Autophagy: a role in metal ion homeostasis?

Nutrient limitation is one of the most common forms of stress encountered by microorganisms in the environment. Surviving this stress depends upon a number of integrated responses, one of the most important of which is autophagy. When the filamentous fungus Aspergillus fumigatus becomes nutrient deprived it undergoes two important processes: the developmental pathway for asexual sporulation (conidiation), and a foraging response that promotes the migration of the hyphal tips into new substrate. To determine the contribution of autophagy to these two functions, we disrupted the A. fumigatus atg1 gene. The data reveal that Atg1 is required for wild-type conidiation of A. fumigatus, but only when nitrogen is limiting. Secondly, we demonstrate that metal ion availability limits the extent to which A. fumigatus can grow without a carbon/nitrogen source and that autophagy is necessary for growth under conditions of metal ion deficiency. These findings indicate that autophagy is responsible for maintaining an adequate supply of nitrogen to support conidiophore development, and provide intriguing new evidence that autophagy is linked to metal ion homeostasis.     

Do the 16 mer, 5'-GUGGUCUGAUGAGGCC-3' and the 25 mer, 5'-GGCCGAAACUCGUAAGAGUCACCAC-3', form a hammerhead ribozyme structure in physiological conditions? An NMR and UV thermodynamic study

In a wide range of salt concentrations, 10-30 mM phosphate buffer containing up to 0.5 M Li2SO4 and 300 mM NaCl, 7.5 mM Mg2+, pH 5.5-7.5, a mixture of the 16 mer and the 25 mer RNA strands does not form a hammerhead in any amount detectable by NMR at 600 MHz. The imino-, amino-, aromatic- and anomeric protons in the NMR spectra of both the 16 mer and the 25 mer RNA have been assigned separately. Both the 16 mer and the 25 mer RNA both take up very stable hairpin structures, and when mixed together there is no major change of conformation in neither oligo-RNA.     

Low resolution X-ray structure of γ-glutamyltranspeptidase from Bacillus licheniformis: Opened active site cleft and a cluster of acid residues potentially involved in the recognition of a metal ion

γ-Glutamyltranspeptidases (γ-GTs) cleave the γ-glutamyl amide bond of glutathione and transfer the released γ-glutamyl group to water (hydrolysis) or acceptor amino acids (transpeptidation). These ubiquitous enzymes play a key role in the biosynthesis and degradation of glutathione, and in xenobiotic detoxification.     

Does kin structure explain the occurrence of workers in a lower termite?

Kinship plays a fundamental role in the origin of social life. It is also predicted to affect numerous details within animal societies, yet recent studies revealed equivocal results. We tested the influence of relatedness for the occurrence of workers in the termite Cryptotermes secundus. Here individuals are developmentally flexible to remain workers or to become dispersing sexuals that found new colonies. Furthermore, colony relatedness naturally increases with inbreeding and decreases when neighboring colonies fuse. Similar to recent studies on social Hymenoptera, our experimental change in relatedness gave equivocal results. Reducing relatedness within colonies did not have an effect, but individuals in inbred colonies were less likely to disperse and more likely to remain workers as predicted by kinship arguments. Several explanations for the interpretation of these equivocal results are provided.     

Does the proposed DSE motif form the active center in the Hermes transposase?

Donor cleavage and strand transfer are two functions performed by transposases during transposition of class II transposable elements. Within transposable elements, the only active center described, to date, facilitating both functions, is the so-called DDE motif. A second motif, R-K-H/K-R-H/W-Y, is found in the site-specific recombinases of the tyrosine recombinase family. While present in many bacterial insertion sequences as well as in the eukaryotic family of mariner/Tc1 elements, the DDE motif was considered absent in other classes of eukaryotic class II elements such as P, and hAT and piggyBac. Based on sequence alignments of a hobo-like element from the nematode Caenorhabditis elegans, to a variety of other hAT transposases and several members of the mariner/Tc1 group, Bigot et al. [Gene 174 (1996) 265] proposed the presence of a DSE motif in hAT transposases. In the present study we tested if each of these three residues is required for transposition of the Hermes element, a member of the hAT family commonly used for insect transformation. While D402N and E572Q mutations lead to knock-out of Hermes function, mutations S535A and S535D did not affect transposition frequency or the choice of integration sites. These data give the first experimental support that D402 and E572 are indeed required for transposition of Hermes. Furthermore, this study indicates that the active center of the Hermes transposase differs from the proposed DSE motif. It remains to be shown if other residues also form the active site of this transposase.     

Does a cytoplasmic bridge connect the CNS axon with the inner loop of myelin?

Sarah Luse (1959) reported over 30 years ago on the presence of a bridge connecting the axon to the myelin sheath in the central nervous system (CNS). This notion has not been accepted in the literature. Wolman (1992) found that the progress of demyelination in some viral diseases affecting the CNS fits the concept of Luse, as the process occurred primarily along the major dense line of myelin, which is in continuity with the cytoplasm of the oligodendroglial cell. Injection of Lucifer yellow (LY) and horseradish peroxidase (HRP) into the vitreous of guinea pigs, with and without iontophoresis, resulted in labeling of the nerve axons and myelin. Labeling of myelin by HRP occurred along the major dense line which indicated that a transient or permanent cytoplasmic bridge connects axons and myelin in the optic nerve.     

CFTR structure and function: is there a role in the kidney?

Cystic fibrosis (CF) is a lethal autosomal recessive genetic disease caused by mutations in the CF transmembrane conductance regulator (CFTR). Mutations in the CFTR gene may result in a defective protein processing that leads to changes in function and regulation of this chloride channel. Despite of the expression of CFTR in the kidney, patients with CF do not present major renal dysfunction, but it is known that both the urinary excretion of proteins and renal capacity to concentrate and dilute urine are altered in these patients. CFTR mRNA is expressed in all nephron segments of rat and human, and this abundance is more prominent in renal cortex and outer medulla renal areas. CFTR protein was detected in apical surface of both proximal and distal tubules of rat kidney but not in the outer medullary collecting ducts. Studies have demonstrated that CFTR does not only transport Cl⁻ but also ATP. ATP transport by CFTR could be involved in the control of other ion transporters such as Na⁺ (ENaC) and K⁺ (renal outer medullary potassium) channels, especially in TAL and CCD. In the kidney, CFTR also might be involved in the endocytosis of low-molecular-weight proteins by proximal tubules. This review is focused on the CFTR function and structure, its role in the renal physiology, and its modulation by hormones involved in the control of extracellular fluid volume.     

Do common eiders nest in kin groups? Microgeographic genetic structure in a philopatric sea duck

We investigated local genetic associations among female Pacific common eiders (Somateria mollissima v‐nigrum) nesting in a stochastic Arctic environment within two groups of barrier islands (Simpson Lagoon and Mikkelsen Bay) in the Beaufort Sea, Alaska. Nonrandom genetic associations were observed among nesting females using regional spatial autocorrelation analyses for distance classes up to 1000 m in Simpson Lagoon. Nearest‐neighbour analyses identified clusters of genetically related females with positive lr values observed for 0–13% and 0–7% of the comparisons in Simpson Lagoon and Mikkelsen Bay, respectively, across years. These results indicate that a proportion of females are nesting in close proximity to more genetically related individuals, albeit at low frequency. Such kin groupings may form through active association between relatives or through natal philopatry and breeding site fidelity. Eiders nest in close association with driftwood, which is redistributed annually by seasonal storms. Yet, genetic associations were still observed. Microgeographic structure may thus be more attributable to kin association than natal philopatry and site fidelity. However, habitat availability may also influence the level of structure observed. Regional structure was present only within Simpson Lagoon and this island group includes at least three islands with sufficient driftwood for colonies, whereas only one island at Mikkelsen Bay has these features. A long‐term demographic study is needed to understand more fully the mechanisms that lead to fine‐scale genetic structure observed in common eiders breeding in the Beaufort Sea.     

Does genomic variation in a foundation species predict arthropod community structure in a riparian forest?

Understanding how genetic variation within a foundation species determines the structure of associated communities and ecosystem processes has been an emerging frontier in ecology. Previous studies in common gardens identified close links between intraspecific variation and multispecies community structure, and these findings are now being evaluated directly in the complex natural ecosystem. In this study, we examined to what extent genomic variation in a foundation tree species explains the structure of associated arthropod communities in the field, comparing with spatial, temporal and environmental factors. In a continuous mixed forest, arthropods were surveyed on 85 mature alders (Alnus hirsuta) in 2 years. Moreover, we estimated Nei's genetic distance among the alders based on 1,077 single nucleotide polymorphisms obtained from restricted‐site‐associated DNA sequencing of the alders’ genome. In both years, we detected significant correlations between genetic distance and dissimilarity of arthropod communities. A generalized dissimilarity modelling indicated that the genetic distance of alder populations was the most important predictor to explain the variance of arthropod communities. Among arthropod functional groups, carnivores were consistently correlated with genetic distance of the foundation species in both years. Furthermore, the extent of year‐to‐year changes in arthropod communities was more similar between more genetically closed alder populations. This study demonstrates that the genetic similarity rule would be primarily prominent in community assembly of plant‐associated arthropods under temporally and spatially variable environments in the field.     

Does the behavioural activation detected after a single dose of a benzodiazepine reflect a withdrawal response?

The effects, in mice, of a single dose of lorazepam or oxazepam were determined, in the holeboard, 24, 48 and 72 hours after treatment. Lorazepam produced significant increases in both spontaneous locomotor activity and in rearing 48 hours after treatment and oxazepam produced a significant overall increase in rearing over the three time points. There was no detectable in vivo receptor occupancy for either drug at the 48 hour time point, so that these effects were not due to residual concentrations of drug in the brain. We therefore suggest that we were detecting a spontaneous withdrawal response to a single dose of benzodiazepine. The increases in both locomotor activity and rearing, detected 48 hours after lorazepam, could be reversed by treating simultaneously with Ro 15-1788 (a benzodiazepine antagonist). When Ro 15-1788 was injected 20 minutes prior to testing, the mice that had been treated 48 hours previously with lorazepam still showed increased locomotor activity and rearing. We conclude that the hyperactivity was not caused by any change in the levels of endogenous substances acting at the benzodiazepine receptor.     

Developmental signaling: Does it bridge the gap between cilia dysfunction and renal cystogenesis?

For more than a decade, evidence has accumulated linking dysfunction of primary cilia to renal cystogenesis, yet molecular mechanisms remain undefined. The pathogenesis of renal cysts is complex, involving multiple cellular aberrations and signaling pathways. Adding to this complexity, primary cilia exhibit multiple roles in a context‐dependent manner. On renal epithelial cells, primary cilia act as mechanosensors and trigger extracellular Ca²⁺ influx in response to laminar fluid flow. During mammalian development, primary cilia mediate the Hedgehog (Hh), Wnt, and Notch pathways, which control cell proliferation and differentiation, and tissue morphogenesis. Further, experimental evidence suggests the developmental state of the kidney strongly influences renal cystic disease. Thus, we review evidence for regulation of Ca²⁺ and cAMP, key molecules in renal cystogenesis, at the primary cilium, the role of Hh, Wnt, and Notch signaling in renal cystic disease, and the interplay between these developmental pathways and Ca²⁺ signaling. Indeed if these developmental pathways influence renal cystogenesis, these may represent novel therapeutic targets that can be integrated into a combination therapy for renal cystic disease. Birth Defects Research (Part C) 102:159–173, 2014. © 2014 Wiley Periodicals, Inc.     

Does a stretched DNA structure dictate the helical geometry of RecA-like filaments?

Proteins in the RecA/Rad51/RadA/UvsX family form helical filaments on DNA in which the DNA is stretched and untwisted. A comparison of the average helical parameters of these filaments from five different proteins, obtained from archaea, eubacteria and eukaryotes, suggests that an intrinsic state of DNA may be responsible for the conservation of these particular filament forms across evolution. In this view, these proteins stabilize this existing state of DNA, rather than induce a novel conformation.     

Ser-796 of β-galactosidase (Escherichia coli) plays a key role in maintaining a balance between the opened and closed conformations of the catalytically important active site loop

A loop (residues 794–803) at the active site of β-galactosidase (Escherichia coli) opens and closes during catalysis. The α and β carbons of Ser-796 form a hydrophobic connection to Phe-601 when the loop is closed while a connection via two H-bonds with the Ser hydroxyl occurs with the loop open. β-Galactosidases with substitutions for Ser-796 were investigated. Replacement by Ala strongly stabilizes the closed conformation because of greater hydrophobicity and loss of H-bonding ability while replacement with Thr stabilizes the open form through hydrophobic interactions with its methyl group. Upon substitution with Asp much of the defined loop structure is lost. The different open-closed equilibria cause differences in the stabilities of the enzyme · substrate and enzyme · transition state complexes and of the covalent intermediate that affect the activation thermodynamics. With Ala, large changes of both the galactosylation (k₂) and degalactosylation (k₃) rates occur. With Thr and Asp, the k₂ and k₃ were not changed as much but large ΔH³ and TΔS³ changes showed that the substitutions caused mechanistic changes. Overall, the hydrophobic and H-bonding properties of Ser-796 result in interactions strong enough to stabilize the open or closed conformations of the loop but weak enough to allow loop movement during the reaction.     

Does one subgenome become dominant in the formation and evolution of a polyploid?

BackgroundPolyploids are common in flowering plants and they tend to have more expanded ranges of distributions than their diploid progenitors. Possible mechanisms underlying polyploid success have been intensively investigated. Previous studies showed that polyploidy generates novel changes and that subgenomes in allopolyploid species often differ in gene number, gene expression levels and levels of epigenetic alteration. It is widely believed that such differences are the results of conflicts among the subgenomes. These differences have been treated by some as subgenome dominance, and it is claimed that the magnitude of subgenome dominance increases in polyploid evolution.ScopeIn addition to changes which occurred during evolution, differences between subgenomes of a polyploid species may also be affected by differences between the diploid donors and changes which occurred during polyploidization. The variable genome components in many plant species are extensive, which would result in exaggerated differences between a subgenome and its progenitor when a single genotype or a small number of genotypes are used to represent a polyploid or its donors. When artificially resynthesized polyploids are used as surrogates for newly formed genotypes which have not been exposed to evolutionary selection, differences between diploid genotypes available today and those involved in the formation of the natural polyploid genotypes must also be considered.ConclusionsContrary to the now widely held views that subgenome biases in polyploids are the results of conflicts among the subgenomes and that one of the parental subgenomes generally retains more genes which are more highly expressed, available results show that subgenome biases mainly reflect legacy from the progenitors and that they can be detected before the completion of polyploidization events. Further, there is no convincing evidence that the magnitudes of subgenome biases have significantly changed during evolution for any of the allopolyploid species assessed.     

Does hunting affect the demography and genetic structure of the greywing francolin Francolinus africanus?

Hunted and unhunted populations of greywing francolin Francolinus africanus have been studied in the eastern Cape Province of South Africa in order to understand the effects of hunting on the demography and genetic structure of these populations. Greywing population density cycled annually for both hunted and unhunted populations. However, there was an apparent pulse of immigration of sub-dominant birds, and earlier reproduction, in the hunted populations immediately after the winter hunting season. Average levels of allozyme heterozygosity (H) for hunted and unhunted populations were both 0.076, and although the proportion of polymorphic loci per sample and the mean number of alleles per locus for each sample were lower for the hunted populations than for the unhunted populations, these differences were not significant. However, the hunted populations displayed higher levels of outbreeding (lower F _IS and F _IT values) than those for unhunted populations. Therefore, it is concluded that although greywing francolin populations contain relatively high levels of genetic heterogeneity, it is probably the increased levels of local immigration following hunting which reduces the effects of any reduction in genetic variation due to a decrease in local population size from hunting.     

Interaction between fast and ultra-slow inactivation in the voltage-gated sodium channel. Does the inactivation gate stabilize the channel structure?

Recently, we reported that mutation A1529D in the domain (D) IV P-loop of the rat skeletal muscle Na(+) channel mu(1) (DIV-A1529D) enhanced entry to an inactivated state from which the channels recovered with an abnormally slow time constant on the order of approximately 100 s. Transition to this "ultra-slow" inactivated state (USI) was substantially reduced by binding to the outer pore of a mutant mu-conotoxin GIIIA. This indicated that USI reflected a structural rearrangement of the outer channel vestibule and that binding to the pore of a peptide could stabilize the pore structure (Hilber, K., Sandtner, W., Kudlacek, O., Glaaser, I. W., Weisz, E., Kyle, J. W., French, R. J., Fozzard, H. A., Dudley, S. C., and Todt, H. (2001) J. Biol. Chem. 276, 27831-27839). Here, we tested the hypothesis that occlusion of the inner vestibule of the Na(+) channel by the fast inactivation gate inhibits ultra-slow inactivation. Stabilization of the fast inactivated state (FI) by coexpression of the rat brain beta(1) subunit in Xenopus oocytes significantly prolonged the time course of entry to the USI. A reduction in USI was also observed when the FI was stabilized in the absence of the beta(1) subunit, suggesting a causal relation between the occurrence of the FI and inhibition of USI. This finding was further confirmed in experiments where the FI was destabilized by introducing the mutations I1303Q/F1304Q/M1305Q. In DIV-A1529D + I1303Q/F1304Q/M1305Q channels, occurrence of USI was enhanced at strongly depolarized potentials and could not be prevented by coexpression of the beta(1) subunit. These results strongly suggest that FI inhibits USI in DIV-A1529D channels. Binding to the inner pore of the fast inactivation gate may stabilize the channel structure and thereby prevent USI. Some of the data have been published previously in abstract form (Hilber, K., Sandtner, W., Kudlacek, O., Singer, E., and Todt, H. (2002) Soc. Neurosci. Abstr. 27, program number 46.12).