Persistence and stability of lotic invertebrate communities in New Zealand

1. Persistence and stability of lotic invertebrate communities were determined at an annual time scale over a 9‐year period (1990–98) at 26 river sites over the northern half of New Zealand. In addition, a number of water quality variables were measured monthly and flow information collected continuously over the same period at each site. 2. The aim of the study was to describe the levels of interannual variability in invertebrate communities, and relate community changes to variability in environmental conditions. The consequences of this temporal variability for the sensitivity of predictive models were also investigated. 3. Levels of change in environmental conditions varied significantly between years, but were relatively similar across sites. In contrast, community persistence (similarity between years in species assemblage composition), and stability (similarity between years with respect to relative abundance of species in the community) both varied significantly between sites, but changes between years were similar. Community stability was highest at sites with relatively harsh flow conditions (high coefficient of variation, high relative size of floods), and was also greater in communities dominated by Ephemeroptera. 4. Relationships between change in environmental conditions and changes in community composition and structure were relatively weak for most individual sites. However, when average levels of change for each of the 26 sites were used, communities showed greater persistence under conditions where flow conditions remained relatively constant. Water quality changes had no significant effect on community persistence when assessed for all 26 sites combined. 5. Results from this study suggest that lotic invertebrate communities fluctuate around a relatively stable state, at least over a 9‐year period. However, the extent of interannual variation in community composition and structure observed, along with the relatively low degree of cluster fidelity observed within a single region, suggests that predictive models based on reference site conditions extrapolated over several years should be applied with caution in New Zealand streams.     

A novel model and molecular therapy for Z alpha-1 antitrypsin deficiency

Animal models that closely resemble human disease can present a challenge. Particularly so in alpha-1 antitrypsin deficiency (α(1)ATD), as the mouse alpha-1 antitrypsin (α(1)AT) cluster encodes five highly related genes compared with the one in humans. The mouse PI2 homologue is closest to the α(1)AT human gene. We have changed the equivalent mouse site that results in the Z variant in man (Glu342Lys) and made both the "M" and "Z" mouse PI2 α(1)AT proteins. We have tested the ability of a small-molecular-weight compound CG to alleviate polymerisation of these mouse α(1)AT proteins as it has been shown to reduce aggregates of Z α(1)AT in man. We found that (1) CG specifically reduces the formation of polymers of recombinant mouse "Z" protein but not "M" protein; (2) whereas there is significantly more α(1)AT secreted from Chinese Hamster Ovary cells transfected with the mouse "M" α(1)AT gene than with the "Z" (20.8?±?3.9 and 6.7?±?3.6, respectively; P?相似文献   

Glycosidic bond specificity of glucansucrases: on the role of acceptor substrate binding residues

Many lactic acid bacteria produce extracellular α-glucan polysaccharides using a glucansucrase and sucrose as glucose donor. The structure and the physicochemical properties of the α-glucans produced are determined by the nature of the glucansucrase. Typically, the α-glucans contain two types of α-glycosidic linkages, for example, (α1-2), (α1-3), (α1-4) or (α1-6), which may be randomly or regularly distributed. Usually, the α-glucan chains are also branched, which gives rise to an additional level of complexity. Even though the first crystal structure was reported in 2010, our current understanding of the structure–function relationships of glucansucrases is not advanced enough to predict the α-glucan specificity from the sequence alone. Nevertheless, based on sequence alignments and site-directed mutagenesis, a few amino acid residues have been identified as being important for the glycosidic bond specificity of glucansucrases. A new development in GH70 research was the identification of a cluster of α-glucan disproportionating enzymes. Here, we discuss the current insights into the structure–function relationships of GH70 enzymes in the light of the recently determined crystal structure of glucansucrases.     

Non-random interactions within and across guilds shape the potential to coexist in multi-trophic ecological communities

Theory posits that the persistence of species in ecological communities is shaped by their interactions within and across trophic guilds. However, we lack empirical evaluations of how the structure, strength and sign of biotic interactions drive the potential to coexist in diverse multi-trophic communities. Here, we model community feasibility domains, a theoretically informed measure of multi-species coexistence probability, from grassland communities comprising more than 45 species on average from three trophic guilds (plants, pollinators and herbivores). Contrary to our hypothesis, increasing community complexity, measured either as the number of guilds or community richness, did not decrease community feasibility. Rather, we observed that high degrees of species self-regulation and niche partitioning allow for maintaining larger levels of community feasibility and higher species persistence in more diverse communities. Our results show that biotic interactions within and across guilds are not random in nature and both structures significantly contribute to maintaining multi-trophic diversity.     

On the mechanism of αC polymer formation in fibrin

Our previous studies revealed that the fibrinogen αC-domains undergo conformational changes and adopt a physiologically active conformation upon their self-association into αC polymers in fibrin. In the present study, we analyzed the mechanism of αC polymer formation and tested our hypothesis that self-association of the αC-domains occurs through the interaction between their N-terminal subdomains and may include β-hairpin swapping. Our binding experiments performed by size-exclusion chromatography and optical trap-based force spectroscopy revealed that the αC-domains self-associate exclusively through their N-terminal subdomains, while their C-terminal subdomains were found to interact with the αC-connectors that tether the αC-domains to the bulk of the molecule. This interaction should reinforce the structure of αC polymers and provide the proper orientation of their reactive residues for efficient cross-linking by factor XIIIa. Molecular modeling of self-association of the N-terminal subdomains confirmed that the hypothesized β-hairpin swapping does not impose any steric hindrance. To "freeze" the conformation of the N-terminal subdomain and prevent the hypothesized β-hairpin swapping, we introduced by site-directed mutagenesis an extra disulfide bond between two β-hairpins of the bovine Aα406-483 fragment corresponding to this subdomain. The experiments performed by circular dichroism revealed that Aα406-483 mutant containing Lys429Cys/Thr463Cys mutations preserved its β-sheet structure. However, in contrast to wild-type Aα406-483, this mutant had lower tendency for oligomerization, and its structure was not stabilized upon oligomerization, in agreement with the above hypothesis. On the basis of the results obtained and our previous findings, we propose a model of fibrin αC polymer structure and molecular mechanism of assembly.     

Structural analysis, enzymatic characterization, and catalytic mechanisms of β-galactosidase from Bacillus circulans sp. alkalophilus

Crystal structures of native and α-D-galactose-bound Bacillus circulans sp. alkalophilus β-galactosidase (Bca-β-gal) were determined at 2.40 and 2.25 ? resolutions, respectively. Bca-β-gal is a member of family 42 of glycoside hydrolases, and forms a 460 kDa hexameric structure in crystal. The protein consists of three domains, of which the catalytic domain has an (α/β)(8) barrel structure with a cluster of sulfur-rich residues inside the β-barrel. The shape of the active site is clearly more open compared to the only homologous structure available in the Protein Data Bank. This is due to the number of large differences in the loops that connect the C-terminal ends of the β-strands to the N-terminal ends of the α-helices within the (α/β)(8) barrel. The complex structure shows that galactose binds to the active site as an α-anomer and induces clear conformational changes in the active site. The implications of α-D-galactose binding with respect to the catalytic mechanism are discussed. In addition, we suggest that β-galactosidases mainly utilize a reverse hydrolysis mechanism for synthesis of galacto-oligosaccharides.     

Aversion to nicotine is regulated by the balanced activity of β4 and α5 nicotinic receptor subunits in the medial habenula

Nicotine dependence is linked to single nucleotide polymorphisms in the CHRNB4-CHRNA3-CHRNA5 gene cluster encoding the α3β4α5 nicotinic acetylcholine receptor (nAChR). Here we show that the β4 subunit is rate limiting for receptor activity, and that current increase by β4 is maximally competed by one of the most frequent variants associated with tobacco usage (D398N in α5). We identify a β4-specific residue (S435), mapping to the intracellular vestibule of the α3β4α5 receptor in close proximity to α5 D398N, that is essential for its ability to increase currents. Transgenic mice with targeted overexpression of Chrnb4 to endogenous sites display a strong aversion to nicotine that can be reversed by viral-mediated expression of the α5 D398N variant in the?medial habenula (MHb). Thus, this study both provides insights into α3β4α5 receptor-mediated mechanisms contributing to nicotine consumption, and identifies the MHb as a critical element in the circuitry controlling nicotine-dependent phenotypes.     

Structural characterization of α‐synuclein in an aggregation prone state

The relation of α‐synuclein (αS) aggregation to Parkinson's disease has long been recognized, but the pathogenic species and its molecular properties have yet to be identified. To obtain insight into the properties of αS in an aggregation‐prone state, we studied the structural properties of αS at acidic pH using NMR spectroscopy and computation. NMR demonstrated that αS remains natively unfolded at lower pH, but secondary structure propensities were changed in proximity to acidic residues. The ensemble of conformations of αS at acidic pH is characterized by a rigidification and compaction of the Asp and Glu‐rich C‐terminal region, an increased probability for proximity between the NAC‐region and the C‐terminal region and a lower probability for interactions between the N‐ and C‐terminal regions.     

Structural forecasting of species persistence under changing environments

The persistence of a species in a given place not only depends on its intrinsic capacity to consume and transform resources into offspring, but also on how changing environmental conditions affect its growth rate. However, the complexity of factors has typically taken us to choose between understanding and predicting the persistence of species. To tackle this limitation, we propose a probabilistic approach rooted on the statistical concepts of ensemble theory applied to statistical mechanics and on the mathematical concepts of structural stability applied to population dynamics models – what we call structural forecasting. We show how this new approach allows us to estimate a probability of persistence for single species in local communities; to understand and interpret this probability conditional on the information we have concerning a system; and to provide out‐of‐sample predictions of species persistence as good as the best experimental approaches without the need of extensive amounts of data.     

Purification and Characterization of a Novel Fungal α-Glucosidase from Mortierella alliacea with High Starch-hydrolytic Activity

The fungal strain Mortierella alliacea YN-15 is an arachidonic acid producer that assimilates soluble starch despite having undetectable α-amylase activity. Here, a α-glucosidase responsible for the starch hydrolysis was purified from the culture broth through four-step column chromatography. Maltose and other oligosaccharides were less preferentially hydrolyzed and were used as a glucosyl donor for transglucosylation by the enzyme, demonstrating distinct substrate specificity as a fungal α-glucosidase. The purified enzyme consisted of two heterosubunits of 61 and 31 kDa that were not linked by a covalent bond but stably aggregated to each other even at a high salt concentration (0.5 M), and behaved like a single 92-kDa component in gel-filtration chromatography. The hydrolytic activity on maltose reached a maximum at 55°C and in a pH range of 5.0-6.0, and in the presence of ethanol, the transglucosylation reaction to form ethyl-α-D-glucoside was optimal at pH 5.0 and a temperature range of 45-50°C.     

Persistence length of human cardiac α-tropomyosin measured by single molecule direct probe microscopy

α-Tropomyosin (αTm) is the predominant tropomyosin isoform in adult human heart and constitutes a major component in Ca2?-regulated systolic contraction of cardiac muscle. We present here the first direct probe images of WT human cardiac αTm by atomic force microscopy, and quantify its mechanical flexibility with three independent analysis methods. Single molecules of bacterially-expressed human cardiac αTm were imaged on poly-lysine coated mica and their contours were analyzed. Analysis of tangent-angle (θ(s)) correlation along molecular contours, second moment of tangent angles (<θ2(s)>), and end-to-end length (L(e-e)) distributions respectively yielded values of persistence length (L(p)) of 41-46 nm, 40-45 nm, and 42-52 nm, corresponding to 1-1.3 molecular contour lengths (L(c)). We also demonstrate that a sufficiently large population, with at least 100 molecules, is required for a reliable L(p) measurement of αTm in single molecule studies. Our estimate that L(p) for αTm is only slightly longer than L(c) is consistent with a previous study showing there is little spread of cooperative activation into near-neighbor regulatory units of cardiac thin filaments. The L(p) determined here for human cardiac αTm perhaps represents an evolutionarily tuned optimum between Ca2? sensitivity and cooperativity in cardiac thin filaments and likely constitutes an essential parameter for normal function in the human heart.     

Divide and conquer? Persistence of infectious agents in spatial metapopulations of hosts

Persistence of an infectious agent in a population is an important issue in epidemiology. It is assumed that spatially fragmenting a population of hosts increases the probability of persistence of an infectious agent and that movement of hosts between the patches is vital for that. The influence of migration on persistence is however often studied in mean-field models, whereas in reality the actual distance travelled can be limited and influence the movement dynamics. We use a stochastic model, where within- and between-patch dynamics are coupled and movement is modelled explicitly, to show that explicit consideration of movement distance makes the relation between persistence of infectious agents and the metapopulation structure of its hosts less straightforward than previously thought. We show that the probability of persistence is largest at an intermediate movement distance of the host and that spatially fragmenting a population of hosts is not necessarily beneficial for persistence.     

Effects of temporal variability on rare plant persistence in annual systems

Traditional conservation biology regards environmental fluctuations as detrimental to persistence, reducing long-term average growth rates and increasing the probability of extinction. By contrast, coexistence models from community ecology suggest that for species with dormancy, environmental fluctuations may be essential for persistence in competitive communities. We used models based on California grasslands to examine the influence of interannual fluctuations in the environment on the persistence of rare forbs competing with exotic grasses. Despite grasses and forbs independently possessing high fecundity in the same types of years, interspecific differences in germination biology and dormancy caused the rare forb to benefit from variation in the environment. Owing to the buildup of grass competitors, consecutive favorable years proved highly detrimental to forb persistence. Consequently, negative temporal autocorrelation, a low probability of a favorable year, and high variation in year quality all benefited the forb. In addition, the litter produced by grasses in a previously favorable year benefited forb persistence by inhibiting its germination into highly competitive grass environments. We conclude that contrary to conventional predictions of conservation and population biology, yearly fluctuations in climate may be essential for the persistence of rare species in invaded habitats.     

Low Energy Conformations for S100 Binding Peptide from the Negative Regulatory Domain of p53

We have computed the low energy conformations of the negative regulatory domain of p53, residues 374–388 using Empirical Conformational Energies of Peptides Program including solvation and computed the statistical weights of distinct conformational states. We find that there are two high probability conformations, one an α-helix from Lys 374–Lys 381, followed by another helical structure involving Lys 382–Glu 388 (statistical weight of 0.48) and an all-α-helix for the entire sequence (statistical weight of 0.23). Both structure are superimposable on the NMR structure of this sequence bound to the S100 protein. The global minimum structure (statistical weight of 0.014) is a beta structure from Gly 374–Arg 379 followed by an α-helix from His 380–Glu 388. Based on these results, we propose a possible strategy for enhancement of p53 anti-tumor activity in cancer cells. Since the structure of this sequence bound to the sirtuin protein, Sir2, is a β-sheet, we further propose that the global minimum may be an intermediate on the α-β structure transition.     

Local structuring factors of invertebrate communities in ephemeral freshwater rock pools and the influence of more permanent water bodies in the region

We used three isolated clusters of small ephemeral rock pools on a sandstone flat in Utah to test the importance of local structuring processes on aquatic invertebrate communities. In the three clusters we characterized all ephemeral rock pools (total: 27) for their morphometry, and monitored their water quality, hydrology and community assemblage during a full hydrocycle. In each cluster we also sampled a set of more permanent interconnected freshwater systems positioned in a wash, draining the water from each cluster of rock pools. This design allowed additional testing for the potential role of more permanent water bodies in the region as source populations for the active dispersers and the effect on the community structure in the rock pools. Species richness and community composition in the rock pools correlated with level of permanence and the ammonia concentration. The length of the rock pool inundation cycle shaped community structure, most probably by inhibiting colonization by some taxa (e.g. tadpoles and insect larvae) through developmental constraints. The gradient in ammonia concentrations probably reflects differences in primary production. The more permanent water bodies in each wash differed both environmentally and in community composition from the connected set of rock pools. A limited set of active dispersers was observed in the rock pools. Our findings indicate that aquatic invertebrate communities in the ephemeral rock pools are mainly structured through habitat permanence, possibly linked with biotic interactions and primary production. Handling editor: S. I. Dodson     

Mutations on the Switch III region and the alpha3 helix of Galpha16 differentially affect receptor coupling and regulation of downstream effectors

Background

Gα₁₆ can activate phospholipase Cβ (PLCβ) directly like Gα_q. It also couples to tetratricopeptide repeat 1 (TPR1) which is linked to Ras activation. It is unknown whether PLCβ and TPR1 interact with the same regions on Gα₁₆. Previous studies on Gα_q have defined two minimal clusters of amino acids that are essential for the coupling to PLCβ. Cognate residues in Gα₁₆ might also be essential for interacting with PLCβ, and possibly contribute to TPR1 interaction and other signaling events.

Results

Alanine mutations were introduced to the two amino acid clusters (246–248 and 259–260) in the switch III region and α3 helix of Gα₁₆. Regulations of PLCβ and STAT3 were partially weakened by each cluster mutant. A mutant harboring mutations at both clusters generally produced stronger suppressions. Activation of Jun N-terminal kinase (JNK) by Gα₁₆ was completely abolished by mutating either clusters. Contrastingly, phosphorylations of extracellular signal-regulated kinase (ERK) and nuclear factor κB (NF-κB) were not significantly affected by these mutations. The interactions between the mutants and PLCβ2 and TPR1 were also reduced in co-immunoprecipitation assays. Coupling between G₁₆ and different categories of receptors was impaired by the mutations, with the effect of switch III mutations being more pronounced than those in the α3 helix. Mutations of both clusters almost completely abolished the receptor coupling and prevent receptor-induced Gβγ release.

Conclusion

The integrity of the switch III region and α3 helix of Gα₁₆ is critical for the activation of PLCβ, STAT3, and JNK but not ERK or NF-κB. Binding of Gα₁₆ to PLCβ2 or TPR1 was reduced by the mutations of either cluster. The same region could also differentially affect the effectiveness of receptor coupling to G₁₆. The studied region was shown to bear multiple functionally important roles of G₁₆.