Identification of a new gene (rat TM6P1) encoding a fasting-inducible, integral membrane protein with six transmembrane domains

We describe the isolation of a new gene that encodes a membrane-integrated protein with six transmembrane domains, termed TM6P1. A 403-bp expressed sequence tag was isolated from fasted rat liver subtracted cDNA library, and its full-length cDNA is 1482 bp long. It contains an open reading frame of 816 bp and is predicted to encode a 271-amino acid protein with a deduced mass of 29520 Da. A sequence homology search failed to show significant correspondence to any known protein in the databank. TM6P1 has six highly hydrophobic domains that are predicted to be transmembrane helices. Consistent with this prediction, the TM6P1-EGFP fusion protein was shown to localize to the plasma membrane. TM6P1 mRNA is widely expressed in rat tissues, with placenta and liver being the most abundant sites. Fasting increased TM6P1 mRNA nearly two-fold in liver. Taken together, our data suggest that TM6P1 is a unique new membrane integral protein that might have a function important during fasting-induced catabolism.     

Lack of Protective Osmolytes Limits Final Cell Density and Volumetric Productivity of Ethanologenic Escherichia coli KO11 during Xylose Fermentation

Limited cell growth and the resulting low volumetric productivity of ethanologenic Escherichia coli KO11 in mineral salts medium containing xylose have been attributed to inadequate partitioning of carbon skeletons into the synthesis of glutamate and other products derived from the citrate arm of the anaerobic tricarboxylic acid pathway. The results of nuclear magnetic resonance investigations of intracellular osmolytes under different growth conditions coupled with those of studies using genetically modified strains have confirmed and extended this hypothesis. During anaerobic growth in mineral salts medium containing 9% xylose (600 mM) and 1% corn steep liquor, proline was the only abundant osmolyte (71.9 nmol ml⁻¹ optical density at 550 nm [OD₅₅₀] unit⁻¹), and growth was limited. Under aerobic conditions in the same medium, twice the cell mass was produced, and cells contained a mixture of osmolytes: glutamate (17.0 nmol ml⁻¹ OD₅₅₀ unit⁻¹), trehalose (9.9 nmol ml⁻¹ OD₅₅₀ unit⁻¹), and betaine (19.8 nmol ml⁻¹ OD₅₅₀ unit⁻¹). Two independent genetic modifications of E. coli KO11 (functional expression of Bacillus subtilis citZ encoding NADH-insensitive citrate synthase; deletion of ackA encoding acetate kinase) and the addition of a metabolite, such as glutamate (11 mM) or acetate (24 mM), as a supplement each increased the intracellular glutamate pool during fermentation, doubled cell growth, and increased volumetric productivity. This apparent requirement for a larger glutamate pool for increased growth and volumetric productivity was completely eliminated by the addition of a protective osmolyte (2 mM betaine or 0.25 mM dimethylsulfoniopropionate), consistent with adaptation to osmotic stress rather than relief of a specific biosynthetic requirement.     

A computational model of in vitro angiogenesis based on extracellular matrix fibre orientation

Recent interest in the process of vascularisation within the biomedical community has motivated numerous new research efforts focusing on the process of angiogenesis. Although the role of chemical factors during angiogenesis has been well documented, the role of mechanical factors, such as the interaction between angiogenic vessels and the extracellular matrix, remains poorly understood. In vitro methods for studying angiogenesis exist; however, measurements available using such techniques often suffer from limited spatial and temporal resolutions. For this reason, computational models have been extensively employed to investigate various aspects of angiogenesis. This paper outlines the formulation and validation of a simple and robust computational model developed to accurately simulate angiogenesis based on length, branching and orientation morphometrics collected from vascularised tissue constructs. Microvessels were represented as a series of connected line segments. The morphology of the vessels was determined by a linear combination of the collagen fibre orientation, the vessel density gradient and a random walk component. Excellent agreement was observed between computational and experimental morphometric data over time. Computational predictions of microvessel orientation within an anisotropic matrix correlated well with experimental data. The accuracy of this modelling approach makes it a valuable platform for investigating the role of mechanical interactions during angiogenesis.     

Effect of acclimation temperature on the upper thermal tolerance of Colorado River cutthroat trout Oncorhynchus clarkii pleuriticus: thermal limits of a North American salmonid

In an effort to explore the thermal limitations of Colorado River cutthroat trout Oncorhynchus clarkii pleuriticus, the critical thermal maxima (T_cmax) of 1+ year Lake Nanita strain O. c. pleuriticus were evaluated when acclimated to 10, 15 and 20° C. The mean ±s.d. T_cmax for O. c. pleuriticus acclimated to 10° C was 24·6 ± 2·0°C (n = 30), for 15° C‐acclimated fish was 26·9 ± 1·5° C (n = 23) and for 20° C‐acclimated fish was 29·4 ± 1·1° C (n = 28); these results showed a marked thermal acclimation effect (Q₁₀ = 1·20). Interestingly, there was a size effect within treatments, wherein the T_cmax of larger fish was significantly lower than that of smaller fish acclimated to the same temperature. The critical thermal tolerances of age 0 year O. c. pleuriticus were also evaluated from three separate populations: Lake Nanita, Trapper Creek and Carr Creek reared under ‘common‐garden’ conditions prior to thermal acclimation. The Trapper Creek population had significantly warmer T_cmax than the Lake Nanita population, but that of the Carr Creek fish had T_cmax similar to both Trapper Creek and Lake Nanita fish. A comparison of these O. c. pleuriticus T_cmax results with those of other stream‐dwelling salmonids suggested that O. c. pleuriticus are less resistant to rapid thermal fluctuations when acclimated to cold temperatures, but can tolerate similar temperatures when acclimated to warmer temperatures.     

A manipulative experiment to evaluate predicted changes in intertidal, macro-faunal assemblages after contamination by heavy metals

Concentrations of heavy metals (zinc, copper and lead) were manipulated experimentally to test the hypotheses about effects on intertidal, soft-sediment assemblages of animals in two sand-flats in Port Hacking, Australia. Hypotheses about changes in the structure and composition of whole assemblages and changes in mean abundance and variability of individual taxa were tested. Specific hypotheses were derived a priori from repeated observations of assemblages in urban and non-urban areas of Port Hacking.After manipulation, concentrations of metals were similar to those in sediments near urban areas. Nevertheless, responses of assemblages to the increased concentrations of metals were weak. Polychaetes, spionids and amphipods responded to experimental treatments. Changes were, however, not consistent among times and places and generally not in agreement with what had been predicted. Significant spatial and temporal variability were detected for all variables investigated. Increased concentrations of metals did not affect variability or overall structure of assemblages. Thus, there was little evidence that increased concentrations of metals caused benthic assemblages in pristine areas to become more similar to those in areas contaminated by human activities.Several potential explanations for the discrepancy between previously observed correlative patterns and the results presented here are discussed. These include a critical assessment of different aspects of the experimental study, such as lack of statistical power, insufficient basis for prediction, artefacts due to experimental procedures and issues to do with the difference between evidence based on correlation and manipulation. Explicit comparisons showed that there were significant effects of physical disturbance due to repeated sampling and that assemblages of animals at the start of the experiment were different from those previously observed in uncontaminated areas. These observations were surprising and made interpretation more difficult. Nevertheless, it is possible that the metals investigated really contribute only marginally to previously observed differences between urban and non-urban areas. Repeated comparisons between observations of patterns and manipulative experiments like these can only improve the basis for prediction and the power of current mechanistic models.     

三种绿叶挥发性物质对云南切梢小蠹寄主定位行为的干扰作用

为了研究环境中非寄主阔叶植物释放出的绿叶挥发性物质（GLVs）对针叶树蛀干害虫云南切梢小蠹Tomicus yunnanesis的影响, 选取了(E)-2-己烯醛、 (E)-2-己烯醇和(Z)-3-己烯醇3种释放量较大的绿叶挥发性物质, 通过室内松梢取食试验测试了单组分及两两混合后对云南切梢小蠹寄主定位行为的干扰作用。结果表明： 源于阔叶植物的3种绿叶挥发性物质及其混合物能够不同程度干扰云南切梢小蠹的寄主定位行为。当虫放入广口瓶12 h后, 3个单组分绿叶挥发性物质处理组［A： (E)-2-己烯醛, P＜0.01; B： (E)-2-己烯醇, P＜0.01; C： (Z)-3-己烯醇, P＜0.01］及2个混合组分［D： (E)-2-己烯醛+(E)-2-己烯醇, P＜0.01）; E： (E)-2-己烯醛+(Z)-3-己烯醇, P＜0.01］中滞留在松梢外部的虫数与对照组相比都有显著性差异, 绿叶挥发性物质的存在显著降低了云南切梢小蠹侵害云南松松梢的概率。但是, 24 h后只有D组（P＜0.01）和E组（P＜0.01）滞留在松梢外部的虫数与对照组相比具有显著性差异, 在48 h后只有D组（P＜0.01）与对照相比仍具有显著性差异。本研究为利用非寄主植物的次生代谢产物防治云南切梢小蠹进行了有益的探索。     

Specificity and Structure of a High Affinity Activin Receptor-like Kinase 1 (ALK1) Signaling Complex

Activin receptor-like kinase 1 (ALK1), an endothelial cell-specific type I receptor of the TGF-β superfamily, is an important regulator of normal blood vessel development as well as pathological tumor angiogenesis. As such, ALK1 is an important therapeutic target. Thus, several ALK1-directed agents are currently in clinical trials as anti-angiogenic cancer therapeutics. Given the biological and clinical importance of the ALK1 signaling pathway, we sought to elucidate the biophysical and structural basis underlying ALK1 signaling. The TGF-β family ligands BMP9 and BMP10 as well as the three type II TGF-β family receptors ActRIIA, ActRIIB, and BMPRII have been implicated in ALK1 signaling. Here, we provide a kinetic and thermodynamic analysis of BMP9 and BMP10 interactions with ALK1 and type II receptors. Our data show that BMP9 displays a significant discrimination in type II receptor binding, whereas BMP10 does not. We also report the crystal structure of a fully assembled ternary complex of BMP9 with the extracellular domains of ALK1 and ActRIIB. The structure reveals that the high specificity of ALK1 for BMP9/10 is determined by a novel orientation of ALK1 with respect to BMP9, which leads to a unique set of receptor-ligand interactions. In addition, the structure explains how BMP9 discriminates between low and high affinity type II receptors. Taken together, our findings provide structural and mechanistic insights into ALK1 signaling that could serve as a basis for novel anti-angiogenic therapies.     

Biannual Spawning and Temporal Reproductive Isolation in Acropora Corals

Coral spawning on the oceanic reef systems of north-western Australia was recently discovered during autumn and spring, but the degree to which species and particularly colonies participated in one or both of these spawnings was unknown. At the largest of the oceanic reef systems, the participation by colonies in the two discrete spawning events was investigated over three years in 13 species of Acropora corals (n = 1,855 colonies). Seven species spawned during both seasons; five only in autumn and one only in spring. The majority of tagged colonies (n = 218) spawned once a year in the same season, but five colonies from three species spawned during spring and autumn during a single year. Reproductive seasonality was not influenced by spatial variation in habitat conditions, or by Symbiodinium partners in the biannual spawner Acropora tenuis. Colonies of A. tenuis spawning during different seasons separated into two distinct yet cryptic groups, in a bayesian clustering analysis based on multiple microsatellite markers. These groups were associated with a major genetic divergence (G”_ST = 0.469), despite evidence of mixed ancestry in a small proportion of individuals. Our results confirm that temporal reproductive isolation is a common feature of Acropora populations at Scott Reef and indicate that spawning season is a genetically determined trait in at least A. tenuis. This reproductive isolation may be punctuated occasionally by interbreeding between genetic groups following favourable environmental conditions, when autumn spawners undergo a second annual gametogenic cycle and spawn during spring.     

Identification of a selective nonpeptide antagonist of the anaphylatoxin C3a receptor that demonstrates antiinflammatory activity in animal models

The anaphylatoxin C3a is a potent chemotactic peptide and inflammatory mediator released during complement activation which binds to and activates a G-protein-coupled receptor. Molecular cloning of the C3aR has facilitated studies to identify nonpeptide antagonists of the C3aR. A chemical lead that selectively inhibited the C3aR in a high throughput screen was identified and chemically optimized. The resulting antagonist, N(2)-[(2,2-diphenylethoxy)acetyl]-L-arginine (SB 290157), functioned as a competitive antagonist of (125)I-C3a radioligand binding to rat basophilic leukemia (RBL)-2H3 cells expressing the human C3aR (RBL-C3aR), with an IC(50) of 200 nM. SB 290157 was a functional antagonist, blocking C3a-induced C3aR internalization in a concentration-dependent manner and C3a-induced Ca(2+) mobilization in RBL-C3aR cells and human neutrophils with IC(50)s of 27.7 and 28 nM, respectively. SB 290157 was selective for the C3aR in that it did not antagonize the C5aR or six other chemotactic G protein-coupled receptors. Functional antagonism was not solely limited to the human C3aR; SB 290157 also inhibited C3a-induced Ca(2+) mobilization of RBL-2H3 cells expressing the mouse and guinea pig C3aRS: It potently inhibited C3a-mediated ATP release from guinea pig platelets and inhibited C3a-induced potentiation of the contractile response to field stimulation of perfused rat caudal artery. Furthermore, in animal models, SB 290157, inhibited neutrophil recruitment in a guinea pig LPS-induced airway neutrophilia model and decreased paw edema in a rat adjuvant-induced arthritis model. This selective antagonist may be useful to define the physiological and pathophysiological roles of the C3aR.     

Mathematical Modelling of Mycobacterium tuberculosis VNTR Loci Estimates a Very Slow Mutation Rate for the Repeats

Minisatellites are highly variable tandem repeats used for over 20 years in humans for DNA fingerprinting. In prokaryotes fingerprinting techniques exploiting VNTR (variable number of tandem repeats) polymorphisms have become widely used recently in bacterial typing. However although many investigations into the mechanisms underlying minisatellite variation in humans have been performed, relatively little is known about the processes that mediate bacterial minisatellite polymorphism. An understanding of this is important since it will influence how the results from VNTR experiments are interpreted. The minisatellites of Mycobacterium tuberculosis are well characterized since they are some of the few polymorphic loci in what is otherwise a very homogeneous organism. Using VNTR results from a well-defined and characterized set of M. tuberculosis strains we show that the repeats at a locus are likely to evolve by stepwise contraction or expansion in the number of repeats. A stochastic continuous-time population mathematical model was developed to simulate the evolution of the repeats. This allowed estimation of the tendency of the repeats to increase or decrease and the rate at which they change. The majority of loci tend to lose rather than gain repeats. All of the loci mutate extremely slowly, with an average rate of 2.3 x 10(-8), which is 350 times slower than that of a set of VNTR repeats with similar diversity observed experimentally in Escherichia coli. This suggests that the VNTR profile of a strain of M. tuberculosis will be indicative of its clonal lineage and will be unlikely to vary in epidemiologically-related strains.