Multiplex PCR as a tool for validating plasmid content of Borrelia burgdorferi

Borrelia burgdorferi has an unusual genomic structure containing 21 plasmids. These plasmids carry genes that are essential for infectivity and survival of the spirochetes in vivo. Several plasmids are lost during cultivation in vitro, which might lead to a heterogeneous population after multiple passages and loss of infectivity in laboratory animals. Herein, we present a simple and inexpensive multiplex PCR method that detects the complete plasmid profile of B. burgdorferi B31 in just two PCR tubes.     

An RND-type efflux system in Borrelia burgdorferi is involved in virulence and resistance to antimicrobial compounds

Borrelia burgdorferi is remarkable for its ability to thrive in widely different environments due to its ability to infect various organisms. In comparison to enteric Gram-negative bacteria, these spirochetes have only a few transmembrane proteins some of which are thought to play a role in solute and nutrient uptake and excretion of toxic substances. Here, we have identified an outer membrane protein, BesC, which is part of a putative export system comprising the components BesA, BesB and BesC. We show that BesC, a TolC homolog, forms channels in planar lipid bilayers and is involved in antibiotic resistance. A besC knockout was unable to establish infection in mice, signifying the importance of this outer membrane channel in the mammalian host. The biophysical properties of BesC could be explained by a model based on the channel-tunnel structure. We have also generated a structural model of the efflux apparatus showing the putative spatial orientation of BesC with respect to the AcrAB homologs BesAB. We believe that our findings will be helpful in unraveling the pathogenic mechanisms of borreliae as well as in developing novel therapeutic agents aiming to block the function of this secretion apparatus.     

Complete Genome Sequence of Borrelia afzelii K78 and Comparative Genome Analysis

The main Borrelia species causing Lyme borreliosis in Europe and Asia are Borrelia afzelii, B. garinii, B. burgdorferi and B. bavariensis. This is in contrast to the United States, where infections are exclusively caused by B. burgdorferi. Until to date the genome sequences of four B. afzelii strains, of which only two include the numerous plasmids, are available. In order to further assess the genetic diversity of B. afzelii, the most common species in Europe, responsible for the large variety of clinical manifestations of Lyme borreliosis, we have determined the full genome sequence of the B. afzelii strain K78, a clinical isolate from Austria. The K78 genome contains a linear chromosome (905,949 bp) and 13 plasmids (8 linear and 5 circular) together presenting 1,309 open reading frames of which 496 are located on plasmids. With the exception of lp28-8, all linear replicons in their full length including their telomeres have been sequenced. The comparison with the genomes of the four other B. afzelii strains, ACA-1, PKo, HLJ01 and Tom3107, as well as the one of B. burgdorferi strain B31, confirmed a high degree of conservation within the linear chromosome of B. afzelii, whereas plasmid encoded genes showed a much larger diversity. Since some plasmids present in B. burgdorferi are missing in the B. afzelii genomes, the corresponding virulence factors of B. burgdorferi are found in B. afzelii on other unrelated plasmids. In addition, we have identified a species specific region in the circular plasmid, cp26, which could be used for species determination. Different non-coding RNAs have been located on the B. afzelii K78 genome, which have not previously been annotated in any of the published Borrelia genomes.     

African Elephants Loxodonta africana Amplify Browse Heterogeneity in African Savanna

There is a growing concern that the feeding habits of the African elephant, which include pushing over, uprooting and snapping trees, may have a negative impact on other herbivores. Browsed trees are known to respond by either increasing production (shoots and leaves) or defence (secondary compounds). It is not clear, however, what proportion of the browsed biomass can be made available at lower feeding heights after a tree is pushed over or snapped; thus, it is also unclear how the forage quality is affected. In a field survey in Kruger National Park, South Africa, 708 Mopane trees were measured over four elephant utilization categories: snapped trees, pushed‐over trees, uprooted trees and control trees. The elephants' impact on the leaf biomass distribution was quantified, and the forage quality (Ca, P, K and Mg, N, digestibility and condensed tannin [CT] concentrations) were analyzed. Pushed‐over and uprooted trees had the maximum leaf biomass at lower heights (<1 m), snapped trees at medium heights (1–2 m) and control trees at higher heights (>2 m). In all three utilization categories, the minimum leaf biomass was seven times higher than it was for control trees at a height of below 1 m. Leaf nitrogen content increased in all three categories and was significantly higher in snapped trees. CT concentrations increased slightly in all trees that were utilized by elephants, especially on granitic soils in the dry season. The results provide the insight that elephants facilitate the redistribution and availability of browse and improve the quality, which may positively affect small browsing herbivores.     

Prevalence of wood characters in eastern North America: what characters are most promising for interpreting climates from fossil wood?

The frequency of wood-anatomical characters in the eastern North America dicotyledonous tree flora shows spatial variance that can be related to climate (40% of the variation in 18 characters is explained by temperature and precipitation). Percent of taxa with rings varies with mean annual temperature, but the relationship is weak and the difficulties in making determinations as to presence or absence of rings make this character a problematic climatic indicator. Significant climate sensitivity is seen among characters pertaining to: a) vessel size and density (in diffuse-porous woods); 2) vessel arrangement; 3) parenchyma types; and 4) rays. Overall, the anatomical variables can be used to represent 82% of the variance in total precipitation and 91% of the variance in mean annual temperature within the study area. These results demonstrate the possibility of deriving a multivariate representation of the response of wood to climate that will be useful in climate reconstruction and comprise a source of information similar to that obtainable from leaf morphology and permitting estimates of precipitation as well as temperature.     

Trees improve grass quality for herbivores in African savannas

The tree–grass interactions of African savannas are mainly determined by varying rainfall patterns and soil fertility. Large savanna trees are known to modify soil nutrient conditions, but whether this has an impact on the quality of herbaceous vegetation is unclear. However, if this were the case, then the removal of trees might also affect the structure and quality of the grass layer. We studied the impact of large nitrogen- and non-nitrogen fixing trees on the sub-canopy (SC) grass layer in low- and high-rainfall areas of differing soil fertility in eastern and southern Africa. We compared the structure and nutrient levels of SC grasses with those outside the canopy. Grass leaf nitrogen and phosphorus contents beneath tree canopies were elevated at all study sites and were up to 25% higher than those outside the canopy in the site of lowest rainfall and soil fertility. Grass leaf fibre and organic matter (OM) contents were slightly enhanced beneath tree canopies. At the site of highest rainfall and soil fertility, grasses beneath the canopy had significantly lower ratios of stem:leaf biomass and dead:living leaf material. Grass species composition differed significantly, with the highly nutritious Panicum spp. being most abundant underneath tree crowns. In the two drier study sites, soil nitrogen and OM contents were enhanced by 30% beneath trees. N-fixation capacity of trees did not contribute to the improved quality of grass under the canopy. We conclude that trees improve grass quality, especially in dry savannas. In otherwise nutrient-poor savanna grasslands, the greater abundance of high-quality grass species with higher contents of N and P and favourable grass structure beneath trees could attract grazing ungulates. As these benefits may be lost with tree clearance, trees should be protected in low fertility savannas and their benefits for grazing wildlife recognised in conservation strategies.     

Scenario modeling for conservation management in the En Afeq Nature Reserve,Israel

Abstract. Conservation management has significant gaps between (1) collection and storage of biological data, (2) data analysis, and (3) application of results. In order to improve management decision-making, it is necessary to bridge these gaps. One of the most promising approaches uses computer-based decision support systems (DSS): interactive models of the system in question—for example, a nature reserve. One kind of DSS is scenario modeling: spatially-based models which (1) use expert opinion and data on vegetation, geology, hydrology, and management, (2) to project changes in landscape through time, (3) on the basis of changes in driving environmental factors. Scenario models are essentially graphic hypotheses, predicting changes in landscape with a specified change in driving factors, which can then be verified or falsified by monitoring. This paper presents an application of this approach to an Israeli nature reserve, the En Afeq Reserve in western Galilee. Our project tests the possibility of improving Israeli conservation management by using methods now standard for nature reserves in the Netherlands.     

Avian Neo-Sex Chromosomes Reveal Dynamics of Recombination Suppression and W Degeneration

How the avian sex chromosomes first evolved from autosomes remains elusive as 100 million years (My) of divergence and degeneration obscure their evolutionary history. The Sylvioidea group of songbirds is interesting for understanding avian sex chromosome evolution because a chromosome fusion event ∼24 Ma formed “neo-sex chromosomes” consisting of an added (new) and an ancestral (old) part. Here, we report the complete female genome (ZW) of one Sylvioidea species, the great reed warbler (Acrocephalus arundinaceus). Our long-read assembly shows that the added region has been translocated to both Z and W, and whereas the added-Z has retained its gene order the added-W part has been heavily rearranged. Phylogenetic analyses show that recombination between the homologous added-Z and -W regions continued after the fusion event, and that recombination suppression across this region took several million years to be completed. Moreover, recombination suppression was initiated across multiple positions over the added-Z, which is not consistent with a simple linear progression starting from the fusion point. As expected following recombination suppression, the added-W show signs of degeneration including repeat accumulation and gene loss. Finally, we present evidence for nonrandom maintenance of slowly evolving and dosage-sensitive genes on both ancestral- and added-W, a process causing correlated evolution among orthologous genes across broad taxonomic groups, regardless of sex linkage.     

Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird‐of‐paradise

Genome assemblies are currently being produced at an impressive rate by consortia and individual laboratories. The low costs and increasing efficiency of sequencing technologies now enable assembling genomes at unprecedented quality and contiguity. However, the difficulty in assembling repeat‐rich and GC‐rich regions (genomic “dark matter”) limits insights into the evolution of genome structure and regulatory networks. Here, we compare the efficiency of currently available sequencing technologies (short/linked/long reads and proximity ligation maps) and combinations thereof in assembling genomic dark matter. By adopting different de novo assembly strategies, we compare individual draft assemblies to a curated multiplatform reference assembly and identify the genomic features that cause gaps within each assembly. We show that a multiplatform assembly implementing long‐read, linked‐read and proximity sequencing technologies performs best at recovering transposable elements, multicopy MHC genes, GC‐rich microchromosomes and the repeat‐rich W chromosome. Telomere‐to‐telomere assemblies are not a reality yet for most organisms, but by leveraging technology choice it is now possible to minimize genome assembly gaps for downstream analysis. We provide a roadmap to tailor sequencing projects for optimized completeness of both the coding and noncoding parts of nonmodel genomes.     

Development of intraspecific size variation in black coucals,white-browed coucals and ruffs from hatching to fledging

Most studies on sexual size dimorphism address proximate and functional questions related to adults, but sexual size dimorphism usually develops during ontogeny and developmental trajectories of sexual size dimorphism are poorly understood. We studied three bird species with variation in adult sexual size dimorphism: black coucals (females 69% heavier than males), white-browed coucals (females 13% heavier than males) and ruffs (males 70% heavier than females). Using a flexible Bayesian generalized additive model framework (GAMM), we examined when and how sexual size dimorphism developed in body mass, tarsus length and bill length from hatching until fledging. In ruffs, we additionally examined the development of intrasexual size variation among three morphs (Independents, Satellites and Faeders), which creates another level of variation in adult size of males and females. We found that 27–100% of the adult inter- and intrasexual size variation developed until fledging although none of the species completed growth during the observational period. In general, the larger sex/morph grew more quickly and reached its maximal absolute growth rate later than the smaller sex/morph. However, when the daily increase in body mass was modelled as a proportion, growth patterns were synchronized between and within sexes. Growth broadly followed sigmoidal asymptotic models, however only with the flexible GAMM approach, residual distributions were homogeneous over the entire observation periods. These results provide a platform for future studies to relate variation in growth to selective pressures and proximate mechanisms in these three species, and they highlight the advantage of using a flexible model approach for examining growth variation during ontogeny.