Biologically driven isotopic fractionations in bivalves: from palaeoenvironmental problem to palaeophysiological proxy

Traditional bulk stable isotope (δ¹⁸O and δ¹³C) and clumped isotope (Δ₄₇) records from bivalve shells provide invaluable histories of Earth's local and global climate change. However, biologically driven isotopic fractionations (BioDIFs) can overprint primary environmental signals in the shell. Here, we explore how conventional measurements of δ¹⁸O, δ¹³C, and Δ₄₇ in bivalve shells can be re-interpreted to investigate these physiological processes deliberately. Using intrashell Δ₄₇ and δ¹⁸O alignment as a proxy for equilibrium state, we separately examine fractionations and/or disequilibrium occurring in the two major stages of the biomineralisation process: the secretion of the extrapallial fluid (EPF) and the precipitation of shell material from the EPF. We measured δ¹⁸O, δ¹³C, and Δ₄₇ in fossil shells representing five genera (Lahillia, Dozyia, Eselaevitrigonia, Nordenskjoldia, and Cucullaea) from the Maastrichtian age [66–69 million years ago (Ma)] López de Bertodano Formation on Seymour Island, Antarctica. Material was sampled from both the outer and inner shell layers (OSL and ISL, respectively), which precipitate from separate EPF reservoirs. We find consistent δ¹⁸O values across the five taxa, indicating that the composition of the OSL can be a reliable palaeoclimate proxy. However, relative to the OSL baseline, ISLs of all taxa show BioDIFs in one or more isotopic parameters. We discuss/hypothesise potential origins of these BioDIFs by synthesising isotope systematics with the physiological processes underlying shell biomineralisation. We propose a generalised analytical and interpretive framework that maximises the amount of palaeoenvironmental and palaeobiological information that can be derived from the isotopic composition of fossil shell material, even in the presence of previously confounding ‘vital effects’. Applying this framework in deep time can expand the utility of δ¹⁸O, δ¹³C, and Δ₄₇ measurements from proxies of past environments to proxies for certain biomineralisation strategies across space, time, and phylogeny among Bivalvia and other calcifying organisms.     

Disturbance and trajectory of change in a stream fish community over four decades

Communities can change gradually or abruptly, and directionally (to an alternate state) or non-directionally. We briefly review the history of theoretical and empirical perspectives on community change, and propose a new framework for viewing temporal trajectories of communities in multivariate space. We used a stream fish dataset spanning 40 years (1969–2008) in southern Oklahoma, USA, emphasizing our own 1981–2008 collections which included well-documented, extreme drought and flood events, to assess dynamics of and environmental factors affecting the fish community. We evaluated the trajectory of the Brier Creek community in multivariate space relative to trajectories in 27 published studies, and for Brier Creek fish, tested hypotheses about gradual versus event-driven changes and persistence of shifts to alternate states. Most species were persistent, qualitatively, across the four decades, but varied widely in abundance, with some having unusually strong reproduction after extreme droughts. The community had an early period of relatively gradual and directional change, but greater displacement than predicted at random after two consecutive extreme droughts midway through the study (1998 and 2000). But, the community subsequently returned toward its former state in the last decade. This fish community is characterized by species that are tolerant of environmental extremes, and have life history traits that facilitate population recovery. The community appears “loosely stable” about a long-term average condition, but the impacts of the two consecutive droughts were substantial, and may foretell future dynamics of this or other communities in a changed global climate if disturbance events become more frequent or severe.     

Hepatitis C virus envelope glycoprotein E2 glycans modulate entry, CD81 binding, and neutralization

Hepatitis C virus (HCV) is a major human pathogen that causes serious liver disease, including cirrhosis and hepatocellular carcinoma. The primary target cells of HCV are hepatocytes, and entry is restricted by interactions of the envelope glycoproteins, E1 and E2, with cellular receptors. E1 and E2 form noncovalently linked heterodimers and are heavily glycosylated. Glycans contribute to protein folding and transport as well as protein function. In addition, glycans associated with viral envelopes mask important functional domains from the immune system and attenuate viral immunogenicity. Here, we explored the role of N- and O-linked glycans on E2, which is the receptor binding subunit of the HCV envelope. We identified a number of glycans that are critical for viral entry. Importantly, we showed that the removal of several glycans significantly increased the inhibition of entry by sera from HCV-positive individuals. Only some of the glycans that affected entry and neutralization were also important for CD81 binding. Our results show that HCV envelope-associated glycans play a crucial role in masking functionally important regions of E2 and suggest a new strategy for eliciting highly neutralizing antibodies against this virus.     

Production and purification of the bacterial autolysin N-acetylmuramoyl-L-alanine amidase B from Pseudomonas aeruginosa

The bacterial cell wall heteropolymer peptidoglycan is not a static structure as it is constantly being made and recycled throughout the bacterium's life cycle. This turnover of peptidoglycan is a highly coordinated event involving a complement of autolytic enzymes that include those with specificity for either the carbohydrate or the peptide linkages of peptidoglycan. One major class of these autolysins are the N-acetylmuramoyl-L-alanine amidases which cleave the amide linkage between the stem peptides and the lactyl moiety of muramoyl residues. They are required in the periplasm for cell separation during division and in both the periplasm and cytoplasm to trim soluble released PG fragments during turnover for recycling. The gene encoding N-acetylmuramoyl-L-alanine amidase B in Pseudomonas aeruginosa was cloned and over-expressed in Escherichia coli. The recombinant protein with a C-terminal His-tag was purified to apparent homogeneity by a combination of affinity and cation-exchange chromatographies using Ni(2+)NTA-agarose and Source S, respectively. Four separate assays involving zymography, light scattering, HPLC and MALDI-TOF mass spectrometry were used to confirm the activity of the protein as an N-acetylmuramoyl-L-alanine amidase.     

Effects of maternal and embryo characteristics on post-fertilization provisioning in fishes of the genus <Emphasis Type="Italic">Gambusia</Emphasis>

Maternal provisioning of embryos in Gambusia (Poeciliidae) entails both production of large, yolky eggs and mother-to-embryo transfer of nutrients, the latter of which is readily quantified using injection of radiolabeled nutrients. We assayed patterns of nutrient transfer in broods of 26 Gambusia geiseri and 23 Gambusia affinis females, using injection of tritiated leucine. We examined maternal and embryo characteristics affecting the instantaneous rate of transfer and characterized the pattern of transfer to individual embryos within broods. Maternal (female size and condition) and brood characteristics (mean embryo size, developmental stage, brood size) did not predict the mean level of nutrient transfer to embryos in a brood for either species. Within broods, individual provisioning of embryos was not related to developmental stage, but was related to embryo mass in G. affinis with nutrient transfer higher to larger embryos. In addition, overall within-brood variation in nutrient transfer, measured as coefficient of variation in embryo radioactivity, was higher in G. affinis than in G. geiseri.     

A high-density consensus map of barley linking DArT markers to SSR,RFLP and STS loci and agricultural traits

Background

Wheat is an excellent species to study freezing tolerance and other abiotic stresses. However, the sequence of the wheat genome has not been completely characterized due to its complexity and large size. To circumvent this obstacle and identify genes involved in cold acclimation and associated stresses, a large scale EST sequencing approach was undertaken by the Functional Genomics of Abiotic Stress (FGAS) project.

Results

We generated 73,521 quality-filtered ESTs from eleven cDNA libraries constructed from wheat plants exposed to various abiotic stresses and at different developmental stages. In addition, 196,041 ESTs for which tracefiles were available from the National Science Foundation wheat EST sequencing program and DuPont were also quality-filtered and used in the analysis. Clustering of the combined ESTs with d2_cluster and TGICL yielded a few large clusters containing several thousand ESTs that were refractory to routine clustering techniques. To resolve this problem, the sequence proximity and "bridges" were identified by an e-value distance graph to manually break clusters into smaller groups. Assembly of the resolved ESTs generated a 75,488 unique sequence set (31,580 contigs and 43,908 singletons/singlets). Digital expression analyses indicated that the FGAS dataset is enriched in stress-regulated genes compared to the other public datasets. Over 43% of the unique sequence set was annotated and classified into functional categories according to Gene Ontology.

Conclusion

We have annotated 29,556 different sequences, an almost 5-fold increase in annotated sequences compared to the available wheat public databases. Digital expression analysis combined with gene annotation helped in the identification of several pathways associated with abiotic stress. The genomic resources and knowledge developed by this project will contribute to a better understanding of the different mechanisms that govern stress tolerance in wheat and other cereals.     

Stress hormone masculinizes female morphology and behaviour

Sex steroids play major roles in vertebrate sexual differentiation. Unexpectedly, we now find that exposure to elevated levels of the naturally occurring stress hormone cortisol can also masculinize sexually dimorphic morphological characters and behaviour in adult female mosquitofish (Gambusia affinis) in a dose-dependent manner. Females masculinized by cortisol developed elongated anal fins with distal tip features similar to those of mature males. Most masculinized females also attempted to copulate when placed with normal females. Although the mechanism of masculinization is currently unknown, we propose a role for an enzyme that both inactivates cortisol and catalyzes the final step in synthesis of a major teleost androgen. This mechanism may also help explain some previously reported effects of stress on sexual development across vertebrate taxa. Our findings underscore the need to understand the full range of chemicals, both naturally occurring hormones and human-produced endocrine disruptors, that can influence sexual differentiation and reproductive function.     

Adaptive Changes in Cardiac Fibroblast Morphology and Collagen Organization as a Result of Mechanical Environment

There is a growing body of work in the literature that demonstrates the significant differences between 2D versus 3D environments in cell morphologies, spatial organization, cell-ECM interactions, and cell signaling. The 3D environments are generally considered more realistic tissue models both because they offer cells a surrounding environment rather than just a planar surface with which to interact, and because they provide the potential for more diverse mechanical environments. Many studies have examined cellular-mediated contraction of 3D matrices; however, because the 3D environment is much more complex and the scale more difficult to study, little is known regarding how mechanical environment, cell and collagen architecture, and collagen remodeling are linked. In the current work, we examine the spatial arrangement of neonatal cardiac fibroblasts and the associated collagen organization in constrained and unconstrained collagen gels over a 24 h period. Collagen gels that are constrained by their physical attachment to a mold and similar gels, which have been detached (unconstrained) from the mold and subsequently contract, offer two simple mechanical models by which the mechanisms of tissue homeostasis and wound repair might be examined. Our observations suggest the presence of two mechanical regimes in the unconstrained gels: an outer ring where cells orient circumferentially and local collagen aligns with the elongated cells; and a central region where unaligned stellate/bipolar cells are radially surrounded by collagen, similar to that seen throughout constrained gels. The evolving organization of cell alignment and surrounding collagen organization suggests that cellular response may be due to the cellular perception of the apparent stiffness of local physical environment.     

Early phase bronchoconstriction in the mouse requires allergen-specific IgG

Allergen provocation of allergic asthma patients is often characterized by an initial period of bronchoconstriction, or early phase reaction (EPR), that leads to maximal airway narrowing within 15-30 min, followed by a recovery period returning airway function to baseline within 1-2 h. In this study, we used a defined OVA provocation model and mice deficient for specific leukocyte populations to investigate the cellular/molecular origins of the EPR. OVA-sensitized/challenged wild-type (C57BL/6J) mice displayed an EPR following OVA provocation. However, this response was absent in gene knockout animals deficient of either B or T cells. Moreover, transfer of OVA-specific IgG, but not IgE, before the OVA provocation, was capable of inducing the EPR in both strains of lymphocyte-deficient mice. Interestingly, an EPR was also observed in sensitized/challenged mast cell-deficient mice following an OVA provocation. These data show that the EPR in the mouse is an immunologically based pathophysiological response that requires allergen-specific IgG but occurs independent of mast cell activities. Thus, in the mouse the initial period of bronchoconstriction following allergen exposure may involve neither mast cells nor IgE-mediated events.