Recent amplification of the kangaroo endogenous retrovirus, KERV, limited to the centromere

Mammalian retrotransposons, transposable elements that are processed through an RNA intermediate, are categorized as short interspersed elements (SINEs), long interspersed elements (LINEs), and long terminal repeat (LTR) retroelements, which include endogenous retroviruses. The ability of transposable elements to autonomously amplify led to their initial characterization as selfish or junk DNA; however, it is now known that they may acquire specific cellular functions in a genome and are implicated in host defense mechanisms as well as in genome evolution. Interactions between classes of transposable elements may exert a markedly different and potentially more significant effect on a genome than interactions between members of a single class of transposable elements. We examined the genomic structure and evolution of the kangaroo endogenous retrovirus (KERV) in the marsupial genus Macropus. The complete proviral structure of the kangaroo endogenous retrovirus, phylogenetic relationship among relative retroviruses, and expression of this virus in both Macropus rufogriseus and M. eugenii are presented for the first time. In addition, we show the relative copy number and distribution of the kangaroo endogenous retrovirus in the Macropus genus. Our data indicate that amplification of the kangaroo endogenous retrovirus occurred in a lineage-specific fashion, is restricted to the centromeres, and is not correlated with LINE depletion. Finally, analysis of KERV long terminal repeat sequences using massively parallel sequencing indicates that the recent amplification in M. rufogriseus is likely due to duplications and concerted evolution rather than a high number of independent insertion events.     

Thermal biology of African lovebirds and Australian grass parakeets

We compared aspects of the thermal biology of two groups of small parrots, of similar body mass, each derived from a range of habitat types, varying in aridity, but indigenous to either southern Africa or Australia. By accounting for phylogenetic differences, we were able to question whether arid zone species have lower metabolic rates and greater thermal tolerances than mesic species in relation to the “pre-adapted” and “post-arrival adaptation” hypotheses. Four species of African lovebird (Agapornis) and four species of Australian grass parakeet (one Neopsephotus and three Neophema species) were investigated. The Rosy-faced Lovebird (Agapornis roseicollis), Bourke's Parakeet (Neopsephotus bourkii) and the Scarlet-chested Parakeet (Neophema splendida) were categorised as arid zone species, Fischer's Lovebird (Agapornis fischeri), the Black-masked Lovebird (Agapornis personatus) and the Elegant Parakeet (Neophema elegans) as semi-arid zone species, and the Black-cheeked Lovebird (Agapornis nigrigenis) and the Turquoise Parakeet (Neophema pulchella) as mesic zone species. Conventional and phylogenetically independent statistical methods yielded no significant differences in the basal metabolic rates of birds from different habitats or between the species assemblages from Africa and Australia.     

TGFbeta superfamily signaling: notes from the desert

The TGFbeta pathways play crucial roles in many developmental events, as well as contributing to many disease states. To provide a venue for both signaling and developmental research on TGFbeta, a FASEB-sponsored bi-annual meeting was initiated six years ago, the fourth of which was organized by Caroline Hill and Michael O'Connor and took place this July in Tucson, Arizona. The meeting highlighted major advances in our understanding of the structural and biochemical aspects of TGFbeta superfamily signaling, its intersection with other pathways, and its contribution to disease.     

Biochemical and genetic engineering strategies to enhance hydrogen production in photosynthetic algae and cyanobacteria

As an energy carrier, hydrogen gas is a promising substitute to carbonaceous fuels owing to its superb conversion efficiency, non-polluting nature, and high energy content. At present, hydrogen is predominately synthesized via chemical reformation of fossil fuels. While various biological methods have been extensively explored, none of them is justified as economically feasible. A sustainable platform for biological production of hydrogen will certainly impact the biofuel market. Among a selection of biological systems, algae and cyanobacteria have garnered major interests as potential cell factories for hydrogen production. In conjunction with photosynthesis, these organisms utilize inexpensive inorganic substrates and solar energy for simultaneous biosynthesis and hydrogen evolution. However, the hydrogen yield associated with these organisms remains far too low to compete with the existing chemical systems. This article reviews recent advances of biochemical, bioprocess, and genetic engineering strategies in circumventing technological limitations to hopefully improve the applicative potential of these photosynthetic hydrogen production systems.     

Fruit Flies in Biomedical Research

Many scientists complain that the current funding situation is dire. Indeed, there has been an overall decline in support in funding for research from the National Institutes of Health and the National Science Foundation. Within the Drosophila field, some of us question how long this funding crunch will last as it demotivates principal investigators and perhaps more importantly affects the long-term career choice of many young scientists. Yet numerous very interesting biological processes and avenues remain to be investigated in Drosophila, and probing questions can be answered fast and efficiently in flies to reveal new biological phenomena. Moreover, Drosophila is an excellent model organism for studies that have translational impact for genetic disease and for other medical implications such as vector-borne illnesses. We would like to promote a better collaboration between Drosophila geneticists/biologists and human geneticists/bioinformaticians/clinicians, as it would benefit both fields and significantly impact the research on human diseases.     

Evidence that Early Carboniferous ostracods colonised coastal flood plain brackish water environments

A study of the stable isotope composition (δ¹⁸O, δ¹³C) of biogenic (ostracod, mollusc) and authigenic carbonates in the Ballagan Formation, Lower Carboniferous of Scotland, coupled with evidence from sedimentology and associated fossil fauna and flora, supports the argument that this formation was deposited in a coastal flood plain setting, in brackish (0.5 < 30‰ NaCl) and hypersaline (> 40‰ NaCl) waters, but in the absence of persistent normal marine conditions. The oxygen isotope data from the Ballagan Formation divide into three clusters: a diagenetic field defined by low δ¹⁸O (< − 11‰ VPDB); an intermediary field (δ¹⁸O − 11‰ to − 9‰) composed of a mixture of known primary and secondary (diagenetic) carbonates; and samples within the range of − 9‰ to − 4‰ which, as far as we can ascertain, are largely unaltered. No samples give typical Early Carboniferous δ¹⁸O marine values. Average marine carbonates from Europe have δ¹⁸O between − 4‰ to − 3‰. The Ballagan Formation carbonates were probably deposited in evaporated freshwater and/or brackish water. This conclusion is supported by the presence of evaporites (gypsum, anhydrite, halite pseudomorphs) and common desiccation-cracked mudstone surfaces throughout the Ballagan Formation, suggesting conditions of fluctuating salinity in ephemeral bodies of water. The stable isotope data support the notion that the ostracod assemblages of the Ballagan Formation were colonising brackish water and hypersaline ecologies on a coastal flood plain during the Early Carboniferous, a stage of development that may have encouraged their colonisation of fully non-marine (limnetic) environments during the later Carboniferous. The ostracods include cytherellacean and kloedenellacean species known from marginal marine sites elsewhere, but probably tolerant of brackish water, podocopid species such as ‘Bythocypris’ aequalis that may have been adapted for brackish water settings on coastal flood plains (ephemeral lakes and lagoons), and paraparchitacean-dominated assemblages that may signal harsh (hypersaline or desiccating) environments.     

Reliance on head versus eyes in the gaze following of great apes and human infants: the cooperative eye hypothesis

As compared with other primates, humans have especially visible eyes (e.g., white sclera). One hypothesis is that this feature of human eyes evolved to make it easier for conspecifics to follow an individual's gaze direction in close-range joint attentional and communicative interactions, which would seem to imply especially cooperative (mututalistic) conspecifics. In the current study, we tested one aspect of this cooperative eye hypothesis by comparing the gaze following behavior of great apes to that of human infants. A human experimenter "looked" to the ceiling either with his eyes only, head only (eyes closed), both head and eyes, or neither. Great apes followed gaze to the ceiling based mainly on the human's head direction (although eye direction played some role as well). In contrast, human infants relied almost exclusively on eye direction in these same situations. These results demonstrate that humans are especially reliant on eyes in gaze following situations, and thus, suggest that eyes evolved a new social function in human evolution, most likely to support cooperative (mututalistic) social interactions.