Interpreting the flock algorithm: a reply to Anderson & Barry (2015).

Anderson & Barry (Molecular Ecology Resources, 2015, 10, 1020-1030) compared a reprogrammed version of flock (Duchesne & Turgeon , Molecular Ecology Resources, 2009, 9, 1333-1344), flockture, to a particular model of structure (Pritchard , Genetics, 2000, 155, 945-959) that they propose is equivalent to flock, a non-MCMC, non-Bayesian algorithm. They conclude that structure performs better than flockture at clustering individuals from simulated populations with very low level of differentiation (FST c. 0.008) based on 15 microsatellites or 96 SNPs. We rather consider that both algorithms failed, with proportions of correct allocations lower than 50%. The authors also noted the slightly better performance of flockture with SNPs at intermediate FST values (c. 0.02-0.04) but did not comment. Finally, we disagree with the way the processing time of each program was compared. When compared on the basis of a run leading to a clustering solution, the main output of any clustering algorithm, flock, is, as users can readily experience, much faster. In all, we feel that flock performs at least as well as structure as a clustering algorithm. Moreover, flock has two major assets: high speed and clear, well validated, rules to estimate K, the number of populations. It thus provides a valuable addition to the set of tools at the disposal of the many researchers dealing with real empirical data sets.

FLOCK: a method for quick mapping of admixture without source samples.

Identifying and estimating individual and/or population admixture is a very common objective in evolution and conservation biology. There are many situations where samples from one or many of the putatively hybridizing entities are not available or easily identified. Here we describe FLOCK, a new method especially designed to provide spatial and/or temporal admixture maps in the absence of one or several source samples. FLOCK is a non-Bayesian method and therefore differs substantially from previous clustering algorithms. Its working principle is repeated re-allocation of all collected specimens (total sample) to the k subsamples, each re-allocation being more effective than the previous one in attracting genetically similar individuals. This snowball effect, more formally referred to as a positive feedback mechanism, makes FLOCK an efficient and quick sorting process. The usage of FLOCK is illustrated with two empirical situations which have been thoroughly analysed previously with other approaches. A number of simulations were run to better assess the power of the FLOCK algorithm. Performance comparisons were made between the FLOCK and Structure algorithms. When non-negligible numbers of pure genotypes were present, the two performed equally well. However, FLOCK proved significantly more powerful in the absence of pure genotypes. Moreover, FLOCK showed more potential for fast processing. Run times were shown to increase linearly with size of total sample and with size of k, the number of reference samples from which admixture mapping is performed.

X-ray spectroscopy studies on the surface structural characteristics and electronic properties of platinum nanoparticles.

The surface structural characteristics and electronic behavior of three platinum nanoparticle (NP) samples prepared with tertiary amine (Pt-TA), primary amine (Pt-PA), and thiol (Pt-SR) molecules were studied using Pt 4f, 5d, and S 2p x-ray photoelectron spectroscopy (XPS), Pt L(3)-edge x-ray absorption spectroscopy (XAS), and theoretical projected local density of states (l-DOS) calculations. Transmission electron microscopy and XPS composition analysis indicated that the three NPs were all very small (1-2 nm), the NP size decreasing in the order of Pt-TA>Pt-PA approximately Pt-SR. All the three samples showed a positive Pt 4f binding energy (BE) shift relative to that of the bulk, in the order of bulk

Stable genetic polymorphism in heterogeneous environments: balance between asymmetrical dispersal and selection in the acorn barnacle.

Elucidating the processes responsible for maintaining polymorphism at ecologically relevant genes is intimately related to understanding the interplay between selection imposed by habitat heterogeneity and a species' capacity for dispersal in the face of environmental constraints. In this paper, we used a model-based approach to solve equilibria of balanced polymorphism, given values of fitness and larval dispersal among different habitats in the acorn barnacle Semibalanus balanoides from the Gulf of St Lawrence. Our results showed that allele frequencies observed at both MPI* and GPI* loci represented stable equilibria, given empirical estimates of fitness values, and that considerably more larvae dispersed from one region (north) to the other (south) than vice versa. Dispersal conditions were predicted to be similar for the maintenance of polymorphism at both loci. Moreover, the values of asymmetrical dispersal required by the model to reach stable equilibria were compatible with empirical estimates of larval dispersal and oceanic circulation documented in this system. Overall, this study illustrated the usefulness of a modified and computable version of Bulmer's model (1972) in order to test hypotheses of balanced polymorphism resulting from interactions between spatial selection and asymmetrical dispersal.

Parallelism in gene transcription among sympatric lake whitefish (Coregonus clupeaformis Mitchill) ecotypes.

Abstract We tested the hypothesis that phenotypic parallelism between dwarf and normal whitefish ecotypes (Coregonus clupeaformis, Salmonidae) is accompanied by parallelism in gene transcription. The most striking phenotypic differences between these forms implied energetic metabolism and swimming activity. Therefore, we predicted that genes showing parallel expression should mainly belong to functional groups associated with these phenotypes. Transcriptome profiles were obtained from white muscle by using a 3557 cDNA gene microarray developed for the Atlantic salmon (Salmo salar). A total of 1181 genes expressed in both lake populations hybridized on the array. Significant differential expression between ecotypes was detected for 134 (11.3%) and 195 (16.5%) gene clones in Cliff Lake and Indian Pond, respectively. Fifty-one genes (4.3%) showed parallel differential expression between lakes, among which 35 were expressed in opposite directions. Sixteen genes (1.35%) showed true parallelism of transcription, which mainly belonged to energetic metabolism and regulation of muscle contraction functional groups. Variance in expression was significantly reduced for these genes compared to those not showing directionality in parallelism of expression. Candidate genes associated with parallelism in swimming activity and energetic metabolism based on their level and variance in expression were identified. These results add to the growing evidence that parallel phenotypic evolution also involves parallelism at both the genotypic and regulatory level, which may at least partly be associated with genetic constraints. It also provides further evidence for the determinant role of divergent natural selection in driving phenotypic divergence, and perhaps reproductive isolation, in the adaptive radiation of lake whitefish. This study adds to a nascent field employing microarrays as powerful tools for investigating the evolutionary processes of adaptive divergence among natural populations.

'Good genes as heterozygosity': the major histocompatibility complex and mate choice in Atlantic salmon (Salmo salar).

According to the theory of mate choice based on heterozygosity, mates should choose each other in order to increase the heterozygosity of their offspring. In this study, we tested the 'good genes as heterozygosity' hypothesis of mate choice by documenting the mating patterns of wild Atlantic salmon (Salmo salar) using both major histocompatibility complex (MHC) and microsatellite loci. Specifically, we tested the null hypotheses that mate choice in Atlantic salmon is not dependent on the relatedness between potential partners or on the MHC similarity between mates. Three parameters were assessed: (i) the number of shared alleles between partners (x and y) at the MHC (M(xy)), (ii) the MHC amino-acid genotypic distance between mates' genotypes (AA(xy)), and (iii) genetic relatedness between mates (r(xy)). We found that Atlantic salmon choose their mates in order to increase the heterozygosity of their offspring at the MHC and, more specifically, at the peptide-binding region, presumably in order to provide them with better defence against parasites and pathogens. This was supported by a significant difference between the observed and expected AA(xy) (p = 0.0486). Furthermore, mate choice was not a mechanism of overall inbreeding avoidance as genetic relatedness supported a random mating scheme (p = 0.445). This study provides the first evidence that MHC genes influence mate choice in fish.

Potential of microsatellites for individual assignment: the North Atlantic redfish (genus Sebastes) species complex as a case study.

We used the four redfish taxa (genus Sebastes) from the North Atlantic to evaluate the potential of multilocus genotype information obtained from microsatellites in assigning individuals at two different levels of group divergence. We first tested the hypothesis that microsatellites can diagnostically discriminate individual redfish from different groups. Second, we compared two different methods to quantify the effect of number of loci and likelihood stringency levels on the power of microsatellites for redfish group membership. The potential of microsatellites to discriminate individuals from different taxa was illustrated by a shared allele distance tree in which four major clusters corresponding to each taxa were defined. Concomitant with this strong discrimination, microsatellites also proved to be powerful in reclassifying specimens to the taxon of origin, using either an empirical or simulated method of estimating assignment success. By testing for the effect of both the number of loci and the level of stringency on the assignment success, we found that 95% of all specimens were still correctly reclassified with only four loci at the most commonly used criterion of log0. In contrast, the results obtained at the population level within taxa highlighted several problems of assignment that may occur at low levels of divergence. Namely, a drastic decrease of success with increasing stringency illustrated the lack of power of our set of loci. Strong discrepancy was observed between results obtained from the empirical and simulated methods. Finally, the highest assignment success was obtained when reducing the number of loci used, an observation previously reported in studies of human populations.

Binding and utilization of human transferrin by Prevotella nigrescens.

To survive and multiply within their hosts, pathogens must possess efficient iron-scavenging mechanisms. In the present study, we investigate the capacity of Prevotella nigrescens and Prevotella intermedia to use various sources of iron for growth and characterize the transferrin-binding activity of P. nigrescens. Iron-saturated human transferrin and lactoferrin, but not ferric chloride and the iron-free form of transferrin, could be used as sources of iron by P. nigrescens and P. intermedia. Neither siderophore activity nor ferric reductase activity could be detected in P. nigrescens and P. intermedia. However, both species showed transferrin-binding activity as well as the capacity to proteolytically cleave transferrin. To various extents, all strains of P. nigrescens and P. intermedia tested demonstrated transferrin-binding activity. The activity was heat and protease sensitive. The capacity of P. nigrescens to bind transferrin was decreased when cells were grown in the presence of hemin. Preincubation of bacterial cells with hemin, hemoglobin, lactoferrin, fibrinogen, immunoglobulin G, or laminin did not affect transferrin-binding activity. The transferrin-binding protein could be extracted from the cell surface of P. nigrescens by treatment with a zwitterionic detergent. Subjecting the cell surface extract to affinity chromatography on an agarose-transferrin column revealed that it contained a protein having an estimated molecular mass of 37 kDa and possessing transferrin-binding activity. The transferrin-binding activity of P. nigrescens and P. intermedia may permit the bacteria to obtain iron for survival and growth in periodontal pockets.

Structural changes with aging in cortical bone of the human tibia.

Structural modifications are considered to play a significant role in the age-related alterations of bone quality and strength. Senescent compact bone is characterized by an increasing heterogeneity of aspects, including high numbers of lowly mineralized osteons as well as the presence of osteons with hypermineralized lamellae or with a notched haversian canal wall, and of double-zone osteons. These latter three types of osteons are different from the structures involved in the haversian remodeling. In the present study, blocks of midshaft tibia from 7 young men (18-39 years), 14 aged men (50-92 years) and 15 aged women (57-96 years) were embedded in methyl methacrylate in order to perform microradiographic and histomorphometric analysis of undecalcified sections. The intracortical porosity was higher in the aged men than in the young ones, as were the numbers of haversian structures and, to a lesser extent, the diameters of the haversian canals. The aged women showed the same tendency, with cortical porosity still higher than in the men. The osteons with hypermineralized lamellae, those with a notched canal and the double-zone osteons appear to constitute large subgroups of the total haversian population, even in the early adult life. Among them, only the osteons with a notched canal wall increased in frequency with age. The 3 types are much more numerous than the structures involved in the typical haversian remodeling. The correlations between their frequencies as well as their significant topographic association corroborates the hypothesis that the hypermineralized lamellae may crumble down because of their excessive brittleness, giving rise to the haversian canals with notched walls. These enlarged canals could be refilled by bone apposition and result in the double-zone osteons. The 3 types of osteons could constitute different steps of one mechanism of bone desintegration and repair occurring very progressively, which might contribute to modify the bone quality and to increase the intracortical porosity.

Aging effect on inductive capacity of human demineralized bone matrix.

Demineralized bone powder (DBP) prepared from human cortical bone was implanted into subcutaneous pouches of athymic Nu/Nu mice for 28 days. The osteoinductive capacity was evaluated by histomorphometry of the induced cartilage and bone, and by alkaline phosphatase activity in the implant. Very small amounts of new bone and cartilage were found at histological analysis, confirming that human DBP is much less osteoinductive than that from other species. Whereas the morphometric data of the implants from the young and aged donors were not significantly different, the alkaline phosphatase activity was significantly lower in the implants from the old donors than from the younger ones. This difference between the morphometric and biochemical results could reflect the fact that the enzymatic activity is already present in the osteoprogenitor cells. At 28 days, the osteoblastic activity in contact with DBP from the aged group is characterized by a decrease in the enzymatic amount which is not yet visible at the tissue level. This tendency to a decrease in the osteoinductive capacity of bone matrix is an additional aspect of the age-related alterations which occur in bone tissue and could be attributed to modifications of different proteins of the bone matrix, including bone morphogenetic protein.

Demonstration of adherence properties of Porphyromonas gingivalis outer membrane vesicles using a new microassay.

Vesicles made by Porphyromonas gingivalis possess several biological activities, including the ability to adhere to oral surfaces and to bacteria. In this study, a new and simple method was developed to measure the adherence capability of outer membrane vesicles from P. gingivalis. Vesicles were conjugated to fluorescent microspheres (0.7 micron) and added to wells of a Teflon-coated microscope slide previously covered with a variety of soluble ligands. After incubation and washes, the number of fluorescent microspheres per microscopic field were counted. Vesicle-coated microspheres attached best to gelatin (> 200 per field), whereas other compounds (such as fibronectin, fibrinogen, collagen and laminin) provided moderate attachment, and no attachment was observed to bovine serum albumin. Adherence to any of the tested ligands was not observed when fluorescent microspheres were conjugated to bovine serum albumin or lipopolysaccharides from P. gingivalis. The adherence of vesicle-coated microspheres to ligands was not significantly affected when the pH of the reaction mixture was between 4 and 10. None of the tested carbohydrates lowered the attachment capability of vesicle-coated microspheres to substrates. When vesicle-coated microspheres were treated with trypsin and chymotrypsin or heated, this resulted in a significant loss of attachment, suggesting a possible involvement of proteinaceous molecules in the process. The present study confirms that vesicles of P. gingivalis are capable of attachment to various molecules and indicate their potential role in colonization.

Effect of Escherichia coli heat-stable enterotoxin on cell volume and intracellular inorganic ions of rat intestinal cells.

1.--Electron micrographs of rat jejunum mucosa incubated for 1 h in the presence of Escheria coli heat-stable enterotoxin (STa) in the lumen shows alterations of villous cells as well as of crypt cells. The brush border of mature enterocytes is partially desintegrated and covered with a thick mucus. Crypts are occupied on half of their height by cells very similar to Paneth cells, loaded with numerous large dark inclusions. 2.--Cell volume and intracellular inorganic ion concentrations have been estimated in mucosal scrapings of jejunum sacs, incubated in vitro for 1 or 3 h. The quick action (1 h of incubation) of STa is a swelling of the intestinal calls accompanied by an increase in Na+, Cl- and Ca2+ intracellular concentrations and a decrease in the K+ and Mg2+ ones. The delayed action (3 h of incubation) is an increase of extracellular space and a decrease in cell volume; and at the same time the intracellular concentration of Na+, Cl-, K+, Ca2+ and Mg2+ is augmented. 3.--After 3 h of incubation intestinal cells from the other levels of intestine (duodenum, ileum and colon) show the same variations in cell volume and intracellular inorganic ion concentrations under the influence of STa, as those recorded in the jejunum. 4.--The present work favours the hypothesis that all intestinal cells, villous or cryptic, are involved in the alteration of fluid ion transport ending in diarrhea.

[Hypolemmal cisterns and epileptogenic foci]. / Citernes hypolemmales et foyers épileptogènes.

A particularly great number of neuronal subsurface cisterns was found in the cerebral cortex of rats in the vicinity of epileptic foci. This phenomenon is worthwhile considering if one remembers the generally admitted role of these cisterns: transmission of ions or of electric potentials.

[A postsynaptic type nodal axon]. / Un axone nodal de type post-synaptique.

A node of Ranvier in which the nodal axon is post-synaptic to a terminal axon was found in the cerebral cortex of the rat near by an epileptic focus. This type of synapse is in itself a rare observation but is also worthwile considering because of its vicinity with this focus.

[Phosphorylase and glucosyltransferases at the level of reactive astrocytes. A histochemical study]. / Phosphorylase et glycosyltransférases au niveau des astrocytes réactionnels. Etude histochimique.

Implantation of cobalt powder in the cerebral cortex of rat determines an epileptogenic focus where two types of reactive astrocytes are observed. The first type is mostly represented in the subcortical white matter but it does exist in the cortex around the implant. Phosphorylase and branching enzyme are both very active in these cells which are filled with glycogen. The second type is limited to the cortex and phosphorylase activity leads to an unbranched polysaccharid. These cells correspond to the "activated astrocytes" described by the authors in a previous paper and observed round irritative lesions which, in the cerebral cortex, produce epileptogenic foci.