Population Genetics of the Carinate Pillsnail, \u3ci\u3eEuchemotrema hubrichti\u3c/i\u3e: Genetic Structure on a Small Spatial Scale

Euchemotrema hubrichti (Pilsbry HA (1940) Volume 1, Part 2. Monographs of the Academy of Natural Sciences, Philadelphia, 3, I-VI, 2, 575–994, I-IX) is a polygyrid land snail known only from the Larue Pine Hills region of southwestern Illinois, USA. Despite the restricted range of the species, observations in the field suggested that patterns of genetic variation within E. hubrichti might show geographic structure. To assess the dispersal potential of E. hubrichti, a mark-recapture experiment was performed at two sites \u3c100 meters apart. To evaluate the geographic distribution of genetic\u3evariation, a region of the mitochondrial cytochrome c oxidase subunit I gene was sequenced from 53 snails collected from sites spanning the species range. Mark-recapture experiments suggested that population sizes at two sites were low and migration between sites was not detected. AMOVA and nested clade analysis (NCA) revealed significant genetic structure among sites. Two sites in particular appeared to be isolated from the others based on nested clade analysis. AMOVA also detected significant genetic differentiation among sites, but partitioning the data into two groups (populations 1 and 2) based on the NCA results did not explain a significant amount of genetic variation. Coalescent methods suggested that population sizes and migration rates for populations 1 and 2 are unequal. These patterns are likely due to the low dispersal ability of E. hubrichti and patchiness of preferred E. hubrichti habitat rather than an ancient vicariant event. These preliminary findings have implications both for the conservation of this species and for the population genetics of any spatially restricted endemic species with low dispersal ability

Bilaterian Phylogeny Based on Analyses of a Region of the Sodium-potassium ATPase beta-subunit Gene

Molecular investigations of deep-level relationships within and among the animal phyla have been hampered by a lack of slowly evolving genes that are amenable to study by molecular systematists. To provide new data for use in deep-level metazoan phylogenetic studies, primers were developed to amplify a 1.3-kb region of the alpha subunit of the nuclear-encoded sodium-potassium ATPase gene from 31 bilaterians representing several phyla. Maximum parsimony, maximum likelihood, and Bayesian analyses of these sequences (combined with ATPase sequences for 23 taxa downloaded from GenBank) yield congruent trees that corroborate recent findings based on analyses of other data sets (e.g., the 18S ribosomal RNA gene). The ATPase-based trees support monophyly for several clades (including Lophotrochozoa, a form of Ecdysozoa, Vertebrata, Mollusca, Bivalvia, Gastropoda, Arachnida, Hexapoda, Coleoptera, and Diptera) but do not support monophyly for Deuterostomia, Arthropoda, or Nemertea. Parametric bootstrapping tests reject monophyly for Arthropoda and Nemertea but are unable to reject deuterostome monophyly. Overall, the sodium-potassium ATPase alpha-subunit gene appears to be useful for deep-level studies of metazoan phylogeny

Discovery of the photosynthetic relatives of the "Maltese mushroom" Cynomorium

BACKGROUND: Although recent molecular phylogenetic studies have identified the photosynthetic relatives of several enigmatic holoparasitic angiosperms, uncertainty remains for the last parasitic plant order, Balanophorales, often considered to include two families, Balanophoraceae and Cynomoriaceae. The nonphotosynthetic (holoparasitic) flowering plant Cynomorium coccineum has long been known to the Muslim world as "tarthuth" and to Europeans as the "Maltese mushroom"; C. songaricum is known in Chinese medicine as "suo yang." Interest in these plants is increasing and they are being extensively collected from wild populations for use in herbal medicines. RESULTS: Here we report molecular phylogenetic analyses of nuclear ribosomal DNA and mitochondrial matR sequence data that strongly support the independent origin of Balanophoraceae and Cynomoriaceae. Analyses of single gene and combined gene data sets place Cynomorium in Saxifragales, possibly near Crassulaceae (stonecrop family). Balanophoraceae appear related to Santalales (sandalwood order), a position previously suggested from morphological characters that are often assumed to be convergent. CONCLUSION: Our work shows that Cynomorium and Balanophoraceae are not closely related as indicated in all past and present classifications. Thus, morphological features, such as inflorescences bearing numerous highly reduced flowers, are convergent and were attained independently by these two holoparasite lineages. Given the widespread harvest of wild Cynomorium species for herbal medicines, we here raise conservation concerns and suggest that further molecular phylogenetic work is needed to identify its photosynthetic relatives. These relatives, which will be easier to cultivate, should then be examined for phytochemical activity purported to be present in the more sensitive Cynomorium

Phylogenetic inference in Rafflesiales: the influence of rate heterogeneity and horizontal gene transfer

BACKGROUND: The phylogenetic relationships among the holoparasites of Rafflesiales have remained enigmatic for over a century. Recent molecular phylogenetic studies using the mitochondrial matR gene placed Rafflesia, Rhizanthes and Sapria (Rafflesiaceae s. str.) in the angiosperm order Malpighiales and Mitrastema (Mitrastemonaceae) in Ericales. These phylogenetic studies did not, however, sample two additional groups traditionally classified within Rafflesiales (Apodantheaceae and Cytinaceae). Here we provide molecular phylogenetic evidence using DNA sequence data from mitochondrial and nuclear genes for representatives of all genera in Rafflesiales. RESULTS: Our analyses indicate that the phylogenetic affinities of the large-flowered clade and Mitrastema, ascertained using mitochondrial matR, are congruent with results from nuclear SSU rDNA when these data are analyzed using maximum likelihood and Bayesian methods. The relationship of Cytinaceae to Malvales was recovered in all analyses. Relationships between Apodanthaceae and photosynthetic angiosperms varied depending upon the data partition: Malvales (3-gene), Cucurbitales (matR) or Fabales (atp1). The latter incongruencies suggest that horizontal gene transfer (HGT) may be affecting the mitochondrial gene topologies. The lack of association between Mitrastema and Ericales using atp1 is suggestive of HGT, but greater sampling within eudicots is needed to test this hypothesis further. CONCLUSIONS: Rafflesiales are not monophyletic but composed of three or four independent lineages (families): Rafflesiaceae, Mitrastemonaceae, Apodanthaceae and Cytinaceae. Long-branch attraction appears to be misleading parsimony analyses of nuclear small-subunit rDNA data, but model-based methods (maximum likelihood and Bayesian analyses) recover a topology that is congruent with the mitochondrial matR gene tree, thus providing compelling evidence for organismal relationships. Horizontal gene transfer appears to be influencing only some taxa and some mitochondrial genes, thus indicating that the process is acting at the single gene (not whole genome) level

A k-shell decomposition method for weighted networks

We present a generalized method for calculating the k-shell structure of weighted networks. The method takes into account both the weight and the degree of a network, in such a way that in the absence of weights we resume the shell structure obtained by the classic k-shell decomposition. In the presence of weights, we show that the method is able to partition the network in a more refined way, without the need of any arbitrary threshold on the weight values. Furthermore, by simulating spreading processes using the susceptible-infectious-recovered model in four different weighted real-world networks, we show that the weighted k-shell decomposition method ranks the nodes more accurately, by placing nodes with higher spreading potential into shells closer to the core. In addition, we demonstrate our new method on a real economic network and show that the core calculated using the weighted k-shell method is more meaningful from an economic perspective when compared with the unweighted one.Comment: 17 pages, 6 figure

In situ efficacy of an experimental toothpaste on enamel rehardening and prevention of demineralisation: a randomised, controlled trial

Background A novel sodium fluoride toothpaste containing lactate ion and polyvinylmethylether-maleic anhydride has been developed to promote enamel remineralisation and resistance to demineralisation. In this in situ study, we compared this toothpaste (‘Test’) with a stannous fluoride-zinc citrate (SnF2-Zn) toothpaste (‘Reference’) (both 1100–1150 ppm fluoride) and a fluoride-free toothpaste (‘Placebo’) using an enamel dental erosion-rehardening model. Methods In each phase of this randomised, investigator-blind, crossover study, participants wore palatal appliances holding bovine enamel specimens with erosive lesions. They brushed their natural teeth with either the Test, Reference or Placebo toothpastes, then swished the resultant slurry. Specimens were removed at 2 h and 4 h post-brushing and exposed to an in vitro acid challenge. Surface microhardness was measured at each stage; enamel fluoride uptake was measured after in situ rehardening. Surface microhardness recovery, relative erosion resistance, enamel fluoride uptake and acid resistance ratio were calculated at both timepoints. Results Sixty two randomised participants completed the study. Test toothpaste treatment yielded significantly greater surface microhardness recovery, relative erosion resistance and enamel fluoride uptake values than either Reference or Placebo toothpastes after 2 and 4 h. The acid resistance ratio value for Test toothpaste was significantly greater than either of the other treatments after 2 h; after 4 h, it was significantly greater versus Placebo only. No treatment-related adverse events were reported. Conclusions In this in situ model, the novel-formulation sodium fluoride toothpaste enhanced enamel rehardening and overall protection against demineralisation compared with a fluoride-free toothpaste and a marketed SnF2-Zn toothpaste

Effects of a sodium fluoride- and phytate-containing dentifrice on remineralisation of enamel erosive lesions—an in situ randomised clinical study

ObjectiveThe objective of this work was to evaluate effects of a dentifrice containing sodium fluoride (1150 ppm F) and the organic polyphosphate phytate (0.85% w/w of the hexa-sodium salt) on in situ remineralisation of early enamel erosive lesions and resistance to subsequent demineralisation.Materials and methodsSubjects (n = 62) wore palatal appliances holding eight bovine enamel specimens with pre-formed erosive lesions. They brushed their natural teeth with the phytate test dentifrice (TD); a positive control dentifrice (PC, 1150 ppm fluoride as NaF); a reference dentifrice (RD, disodium pyrophosphate + 1100 ppm fluoride as NaF) or a negative control dentifrice (NC, fluoride-free) in a randomised, double-blind, crossover design. Specimens were removed at 2, 4 and 8 h post-brushing and exposed to an ex vivo acid challenge. Surface microhardness (Knoop) was measured at each stage. The primary efficacy variable was relative erosion resistance (RER); other variables included the surface microhardness recovery (SMHR), acid resistance ratio (ARR) and enamel fluoride uptake (EFU).ResultsAfter 4 h, the results for RER, ARR and EFU were in the order PC > TD = RD > NC with PC > TD = RD = NC for SMHR. Results at 2 and 8 h were generally consistent with the 4 h data. Mineralisation progressed over time. Dentifrices were generally well-tolerated.ConclusionsIn this in situ model, addition of phytate or pyrophosphate to a fluoride dentifrice inhibited the remineralising effect of fluoride. Both formulations still delivered fluoride to the enamel and inhibited demineralisation, albeit to a lesser extent than a polyphosphate-free dentifrice.Clinical relevanceAddition of phytate or pyrophosphate to a fluoride dentifrice may reduce its net anti-erosive properties

Trend-analysis of dental hard-tissue conditions as function of tooth age

Objective This retrospective in-vitro study investigated tooth age effect on dental hard-tissue conditions. Methods Unidentified extracted premolars (n = 1500) were collected and their individual age was estimated (10–100 (±10) years old (yo)) using established dental forensic methods Dental caries, fluorosis and tooth wear (TW) were assessed using the International Caries Detection and Assessment System (ICDAS; 0–5 for crown and 0–2 for root), Thylstrup-Fejerskov (TFI; 0–9) and Basic Erosive Wear Examination (BEWE; 0–3) indices, respectively. Staining and color were assessed using the modified-Lobene (MLI) (0–3) and VITA shade (B1-C4) indices, respectively. Relationships between indices and age were tested using regression models. Results Starting at age ∼10yo, presence of caries increased from 35% to 90% at ∼50yo (coronal), and from 0% to 35% at ∼80yo (root). Caries severity increased from ICDAS 0.5 to 2 at ∼40yo and from ICDAS 0 to 0.5 at ∼60yo for coronal and root caries, respectively. Presence of TW increased from 25% (occlusal) and 15% (smooth-surfaces) to 100% at ∼80yo. TW severity increased from BEWE 0.5 to 2 at ∼50yo (occlusal) and ∼0.3 to 1.5 at ∼50yo (smooth-surfaces). Percentage and severity of fluorosis decreased from 70% to 10% at ∼80yo, and from TFI 1 to 0 at ∼90yo, respectively. Percentage of extrinsic staining increased from 0% to 85% at ∼80yo and its severity increased from MLI 0 to 2 at ∼70yo. Color changed from A3 to B3 at ∼50yo (crown), and from C2 to A4 at ∼85yo (root). Conclusions Aging is proportionally related to the severity of caries, TW, staining, and inversely to dental fluorosis. Teeth become darker with ag