Complete genome sequence of Polynucleobacter necessarius subsp. asymbioticus type strain (QLW-P1DMWA-1(T))

Polynucleobacter necessarius subsp. asymbioticus strain QLW-P1DMWA-1(T) is a planktonic freshwater bacterium affiliated with the family Burkholderiaceae (class Betaproteobacteria). This strain is of interest because it represents a subspecies with cosmopolitan and ubiquitous distribution in standing freshwater systems. The 16S-23S ITS genotype represented by the sequenced strain comprised on average more than 10% of bacterioplankton in its home habitat. While all strains of the subspecies P. necessarius asymbioticus are free-living freshwater bacteria, strains belonging to the only other subspecies, P. necessarius subsp. necessarius are obligate endosymbionts of the ciliate Euplotes aediculatus. The two subspecies of P. necessarius are the instances of two closely related subspecies that differ in their lifestyle (free-living vs. obligate endosymbiont), and they are the only members of the genus Polynucleobacter with completely sequenced genomes. Here we describe the features of P. necessarius subsp. asymbioticus, together with the complete genome sequence and annotation. The 2,159,490 bp long chromosome with a total of 2,088 protein-coding and 48 RNA genes is the first completed genome sequence of the genus Polynucleobacter to be published and was sequenced as part of the DOE Joint Genome Institute Community Sequencing Program 2006.     

Giardia/giardiasis — A perspective on diagnostic and analytical tools

Giardiasis is a gastrointestinal disease of humans and other animals caused by species of parasitic protists of the genus Giardia. This disease is transmitted mainly via the faecal–oral route (e.g., in water or food) and is of socioeconomic importance worldwide. The accurate detection and genetic characterisation of the different species and population variants (usually referred to as assemblages and/or sub-assemblages) of Giardia are central to understanding their transmission patterns and host spectra. The present article provides a background on Giardia and giardiasis, and reviews some key techniques employed for the identification and genetic characterisation of Giardia in biological samples, the diagnosis of infection and the analysis of genetic variation within and among species of Giardia. Advances in molecular techniques provide a solid basis for investigating the systematics, population genetics, ecology and epidemiology of Giardia species and genotypes as well as the prevention and control of giardiasis.     

In Vivo Assessment of Bone Regeneration in Alginate/Bone ECM Hydrogels with Incorporated Skeletal Stem Cells and Single Growth Factors

The current study has investigated the use of decellularised, demineralised bone extracellular matrix (ECM) hydrogel constructs for in vivo tissue mineralisation and bone formation. Stro-1-enriched human bone marrow stromal cells were incorporated together with select growth factors including VEGF, TGF-β3, BMP-2, PTHrP and VitD3, to augment bone formation, and mixed with alginate for structural support. Growth factors were delivered through fast (non-osteogenic factors) and slow (osteogenic factors) release PLGA microparticles. Constructs of 5 mm length were implanted in vivo for 28 days within mice. Dense tissue assessed by micro-CT correlated with histologically assessed mineralised bone formation in all constructs. Exogenous growth factor addition did not enhance bone formation further compared to alginate/bone ECM (ALG/ECM) hydrogels alone. UV irradiation reduced bone formation through degradation of intrinsic growth factors within the bone ECM component and possibly also ECM cross-linking. BMP-2 and VitD3 rescued osteogenic induction. ALG/ECM hydrogels appeared highly osteoinductive and delivery of angiogenic or chondrogenic growth factors led to altered bone formation. All constructs demonstrated extensive host tissue invasion and vascularisation aiding integration and implant longevity. The proposed hydrogel system functioned without the need for growth factor incorporation or an exogenous inducible cell source. Optimal growth factor concentrations and spatiotemporal release profiles require further assessment, as the bone ECM component may suffer batch variability between donor materials. In summary, ALG/ECM hydrogels provide a versatile biomaterial scaffold for utilisation within regenerative medicine which may be tailored, ultimately, to form the tissue of choice through incorporation of select growth factors.     

Remote monitoring of nests using digital camera technology

ABSTRACT.   Although cameras have been used for many years to collect data at birds' nests, recent advances in digital technology have led to increased storage capacity, faster and easier review of data, and reduced power consumption. The development of sophisticated triggering mechanisms, such as video motion detection, herald a new era of portable, energy-efficient systems that require less frequent maintenance. We used a digital infrared camera system to monitor predation events at the nests of ground-nesting Lapwings ( Vanellus vanellus ; N = 40) and tree-nesting Spotted Flycatchers ( Muscicapa striata ; N = 17). Eight predator species were recorded taking eggs or chicks at Lapwing ( N = 10) and Spotted Flycatcher ( N = 7) nests, including red fox ( Vulpes vulpes ), badger ( Meles meles ), sheep ( Ovis aries ), and Carrion Crow ( Corvus corone ) at Lapwing nests and Eurasian Jay ( Garrulus glandarius ), European Buzzard ( Buteo buteo ), Great-spotted Woodpecker ( Dendrocopus major ), and domestic cat ( Felis catus ) at flycatcher nests. We tested three system configurations in an attempt to minimize power requirements and maximize predation-event recording capability. We found that the use of a passive-infrared sensor to awaken the system from standby mode did not compromise reliability and reduced power consumption. With this system, a 38-A h battery operated the system for 120 h with no maintenance at a cost per unit of about $800 (US; or £400 UK Sterling). Further modifications would permit adaptation of the system for a wide range of scientific and nest surveillance operations.     

An essential yeast gene with homology to the exonuclease-encoding XRN1/KEM1 gene also encodes a protein with exoribonuclease activity.

An essential gene, designated HKE1/RAT1, has been isolated from the yeast Saccharomyces cerevisiae and characterized. The gene encodes a protein of 116 kDa (p116) and has significant homology to another yeast gene (XRN1/KEM1) encoding a related protein (p175) with 5'-->3' exonuclease activity as well as activities involving chromosomal DNA pairing and mechanics. Preliminary analysis of an hke1ts mutant reveals a precipitous decline in the translation of mRNA at the nonpermissive temperature. Sporulation of heterozygous HKE1/hke1::URA3 diploids reveals that this gene, unlike the highly related XRN1/KEM1 gene, is essential for cell viability. Overexpression of the homologous gene product, p175, failed to rescue cells lacking a functional p116. In vitro studies demonstrate that p116 is a protein with 5'-->3' exoribonuclease activity, a major activity of the related p175. An immunoreactive RNase activity of 116 kDa is abolished with antiserum against p116. Both the level of this protein and the RNase activity correlate with HKE1 gene dosage. The RNase activity purifies coincidentally with a previously described 116-kDa RNase having 5'-->3' exoribonuclease activity.     

Flight endurance and heating rate vary with both latitude and habitat connectivity in a butterfly species

Environmental factors at both macro‐ecological and landscape scales are likely to affect (meta) population dynamics and species distributions, through direct or indirect effects on individual phenotypes. Although disentangling these scale effects is of prime importance in evolutionary ecology and conservation biology, most studies dealing with the links between phenotype and the environment have mainly focused on the landscape scale, and none has addressed the interactions between effects at both scales. In ectotherms, movement abilities are strongly dependent upon thermoregulation abilities, and thus likely vary with latitude. Moreover, in such species, movement is also highly dependent upon landscape geometry at the landscape scale. Here, we quantified the combined effects of latitude and habitat fragmentation on movement ability in relation with thermoregulation abilities in the butterfly Pieris brassicae as model for understanding the relative contributions of macro‐ecological and landscape scale effects on species’ mobility. We sampled individuals at an early developmental stage (eggs or caterpillars), in natural populations from 27 sites with different degrees of habitat connectivity, along a latitudinal gradient across France and Belgium. Adult flight and heating rate were measured in laboratory controlled conditions and were used as proxies for movement ability and thermoregulation ability, respectively. We found that flight endurance for both sexes and female heating rate increased with latitude. Habitat connectivity had a sex‐dependent effect on both traits: flight endurance in males increased with decreasing habitat connectivity, while the opposite was found in females. Moreover, heating rate increased with increasing habitat connectivity, the effect being stronger in males. Overall, our results highlight the need to integrate intraspecific variation in movement ability at different spatial scales when studying species’ responses to global environmental change.