Redesign of a four-helix bundle protein by phage display coupled with proteolysis and structural characterization by NMR and X-ray crystallography

To test whether it is practical to use phage display coupled with proteolysis for protein design, we used this approach to convert a partially unfolded four-helix bundle protein, apocytochrome b(562), to a stably folded four-helix bundle protein. Four residues expected to form a hydrophobic core were mutated. One residue was changed to Trp to provide a fluorescence probe for studying the protein's physical properties and to partially fill the void left by the heme. The other three positions were randomly mutated. In addition, another residue in the region to be redesigned was substituted with Arg to provide a specific cutting site for protease Arg-c. This library of mutants was displayed on the surface of phage and challenged with protease Arg-c to select stably folded proteins. The consensus sequence that emerged from the selection included hydrophobic residues at only one of the three positions and non-hydrophobic residues at the other two. Nevertheless, the selected proteins were thermodynamically very stable. The structure of a selected protein was characterized using multi-dimensional NMR. All four helices were formed in the structure. Further, site-directed mutagenesis was used to change one of the two non-hydrophobic residues to a hydrophobic residue, which increased the stability of the protein, indicating that the selection result was not based solely on the protein's global stability and that local structural characteristics may also govern the selection. This conclusion is supported by the crystal structure of another mutant that has two hydrophobic residues substituted for the two non-hydrophobic residues. These results suggest that the hydrophobic interactions in the core are not sufficient to dictate the selection and that the location of the cutting site of the protease also influences the selection of structures.     

Molecular genetic analyses of species boundaries in the sea

The tools of molecular genetics have enormous potential for clarifying the nature and age of species boundaries in marine organisms. Below I summarize the genetic implications of various species concepts, and review the results of recent molecular genetic analyses of species boundaries in marine microbes, plants, invertebrates and vertebrates. Excessive lumping, rather than excessive splitting, characterizes the current systematic situation in many groups. Morphologically similar species are often quite distinct genetically, suggesting that conservative systematic traditions or morphological stasis may be involved. Some reproductively isolated taxa exhibit only small levels of genetic differentiation, however. In these cases, large population sizes, slow rates of molecular evolution, and relatively recent origins may contribute to the difficulty in finding fixed genetic markers associated with barriers to gene exchange. The extent to which hybridization blurs species boundaries of marine organisms remains a subject of real disagreement in some groups (e.g. corals). The ages of recently diverged species are largely unknown; many appear to be older than 3 million years, but snails and fishes provide several examples of more recent divergences. Increasingly sophisticated genetic analyses make it easier to distinguish allopatric taxa, but criteria for recognition at the species level are highly inconsistent across studies. Future molecular genetic analyses should help to resolve many of these issues, particularly if coupled with other biological and paleontological approaches.     

Inactivation mode of sodium channels defines the different maximal firing rates of conventional versus atypical midbrain dopamine neurons

Two subpopulations of midbrain dopamine (DA) neurons are known to have different dynamic firing ranges in vitro that correspond to distinct projection targets: the originally identified conventional DA neurons project to the dorsal striatum and the lateral shell of the nucleus accumbens, whereas an atypical DA population with higher maximum firing frequencies projects to prefrontal regions and other limbic regions including the medial shell of nucleus accumbens. Using a computational model, we show that previously identified differences in biophysical properties do not fully account for the larger dynamic range of the atypical population and predict that the major difference is that originally identified conventional cells have larger occupancy of voltage-gated sodium channels in a long-term inactivated state that recovers slowly; stronger sodium and potassium conductances during action potential firing are also predicted for the conventional compared to the atypical DA population. These differences in sodium channel gating imply that longer intervals between spikes are required in the conventional population for full recovery from long-term inactivation induced by the preceding spike, hence the lower maximum frequency. These same differences can also change the bifurcation structure to account for distinct modes of entry into depolarization block: abrupt versus gradual. The model predicted that in cells that have entered depolarization block, it is much more likely that an additional depolarization can evoke an action potential in conventional DA population. New experiments comparing lateral to medial shell projecting neurons confirmed this model prediction, with implications for differential synaptic integration in the two populations.     

How formalin affects the outcome of routine and special stains

The discovery of formaldehyde for preserving tissue structures produced a new dimension in microscopy. Preserving structure and morphology became important; therefore, identifying a proper fixing agent for particular structures, chemical entities, and tissues, also became important. The methods for demonstrating tissue structures evolved and were implemented with careful observation and documentation of the results and outcomes. Formalin was incorporated into many techniques, and provided helpful results in many cases and hindrances in others. The effects of formalin on the outcomes of routine and special staining techniques are reported here.     

Differences among major taxa in the extent of ecological knowledge across four major ecosystems

Existing knowledge shapes our understanding of ecosystems and is critical for ecosystem-based management of the world''s natural resources. Typically this knowledge is biased among taxa, with some taxa far better studied than others, but the extent of this bias is poorly known. In conjunction with the publically available World Registry of Marine Species database (WoRMS) and one of the world''s premier electronic scientific literature databases (Web of Science®), a text mining approach is used to examine the distribution of existing ecological knowledge among taxa in coral reef, mangrove, seagrass and kelp bed ecosystems. We found that for each of these ecosystems, most research has been limited to a few groups of organisms. While this bias clearly reflects the perceived importance of some taxa as commercially or ecologically valuable, the relative lack of research of other taxonomic groups highlights the problem that some key taxa and associated ecosystem processes they affect may be poorly understood or completely ignored. The approach outlined here could be applied to any type of ecosystem for analyzing previous research effort and identifying knowledge gaps in order to improve ecosystem-based conservation and management.     

Aspects of benthic decapod diversity and distribution from rocky nearshore habitat at geographically widely dispersed sites

Relationships of diversity, distribution and abundance of benthic decapods in intertidal and shallow subtidal waters to 10 m depth are explored based on data obtained using a standardized protocol of globally-distributed samples. Results indicate that decapod species richness overall is low within the nearshore, typically ranging from one to six taxa per site (mean = 4.5). Regionally the Gulf of Alaska decapod crustacean community structure was distinguishable by depth, multivariate analysis indicating increasing change with depth, where assemblages of the high and mid tide, low tide and 1 m, and 5 and 10 m strata formed three distinct groups. Univariate analysis showed species richness increasing from the high intertidal zone to 1 m subtidally, with distinct depth preferences among the 23 species. A similar depth trend but with peak richness at 5 m was observed when all global data were combined. Analysis of latitudinal trends, confined by data limitations, was equivocal on a global scale. While significant latitudinal differences existed in community structure among ecoregions, a semi-linear trend in changing community structure from the Arctic to lower latitudes did not hold when including tropical results. Among boreal regions the Canadian Atlantic was relatively species poor compared to the Gulf of Alaska, whereas the Caribbean and Sea of Japan appeared to be species hot spots. While species poor, samples from the Canadian Atlantic were the most diverse at the higher infraordinal level. Linking 11 environmental variables available for all sites to the best fit family-based biotic pattern showed a significant relationship, with the single best explanatory variable being the level of organic pollution and the best combination overall being organic pollution and primary productivity. While data limitations restrict conclusions in a global context, results are seen as a first-cut contribution useful in generating discussion and more in-depth work in the still poorly understood field of biodiversity distribution.     

Ecological speciation in anemone‐associated snapping shrimps (Alpheus armatus species complex)

Divergent natural selection driven by competition for limited resources can promote speciation, even in the presence of gene flow. Reproductive isolation is more likely to result from divergent selection when the partitioned resource is closely linked to mating. Obligate symbiosis and host fidelity (mating on or near the host) can provide this link, creating ideal conditions for speciation in the absence of physical barriers to dispersal. Symbiotic organisms often experience competition for hosts, and host fidelity ensures that divergent selection for a specific host or host habitat can lead to speciation and strengthen pre‐existing reproductive barriers. Here, we present evidence that diversification of a sympatric species complex occurred despite the potential for gene flow and that partitioning of host resources (both by species and by host habitat) has contributed to this diversification. Four species of snapping shrimps (Alpheus armatus, A. immaculatus, A. polystictus and A. roquensis) are distributed mainly sympatrically in the Caribbean, while the fifth species (A. rudolphi) is restricted to Brazil. All five species are obligate commensals of sea anemones with a high degree of fidelity and ecological specificity for host species and habitat. We analysed sequence data from 10 nuclear genes and the mitochondrial COI gene in 11–16 individuals from each of the Caribbean taxa and from the only available specimen of the Brazilian taxon. Phylogenetic analyses support morphology‐based species assignments and a well‐supported Caribbean clade. The Brazilian A. rudolphi is recovered as an outgroup to the Caribbean taxa. Isolation–migration coalescent analysis provides evidence for historical gene flow among sympatric sister species. Our data suggest that both selection for a novel host and selection for host microhabitat may have promoted diversification of this complex despite gene flow.     

Is endothelial-nitric-oxide-synthase-derived nitric oxide involved in cardiac hypoxia/reoxygenation-related damage?

Nitric oxide (NO) has been reported to act both as a destructive and a protective agent in the pathogenesis of the injuries that occur during hypoxia/reoxygenation (H/R). It has been suggested that this dual role of NO depends directly on the isoform of NO synthase (NOS) involved. In this work, we investigate the role that NO derived from endothelial NOS (eNOS) plays in cardiac H/R-induced injury. Wistar rats were submitted to H/R (hypoxia for 30 min; reoxygenation of 0 h, 12 h and 5 days), with or without prior treatment using the selective eNOS inhibitor l-NIO (20 mg/kg). Lipid peroxidation, apoptosis and protein nitration, as well as NO production (NOx), were analysed. The results showed that l-NIO administration lowered NOx levels in all the experimental groups. However, no change was found in the lipid peroxidation level, the percentage of apoptotic cells or nitrated protein expression, implying that eNOS-derived NO may not be involved in the injuries occurring during H/R in the heart. We conclude that l-NIO would not be useful in alleviating the adverse effects of cardiac H/R.     

Scraping through the ice: uncovering the role of TRPM8 in cold transduction

The proper detection of environmental temperatures is essential for the optimal growth and survival of organisms of all shapes and phyla, yet only recently have the molecular mechanisms for temperature sensing been elucidated. The discovery of temperature-sensitive ion channels of the transient receptor potential (TRP) superfamily has been pivotal in explaining how temperatures are sensed in vivo, and here we will focus on the lone member of this cohort, TRPM8, which has been unequivocally shown to be cold sensitive. TRPM8 is expressed in somatosensory neurons that innervate peripheral tissues such as the skin and oral cavity, and recent genetic evidence has shown it to be the principal transducer of cool and cold stimuli. It is remarkable that this one channel, unlike other thermosensitive TRP channels, is associated with both innocuous and noxious temperature transduction, as well as cold hypersensitivity during injury and, paradoxically, cold-mediated analgesia. With ongoing research, the field is getting closer to answering a number of fundamental questions regarding this channel, including the cellular mechanisms of TRPM8 modulation, the molecular context of TRPM8 expression, as well as the full extent of the role of TRPM8 in cold signaling in vivo. These findings will further our understanding of basic thermotransduction and sensory coding, and may have important implications for treatments for acute and chronic pain.