Intact Cluster Research Articles

Everyday-like memory and its cognitive correlates in healthy older adults and in young patients with traumatic brain injury: a pilot study based on virtual reality

Purpose State: A pilot-study with a comparison approach between aging and traumatic brain injury (TBI) is proposed to investigate everyday object memory patterns using a virtual HOMES test. Methods: Sixteen young controls, 15 older adults and 15 TBI patients underwent the HOMES test and traditional tests. Results: Older adults and TBI patients exhibited similar HOMES performances: poor recall, a greater recognition benefit, high false recognitions, but intact clustering and proactive interference effects. The age-related differences for HOMES measures were mainly mediated by executive functioning, while the HOMES performances in the TBI group were correlated with memory measures. Conclusion: The differential cognitive mediating effects for a similar everyday-like memory pattern are discussed by highlighting the need for more cautious interpretations of cognitive mechanisms behind similar behavioral patterns in different populations especially in clinical and rehabilitation settings.Implication for RehabilitationVirtual reality might provide ecological scenarios to assess the multiple processes of everyday memory in elderly people as well as in TBI patients.A similar pattern of Everyday-like memory failures might result from different cognitive origins among different neuropsychological patients.The assessment of specific cognitive origins of Everyday-like memory impairments deserves consideration for drawing up relevant rehabilitative programs that match the specific cognitive needs of patients for performing everyday memory tasks.

Investigating energetics of Au8 on graphene/Ru(0001) using a genetic algorithm and density functional theory

Gold nanoparticles have been extensively studied for their catalytic activity both theoretically and experimentally. The moiré pattern formed by graphene supported on single crystal substrates creates a useful environment where the properties of Au nanoclusters can be studied, provided the structure and evolution of these clusters can be controlled. We used a genetic algorithm combined with DFT calculations to predict the lowest energy structures of a Au8 cluster on graphene/Ru(0001). The most stable cluster forms a double-layer Au wall structure for Au8 in the fcc region of the moiré pattern, where the Au8 cluster is most strongly adsorbed. Further calculations give estimates for the net diffusion barrier of Au8 as an intact cluster on the surface. Our results are consistent with the Au island structure experimentally observed on graphene/Ru(0001), and support the hypothesis that Au clusters aggregate through Oswald ripening with Au dimers being the most important diffusing species.

Spectroscopic Monitoring of the Acidity of Water Films on Ru(0001): Orientation‐Specific Acidity of Adsorbed Water

We examined the acid–base properties of water films adsorbed onto a Ru(0001) substrate by using surface spectroscopic methods in vacuum environments. Ammonia adsorption experiments combined with low-energy sputtering (LES), reactive ion scattering (RIS), reflection–absorption infrared spectroscopy (RAIRS) and temperature-programmed desorption (TPD) measurements showed that the adsorbed water is acidic enough to transfer protons to ammonia. Only the water molecules in an intact water monolayer and water clusters larger than the hexamer exhibit such acidity, whereas small clusters, a thick ice film or a partially dissociated water monolayer that contains OH, H2O and H species are not acidic. The observations indicate the orientation-specific acidity of adsorbed water. The acidity stems from water molecules with H-down adsorption geometry present in the monolayer. However, the dissociation of water into H and OH on the surface does not promote but rather suppresses the proton transfer to ammonia.

Diastereomeric control of enantioselectivity: evidence for metal cluster catalysis.

Enantioselective hydrogenation of tiglic acid effected by diastereomers of the general formula [(μ-H)2Ru3(μ3-S)(CO)7(μ-P-P*)] (P-P* = chiral Walphos diphosphine ligand) strongly supports catalysis by intact Ru3 clusters. A catalytic mechanism involving Ru3 clusters has been established by DFT calculations.

Establishing a Au Nanoparticle Size Effect in the Oxidation of Cyclohexene Using Gradually Changing Au Catalysts

The effect of the size of gold nanoparticles on their catalytic activity in aerobic oxidation of cyclohexene was established using supported gold nanoparticles that gradually undergo a change in size during the catalytic reaction. Two triphenylphosphine-stabilized clusters, Au9(PPh3)8(NO3)3 and Au101(PPh3)21Cl5, were synthesized and deposited on SiO2. The clusters did not retain their structure during the catalytic reaction; larger particles with mean diameters of ∼5–10 nm gradually formed. By combining kinetic experiments with the monitoring of catalyst transformations using transmission electron microscopy, diffuse-reflectance ultraviolet–visible spectroscopy, and X-ray photoelectron spectroscopy, we showed that catalytic activity appeared only after >2 nm Au0 particles had formed, while intact clusters and phosphine-free <2 nm particles were inactive in cyclohexene oxidation under the studied conditions.

Correction: Heterologous Reconstitution of the Intact Geodin Gene Cluster in Aspergillus nidulans through a Simple and Versatile PCR Based Approach

The third author was incorrectly indicated as a Corresponding Author of the article. This author should instead be noted as having contributed to the article equally with the first two authors. In addition, the third author's name was spelled incorrectly. The correct name is: Diana Chinyere Anyaogu.

Monothiol Glutaredoxins Can Bind Linear [Fe3S4]+ and [Fe4S4]2+ Clusters in Addition to [Fe2S2]2+ Clusters: Spectroscopic Characterization and Functional Implications

Saccharomyces cerevisiae mitochondrial glutaredoxin 5 (Grx5) is the archetypical member of a ubiquitous class of monothiol glutaredoxins with a strictly conserved CGFS active-site sequence that has been shown to function in biological [Fe2S2](2+) cluster trafficking. In this work, we show that recombinant S. cerevisiae Grx5 purified aerobically, after prolonged exposure of the cell-free extract to air or after anaerobic reconstitution in the presence of glutathione, predominantly contains a linear [Fe3S4](+) cluster. The excited-state electronic properties and ground-state electronic and vibrational properties of the linear [Fe3S4](+) cluster have been characterized using UV-vis absorption/CD/MCD, EPR, Mössbauer, and resonance Raman spectroscopies. The results reveal a rhombic S = 5/2 linear [Fe3S4](+) cluster with properties similar to those reported for synthetic linear [Fe3S4](+) clusters and the linear [Fe3S4](+) clusters in purple aconitase. Moreover, the results indicate that the Fe-S cluster content previously reported for many monothiol Grxs has been misinterpreted exclusively in terms of [Fe2S2](2+) clusters, rather than linear [Fe3S4](+) clusters or mixtures of linear [Fe3S4](+) and [Fe2S2](2+) clusters. In the absence of GSH, anaerobic reconstitution of Grx5 yields a dimeric form containing one [Fe4S4](2+) cluster that is competent for in vitro activation of apo-aconitase, via intact cluster transfer. The ligation of the linear [Fe3S4](+) and [Fe4S4](2+) clusters in Grx5 has been assessed by spectroscopic, mutational, and analytical studies. Potential roles for monothiol Grx5 in scavenging and recycling linear [Fe3S4](+) clusters released during protein unfolding under oxidative stress conditions and in maturation of [Fe4S4](2+) cluster-containing proteins are discussed in light of these results.

Arabidopsis thaliana Nfu2 Accommodates [2Fe-2S] or [4Fe-4S] Clusters and Is Competent for in Vitro Maturation of Chloroplast [2Fe-2S] and [4Fe-4S] Cluster-Containing Proteins

Nfu-type proteins are essential in the biogenesis of iron-sulfur (Fe-S) clusters in numerous organisms. A number of phenotypes including low levels of Fe-S cluster incorporation are associated with the deletion of the gene encoding a chloroplast-specific Nfu-type protein, Nfu2 from Arabidopsis thaliana (AtNfu2). Here, we report that recombinant AtNfu2 is able to assemble both [2Fe-2S] and [4Fe-4S] clusters. Analytical data and gel filtration studies support cluster/protein stoichiometries of one [2Fe-2S] cluster/homotetramer and one [4Fe-4S] cluster/homodimer. The combination of UV-visible absorption and circular dichroism and resonance Raman and Mössbauer spectroscopies has been employed to investigate the nature, properties, and transfer of the clusters assembled on Nfu2. The results are consistent with subunit-bridging [2Fe-2S](2+) and [4Fe-4S](2+) clusters coordinated by the cysteines in the conserved CXXC motif. The results also provided insight into the specificity of Nfu2 for the maturation of chloroplastic Fe-S proteins via intact, rapid, and quantitative cluster transfer. [2Fe-2S] cluster-bound Nfu2 is shown to be an effective [2Fe-2S](2+) cluster donor for glutaredoxin S16 but not glutaredoxin S14. Moreover, [4Fe-4S] cluster-bound Nfu2 is shown to be a very rapid and efficient [4Fe-4S](2+) cluster donor for adenosine 5'-phosphosulfate reductase (APR1), and yeast two-hybrid studies indicate that APR1 forms a complex with Nfu2 but not with Nfu1 and Nfu3, the two other chloroplastic Nfu proteins. This cluster transfer is likely to be physiologically relevant and is particularly significant for plant metabolism as APR1 catalyzes the second step in reductive sulfur assimilation, which ultimately results in the biosynthesis of cysteine, methionine, glutathione, and Fe-S clusters.

Heterologous reconstitution of the intact geodin gene cluster in Aspergillus nidulans through a simple and versatile PCR based approach.

Fungal natural products are a rich resource for bioactive molecules. To fully exploit this potential it is necessary to link genes to metabolites. Genetic information for numerous putative biosynthetic pathways has become available in recent years through genome sequencing. However, the lack of solid methodology for genetic manipulation of most species severely hampers pathway characterization. Here we present a simple PCR based approach for heterologous reconstitution of intact gene clusters. Specifically, the putative gene cluster responsible for geodin production from Aspergillus terreus was transferred in a two step procedure to an expression platform in A. nidulans. The individual cluster fragments were generated by PCR and assembled via efficient USER fusion prior to transformation and integration via re-iterative gene targeting. A total of 13 open reading frames contained in 25 kb of DNA were successfully transferred between the two species enabling geodin synthesis in A. nidulans. Subsequently, functions of three genes in the cluster were validated by genetic and chemical analyses. Specifically, ATEG_08451 (gedC) encodes a polyketide synthase, ATEG_08453 (gedR) encodes a transcription factor responsible for activation of the geodin gene cluster and ATEG_08460 (gedL) encodes a halogenase that catalyzes conversion of sulochrin to dihydrogeodin. We expect that our approach for transferring intact biosynthetic pathways to a fungus with a well developed genetic toolbox will be instrumental in characterizing the many exciting pathways for secondary metabolite production that are currently being uncovered by the fungal genome sequencing projects.

Allying with armored snails: the complete genome of gammaproteobacterial endosymbiont

Deep-sea vents harbor dense populations of various animals that have their specific symbiotic bacteria. Scaly-foot gastropods, which are snails with mineralized scales covering the sides of its foot, have a gammaproteobacterial endosymbiont in their enlarged esophageal glands and diverse epibionts on the surface of their scales. In this study, we report the complete genome sequencing of gammaproteobacterial endosymbiont. The endosymbiont genome displays features consistent with ongoing genome reduction such as large proportions of pseudogenes and insertion elements. The genome encodes functions commonly found in deep-sea vent chemoautotrophs such as sulfur oxidation and carbon fixation. Stable carbon isotope ((13)C)-labeling experiments confirmed the endosymbiont chemoautotrophy. The genome also includes an intact hydrogenase gene cluster that potentially has been horizontally transferred from phylogenetically distant bacteria. Notable findings include the presence and transcription of genes for flagellar assembly, through which proteins are potentially exported from bacterium to the host. Symbionts of snail individuals exhibited extreme genetic homogeneity, showing only two synonymous changes in 19 different genes (13 810 positions in total) determined for 32 individual gastropods collected from a single colony at one time. The extremely low genetic individuality in endosymbionts probably reflects that the stringent symbiont selection by host prevents the random genetic drift in the small population of horizontally transmitted symbiont. This study is the first complete genome analysis of gastropod endosymbiont and offers an opportunity to study genome evolution in a recently evolved endosymbiont.

Homeostatic Competition between Phasic and Tonic Inhibition

The GABAA receptors are the major inhibitory receptors in the brain and are localized at both synaptic and extrasynaptic membranes. Synaptic GABAA receptors mediate phasic inhibition, whereas extrasynaptic GABAA receptors mediate tonic inhibition. Both phasic and tonic inhibitions regulate neuronal activity, but whether they regulate each other is not very clear. Here, we investigated the functional interaction between synaptic and extrasynaptic GABAA receptors through various molecular manipulations. Overexpression of extrasynaptic α6β3δ-GABAA receptors in mouse hippocampal pyramidal neurons significantly increased tonic currents. Surprisingly, the increase of tonic inhibition was accompanied by a dramatic reduction of the phasic inhibition, suggesting a possible homeostatic regulation of the total inhibition. Overexpressing the α6 subunit alone induced an up-regulation of δ subunit expression and suppressed phasic inhibition similar to overexpressing the α6β3δ subunits. Interestingly, blocking all GABAA receptors after overexpressing α6β3δ receptors could not restore the synaptic GABAergic transmission, suggesting that receptor activation is not required for the homeostatic interplay. Furthermore, insertion of a gephyrin-binding-site (GBS) into the α6 and δ subunits recruited α6(GBS)β3δ(GBS) receptors to postsynaptic sites but failed to rescue synaptic GABAergic transmission. Thus, it is not the positional effect of extrasynaptic α6β3δ receptors that causes the down-regulation of phasic inhibition. Overexpressing α5β3γ2 subunits similarly reduced synaptic GABAergic transmission. We propose a working model that both synaptic and extrasynaptic GABAA receptors may compete for limited receptor slots on the plasma membrane to maintain a homeostatic range of the total inhibition.

Ions colliding with clusters of fullerenes—Decay pathways and covalent bond formations

We report experimental results for the ionization and fragmentation of weakly bound van der Waals clusters of n C60 molecules following collisions with Ar(2+), He(2+), and Xe(20+) at laboratory kinetic energies of 13 keV, 22.5 keV, and 300 keV, respectively. Intact singly charged C60 monomers are the dominant reaction products in all three cases and this is accounted for by means of Monte Carlo calculations of energy transfer processes and a simple Arrhenius-type [C60]n(+) → C60(+)+(n-1)C60 evaporation model. Excitation energies in the range of only ~0.7 eV per C60 molecule in a [C60]13(+) cluster are sufficient for complete evaporation and such low energies correspond to ion trajectories far outside the clusters. Still we observe singly and even doubly charged intact cluster ions which stem from even more distant collisions. For penetrating collisions the clusters become multiply charged and some of the individual molecules may be promptly fragmented in direct knock-out processes leading to efficient formations of new covalent systems. For Ar(2+) and He(2+) collisions, we observe very efficient C119(+) and C118(+) formation and molecular dynamics simulations suggest that they are covalent dumb-bell systems due to bonding between C59(+) or C58(+) and C60 during cluster fragmentation. In the Ar(2+) case, it is possible to form even smaller C120-2m(+) molecules (m = 2-7), while no molecular fusion reactions are observed for the present Xe(20+) collisions.

Identification of an intact ParaHox cluster with temporal colinearity but altered spatial colinearity in the hemichordate Ptychodera flava

BackgroundParaHox and Hox genes are thought to have evolved from a common ancestral ProtoHox cluster or from tandem duplication prior to the divergence of cnidarians and bilaterians. Similar to Hox clusters, chordate ParaHox genes including Gsx, Xlox, and Cdx, are clustered and their expression exhibits temporal and spatial colinearity. In non-chordate animals, however, studies on the genomic organization of ParaHox genes are limited to only a few animal taxa. Hemichordates, such as the Enteropneust acorn worms, have been used to gain insights into the origins of chordate characters. In this study, we investigated the genomic organization and expression of ParaHox genes in the indirect developing hemichordate acorn worm Ptychodera flava.ResultsWe found that P. flava contains an intact ParaHox cluster with a similar arrangement to that of chordates. The temporal expression order of the P. flava ParaHox genes is the same as that of the chordate ParaHox genes. During embryogenesis, the spatial expression pattern of PfCdx in the posterior endoderm represents a conserved feature similar to the expression of its orthologs in other animals. On the other hand, PfXlox and PfGsx show a novel expression pattern in the blastopore. Nevertheless, during metamorphosis, PfXlox and PfCdx are expressed in the endoderm in a spatially staggered pattern similar to the situation in chordates.ConclusionsOur study shows that P. flava ParaHox genes, despite forming an intact cluster, exhibit temporal colinearity but lose spatial colinearity during embryogenesis. During metamorphosis, partial spatial colinearity is retained in the transforming larva. These results strongly suggest that intact ParaHox gene clustering was retained in the deuterostome ancestor and is correlated with temporal colinearity.

Intact cluster and chordate-like expression of ParaHox genes in a sea star

BackgroundThe ParaHox genes are thought to be major players in patterning the gut of several bilaterian taxa. Though this is a fundamental role that these transcription factors play, their activities are not limited to the endoderm and extend to both ectodermal and mesodermal tissues. Three genes compose the ParaHox group: Gsx, Xlox and Cdx. In some taxa (mostly chordates but to some degree also in protostomes) the three genes are arranged into a genomic cluster, in a similar fashion to what has been shown for the better-known Hox genes. Sea urchins possess the full complement of ParaHox genes but they are all dispersed throughout the genome, an arrangement that, perhaps, represented the primitive condition for all echinoderms. In order to understand the evolutionary history of this group of genes we cloned and characterized all ParaHox genes, studied their expression patterns and identified their genomic loci in a member of an earlier branching group of echinoderms, the asteroid Patiria miniata.ResultsWe identified the three ParaHox orthologs in the genome of P. miniata. While one of them, PmGsx is provided as maternal message, with no zygotic activation afterwards, the other two, PmLox and PmCdx are expressed during embryogenesis, within restricted domains of both endoderm and ectoderm. Screening of a Patiria bacterial artificial chromosome (BAC) library led to the identification of a clone containing the three genes. The transcriptional directions of PmGsx and PmLox are opposed to that of the PmCdx gene within the cluster.ConclusionsThe identification of P. miniata ParaHox genes has revealed the fact that these genes are clustered in the genome, in contrast to what has been reported for echinoids. Since the presence of an intact cluster, or at least a partial cluster, has been reported in chordates and polychaetes respectively, it becomes clear that within echinoderms, sea urchins have modified the original bilaterian arrangement. Moreover, the sea star ParaHox domains of expression show chordate-like features not found in the sea urchin, confirming that the dynamics of gene expression for the respective genes and their putative regulatory interactions have clearly changed over evolutionary time within the echinoid lineage.

Time is of the essence for ParaHox homeobox gene clustering

ParaHox genes, and their evolutionary sisters the Hox genes, are integral to patterning the anterior-posterior axis of most animals. Like the Hox genes, ParaHox genes can be clustered and exhibit the phenomenon of colinearity - gene order within the cluster matching gene activation. Two new instances of ParaHox clustering provide the first examples of intact clusters outside chordates, with gene expression lending weight to the argument that temporal colinearity is the key to understanding clustering.See research articles: http://www.biomedcentral.com/1741-7007/11/68 and http://www.biomedcentral.com/1471-2148/13/129

Mass Spectrometry and Gas‐Phase Chemistry of Bismuth–Oxido Clusters

The mass spectrometric characterisation of bismuth-oxido clusters is described together with tandem mass spectrometric experiments aimed at investigating their gas-phase chemistry. Clusters with different ligand shells (nitrate, salicylates, and methacrylate) and different sizes ({Bi6 O8 }, {Bi22 O26 }, and {Bi38 O45 }) were selected for this study. The following aspects were addressed by (tandem) electrospray ionisation Fourier-transform ion-cyclotron-resonance (ESI-FTICR) mass spectrometry: 1) Electrospray ionisation was used successfully for the generation of intact cluster ions, but led to rather complicated distributions of charge states and solvent adducts. The cluster core remained intact. 2) Mass spectrometry was used to follow the cluster growth from {Bi6 O8 } to {Bi22 O27 } and finally {Bi38 O45 } clusters. These experiments revealed that careful tuning of the conditions is required to avoid precipitates forming that hamper ESI ionisation. The stages of growth strongly depend on the experimental conditions. 3) Fragmentation experiments in the gas phase performed with the {Bi22 O27 } clusters obtained in the growth experiments resulted in the preferential formation of {Bi6 O8 } fragments and point to the particular stability of this cluster and its role in cluster growth. 4) Solution-phase ligand-exchange reactions on {Bi22 O26 } salicylate clusters were qualitatively monitored by mass spectrometry, but were limited by the complicated ion series formed that led to overlapping isotope patterns. 5) A number of fragmentation reactions occurred within the ligand shell when the clusters surrounded by an organic ligand shell were subjected to infrared multiphoton dissociation experiments. 6) For the nitrate clusters, fragmentation within the core was observed yielding {Bi6 O8 } fragments together with the corresponding clusters of reduced size.

Clustering and Switching Strategies During the Semantic Fluency Task in Men with Frontal Lobe Lesions and in Men with Schizophrenia

Differences in semantic clustering and switching were examined in men with frontal lobe lesions, men with schizophrenia and healthy men. Men with frontal lobe lesions and men with schizophrenia generated fewer words than healthy men and presented intact clustering, but decreased switching during the semantic fluency task. However, after controlling for the number of words produced, between-group differences in switching disappeared. These findings suggest that all three groups used similar strategies of clustering and switching during the semantic fluency task, although men with frontal lobe lesions and men with schizophrenia did it less efficiently than healthy men.

The type VI secretion system encoded in SPI-6 plays a role in gastrointestinal colonization and systemic spread of Salmonella enterica serovar Typhimurium in the chicken.

The role of the Salmonella Pathogenicity Islands (SPIs) in pathogenesis of Salmonella enterica Typhimurium infection in the chicken is poorly studied, while many studies have been completed in murine models. The Type VI Secretion System (T6SS) is a recently described protein secretion system in Gram-negative bacteria. The genus Salmonella contains five phylogenetically distinct T6SS encoded in differentially distributed genomic islands. S. Typhimurium harbors a T6SS encoded in SPI-6 (T6SSSPI-6), which contributes to the ability of Salmonella to colonize mice. On the other hand, serotype Gallinarum harbors a T6SS encoded in SPI-19 (T6SSSPI-19) that is required for colonization of chicks. In this work, we investigated the role of T6SSSPI-6 in infection of chicks by S. Typhimurium. Oral infection of White Leghorn chicks showed that a ΔT6SSSPI-6 mutant had reduced colonization of the gut and internal organs, compared with the wild-type strain. Transfer of the intact T6SSSPI-6 gene cluster into the T6SS mutant restored bacterial colonization. In addition, our results showed that transfer of T6SSSPI-19 from S. Gallinarum to the ΔT6SSSPI-6 mutant of S. Typhimurium not only complemented the colonization defect but also resulted in a transient increase in the colonization of the cecum and ileum of chicks at days 1 and 3 post-infection. Our data indicates that T6SSSPI-6 contributes to chicken colonization and suggests that both T6SSSPI-6 and T6SSSPI-19 perform similar functions in vivo despite belonging to different phylogenetic families.

Tail Tip Proteins Related to Bacteriophage λ gpL Coordinate an Iron-Sulfur Cluster

The assembly of long non-contractile phage tails begins with the formation of the tail tip complex (TTC). TTCs are multi-functional protein structures that mediate host cell adsorption and genome injection. The TTC of phage λ is assembled from multiple copies of eight different proteins, including gpL. Purified preparations of gpL and several homologues all displayed a distinct reddish color, suggesting the binding of iron by these proteins. Further characterization of the gpL homologue from phage N15, which was most amenable to in vitro analyses, showed that it contains two domains. The C-terminal domain was demonstrated to coordinate an iron-sulfur cluster, providing the first example of a viral structural protein binding to this type of metal group. We characterized the iron-sulfur cluster using inductively coupled plasma-atomic emission spectroscopy, absorbance spectroscopy, and electron paramagnetic resonance spectroscopy and found that it is an oxygen-sensitive [4Fe-4S]2+ cluster. Four highly conserved cysteine residues were shown to be required for coordinating the iron-sulfur cluster, and substitution of any of these Cys residues with Ser or Ala within the context of λ gpL abolished biological activity. These data imply that the intact iron-sulfur cluster is required for function. The presence of four conserved Cys residues in the C-terminal regions of very diverse gpL homologues suggest that utilization of an iron-sulfur cluster is a widespread feature of non-contractile tailed phages that infect Gram-negative bacteria. In addition, this is the first example of a viral structural protein that binds an iron-sulfur cluster.

Draft Genome Sequence of Streptomyces bottropensis ATCC 25435, a Bottromycin-Producing Actinomycete

A series of bottromycin antibiotics have been isolated and identified from Streptomyces bottropensis strain ATCC 25435. Here, a draft genome sequence of S. bottropensis ATCC 25435 is presented. The genome carries an intact biosynthetic gene cluster for bottromycin antibiotics, which provides insight into the combinatorial biosynthesis of bottromycin antibiotics.