic regions of banana bunchy top virus (BBTV) DNA-1 to -5 were fused to the green fluorescent protein (GFP) and uidA reporter genes and assessed for promoter activity in transgenic banana (Musa spp. cv. Bluggoe). Promoter activity associated with the BBTV-derived promoters was transgene dependent with greatest activity observed using the GFP reporter. The BBTV promoters (BT1 to BT5) directed expression primarily in vascular-associated cells, although levels of activity varied between individual promoters. Promoters BT4 and BT5 directed the highest levels of GFP expression, while activity from BT1, BT2 and BT3 promoters was considerably weaker. Intron-mediated enhancement, using the maize polyubiquitin 1 (ubi1) intron, generated a significant increase in GUS expression directed by the BBTV promoters in transgenic plants. Received: 17 May 1999 / Revision received: 3 November 1999 / Accepted: 4 November 1999