Structure,Dynamics, and Allosteric Potential of Ionotropic Glutamate Receptor N-Terminal Domains

Ionotropic glutamate receptors (iGluRs) are tetrameric cation channels that mediate synaptic transmission and plasticity. They have a unique modular architecture with four domains: the intracellular C-terminal domain (CTD) that is involved in synaptic targeting, the transmembrane domain (TMD) that forms the ion channel, the membrane-proximal ligand-binding domain (LBD) that binds agonists such as L-glutamate, and the distal N-terminal domain (NTD), whose function is the least clear. The extracellular portion, comprised of the LBD and NTD, is loosely arranged, mediating complex allosteric regulation and providing a rich target for drug development. Here, we briefly review recent work on iGluR NTD structure and dynamics, and further explore the allosteric potential for the NTD in AMPA-type iGluRs using coarse-grained simulations. We also investigate mechanisms underlying the established NTD allostery in NMDA-type iGluRs, as well as the fold-related metabotropic glutamate and GABA_B receptors. We show that the clamshell motions intrinsically favored by the NTD bilobate fold are coupled to dimeric and higher-order rearrangements that impact the iGluR LBD and ultimately the TMD. Finally, we explore the dynamics of intact iGluRs and describe how it might affect receptor operation in a synaptic environment.     

Rhagada revisited: on the taxonomy of species from the Kimberley and Dampierland,Western Australia (Pulmonata,Camaenidae)

The genus Rhagada is the second most diverse camaenid genus in Australia. We examined anatomical and mitochondrial characters of previously unidentified material from the Kimberley that was earmarked to potentially represent new species in recently published molecular phylogenetic studies. Our comparisons revealed that specimens from Gibbings Island (‘R. sp. Gibbings’) were morphologically and genetically most similar to Rhagada cygna from the Dampier Peninsula. Hence, ‘R. sp. Gibbings’ is considered to be identical to R. cygna. In addition, we found that R. cygna as so delimited is not clearly distinguished from the second species on the Dampier Peninsula, Rhagada bulgana. Both species differ rather subtly in anatomical and mitochondrial characters, indicating their close relationships and potentially incomplete evolutionary differentiation. Furthermore, we describe two new species based on comparative morphology and mitochondrial sequences: Rhagada worora n. sp. from the Prince Regent Reserve in the Kimberley and Rhagada karajarri n. sp. from Dampierland. The present study confirms that species in Rhagada are best identified by means of both morphological and molecular data.

http://zoobank.org/urn:lsid:zoobank.org:pub:556E1866-6F9E-4CC0-8ACF-CD56E929501F     

Tsunami impact on the population development of a critically endangered hummingbird species of a Pacific island

It is a long-standing question how tsunamis can influence wild populations of animals and plants. Here, we assessed short-term changes in the population of the critically endangered Juan Fernández Firecrown (Sephanoides fernandensis) by using abundance data recorded 1 year before and 1 year after the 2010 Chilean tsunami. We tested that the abundance of Firecrowns declined in the areas where the tsunami caused the massive loss of Cabbage Trees, an important seasonal nectar source for Firecrowns. The abundance of Juan Fernández Firecrowns decreased after the tsunami, but also was affected by the habitat type, altitude, and the abundance of Cabbage Trees. Firecrowns tended to be more abundant in settlement areas than in native forest whereas the reduction in Firecrown abundance after the tsunami was more intense in settlement areas than in native forest. As expected, this habitat effect was dependent on the massive loss of Cabbage Trees in settlement areas following the tsunami. In spite of the short-term nature of our data, our results are conclusive in showing that the loss of an important food source causes short-term changes in the distribution and abundance of Firecrowns, which, in turn, could contribute to population decline.     

Jasmonic acid perception by COI1 involves inositol polyphosphates in Arabidopsis thaliana

Plant responses to wounding are part of their defense responses against insects, and are tightly regulated. The isoleucin conjugate of jasmonic acid (JA‐Ile) is a major regulatory molecule. We have previously shown that inositol polyphosphate signals are required for defense responses in Arabidopsis; however, the way in which inositol polyphosphates contribute to plant responses to wounding has so far remained unclear. Arabidopsis F‐box proteins involved in the perception of JA‐Ile (COI1) and auxin (TIR1) are structurally similar. Because TIR1 has recently been shown to contain inositol hexakisphosphate (InsP₆) as a co‐factor of unknown function, here we explored the possibility that InsP₆ or another inositol polyphosphate is required for COI1 function. In support of this hypothesis, COI1 variants with changes in putative inositol polyphosphate coordinating residues exhibited a reduced interaction with the COI1 target, JAZ9, in yeast two‐hybrid tests. The equivalent COI1 variants displayed a reduced capability to rescue jasmonate‐mediated root growth inhibition or silique development in Arabidopsis coi1 mutants. Yeast two‐hybrid tests using wild‐type COI1 in an ipk1Δ yeast strain exhibiting increased levels of inositol pentakisphosphate (InsP₅) and reduced levels of InsP₆ indicate an enhanced COI1/JAZ9 interaction. Consistent with these findings, Arabidopsis ipk1‐1 mutants, also with increased InsP₅ and reduced InsP₆ levels, showed increased defensive capabilities via COI1‐mediated processes, including wound‐induced gene expression, defense against caterpillars or root growth inhibition by jasmonate. The combined data from experiments using mutated COI1 variants, as well as yeast and Arabidopsis backgrounds altered in inositol polyphosphate metabolism, indicate that an inositol polyphosphate, and probably InsP₅, contributes to COI1 function.     

Cellular aging leads to functional heterogeneity of hematopoietic stem cells: a modeling perspective

Hematopoietic stem cells (HSCs) are the source for the life-long supply of functional cells in peripheral blood while they simultaneously maintain their own reserve pool. However, there is accumulating evidence that HSCs are themselves subject to quantitative and qualitative exhaustion. Although several processes linked to mitotic activity can potentially account for the observed aging phenomena (e.g., DNA damage, telomere shortening, epigenetic modification), a precise understanding of HSC exhaustion is still missing. It is particularly unclear how individual aging processes on the single-cell level translate on the phenotypic level of the overall tissue and whether there is a functional implication of an age-structured HSC population. We address these issues by applying a novel mathematical model of HSC organization in which division-specific, cumulative alterations of stem cell quality determine the phenotypic and functional appearance of the overall cell population. Adapting the model to a number of basic experimental findings, we quantify the level of additional heterogeneity that is introduced by a population of individually aging cells. Based on this model, we are able to conclude that division-dependent processes of cellular aging explain a wide range of phenomena on HSC exhaustion and that HSC aging needs to be considered as a highly heterogeneous process. We furthermore report that functional heterogeneity between young and old HSCs appears closely similar to the phenomena described for long- and short-term repopulating cells. We speculate whether differential, division-coupled stem cell aging introduces an intra-animal variability that also accounts for heterogeneity with respect to the repopulation ability of HSCs.     

Detection of viral sequence fragments of HIV-1 subfamilies yet unknown

Background  

Methods of determining whether or not any particular HIV-1 sequence stems - completely or in part - from some unknown HIV-1 subtype are important for the design of vaccines and molecular detection systems, as well as for epidemiological monitoring. Nevertheless, a single algorithm only, the Branching Index (BI), has been developed for this task so far. Moving along the genome of a query sequence in a sliding window, the BI computes a ratio quantifying how closely the query sequence clusters with a subtype clade. In its current version, however, the BI does not provide predicted boundaries of unknown fragments.     

Bone regeneration: stem cell therapies and clinical studies in orthopaedics and traumatology

Regenerative medicine seeks to repair or replace damaged tissues or organs, with the goal to fully restore structure and function without the formation of scar tissue. Cell based therapies are promising new therapeutic approaches in regenerative medicine. By using mesenchymal stem cells, good results have been reported for bone engineering in a number of clinical studies, most of them investigator initiated trials with limited scope with respect to controls and outcome. With the implementation of a new regulatory framework for advanced therapeutic medicinal products, the stage is set to improve both the characterization of the cells and combination products, and pave the way for improved controlled and well-designed clinical trials. The incorporation of more personalized medicine approaches, including the use of biomarkers to identify the proper patients and the responders to treatment, will be contributing to progress in the field. Both translational and clinical research will move the boundaries in the field of regenerative medicine, and a coordinated effort will provide the clinical breakthroughs, particularly in the many applications of bone engineering.