Jaw muscle fiber type distribution in Hawaiian gobioid stream fishes: histochemical correlations with feeding ecology and behavior

Differences in fiber type distribution in the axial muscles of Hawaiian gobioid stream fishes have previously been linked to differences in locomotor performance, behavior, and diet across species. Using ATPase assays, we examined fiber types of the jaw opening sternohyoideus muscle across five species, as well as fiber types of three jaw closing muscles (adductor mandibulae A1, A2, and A3). The jaw muscles of some species of Hawaiian stream gobies contained substantial red fiber components. Some jaw muscles always had greater proportions of white muscle fibers than other jaw muscles, independent of species. In addition, comparing across species, the dietary generalists (Awaous guamensis and Stenogobius hawaiiensis) had a lower proportion of white muscle fibers in all jaw muscles than the dietary specialists (Lentipes concolor, Sicyopterus stimpsoni, and Eleotris sandwicensis). Among Hawaiian stream gobies, generalist diets may favor a wider range of muscle performance, provided by a mix of white and red muscle fibers, than is typical of dietary specialists, which may have a higher proportion of fast-twitch white fibers in jaw muscles to help meet the demands of rapid predatory strikes or feeding in fast-flowing habitats.     

Engineering central metabolic pathways for high-level flavonoid production in Escherichia coli

The identification of optimal genotypes that result in improved production of recombinant metabolites remains an engineering conundrum. In the present work, various strategies to reengineer central metabolism in Escherichia coli were explored for robust synthesis of flavanones, the common precursors of plant flavonoid secondary metabolites. Augmentation of the intracellular malonyl coenzyme A (malonyl-CoA) pool through the coordinated overexpression of four acetyl-CoA carboxylase (ACC) subunits from Photorhabdus luminescens (PlACC) under a constitutive promoter resulted in an increase in flavanone production up to 576%. Exploration of macromolecule complexes to optimize metabolic efficiency demonstrated that auxiliary expression of PlACC with biotin ligase from the same species (BirAPl) further elevated flavanone synthesis up to 1,166%. However, the coexpression of PlACC with Escherichia coli BirA (BirAEc) caused a marked decrease in flavanone production. Activity improvement was reconstituted with the coexpression of PlACC with a chimeric BirA consisting of the N terminus of BirAEc and the C terminus of BirAPl. In another approach, high levels of flavanone synthesis were achieved through the amplification of acetate assimilation pathways combined with the overexpression of ACC. Overall, the metabolic engineering of central metabolic pathways described in the present work increased the production of pinocembrin, naringenin, and eriodictyol in 36 h up to 1,379%, 183%, and 373%, respectively, over production with the strains expressing only the flavonoid pathway, which corresponded to 429 mg/liter, 119 mg/liter, and 52 mg/liter, respectively.     

Cell bank characterization and fermentation optimization for production of recombinant heavy chain C-terminal fragment of botulinum neurotoxin serotype E (rBoNTE(H(c)): antigen E) by Pichia pastoris

A process was developed for production of a candidate vaccine antigen, recombinant C-terminal heavy chain fragment of the botulinum neurotoxin serotype E, rBoNTE(H(c)) in Pichia pastoris. P. pastoris strain GS115 was transformed with the rBoNTE(H(c)) gene inserted into pHILD4 Escherichia coli-P. pastoris shuttle plasmid. The clone was characterized for genetic stability, copy number, and BoNTE(H(c)) sequence. Expression of rBoNTE(H(c)) from the Mut(+) HIS4 clone was confirmed in the shake-flask, prior to developing a fed-batch fermentation process at 5 and 19 L scale. The fermentation process consists of a glycerol growth phase in batch and fed-batch mode using a defined medium followed by a glycerol/methanol transition phase for adaptation to growth on methanol and a methanol induction phase resulting in the production of rBoNTE(H(c)). Specific growth rate, ratio of growth to induction phase, and time of induction were critical for optimal rBoNTE(H(c)) production and minimal proteolytic degradation. A computer-controlled exponential growth model was used for process automation and off-gas analysis was used for process monitoring. The optimized process had an induction time of 9 h on methanol and produced up to 3 mg of rBoNTE(H(c)) per gram wet cell mass as determined by HPLC and Western blot analysis.     

Structural characterization of a ribose-5-phosphate isomerase B from the pathogenic fungus Coccidioides immitis

Background

F-spondin is a multi-domain extracellular matrix (ECM) protein and a contact-repellent molecule that directs axon outgrowth and cell migration during development. The reelin_N domain and the F-spondin domain (FS domain) comprise a proteolytic fragment that interacts with the cell membrane and guides the projection of commissural axons to floor plate. The FS domain is found in F-spondins, mindins, M-spondin and amphiF-spondin.

Results

We present the crystal structure of human F-spondin FS domain at 1.95Å resolution. The structure reveals a Ca²⁺-binding C2 domain variant with an 8-stranded antiparallel β-sandwich fold. Though the primary sequences of the FS domains of F-spondin and mindin are less than 36% identical, their overall structures are very similar. The unique feature of F-spondin FS domain is the presence of three disulfide bonds associated with the N- and C-termini of the domain and a highly conserved N-linked glycosylation site. The integrin-binding motif found in mindin is not conserved in the F-spondin FS domain.

Conclusion

The structure of the F-spondin FS domain completes the structural studies of the multiple-domain ECM molecule. The homology of its core structure to a common Ca²⁺- and lipid-binding C2 domain suggests that the F-spondin FS domain may be responsible for part of the membrane targeting of F-spondin in its regulation of axon development. The structural properties of the FS domain revealed in this study pave the way for further exploration into the functions of F-spondin.     

ELECTRON MICROSCOPIC OBSERVATIONS OF RAT AND MOUSE CEREBELLUM IN TISSUE CULTURE

Closely ordered stages of myelin formation in cultures of newborn rat and mouse cerebellum, selected by direct light microscopy, were studied with the electron microscope. Electron micrographs of these cultures reveal the presence of neurons, axons, neuroglia, microglia, and ependymal cells. The appearance of the neuron is identical to that previously described in vivo. The neuroglial cell has long, branching processes, and its cytoplasm is characterized by packets of long, narrow fibrils. During myelin formation, a glial cell process surrounds the axon. This process may form an internal mesaxon and may spiral for several turns around the axon. Other glial cell processes may interdigitate with or overlay the innermost process to contribute to the multilamellated structure. The glial processes flatten and the cytoplasmic surfaces of the cell membrane come into contact to form the lamellae of the myelin sheath. These adhesions may be temporarily incomplete as evidenced by sequestered islands of glial cytoplasm among the myelin lamellae. Ultimately, a compact, apparently spiral, myelin sheath is formed. These findings are discussed in relation to in vivo central myelin formation.     

Differences between observed and predicted energy costs at rest and during exercise in three subsistence-level populations

Estimates of daily energy expenditure are important for many areas of research in human ecology and adaptability. The most common technique for estimating human energy expenditure under field conditions, the factorial method, generally relies on activity-specific energy costs derived from published sources, based largely on North American and European subjects. There is concern that such data may not be appropriate for non-Western populations because of differences in metabolic costs. The present study addresses this concern by comparing measured vs. predicted energy costs at rest and during sub-maximal exercise in 83 subjects (52 males, 31 females) from three subsistence-level populations (Siberian herders and high-land and coastal Ecuadorian farmers). Energy costs at rest (i.e., lying, sitting and standing) and while performing a standard stepping exercise did not significantly differ among the three groups. However, resting energy costs were significantly elevated over predicted levels (+16% in men, +11% in women), whereas exercising costs were comparable to predicted values (?6% in men, +3% in women). Elevations in resting energy needs appear to reflect responses to thermal stress. These results indicate that temperature adjustments of resting energy costs are critical for accurately predicting daily energy needs among traditionally living populations. o 1996 Wiley-Liss, Inc.     

Cellular retinoic acid-binding protein and its relationship to the biological activity of four synthetic retinoids in hamster tracheal organ culture

Summary The mechanism of action of retinoid in reversing keratinization in hamster trachea is yet unknown. The purpose of this study was to determine if cellular retinoic acid binding protein (CRABP) is present in tracheal epithelium following incubation in serum-free, vitamin A-deficient culture medium for 10 days, and if the effectiveness of a retinoid in reversing keratinization in organ culture is correlated with its ability to compete for CRABP sites. The cytosol prepared from tracheal cultures contained CRABP at a concentration of 2.61 pmoles per mg protein. Of the four retinoids with carboxyl end group selected for the study, two of the biological active retinoids competed for the CRABP sites. However, no correlation was observed between the biological activity of the inactive retinoids and their ability to associate with the CRABP sites. These results indicate that even though the action of retinoid may be mediated by retinoid binding protein, it cannot be used as a sole predicator of retinoid response in hamster trachea. This investigation was supported by Contract N01-CP-31012 and U. S. P. H. Grants CA30512 and CA32428, which were awarded by the Division of Cancer Etiology, National Cancer Institute, DHHS. Editor's Statement Tracheal organ cultures provide a useful model for the study of epithelial differentiation and carcinogenesis. Much attention has been given to the action of retinoids in this process. Mehta et al. demonstrate a lack of correlation between biological activity and specific cytosolic binding of members of this class of compounds, pointing out the need for a more complete biochemical understanding of the mechanism of action and active forms of retinoids in this and other systems in vivo and in vitro. David W. Barnes     

Deep sequencing reveals clonal evolution patterns and mutation events associated with relapse in B-cell lymphomas

Background

Molecular mechanisms associated with frequent relapse of diffuse large B-cell lymphoma (DLBCL) are poorly defined. It is especially unclear how primary tumor clonal heterogeneity contributes to relapse. Here, we explore unique features of B-cell lymphomas - VDJ recombination and somatic hypermutation - to address this question.

Results

We performed high-throughput sequencing of rearranged VDJ junctions in 14 pairs of matched diagnosis-relapse tumors, among which 7 pairs were further characterized by exome sequencing. We identify two distinctive modes of clonal evolution of DLBCL relapse: an early-divergent mode in which clonally related diagnosis and relapse tumors diverged early and developed in parallel; and a late-divergent mode in which relapse tumors developed directly from diagnosis tumors with minor divergence. By examining mutation patterns in the context of phylogenetic information provided by VDJ junctions, we identified mutations in epigenetic modifiers such as KMT2D as potential early driving events in lymphomagenesis and immune escape alterations as relapse-associated events.

Conclusions

Altogether, our study for the first time provides important evidence that DLBCL relapse may result from multiple, distinct tumor evolutionary mechanisms, providing rationale for therapies for each mechanism. Moreover, this study highlights the urgent need to understand the driving roles of epigenetic modifier mutations in lymphomagenesis, and immune surveillance factor genetic lesions in relapse.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0432-0) contains supplementary material, which is available to authorized users.     

THE EFFECTIVE SIZE OF A HIERARCHICALLY STRUCTURED POPULATION

A knowledge of the effective size of a population (N_e) is important in understanding its current and future evolutionary potential. Unfortunately, the effective size of a hierarchically structured population is not, in general, equal to the sum of its parts. In particular, the inbreeding structure has a major influence on N_e. Here I link N_e to Wright's hierarchical measures of inbreeding, F_IS and F_ST, for an island-structured population (or metapopulation) of size N_T. The influence of F_ST depends strongly on the degree to which island productivity is regulated. In the absence of local regulation (the interdemic model), interdemic genetic drift reduces N_e. When such drift is combined with local inbreeding under otherwise ideal conditions, the effects of F_IS and F_ST are identical: increasing inbreeding either within or between islands reduces N_e, with N_e = N_T/[(1 + F_IS)(1 + F_ST) ? 2F_ISF_ST]. However, if islands are all equally productive because of local density regulation (the traditional island model), then N_e = N_T/[(1 + F_IS)(1 –F_ST)] and the effect of F_ST is reversed. Under the interdemic model, random variation in the habitat quality (and hence productivity) of islands act to markedly decrease N_e. This variation has no effect under the island model because, by definition, all islands are equally productive. Even when no permanent island structure exists, spatial differences in habitat quality can significantly increase the overall variance in reproductive success of both males and females and hence lower N_e. Each of these basic results holds when other nonideal factors are added to the model. These factors, deviations from a 1:1 sex ratio, greater than Poisson variance in female reproductive success, and variation in male mating success due to polygynous mating systems, all act to lower N_e. The effects of male and female variance on N_e have important differences because only females affect island productivity. Finally, it is noted that to use these relationships, F_IS and F_ST must be estimated according to Wright's definition (and corrected to have a zero expectation under the null model). A commonly used partitioning (θ, θ_g) can be biased if either island size or the number of islands is small.