Past vegetation dynamics in the Yellowstone region highlight the vulnerability of mountain systems to climate change

Aim

Reconstruct the long‐term ecosystem dynamics of the region across an elevational gradient as they relate to climate and local controls. In particular, we (1) describe the dominant conifers' history; (2) assess changes in vegetation composition and distribution; and (3) note periods of abrupt change versus stability as means of better understanding vegetation responses to environmental variability.

Location

Greater Yellowstone Ecosystem (GYE; USA).

Time period

16.5 ka bp ‐present.

Major taxa studied

Juniperus, Picea, Abies, Pinus, Pseudotsuga.

Methods

The vegetation reconstruction was developed from 15 pollen records. Results were interpreted based on modern pollen–vegetation relationships estimated from a suite of regression‐based approaches.

Results

Calibrated pollen data suggest that late‐glacial vegetation, dominated by shrubs and Juniperus, lacks a modern counterpart in the area. Picea, Abies and Pinus expanded at 16 ka bp in association with postglacial warming and co‐occurred in mixed‐conifer parkland/forest after 12 ka bp . This association along with Pinus contorta forest, which was present after 9 ka bp , has persisted with little change at middle and high elevations to the present day. This stability contrasts with the dynamic history of plant communities at low elevations, where shifts between parkland, steppe and forest over the last 8,000 years were likely driven by variations in effective moisture and fire.

Main conclusions

The postglacial vegetation history of the GYE highlights the dynamic nature of mountain ecosystems and informs on their vulnerability to future climate change: (1) most of the conifers have been present in the area for >12,000 years and survived climate change by adjusting their elevational ranges; (2) some plant associations have exhibited stability over millennia as a result of nonclimatic controls; and (3) present‐day forest cover is elevationally more compressed than at any time in history, probably due to the legacy of the Medieval Climate Anomaly and the Little Ice Age.     

Competition between Delta and the Abruptex domain of Notch

Background  

Extracellular domains of the Notch family of signalling receptors contain many EGF repeat domains, as do their major ligands. Some EGF repeats are modified by O-fucosylation, and most have no identified role in ligand binding.     

Conservation prioritisation through genomic reconstruction of demographic histories applied to two endangered suids in the Malay Archipelago

Aim

The biodiversity of the Malay Archipelago is the product of the region's rich biogeographical history with periods of island connectivity and isolation during the Pleistocene glacial cycles. Here, the case of two endemic suid species, the Javan (Sus verrucosus) and Bawean (S. blouchi) warty pigs, was used to illustrate how biogeographic processes and recent anthropogenic pressures can shape demographic histories with significant implications for species conservation.

Location

Malay Archipelago, with focus on Bawean and Java.

Methods

We employed genome-wide single nucleotide polymorphisms from the Porcine SNP60 v2 BeadChip to assess interspecific genetic differentiation, to estimate divergence times and to perform demographic model selection.

Results

In contrast to the hypothesis of recent divergence during the last glacial maximum, S. blouchi was found to have diverged from S. verrucosus at least 166 k years ago following a founder event. The contemporary S. blouchi population was characterised by a recent bottleneck that reduced the effective population size to less than 20. The genomic assessment supports the single species status of S. blouchi, as was previously proposed based on morphometrics. The demographic history of S. verrucosus showed evidence of secondary contact with the sympatric banded pig (S. scrofa vittatus) that colonised Java 70 k years ago.

Main Conclusions

While the Javan and Bawean warty pigs have persisted throughout the Pleistocene climatic oscillations, contemporary pressures from human activities threaten their survival and immediate action should be taken to grant legal protection to both S. verrucosus and S. blouchi. This study highlighted the use of demographic history modelling using genomic data to identify evolutionary significant units and inform conservation.     

Environmental amoebae do not support the long‐term survival of virulent mycobacteria

Aims

To test the hypothesis that Mycobacterium bovis can persist in the environment within protozoa.

Methods and Results

In this study, we used a novel approach to detect internalized mycobacteria in environmental protozoa from badger latrines. Acid‐fast micro‐organisms were visualized in isolated amoebae, although we were unable to identify them to species level as no mycobacteria were grown from these samples nor was M. bovis detected by IS6110 PCR. Co‐incubation of Acanthamoeba castellanii with virulent M. bovis substantially reduced levels of bacilli, indicating that the amoebae have a negative effect on the persistence of M. bovis.

Conclusions

The internalization of mycobacteria in protozoa might be a rare event under environmental conditions. The results suggest that amoebae might contribute to the inactivation of M. bovis rather than representing a potential environmental reservoir.

Significance and Impact of the Study

Protozoa have been suggested to act as an environmental reservoir for M. bovis. The current study suggests that environmental amoebae play at most a minor role as potential reservoirs of M. bovis and that protozoa might inhibit persistence of M. bovis in the environment.     

Effect of a disinfection strategy on the methicillin‐resistant Staphylococcus aureus CC398 prevalence of sows,their piglets and the barn environment

Aims

To assess, in a cleaned and disinfected barn environment, the efficacy of an animal disinfection strategy to reduce the livestock‐associated methicillin‐resistant Staphylococcus aureus (LA‐MRSA) prevalence in sows, their offspring and the barn environment.

Methods and Results

On each farm, six sow rounds were sampled; sows were divided into either a test or control group. Per round, 20 sows and 40 of their piglets were sampled at different time points together with the barn environment. The disinfection strategy of the test groups consisted of washing the sows with a shampoo followed by disinfection of the skin with a solution containing chlorhexidine digluconate and isopropanol. On the first day of disinfection and 6 days after stopping the disinfection, a significant decrease (P < 0·01) of on average 68 and 66% in sow MRSA prevalence was observed on both farms, whereas no decrease was seen in the control groups. Just before weaning, 21–28 days after the end of the disinfection strategy, the difference in MRSA prevalence between both groups was reduced to 4% and no longer significant (P = 0·20). The MRSA prevalence of the piglets in the test groups was significantly lower (26%; P < 0·01) 6 days after the end of disinfection. Just before weaning, this difference was reduced to 5% but still significant (P < 0·01). In the swine nursery unit, no significant difference (P = 0·99) was seen between both groups. Based on semi‐quantitative counts, a relationship (r² > 0·6; P < 0·01) was seen between MRSA contamination in the barn environment and the MRSA prevalence in pigs.

Conclusion

Results show that the tested disinfection strategy reduces temporarily the sow and piglet MRSA status, but does not result in a final reduction in MRSA at weaning or in the nursery unit.

Significance and Impact of the Study

First report on the efficacy of an animal disinfection strategy to reduce LA‐MRSA prevalence in sows, their offspring and the barn environment.     

Ankyrin repeat domain-encoding genes in the wPip strain of Wolbachia from the Culex pipiens group

Background  

Wolbachia are obligate endosymbiotic bacteria maternally transmitted through the egg cytoplasm that are responsible for several reproductive disorders in their insect hosts, such as cytoplasmic incompatibility (CI) in infected mosquitoes. Species in the Culex pipiens complex display an unusually high number of Wolbachia-induced crossing types, and based on present data, only the wPip strain is present.     

The effect of growth media and physical treatments on the adhesion properties of canine probiotics

Aims

The manufacturing processes have been reported to influence the properties of probiotics with potential impact on health properties. The aim was to investigate the effect of different growth media and inactivation methods on the properties of canine‐originated probiotic bacteria alone and in combination mixture.

Methods and Results

Three established dog probiotics, Lactobacillus fermentum VET9A, Lactobacillus plantarum VET14A and Lactobacillus rhamnosus VET16A, and their combination mixture were evaluated for their adhesion to dog mucus. The effect of different growth media, one reflecting laboratory and the other manufacturing conditions, and inactivation methods (95°C, 80°C and UV irradiation) on the mucus adhesion of the probiotic strains was characterized. Evaluation of dog probiotics was supported by cell visualization using transmission electron microscopy (TEM). Higher adhesion percentage was reported for probiotic strains growing in laboratory rather than in manufacturing conditions (P < 0·05). Inactivation by heat (95°C, 80°C) decreased the adhesion properties when strains were cultivated in soy‐based growth media compared with those grown in MRS broth (P < 0·05). TEM observations uncovered differences in cell‐surface components in nonviable forms of probiotic strains as compared with their viable forms.

Conclusions

Manufacturing process conditions such as growth media and pretreatment methods may significantly affect the adhesive ability of the tested strains.

Significance and Impact of the Study

Growth conditions, growth media, pretreatment methods and different probiotic combinations should be carefully considered for quality control of existing probiotics and for identification of new probiotics for dogs. These may also have an impact on health benefits for the host.     

Transformation of Anaplasma phagocytophilum

Background  

Tick-borne pathogens cause emerging zoonoses, and include fastidious organisms such as Anaplasma phagocytophilum. Because of their obligate intracellular nature, methods for mutagenesis and transformation have not been available.     

Bacillus amyloliquefaciens ssp. plantarum strains as potential protective starter cultures for the production of Bikalga,an alkaline fermented food

Aims

To identify and screen dominant Bacillus spp. strains isolated from Bikalga, fermented seeds of Hibiscus sabdariffa for their antimicrobial activities in brain heart infusion (BHI) medium and in a H. sabdariffa seed‐based medium. Further, to characterize the antimicrobial substances produced.

Methods and Results

The strains were identified by gyrB gene sequencing and phenotypic tests as B. amyloliquefaciens ssp. plantarum. Their antimicrobial activity was determined by the agar spot and well assay, being inhibitory to a wide range of Gram‐positive and Gram‐negative pathogenic bacteria and fungi. Antimicrobial activity against Bacillus cereus was produced in H. sabdariffa seed‐based medium. PCR results revealed that the isolates have potential for the lipopeptides iturin, fengycin, surfactin, the polyketides difficidin, macrolactin, bacillaene and the dipeptide bacilysin production. Ultra‐high‐performance liquid chromatography‐time of flight mass spectrometry analysis of antimicrobial substance produced in BHI broth allowed identification of iturin, fengycin and surfactin.

Conclusions

The Bacillus amyloliquefaciens ssp. plantarum exhibited broad‐spectrum antifungal and antibacterial properties. They produced several lipopeptide antibiotics and showed good potential for biological control of Bikalga.

Significance and Impact of the Study

Pathogenic bacteria often occur in spontaneous food fermentations. This is the first report to identify indigenous B. amyloliquefaciens ssp. plantarum strains as potential protective starter cultures for safeguarding Bikalga.     

Characterization of 13 multi-drug resistant <Emphasis Type="Italic">Salmonella</Emphasis> serovars from different broiler chickens associated with those of human isolates

Background  

Salmonella are frequently isolated from chickens and their products. Prevalent serogroups and serovars of Salmonella as well as their genotypes and antibiograms were determined for cloacal samples from 1595 chickens. To understand the possible serovar and H antigens for transmission between chicken and human, serovars and their H antigens of 164 chicken and 5314 human isolates were compared.     

Efflux pump genes of the resistance-nodulation-division family in Burkholderia cenocepacia genome

Background  

Burkholderia cenocepacia is recognized as opportunistic pathogen that can cause lung infections in cystic fibrosis patients. A hallmark of B. cenocepacia infections is the inability to eradicate the organism because of multiple intrinsic antibiotic resistance. As Resistance-Nodulation-Division (RND) efflux systems are responsible for much of the intrinsic multidrug resistance in Gram-negative bacteria, this study aims to identify RND genes in the B. cenocepacia genome and start to investigate their involvement into antimicrobial resistance.     

Characterization of the dsDNA prophage sequences in the genome of <Emphasis Type="Italic">Neisseria gonorrhoeae</Emphasis> and visualization of productive bacteriophage

Background  

Bioinformatic analysis of the genome sequence of Neisseria gonorrhoeae revealed the presence of nine probable prophage islands. The distribution, conservation and function of many of these sequences, and their ability to produce bacteriophage particles are unknown.     

Complete PHB mobilization in Escherichia coli enhances the stress tolerance: a potential biotechnological application

Background  

Poly-β-hydroxybutyrate (PHB) mobilization in bacteria has been proposed as a mechanism that can benefit their host for survival under stress conditions. Here we reported for the first time that a stress-induced system enabled E. coli, a non-PHB producer, to mobilize PHB in vivo by mimicking natural PHB accumulation bacteria.     

Antibacterial and antifungal activities of pyroligneous acid from wood of Eucalyptus urograndis and Mimosa tenuiflora

Aims

This work aimed to evaluate the antibacterial and antifungal activities of two types of pyroligneous acid (PA) obtained from slow pyrolysis of wood of Mimosa tenuiflora and of a hybrid of Eucalyptus urophylla × Eucalyptus grandis.

Methods and Results

Wood wedges were carbonized on a heating rate of 1·25°C min^?1 until 450°C. Pyrolysis smoke was trapped and condensed to yield liquid products. Crude pyrolysis liquids were bidistilled under 5 mmHg vacuum yielding purified PA. Multi‐antibiotic‐resistant strains of Escherichia coli, Pseudomonas aeruginosa (ATCC 27853) and Staphylococcus aureus (ATCC 25923) had their sensitivity to PA evaluated using agar diffusion test. Two yeasts were evaluated as well, Candida albicans (ATCC 10231) and Cryptococcus neoformans. GC‐MS analysis of both PAs was carried out to obtain their chemical composition. Regression analysis was performed, and models were adjusted, with diameter of inhibition halos and PA concentration (100, 50 and 20%) as parameters. Identity of regression models and equality of parameters in polynomial orthogonal equations were verified. Inhibition halos were observed in the range 15–25 mm of diameter.

Conclusions

All micro‐organisms were inhibited by both types of PA even in the lowest concentration of 20%.

Significance and Impact of the Study

The feasibility of the usage of PAs produced with wood species planted in large scale in Brazil was evident and the real potential as a basis to produce natural antibacterial and antifungal agents, with real possibility to be used in veterinary and zootechnical applications.     

The isolation and mapping of a novel hydroxycinnamoyltransferase in the globe artichoke chlorogenic acid pathway

Background  

The leaves of globe artichoke and cultivated cardoon (Cynara cardunculus L.) have significant pharmaceutical properties, which mainly result from their high content of polyphenolic compounds such as monocaffeoylquinic and dicaffeoylquinic acid (DCQ), and a range of flavonoid compounds.     

Simplified production and concentration of HIV-1-based lentiviral vectors using HYPERFlask vessels and anion exchange membrane chromatography

Background  

During the past twelve years, lentiviral (LV) vectors have emerged as valuable tools for transgene delivery because of their ability to transduce nondividing cells and their capacity to sustain long-term transgene expression in target cells in vitro and in vivo. However, despite significant progress, the production and concentration of high-titer, high-quality LV vector stocks is still cumbersome and costly.     

A comparative study of protein synthesis in <Emphasis Type="Italic">in vitro</Emphasis> systems: from the prokaryotic reconstituted to the eukaryotic extract-based

Background  

Cell-free protein synthesis is not only a rapid and high throughput technology to obtain proteins from their genes, but also provides an in vitro platform to study protein translation and folding. A detailed comparison of in vitro protein synthesis in different cell-free systems may provide insights to their biological differences and guidelines for their applications.     

Formulation of novel lipid-coated magnetic nanoparticles as the probe for in vivo imaging

Background  

Application of superparamagnetic iron oxide nanoparticles (SPIOs) as the contrast agent has improved the quality of magnetic resonance (MR) imaging. Low efficiency of loading the commercially available iron oxide nanoparticles into cells and the cytotoxicity of previously formulated complexes limit their usage as the image probe. Here, we formulated new cationic lipid nanoparticles containing SPIOs feasible for in vivo imaging.