The complete mitochondrial genome of the leafminer Liriomyza sativae (Diptera: Agromyzidae): great difference in the A+T-rich region compared to Liriomyza trifolii

The complete mitochondrial genome sequence of Liriomyza sativae Blanchard (15,551 bp) was determined and analyzed in this study. The circular genome contained 37 genes including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and an A + T-rich region. The initiation codons of COI and ND1 were ‘ATCA’ and ‘GTG’, respectively. ND2 gene used the truncated termination codon ‘T’. All the tRNA genes had the typical cloverleaf secondary structures except for tRNA^Ser(AGN) gene, which was found with the absence of a DHU arm. In addition, a tRNA-like secondary structure (tRNA^Met) was found in the A + T-rich region. The great difference was that the length of L. sativae A + T-rich region was 597 bp shorter than that of Liriomyza trifolii (Burgess). Meanwhile, some minor differences such as ‘TATA’ block were also observed in L. sativae in contrast to ‘TACA’ block in L. trifolii. There were also some essential structure elements such as ‘TATA’ block, ‘G(A)_nT’ block, poly-T stretch and stem-and-loop structure in the A + T-rich region of L. sativae mitochondrial genome.     

Quality of T-cells after stimulation with leukemia-derived dendritic cells (DC) from patients with acute myeloid leukemia (AML) or myeloid dysplastic syndrome (MDS) is predictive for their leukemia cytotoxic potential

Myeloid leukemic cells can differentiate into leukemia-derived dendritic cells (DC_leu), presenting known/unknown leukemic-antigens. Induced anti-leukemic T-cell-responses are variable. To further elicit DC/DC_leu-induced T-cell-response-patterns we performed (functional)flow-cytometry/fluorolysis-assays before/after mixed lymphocyte cultures (MLC) of matched (allogeneic) donor-T-cells (n = 6), T-cells prepared at relapse after stem cell transplantation (n = 4) or (autologous) patients’-T-cells (n = 7) with blast-containing-mononuclear-cells (‘MNC’) or DC_leu-containing DC (‘DC’). Compared to ‘MNC’ ‘DC’ were better mediators of anti-leukaemic T-cell-activity, although not in every case effective. We could define cut-off proportions of mature DC, DC_leu, proliferating, CD4⁺, CD8⁺ and non-naive T-cells after ‘MNC’- or ‘DC’-stimulation, that were predictive for an anti-leukemic-activity of stimulated T-cells as well as a response to immunotherapy. Interestingly especially ratios >1 of CD4:CD8 or CD45RO:CD45RA T-cells were predictive for anti-leukemic function after DC-stimulation.In summary the composition and quality of DC and T-cells after a MLC-stimulating-phase is predictive for a successful ex-vivo and in-vivo anti-leukemic response, especially with respect to proportions of proliferating, CD4⁺ and CD45RO⁺ T-cells. Successful cytotoxicity and the development of a T-cell-memory after ‘DC’-stimulation could be predictive for the clinical course of the disease and may pave the way to develop adoptive immunotherapy, especially for patients at relapse after SCT.     

Pseudomonas protegens sp. nov., widespread plant-protecting bacteria producing the biocontrol compounds 2,4-diacetylphloroglucinol and pyoluteorin

Fluorescent Pseudomonas strains producing the antimicrobial secondary metabolite 2,4-diacetylphloroglucinol (Phl) play a prominent role in the biocontrol of plant diseases. A subset of Phl-producing fluorescent Pseudomonas strains, which can additionally synthesize the antimicrobial compound pyoluteorin (Plt), appears to cluster separately from other fluorescent Pseudomonas spp. based on 16S rRNA gene analysis and shares at most 98.4% 16S rRNA gene sequence identity with any other Pseudomonas species. In this study, a polyphasic approach based on molecular and phenotypic methods was used to clarify the taxonomy of representative Phl⁺ Plt⁺ strains isolated from tobacco, cotton or wheat on different continents. Phl⁺ Plt⁺ strains clustered separately from their nearest phylogenetic neighbors (i.e. species from the ‘P. syringae’, ‘P. fluorescens’ and ‘P. chlororaphis’ species complexes) based on rpoB, rpoD or gyrB phylogenies. DNA-DNA hybridization experiments clarified that Phl⁺ Plt⁺ strains formed a tight genomospecies that was distinct from P. syringae, P. fluorescens, or P. chlororaphis type strains. Within Phl⁺ strains, the Phl⁺ Plt⁺ strains were differentiated from other biocontrol fluorescent Pseudomonas strains that produced Phl but not Plt, based on phenotypic and molecular data. Discriminative phenotypic characters were also identified by numerical taxonomic analysis and siderotyping. Altogether, this polyphasic approach supported the conclusion that Phl⁺ Plt⁺ fluorescent Pseudomonas strains belonged to a novel species for which the name Pseudomonas protegens is proposed, with CHA0^T (=CFBP 6595^T, =DSM 19095^T) as the type strain.     

Syntheses, structures and vibrational spectroscopy of some 1:2 and 1:3 adducts of silver(I) oxyanion salts with pyridine and piperidine bases containing non-coordinating 2(,6)-substituents

Synthetic, single crystal X-ray structural characterizations and vibrational spectroscopic studies are recorded for a number of adducts of 1:2 stoichiometry of silver(I) oxyanion salts for oxyanions of differing basicity (perchlorate, nitrate, carboxylate (as trifluoroacetate (≡‘tfa’))), with a variety of pyridine (≡‘py’) or piperidine (≡‘pip’) bases hindered in the 2- (and, sometimes, 6-) position(s) by methyl or non-coordinating functionalities of other types, the ligands employed being 2-methylpyridine (‘2mp’), 2,6-dimethylpyridine (‘lut’), 2,4,6-trimethylpyridine (‘coll’), quinoline (‘quin’), 2,2,6,6-tetramethylpiperidine (‘tmp’), 2-amino-,6-methylpyridine (‘nmp’), 2-methoxypyridine (‘mop’) and 2-cyanomethylpyridine (‘pcn’); studies are also recorded of adducts with the parent, ‘py’, base and with 4-cyanopyridine (‘cnp’). In the majority of the complexes, the NAgN motif predominates, as might be expected, variously distorted from linearity in response to changes in (competing) basicities of the nitrogen base and any nearby anion or solvent molecule; an unusual variation is found in the highly hindered tmp/tfa adduct which is a monohydrate with interacting water displacing the rather basic anion, the converse being the case in the corresponding nitrate, also a monohydrate. With the less-hindered base mpy, both nitrate and trifluoroacetate are binuclear, with O and OCO bridges corresponding to centrosymmetric four- and eight-membered rings, respectively; the quin/nitrate adduct is more complex, also binuclear but with bis(chelating) nitrate. AgNO₃:py (1:3) is found to be binuclear, while with Agtfa/py, a 3:2 adduct [Ag(py)₂][Ag₂(tfa)₃]_(∞|∞) is found with a novel, polymeric, strongly interacting anion. A further pair of 1:3 adducts, AgNO₃:2np (2np = 2-aminopyridine) and Agtfa:nmp, both mononuclear [AgL₃]⁺X⁻ are described, differing in the modes of interaction of silver with the three N-bases. In all simple NAgN systems with aromatic ligands, the pair of ligand ‘planes’ is disposed quasi-parallel.The far-IR spectra of [AgL₂]Y (L = lut, coll; Y = ClO₄, NO₃, tfa) and of [Ag(py)_n](ClO₄) (n = 2,4) have been recorded and the ν(AgN) bands assigned in the range 80-240 cm⁻¹. For the L = lut, coll complexes, there is a clear trend of decreasing ν(AgN) following increasing r(AgN) as the interaction with the counterion increases along the series Y = ClO₄, NO₃, tfa.     

Development of mesenchymal stem cells partially originate from the neural crest

Mesenchymal stem cells (MSCs) are a heterogeneous subset of stromal stem cells isolated from many adult tissues. Previous studies reported that MSCs can differentiate to both mesodermal and neural lineages by a phenomenon referred to as ‘‘dedifferentiation’’ or ‘‘transdifferentiation’’. However, since MSCs have only been defined in vitro, much of their development in vivo is still unknown. Here, we prospectively identified MSCs in the bone marrow from adult transgenic mice encoding neural crest-specific P0-Cre/Floxed-EGFP and Wnt1-Cre/Floxed-EGFP. EGFP-positive MSCs formed spheres that expressed neural crest stem cell genes and differentiated into neurons, glial cells, and myofibroblasts. Interestingly, we observed MSCs both in the GFP⁺ and GFP⁻ fraction and found that there were no significant differences in the in vitro characteristics between these two populations. Our results suggest that MSCs in adult bone marrow have at least two developmental origins, one of which is the neural crest.     

Synthesis and structural characterization of adducts of silver(I) perchlorate with PR3 (R = Ph, cy, o-tolyl) and oligodentate aromatic bases derivative of 2,2′-bipyridyl, L, AgClO4:PR3:L (1:1:1)

Ten novel adducts of the form AgClO₄:PR₃:L (1:1:1) (R = Ph, cy, o-tolyl; L = 2,2′-bipyridyl (‘bpy’), 2,2′-biquinoline (‘bq’), bis(2-pyridyl)amine (‘dpa’), bis(2-picolyl)amine (‘dpca’)) have been synthesized and characterized by analytical, spectroscopic (IR, far-IR, ¹H and ³¹P NMR) and single crystal X-ray diffraction studies. The solid state molecular structures show that the complexes predominantly take the form [(R₃P)AgL]⁺X⁻, with a trigonal PAgN₂ coordination environment, where the approach of the anion or the solvent may perturb the planarity of the silver environment. The ClO₄ anion shows uni- or semi-bidentate coordination, except in the complexes AgClO₄:PR₃:dpca (1:1:1) (R = Ph and o-tolyl), where the anion remains uncoordinated and the dpca donor is a three-coordinate pincer-like ligand.     

Salt-stress induced changes in the leaf proteome of diploid and tetraploid mandarins with contrasting Na and Cl accumulation behaviour

To understand the genotypic variation of citrus to mild salt stress, a proteomic approach has been carried out in parallel on two citrus genotypes (‘Cleopatra’ and ‘Willow leaf’ mandarins), which differ for Na⁺ and Cl⁻ accumulation, and their cognate autotetraploids (4×). Using two-dimensional electrophoresis approximately 910 protein spots were reproducibly detected in control and salt-stressed leaves of all genotypes. Among them, 44 protein spots showing significant variations at least in one genotype were subjected to mass spectrometry analysis for identification. Salt-responsive proteins were involved in several functions, including photosynthetic processes, ROS scavenging, stress defence, and signalling. Genotype factors affect the salt-responsive pattern, especially that of carbon metabolism. The no ion accumulator ‘Cleopatra’ mandarin genotype showed the highest number of salt-responsive proteins, and up-regulation of Calvin cycle-related proteins. Conversely the ion accumulator ‘Willow leaf’ mandarin showed high levels of several photorespiration-related enzymes. A common set of proteins (twelve spots) displayed higher levels in salt-stressed leaves of 2× and 4× ‘Cleopatra’ and 4× ‘Willow leaf’ mandarin. Interestingly, antioxidant enzymes and heat shock proteins showed higher constitutive levels in 4× ‘Cleopatra’ mandarin and 4× ‘Willow leaf’ mandarin compared with the cognate 2× genotype. This work provides for the first time information on the effect of 8 weeks of salt stress on citrus genotypes contrasting for ion accumulation and their cognate autotetraploids. Results underline that genetic factors have a predominant effect on the salt response, although a common stress response independent from genotype was also found.     

Molecular characterization and expression analysis of ubiquitin-activating enzyme E1 gene in Citrus reticulata

Ubiquitin-activating enzyme E1 (UBE1) catalyzes the first step in the ubiquitination reaction, which targets a protein for degradation via a proteasome pathway. UBE1 plays an important role in metabolic processes. In this study, full-length cDNA and DNA sequences of UBE1 gene, designated CrUBE1, were obtained from ‘Wuzishatangju’ (self-incompatible, SI) and ‘Shatangju’ (self-compatible, SC) mandarins. 5 amino acids and 8 bases were different in cDNA and DNA sequences of CrUBE1 between ‘Wuzishatangju’ and ‘Shatangju’, respectively. Southern blot analysis showed that there existed only one copy of the CrUBE1 gene in genome of ‘Wuzishatangju’ and ‘Shatangju’. The temporal and spatial expression characteristics of the CrUBE1 gene were investigated using semi-quantitative RT-PCR (SqPCR) and quantitative real-time PCR (qPCR). The expression level of the CrUBE1 gene in anthers of ‘Shatangju’ was approximately 10-fold higher than in anthers of ‘Wuzishatangju’. The highest expression level of CrUBE1 was detected in pistils at 7 days after self-pollination of ‘Wuzishatangju’, which was approximately 5-fold higher than at 0 h. To obtain CrUBE1 protein, the full-length cDNA of CrUBE1 genes from ‘Wuzishatangju’ and ‘Shatangju’ were successfully expressed in Pichia pastoris. Pollen germination frequency of ‘Wuzishatangju’ was significantly inhibited with increasing of CrUBE1 protein concentrations from ‘Wuzishatangju’.     

Synthesis and structural characterization of adducts of silver(I) carboxylate salts AgX (X = CF3COO, CH3COO) with ER3 (E = P, As; R = Ph, cy, o-tolyl) and oligodentate aromatic bases derivative of 2,2′-bipyridyl, L, AgX:PR3:L (1:1:1)

Twenty-one adducts of the form AgX:ER₃:L (1:1:1) (X = CF₃COO (‘tfa’), CH₃COO (‘ac’), E = P, As; R = Ph, cy, o-tolyl; L = 2,2′-bipyridyl (‘bpy’)-based ligand) have been synthesized and characterized by analytical, spectroscopic (IR, far-IR, ¹H, ¹⁹F and ³¹P NMR) and single crystal X-ray diffraction studies. The resulting complexes are predominantly of the form [(R₃E)AgL]⁺X⁻, with a trigonal EAgN₂ coordination environment, the planarity of which may be perturbed by the approach of anion or solvent. The carboxylate anions have been found to be uni-, or semi-bidentate, or also completely ionic, as in the complexes [Ag(PPh₃)(bpy)(H₂O)](tfa) and [Ag(PPh₃)(dpk · H₂O)](tfa) (‘dpk · H₂O’ = bis(2-pyridyl)ketone (hydrated)). The complexes Agac:PPh₃:dpa (1:1:1) and Agac:P(o-tol)₃:dpa:MeCN (1:1:1:1) are dinuclear, with bridging unidentate acetate and terminal unidentate dpa (‘dpa’ = bis(2-pyridyl)amine).     

Conformational changes and reaction of clostridial glycosylating toxins

The crystal structures of the catalytic fragments of ‘lethal toxin’ from Clostridium sordellii and of ‘α-toxin’ from Clostridium novyi have been established. Almost half of the residues follow the chain fold of the glycosyl-transferase type A family of enzymes; the other half forms large α-helical protrusions that are likely to confer specificity for the respective targeted subgroup of Rho proteins in the cell. In the crystal, the active center of α-toxin contained no substrates and was disassembled, whereas that of lethal toxin, which was ligated with the donor substrate UDP-glucose and cofactor Mn^2 +, was catalytically competent. Surprisingly, the structure of lethal toxin with Ca^2 + (instead of Mn^2 +) at the cofactor position showed a bound donor substrate with a disassembled active center, indicating that the strictly octahedral coordination sphere of Mn^2 + is indispensable to the integrity of the enzyme. The homologous structures of α-toxin without substrate, distorted lethal toxin with Ca^2 + plus donor, active lethal toxin with Mn^2 + plus donor and the homologous Clostridium difficile toxin B with a hydrolyzed donor have been lined up to show the geometry of several reaction steps. Interestingly, the structural refinement of one of the three crystallographically independent molecules of Ca^2 +-ligated lethal toxin resulted in the glucosyl half-chair conformation expected for glycosyl-transferases that retain the anomeric configuration at the C1″ atom. A superposition of six acceptor substrates bound to homologous enzymes yielded the position of the nucleophilic acceptor atom with a deviation of < 1 Å. The resulting donor-acceptor geometry suggests that the reaction runs as a circular electron transfer in a six-membered ring, which involves the deprotonation of the nucleophile by the β-phosphoryl group of the donor substrate UDP-glucose.     

Differential responses of two Stellaria longipes ecotypes to ultraviolet-B radiation and drought stress

Enhanced ultraviolet-B (UVB) radiation and water deficit affect plant growth and development. We determined the effects of UVB and drought stress on growth parameters and chemical attributes of two ecotypes (alpine and prairie) of Stellaria longipes under controlled-environment conditions. Clonal ramets of these ecotypes were grown under three UVB levels (0, 5, and 10 kJ m⁻² d⁻¹) and exposed to two watering regimes (well watered and drought stressed) for 21 days. Compared to the alpine, the prairie ecotype was taller, had higher number of nodes, and greater leaf area and specific leaf weight (leaf dry weight: leaf area), which resulted in increased dry matter in this ecotype. Overall, ‘prairie’ was higher in total chlorophyll (Chl), but lower in Chla:b ratio, flavonoids, and ethylene, than ‘alpine’. In both ecotypes, UVB and drought stress reduced growth and dry matter, whereas UVB increased carotenoids and flavonoids. Drought stress decreased ethylene evolution. These characteristics were also determined in plants growing in the field. In the field-growing plants, ‘prairie’ had higher growth and dry matter, but lower Chla:b ratio and flavonoids, than ‘alpine’. The two ecotypes responded differentially to UVB and watering regime, as ‘prairie’ appeared to be more sensitive to UVB and drought stress than ‘alpine’.     

A study of the effects of ‘Candidatus Phytoplasma mali’ on the psyllid Cacopsylla melanoneura (Hemiptera: Psyllidae)

Cacopsylla melanoneura is a univoltine psyllid vector of ‘Candidatus Phytoplasma mali’, the etiological agent of apple proliferation (AP), a severe disease in European apple orchards. The influence of ‘Ca. P. mali’ on the fitness of C. melanoneura was studied. In the spring of 2007, male-female pairs of field-collected adults were exposed to ‘Ca. P. mali’-infected or healthy ‘Golden Delicious’ apple shoots. Exposure to these diseased shoots did not affect the life span of the adult psyllids. However, significantly fewer eggs were laid on the diseased shoots. Furthermore, fewer of the eggs that were laid on the infected plants hatched. Data suggest a detrimental effect of AP phytoplasma on the fitness of C. melanoneura.     

Potassium(I)thallium(I) heterometallic 3D polymeric mixed-anions compound, succinate-nitrate [K2Tl(μ-C4H4O4)(μ-NO3)]n

A three-dimensional polymeric K^ITl^I heterometallic compound [K₂Tl(μ-C₄H₄O₄)(μ-NO₃)]_n, with mixes succinate and nitrate ligands, has been synthesized and characterized. Its single-crystal X-ray structure shows two types of K⁺-ions with coordination numbers of seven and eight and one Tl⁺-ion with a coordination number of five. However, the arrangement of O-atoms for Tl^I suggests a gap or hole in the coordination geometry around this atom. This ‘hole’ is possibly occupied by a stereochemically ‘active’ electron lone pair of thallium atoms. Two hydrogen atoms of succinate situated 3.26 Å above the proposed site on the lone pair of Tl^I is oriented in such a way that it might be thought to be forming weak Tl-Lp?H-C hydrogen bond or agostic interactions, thus attaining of environment TlO₅H₂.     

Syntheses, structures and vibrational spectroscopy of some unusual silver(I) (pseudo-) halide/unidentate nitrogen base polymers

The meagre (structurally defined) array of 1:2 silver(I) (pseudo-)halide:unidentate nitrogen base adducts is augmented by the single-crystal X-ray structural characterization of the 1:2 silver(I) thiocyanate:piperidine (‘pip’) adduct. It is of the one-dimensional ‘castellated polymer’ type previously recorded for the chloride: ?Ag(pip)₂(μ-SCN)Ag(pip)₂? a single bridging atom (S) linking successive silver atoms. By contrast, in its copper(I) counterpart, also a one-dimensional polymer, the thiocyanate bridges as end-bound SN-ambidentate: ?CuSCNCuSCN? A study of the 1:1 silver(I) bromide:quinoline (‘quin’) adduct is recorded, as the 0.25 quin solvate, isomorphous with its previous reported ‘saddle polymer’ chloride counterpart.Recrystallization of 1:1 silver(I) iodide:tris(2,4,6-trimethoxyphenyl)phosphine (‘tmpp’) mixtures from py and quinoline (‘quin’)/acetonitrile solutions has yielded crystalline materials which have also been characterized by X-ray studies. In both cases the products are salts, the cation in each being the linearly coordinated silver(I) species [Ag(tmpp)₂]⁺, while the anions are, respectively, the discrete [Ag₅I₇(py)₂]²⁻ species, based on the already known but unsolvated [Cu₅I₇]²⁻ discrete, and the polymeric, arrays, and polymeric . The detailed stereochemistry of the [Ag(tmpp)₂]⁺ cation is a remarkably constant feature of all structures, as is its tendency to close-pack in sheets normal to their P-Ag-P axes.The far-IR spectra of the above species and of several related complexes have been recorded and assigned. The vibrational modes of the single stranded polymeric AgX chains in [XAg(pip)₂]_(∞|∞) (X = Cl, SCN) are discussed, and the assignments ν(AgX) = 155, 190 cm⁻¹ (X = Cl) and 208 cm⁻¹ (X = SCN) are made. The ν(AgX) and ν(AgN) modes in the cubane tetramers [XAg(pip)]₄ (X = Br, I) are assigned and discussed in relation to the assignments for the polymeric AgX:pip (1:2) complexes, and those for the polymeric [XAg(quin)]_(∞|∞) (X = Cl, Br) compounds. The far-IR spectra of [Ag(tmpp)₂]₂[Ag₅I₇(py)₂] and its corresponding 2-methylpyridine complex show a single strong band at about 420 cm⁻¹ which is assigned to the coordinated tmpp ligand in [Ag(tmpp)₂]⁺, and a partially resolved triplet at about 90, 110 and 140 cm⁻¹ which is assigned to the ν(AgI) modes of the [Ag₅I₇L₂]²⁻ anion. An analysis of this pattern is given using a model which has been used previously to account for unexpectedly simple ν(CuI) spectra for oligomeric iodocuprate(I) species.     

On resemblance measures for ecological studies, including taxonomic dissimilarities and a zero-adjusted Bray-Curtis coefficient for denuded assemblages

Bray-Curtis similarity is widely employed in multivariate analysis of assemblage data, for sound biological reasons. This paper discusses two problems, however, with its practical application: its behaviour is erratic (or even undefined) for the vanishingly sparse samples that may be found as an end-point to a severe impact gradient, or a start-point in colonisation studies; and, in common with all similarity measures on species-level data, it is sensitive to inconsistency of taxonomic identification through time. It is shown that the latter problem is ameliorated by application of ‘taxonomic dissimilarity’ coefficients, a natural extension of the concept of taxonomic distinctness indices. Two previous suggestions for use with presence/absence data, denoted here by Γ⁺ and Θ⁺, are noted to be simple generalisations of the Bray-Curtis and Kulczynski measures, respectively. Also seen is their ability to permit ordinations of assemblages from wide geographic scales, with no species in common, and for which Bray-Curtis would return zero similarity for all pairs of samples.The primary problem addressed, however, is that of denuded or entirely blank samples. Where it can be convincingly argued that impoverished samples are near-blank from the same cause, rather than by random occurrences from inadequate sample sizes (tow length, core diameter, transect or quadrat size etc.), a simple adjustment to the form of the Bray-Curtis coefficient can generate meaningful MDS displays which would otherwise collapse, and can improve values of the ANOSIM R statistic (increased separation of groups in multivariate space). It is also shown to have no effect at all on the normal functioning of a Bray-Curtis analysis when at least a modest amount of data is present for all samples.Examination of the properties of this ‘zero-adjusted’ Bray-Curtis measure goes hand-in-hand with a wider discussion of the efficacy of competing similarity, distance or dissimilarity coefficients (collectively: resemblance measures) in community ecology. The inherent biological guidelines underlying the ‘Bray-Curtis family’ of measures (including Kulczynski, Sorenson, Ochiai and Canberra dissimilarity) are made explicit. These and other commonly employed measures (e.g. Euclidean, Manhattan, Gower and chi-squared distances) are calculated for several ‘classic’ data sets of impact events or gradients in space and time. Behaviour of particular coefficients is judged against the interpretability of the resulting ordination plots and an objective measure of the ability to discriminate between a priori defined hypotheses, representing impact conditions. A second-stage MDS plot of a set of resemblance coefficients, based on the respective similarities of the multivariate patterns each generates (an MDS of MDS plots, in effect), is seen to be useful in determining which coefficients are extracting essentially different information from the same assemblage matrix. This suggests a mechanism for practical classification of the plethora of resemblance measures defined in the literature. Similarity-based ANOSIM R statistics and Spearman ρ correlations, whose non-parametric structure make them absolutely comparable across different resemblance measures, answer questions about whether the different information extracted by some coefficients is more, or less, helpful to the final biological interpretation.     

Patterns in rotifer diapausing egg banks: Density and viability

Here we present a quantitative study on the density, age and viability of the diapausing egg banks of the rotifer species complex Brachionus plicatilis in the sediments of 15 water bodies from Eastern Spain. Sampled ponds, located in coastal and inland areas, varied in salinity and ranged in size, depth and permanence. By identifying ‘hatched’, ‘deteriorated’ and ‘viable’ diapausing eggs in the sediment samples, we estimated production, hatching and deterioration in relation to the habitat properties of each pond. Our results indicate the presence of large numbers of diapausing eggs in the sediments of almost all of the ponds studied (2-115 eggs cm^− 2). Inland ponds tended to have higher densities than coastal lagoons. The vertical distribution of eggs in the sediments frequently showed a non-decreasing pattern, which suggested a high among-year variation in egg production. Despite maximum age of eggs of 60-80 years, the median age (3-30 years) suggests that rotifer egg banks are young in the studied ponds. Egg senescence is suggested by the declining abundance of ‘healthy-looking’ eggs with depth. The proportion of ‘deteriorated’ eggs ranged 75-99% suggesting that deterioration rates in the sediments are high and vary among habitats. Hatching and deterioration rates, as estimated from the counts of ‘hatched’, ‘deteriorated’ and ‘healthy-looking’ eggs in the sediments, largely varied among ponds. An association between hatching and deterioration rates is suggested by our data. This is in agreement with the hypothesis that hatching rates of diapausing eggs depended not only on the risks associated with the water column, as initially expected by the general theory on diapause, but they are also related to the incidence of deterioration processes in the sediment.     

Exploring the relationship between groundwater geochemical factors and denitrification potentials on a dairy farm in southeast Ireland

Nitrate (NO₃⁻) loss from agriculture to shallow groundwater and transferral to sensitive aquatic ecosystems is of global concern. Denitrifying bioreactor technology, where a solid carbon (C) reactive media intercepts contaminated groundwater, has been successfully used to convert NO₃⁻ to di-nitrogen (N₂) gas. One of the challenges of groundwater remediation research is how to track denitrification potential spatially and temporally within reactive media and subsoil. First, using δ¹⁵N/δ¹⁸O isotopes, eight wells were divided into indicative transformational processes of ‘nitrification’ or ‘denitrification’ wells. Then, using N₂/argon (Ar) ratios these wells were divided into ‘low denitrification potential’ or high denitrification potential’ categories. Secondly, using falling head tests, the saturated hydraulic conductivity (K_sat) in each well was estimated, creating two groups of ‘slow’ (0.06 m day⁻¹) and ‘fast’ (0.13 m day⁻¹) wells, respectively. Thirdly, two ‘low denitrification potential’ wells (one fast and one slow) with high NO₃⁻ concentration were amended with woodchip to enhance denitrification. Water samples were retrieved from all wells using a low flow syringe to avoid de-gassing and analysed for N₂/Ar ratio using membrane inlet mass spectrometry. Results showed that there was good agreement between isotope and chemical (N₂/Ar ratio and dissolved organic C (DOC)) and physio-chemical (dissolved oxygen, temperature, conductivity and pH) parameters. To explain the spatial and temporal distribution of NO₃⁻ and other parameters on site, the development of predictive models using the available datasets for this field site was examined for NO₃⁻, Cl⁻, N₂/Ar and DOC. Initial statistical analysis was directed towards the testing of the effect of woodchip amendment. The analysis was formulated as a repeated measures analysis of the factorial structure for treatment and time. Nitrate concentrations were related to K_sat and water level (p < 0.0001 and p = 0.02, respectively), but did not respond to woodchip addition (p = 0.09). This non-destructive technique allows elucidation of denitrification potential over time and could be used in denitrifying bioreactor technology to assess denitrification hotspots in reactive media, while developing a NO₃⁻ spatial and temporal predictive model for bioreactor site specific conditions.     

Interfacial interactions of glutamate, water and ions with carbon nanopore evaluated by molecular dynamics simulations

Molecular dynamics simulations were used to assess the transport of glutamate, water and ions (Na⁺ and Cl⁻) in a single wall carbon nanopore. The spatial profiles of Na⁺ and Cl⁻ ions are largely determined by the pore wall charges. Co-ions are repelled whereas the counter-ions are attracted by the pore charges, but this ‘rule’ breaks down when the water concentration is set to a level significantly below that in the physiological bulk solution. In such cases water is less able to counteract the ion-wall interactions (electrostatic or non-electrostatic), co-ions are layered near the counter-ions attracted by the wall charges and are thus layered as counter-ions. Glutamate is concentrated near the pore wall even at physiological water concentration, and irrespective of whether the pore wall is neutral or charged (positively or negatively), and its peak levels are up to 40 times above mean values. The glutamate is thus always layered as a counter-ion. Layering of water near the wall is independent of charges on the pore wall, but its peak levels near the wall are ‘only’ 6-8 times above the pore mean values. However, if the mean concentration of water is significantly below the level in the physiological bulk solution, its layering is enhanced, whereas its concentration in the pore center diminishes to very low levels. Reasons for such a ‘paradoxical’ behavior of molecules (glutamate and water) are that the non-electrostatic interactions are (except at very short distances) attractive, and electrostatic interactions (between the charged atoms of the glutamate or water and the pore wall) are also attractive overall. Repulsive interactions (between equally charged atoms) exist, and they order the molecules near the wall, whereas in the pore center the glutamate (and water) angles are largely randomly distributed, except in the presence of an external electric field. Diffusion of molecules and ions is complex. The translational diffusion is in general both inhomogeneous and anisotropic. Non-electrostatic interactions (ion-wall, glutamate-wall or water-wall) powerfully influence diffusion. In the neutral nanopore the effective axial diffusion constants of glutamate, water and Na⁺ and Cl⁻ ions are all < 10% of their values in the bulk, and the electrostatic interactions can reduce them further. Diffusion of molecules and ions is further reduced if the water concentration in the pore is low. Glutamate⁻ is slowed more than water, and ions are reduced the most especially co-ions. In conclusion the interfacial interactions influence the spatial distribution of glutamate, water and ions, and regulate powerfully, in a complex manner and over a very wide range their transport through nanosize pores.     

Sugar reception in the blowfly: a possible Ca(++) involvement

The present study investigates the effects of W-7 (a calmodulin antagonist involved in the Ca⁺⁺ cascade) on the response of the ‘sugar’ and ‘water’ cells of labellar chemosensilla in the blowfly Protophormia terraenovae to stimulation with sucrose or fructose. In order to ascertain whether Ca⁺⁺ conductance is involved, the effects of EGTA, one of the most used Ca⁺⁺ chelating agent, and of SK&F-96365, an inhibitor of receptor mediated calcium influx, were also studied. Our electrophysiological data indicate that W-7 addition strongly depresses the ‘sugar’ chemoreceptor response to both sugars and in the case of sucrose stimulation also influences adaptation rate. The Ca⁺⁺ chelator has no significant effects on the response of the ‘sugar’ cell following stimulation with sucrose, but lowers fructose stimulating effectiveness. In the presence of SK&F-96365 both sucrose and fructose responses are inhibited. A possible transduction mechanism for sugar reception is discussed.