The use of synthetic genes for the expression of ciliate proteins in heterologous systems

The common fish parasite, Ichthyophthirius multifiliis, expresses abundant glycosylated phosphatidylinositol (GPI)-anchored membrane proteins known as immobilization antigens, or i-antigens. These proteins are targets of the host immune response, and have been identified as potential candidates for recombinant subunit vaccine development. Nevertheless, because Ichthyophthirius utilizes a non-standard genetic code, expression of the corresponding gene products, either as subunit antigens in conventional protein expression systems, or as vector-encoded antigens in the case of DNA vaccines, is far from straightforward. To overcome this problem, we utilized 'assembly polymerase chain reaction' to manufacture synthetic versions of two genes (designated IAG52A[G5/CC] and IAG52B[G5/CC]) encoding approximately 52/55 kDa i-antigens from parasite strain G5. This approach made it possible to eliminate unwanted stop codons and substitute the preferred codon usage of channel catfish for the native sequences of the genes. To determine whether the synthetic alleles could be expressed in cells that use the standard genetic code, we introduced IAG52A[G5/CC] into a variety of heterologous cell types and tested for expression either by immunofluorescence light microscopy or Western blotting. When cloned downstream of appropriate promoters, IAG52A[G5/CC] was expressed in Escherichia coli, mammalian COS-7 cells, and channel catfish where it elicited antigen-specific immune responses. Interestingly, the localization pattern of the corresponding gene product in COS-7 cells indicated that while the protein was correctly folded, it was not present on the cell membrane, suggesting that the signal peptides required for GPI-anchor addition differ in ciliate and mammalian systems. Construction of synthetic alleles should have practical utility in the development of vaccines against Ichthyophthirius, and at the same time, provide a general method for the expression of ciliate genes in heterologous systems.     

Biochemical and immunological characterization of pea nuclear intermediate filament proteins

In immunoblot assays, at least three putative nuclear intermediate filament (NIF) proteins were detected in nuclear envelope-matrix (NEM) and lamin (L1) fractions of nuclei from plumules of dark-grown pea (Pisum sativum L.) seedlings. These NIF proteins had apparent molecular masses of ca. 65, 60, and 54 kDa (also referred to as p65, p60, and p54), and appeared as multiple isoelectric forms, with pIs ranging from ca. 4.8 to 6.0. Polyclonal and monoclonal antibodies were raised to the 65-kDa NIF protein bands excised from gels after electrophoresis. These anti-pea antibodies were specifically cross-reactive with the pea nuclear p65, p60, and p54 proteins and also with chicken lamins. Sequence alignment of peptide fragments obtained from the 65- and 60-kDa pea NIF proteins showed similarity with animal intermediate filament proteins such as lamins and keratins and with certain plant proteins predicted to have long coiled-coil domains. These pea NIF proteins were further purified and enriched from the NEM fraction using methods similar to those used for isolating animal lamins. When negatively stained and viewed by transmission electron microscopy, the filaments in the pea lamin (L1) fraction appeared to be 6–12 nm in diameter. As assayed by immunofluorescence cytochemistry using a confocal laser-scanning microscope, fixed pea plumule cells displayed uniform as opposed to peripheral nuclear staining by several of the antibody preparations, both polyclonal and monoclonal. This report describes the biochemical and immunological properties of these pea NIF proteins.Abbreviations IF Intermediate filament - L Lamin fraction - LM Lamina-matrix fraction - MAb JLA20 Anti-chicken actin monoclonal antibody - MAb LN43 Anti-human lamin B2 monoclonal antibody - MAb PL19 Anti-pea lamin #19 monoclonal antibody - MAb TIB 131 Anti-intermediate filament monoclonal antibody - N Nuclei fraction - NEM Nuclear envelope-matrix fraction - NIF Nuclear intermediate filament - PAb PL3 Anti-pea lamin #3 polyclonal antibody     

Rethinking the dispersal of Homo sapiens out of Africa

Current fossil, genetic, and archeological data indicate that Homo sapiens originated in Africa in the late Middle Pleistocene. By the end of the Late Pleistocene, our species was distributed across every continent except Antarctica, setting the foundations for the subsequent demographic and cultural changes of the Holocene. The intervening processes remain intensely debated and a key theme in hominin evolutionary studies. We review archeological, fossil, environmental, and genetic data to evaluate the current state of knowledge on the dispersal of Homo sapiens out of Africa. The emerging picture of the dispersal process suggests dynamic behavioral variability, complex interactions between populations, and an intricate genetic and cultural legacy. This evolutionary and historical complexity challenges simple narratives and suggests that hybrid models and the testing of explicit hypotheses are required to understand the expansion of Homo sapiens into Eurasia.     

Electrostatic and non-electrostatic contributions of proteoglycans to the compressive equilibrium modulus of bovine articular cartilage

This study presents direct experimental evidence for assessing the electrostatic and non-electrostatic contributions of proteoglycans to the compressive equilibrium modulus of bovine articular cartilage. Immature and mature bovine cartilage samples were tested in unconfined compression and their depth-dependent equilibrium compressive modulus was determined using strain measurements with digital image correlation analysis. The electrostatic contribution was assessed by testing samples in isotonic and hypertonic saline; the combined contribution was assessed by testing untreated and proteoglycan-depleted samples.Though it is well recognized that proteoglycans contribute significantly to the compressive stiffness of cartilage, results demonstrate that the combined electrostatic and non-electrostatic contributions may add up to more than 98% of the modulus, a magnitude not previously appreciated. Of this contribution, about two thirds arises from electrostatic effects. The compressive modulus of the proteoglycan-depleted cartilage matrix may be as low as 3 kPa, representing less than 2% of the normal tissue modulus; experimental evidence also confirms that the collagen matrix in digested cartilage may buckle under compressive strains, resulting in crimping patterns. Thus, it is reasonable to model the collagen as a fibrillar matrix that can sustain only tension. This study also demonstrates that residual stresses in cartilage do not arise exclusively from proteoglycans, since cartilage remains curled relative to its in situ geometry even after proteoglycan depletion. These increased insights on the structure–function relationships of cartilage can lead to improved constitutive models and a better understanding of the response of cartilage to physiological loading conditions.     

Seasonal variation in pre‐fledging survival of lesser scaup Aythya affinis: hatch date effects depend on maternal body mass

Among temperate‐breeding birds, offspring survival and reproductive success are often inversely related to timing of breeding. The mechanisms that produce seasonal declines in offspring survival are not fully understood but may be related to temporal changes in parental quality, environmental quality, or both. We analyzed data for lesser scaup Aythya affinis to evaluate hypothesized effects of parental quality and date on pre‐fledging survival. Maternal quality, as indexed by body mass, did not have an independent effect on offspring survival in this species. Maternal body mass did not decline seasonally and did not have an independent effect on duckling survival. Although we did not detect an independent effect of hatch date on duckling survival, duckling survival declined seasonally for broods raised by lightweight females, indicating an interactive effect of maternal mass and date. We hypothesize that this interaction may be driven by seasonally declining food resources coupled with the influence of female condition on the ability to monopolize food resources or remain attentive to the brood. We also tested morphological predictions of the date hypothesis by examining physical characteristics of ducklings. When corrected for age and size, late‐hatched ducklings tended to have marginally larger digestive systems and smaller leg muscles than did early‐hatched birds. Abundances of intestinal parasites acquired through diet decreased marginally in late‐hatched ducklings. Results for digestive system and parasite infection patterns suggested that later‐hatched broods may shift diets, consistent with a contribution of environmental factors to seasonal variation in offspring survival. Taken together, our results suggest that both female attributes and environmental conditions may influence seasonal patterns of offspring survival in this species.     

Dedicated biomass crops can enhance biodiversity in the arable landscape

Suggestions that novel, non‐food, dedicated biomass crops used to produce bioenergy may provide opportunities to diversify and reinstate biodiversity in intensively managed farmland have not yet been fully tested at the landscape scale. Using two of the largest, currently available landscape‐scale biodiversity data sets from arable and biomass bioenergy crops, we take a taxonomic and functional trait approach to quantify and contrast the consequences for biodiversity indicators of adopting dedicated biomass crops on land previously cultivated under annual, rotational arable cropping. The abundance and community compositions of biodiversity indicators in fields of break and cereal crops changed when planted with the dedicated biomass crops, miscanthus and short rotation coppiced (SRC) willow. Weed biomass was consistently greater in the two dedicated biomass crops than in cereals, and invertebrate abundance was similarly consistently higher than in break crops. Using canonical variates analysis, we identified distinct plant and invertebrate taxa and trait‐based communities in miscanthus and SRC willows, whereas break and cereal crops tended to form a single, composite community. Seedbanks were shown to reflect the longer term effects of crop management. Our study suggests that miscanthus and SRC willows, and the management associated with perennial cropping, would support significant amounts of biodiversity when compared with annual arable crops. We recommend the strategic planting of these perennial, dedicated biomass crops in arable farmland to increase landscape heterogeneity and enhance ecosystem function, and simultaneously work towards striking a balance between energy and food security.     

River Red Gum (Eucalyptus camaldulensis Dehnh.) organic matter as a carbon source in the lower Darling River,Australia

The Darling River, in New South Wales, Australia, is a large semi-arid system with a highly variable flow regime, characterised by unpredictable events of flooding and drought. In large lowland rivers like the Darling, lateral (river-floodplain) interactions can greatly influence both physical and biological components of the system. The floodplain and riparian zone of the Darling River is dominated by River Red Gum (RRG), Eucalyptus camaldulensis. The large amount of organic matter they produce accumulates on the floodplain and on benches within the channel, and is subject to alternate periods of flooding and drying as a result of highly variable flows. This paper examines the effect of alternate periods of flooding and drying on the processing of E. camaldulensis organic matter. Results of the 6-month in situ field study, together with results from laboratory experiments comparing dissolved organic carbon (DOC) release from various RRG litter types, suggest that RRG leaves provide the most bio-available source of carbon to the system, while bark may be more important as a habitat for invertebrates and other fauna. Laboratory experiments exploring the effect of drying and re-flooding on litter breakdown and release of DOC suggested that the majority of DOC was released from RRG leaves in the first 24 h of inundation. Also, upon drying and re-flooding of the leaves, a smaller but significant release of DOC occurred. However, an alternative wet/dry cycle did not affect weight loss of the leaf litter. Results of the field and lab experiments suggest that RRG leaves represent an important source of carbon to the Darling River, with inputs being influenced by the highly variable flow regime.