Developing Native Multispecies Sod: An Alternative Rehabilitation Method for Disturbed Lands

Natural and anthropogenic disturbance provides a mechanism for resetting the species assemblage within natural communities. Following anthropogenic disturbance particularly, there are generally more weedy species. Restoration of ecosystem structure and function in disturbed areas could aid in the control of these undesirable species. Attempts to re‐establish vegetation via direct sowing, hydroseeding, drill seeding, imprinting or plugging of either native or non‐native species can be effective, but can result in increased erosion and weed proliferation prior to desirable cover of the intended species. The use of native species for rehabilitation can be preferable because non‐native species are often less suited to the local environment and can pose a threat to the integrity of adjacent ecosystems. Native multispecies sod could become a useful rehabilitation tool, but research is needed to determine which species to use and the appropriate number of species to include. Mixtures of 4–7 native species were grown for 7 months, and clipped dry biomass, species percent abundance, and total ground cover were assessed over time in order to determine the suitability of 20 native species for sod production. Despite differences between mixtures at some harvests, all mixtures established and produced similar biomass by the end of the study. Final percent cover varied widely among species; 16 of the 20 species increased significantly over the course of production. Differences in total ground cover between mixtures were explained by the growth of the particular species rather than any synergistic effect of species diversity.     

The role of Steller sea lions in a large population decline of harbor seals

We provide the first direct evidence that Steller sea lions will prey on harbor seals. Direct observations of predation on marine mammals at sea are rare, but when observed rates of predation are extrapolated, predation mortality may be found to be significant. From 1992 to 2002, harbor seals in Glacier Bay declined steeply, from 6,200 to 2,500 (∼65%). After documenting that Steller sea lions were preying on seals in Glacier Bay, we investigated increased predation by sea lions as a potential explanation for the large decline. In five independent data sets spanning 21–25 yr and including 14,308 d of observations, 13 predation events were recorded. We conducted a fine-scale analysis for an intensively studied haul-out (Spider Island) and a broader analysis of all of Glacier Bay. At Spider Island, estimated predation by sea lions increased and could account for the entirety of annual pup production in 5 of 8 yr since 1995. The predation rate, however, was not proportional to the number of predators. Predation by Steller sea lions is a new source of mortality that contributed to the seal declines; however, life history modeling indicates that it is unlikely that sea lion predation is the sole factor responsible for the large declines.     

Unraveling the molecular basis for ligand binding in truncated hemoglobins: The trHbO Bacillus subtilis case

Truncated hemoglobins (trHbs) are heme proteins present in bacteria, unicellular eukaryotes, and higher plants. Their tertiary structure consists in a 2‐over‐2 helical sandwich, which display typically an inner tunnel/cavity system for ligand migration and/or storage. The microorganism Bacillus subtilis contains a peculiar trHb, which does not show an evident tunnel/cavity system connecting the protein active site with the solvent, and exhibits anyway a very high oxygen association rate. Moreover, resonant Raman results of CO bound protein, showed that a complex hydrogen bond network exists in the distal cavity, making it difficult to assign unambiguously the residues involved in the stabilization of the bound ligand. To understand these experimental results with atomistic detail, we performed classical molecular dynamics simulations of the oxy, carboxy, and deoxy proteins. The free energy profiles for ligand migration suggest that there is a key residue, GlnE11, that presents an alternate conformation, in which a wide ligand migration tunnel is formed, consistently with the kinetic data. This tunnel is topologically related to the one found in group I trHbs. On the other hand, the results for the CO and O₂ bound protein show that GlnE11 is directly involved in the stabilization of the cordinated ligand, playing a similar role as TyrB10 and TrpG8 in other trHbs. Our results not only reconcile the structural data with the kinetic information, but also provide additional insight into the general behaviour of trHbs. Proteins 2010. © 2009 Wiley‐Liss, Inc.     

Folding and membrane insertion of amyloid‐beta (25–35) peptide and its mutants: Implications for aggregation and neurotoxicity

The mechanisms of interfacial folding and membrane insertion of the Alzheimer's amyloid‐β fragment Aβ(25–35) and its less toxic mutant, N27A‐Aβ(25–35) and more toxic mutant, M35A‐Aβ(25–35), are investigated using replica–exchange molecular dynamics in an implicit water‐membrane environment. This study simulates the processes of interfacial folding and membrane insertion in a spontaneous fashion to identify their general mechanisms. Aβ(25–35) and N27A‐Aβ(25–35) peptides share similar mechanisms: the peptides are first located in the membrane hydrophilic region where their C‐terminal residues form helical structures. The peptides attempt to insert themselves into the membrane hydrophobic region using the C‐terminal or central hydrophobic residues. A small portion of peptides can successfully enter the membrane's hydrophobic core, led by their C‐terminal residues, through the formation of continuous helical structures. No detectable amount of M35A‐Aβ(25–35) peptides appeared to enter the membrane's hydrophobic core. The three studied peptides share a similar helical structure for their C‐terminal five residues, and these residues mainly buried within the membrane's hydrophobic region. In contrast, their N‐terminal properties are markedly different. With respect to the Aβ(25–35), the N27A‐Aβ(25–35) forms a more structured helix and is buried deeper within the membrane, which may result in a lower degree of aggregation and a lower neurotoxicity; in contrast, the less structured and more water‐exposed M35A‐Aβ(25–35) is prone to aggregation and has a higher neurotoxicity. Understanding the mechanisms of Aβ peptide interfacial folding and membrane insertion will provide new insights into the mechanisms of neurodegradation and may give structure‐based clues for rational drug design preventing amyloid associated diseases. Proteins 2010. © 2010 Wiley‐Liss, Inc.     

Dissection of the conformational cycle of the multidrug/lipidA ABC exporter MsbA

Recent crystal structures of the multidrug ATP‐binding cassette (ABC) exporters Sav1866 from Staphylococcus aureus, MsbA from Escherichia coli, Vibrio cholera, and Salmonella typhimurium, and mouse ABCB1a suggest a common alternating access mechanism for export. However, the molecular framework underlying this mechanism is critically dependent on assumed conformational relationships between nonidentical crystal structures and therefore requires biochemical verification. The structures of homodimeric MsbA reveal a pair of glutamate residues (E208 and E208′) in the intracellular domains of its two half‐transporters, close to the nucleotide‐binding domains (NBDs), which are in close proximity of each other in the outward‐facing state but not in the inward‐facing state. Using intermolecular cysteine crosslinking between E208C and E208C′ in E. coli MsbA, we demonstrate that the NBDs dissociate in nucleotide‐free conditions and come close on ATP binding and ADP·vanadate trapping. Interestingly, ADP alone separates the half‐transporters like a nucleotide‐free state, presumably for the following catalytic cycle. Our data fill persistent gaps in current studies on the conformational dynamics of a variety of ABC exporters. Based on a single biochemical method, the findings describe a conformational cycle for a single ABC exporter at major checkpoints of the ATPase reaction under experimental conditions, where the exporter is transport active. Proteins 2010. © 2010 Wiley‐Liss, Inc.     

Gain of local structure in an amphipathic peptide does not require a specific tertiary framework

In this work, we studied how an amphipathic peptide of the surface of the globular protein thioredoxin, TRX94‐108, acquires a native‐like structure when it becomes involved in an apolar interaction network. We designed peptide variants where the tendency to form α‐helical conformation is modulated by replacing each of the leucine amino acid residues by an alanine. The induction of structure caused by sodium dodecyl sulfate (SDS) binding was studied by capillary zone electrophoresis, circular dichroism, DOSY‐NMR, and molecular dynamics simulations (MDS). In addition, we analyzed the strength of the interaction between a C18 RP‐HPLC matrix and the peptides. The results presented here reveal that (a) critical elements in the sequence of the wild‐type peptide stabilize a SDS/peptide supramolecular cluster; (b) the hydrophobic nature of the interaction between SDS molecules and the peptide constrains the ensemble of conformations; (c) nonspecific apolar surfaces are sufficient to stabilize peptide secondary structure. Remarkably, MDS shed light on a contact network formed by a limited number of SDS molecules that serves as a structural scaffold preserving the helical conformation of this module. This mechanism might prevail when a peptide with low helical propensity is involved in structure consolidation. We suggest that folding of peptides sharing this feature does not require a preformed tightly‐packed protein core. Thus, the formation of specific tertiary interactions would be the consequence of peptide folding and not its cause. In this scenario, folding might be thought of as a process that includes unspecific rounds of structure stabilization guiding the protein to the native state. Proteins 2010. © 2010 Wiley‐Liss, Inc.     

The effect of calcium on the conformation of cobalamin transporter BtuB

BtuB is a β‐barrel membrane protein that facilitates transport of cobalamin (vitamin B12) from the extracellular medium across the outer membrane of Escherichia coli. It is thought that binding of B12 to BtuB alters the conformation of its periplasm‐exposed N‐terminal residues (the TonB box), which enables subsequent binding of a TonB protein and leads to eventual uptake of B12 into the cytoplasm. Structural studies determined the location of the B12 binding site at the top of the BtuB's β‐barrel, surrounded by extracellular loops. However, the structure of the loops was found to depend on the method used to obtain the protein crystals, which—among other factors—differed in calcium concentration. Experimentally, calcium concentration was found to modulate the binding of the B12 substrate to BtuB. In this study, we investigate the effect of calcium ions on the conformation of the extracellular loops of BtuB and their possible role in B12 binding. Using all‐atom molecular dynamics, we simulate conformational fluctuations of several X‐ray structures of BtuB in the presence and absence of calcium ions. These simulations demonstrate that calcium ions can stabilize the conformation of loops 3–4, 5–6, and 15–16, and thereby prevent occlusion of the binding site. Furthermore, binding of calcium ions to extracellular loops of BtuB was found to enhance correlated motions in the BtuB structure, which is expected to promote signal transduction. Finally, we characterize conformation dynamics of the TonB box in different X‐ray structures and find an interesting correlation between the stability of the TonB box structure and calcium binding. Proteins 2010. © 2009 Wiley‐Liss, Inc.     

Population dynamics of the West Indian sweetpotato weevil Euscepes postfasciatus (Fairmaire): a simulation analysis

The West Indian sweetpotato weevil Euscepes postfasciatus (Fairmaire) is a major pest of the sweet potato Ipomoea batatas (L.) Lam. and this weevil is a target of an eradication program using the Sterile Insect Technique in Okinawa Prefecture, Japan. Understanding the population ecology is essential in the planning of an eradication program; hence, a host‐plant infestation survey and light trap survey have been conducted to monitor the population dynamics of the weevil on Kume Island (Okinawa Prefecture), which is the target area of the trial weevil eradication project. Seasonal tendencies of weevil density were found in these field surveys, but the tendency found in the host‐plant infestation survey was not seen every year, and the effectiveness of the light trap is somewhat suspect. To confirm the reliability of the tendency observed in these field surveys, the present study attempted to explain the tendency by a seasonal temperature change using a temperature‐based model of weevil population dynamics. The seasonal changes of weevil density differed according to host plants and host‐plant fields. The seasonal changes of weevil density inside the host plant Ipomoea indica and outside the host plants in I. indica fields were consistent with those predicted by the model. However, those inside the host plant Ipomoea pes‐caprae in the host‐plant infestation survey were contrary to the predicted ones, and those observed outside host plants in I. pes‐caprae fields by the light trap survey were not in good agreement with the predicted ones. It was concluded that the seasonal change of the weevil density observed in I. indica and I. indica fields can be explained by a seasonal temperature change, but factors other than seasonal temperature change are needed to explain those in I. pes‐caprae and I. pes‐caprae fields.