Assessing the accuracy of ancestral protein reconstruction methods

The phylogenetic inference of ancestral protein sequences is a powerful technique for the study of molecular evolution, but any conclusions drawn from such studies are only as good as the accuracy of the reconstruction method. Every inference method leads to errors in the ancestral protein sequence, resulting in potentially misleading estimates of the ancestral protein's properties. To assess the accuracy of ancestral protein reconstruction methods, we performed computational population evolution simulations featuring near-neutral evolution under purifying selection, speciation, and divergence using an off-lattice protein model where fitness depends on the ability to be stable in a specified target structure. We were thus able to compare the thermodynamic properties of the true ancestral sequences with the properties of “ancestral sequences” inferred by maximum parsimony, maximum likelihood, and Bayesian methods. Surprisingly, we found that methods such as maximum parsimony and maximum likelihood that reconstruct a “best guess” amino acid at each position overestimate thermostability, while a Bayesian method that sometimes chooses less-probable residues from the posterior probability distribution does not. Maximum likelihood and maximum parsimony apparently tend to eliminate variants at a position that are slightly detrimental to structural stability simply because such detrimental variants are less frequent. Other properties of ancestral proteins might be similarly overestimated. This suggests that ancestral reconstruction studies require greater care to come to credible conclusions regarding functional evolution. Inferred functional patterns that mimic reconstruction bias should be reevaluated.     

Hair removal methods: A comparative study for dermoscopy images

Removal and restoration of hair and hair-like regions within skin lesion images is needed so features within lesions can be more effectively analyzed for benign lesions, cancerous lesions, and for cancer discrimination. This paper refers to “melanoma texture” as a rationale for supporting the need for the proposed hair detection and repair techniques, which incompletely represents why hair removal is an important operation for skin lesion analysis. A comparative study of the state-of-the-art hair-repaired methods with a novel algorithm is also proposed by morphological and fast marching schemes. The hair-repaired techniques are evaluated in terms of computational, performance and tumor-disturb patterns (TDP) aspects. The comparisons have been done among (i) linear interpolation, inpainting by (ii) non-linear partial differential equation (PDE) and (iii) exemplar-based repairing techniques. The performance analysis of hair detection quality, was based on the evaluation of the hair detection error (HDE), quantified by statistical metrics and manually used to determine the hair lines from a dermatologist as the ground truth. The results are presented on a set of 100 dermoscopic images. For the two characteristics measured in the experiments the best method is the fast marching hair removal algorithm (HDE: 2.98%, TDP: 4.21%). This proposed algorithm repaired the texture of the melanoma, which becomes consistent with human vision. The comparisons results obtained, indicate that hair-repairing algorithm based on the fast marching method achieve an accurate result.     

A comparative study in methods of cryoprotection for human semen

A comparative study using either glycerol or an egg yolk-citrate-glycerol mix for cryoprotection under the conditions described showed the latter to give a significantly better post-thaw motility. The greatest drop was noted within the first hour, suggesting that freezability of a sample could be judged accurately by rethawing at that time.Controlled studies using scanning electron microscopy clearly showed a greater head disruption after freezing with glycerol and looped tails after centrifugation, which could account for some of the findings of the first part of the study.These findings are reviewed and it is recommended that seminal samples are not centrifuged and that a complex medium be employed for seminal freezing and storing.     

Towards the reconstruction of the bilaterian ancestral pre-MHC region

In this article, we describe how we reconstructed a precise, minimal proto-MHC region in the ancestor of euchordates, which was based on a comparison of the MHC-paralogy group of vertebrate with the MHC-like chromosome of cephalochordates. This deduced ancestral region was compared with the genomes of extant species, other deuterostomes and protostomes. Our analysis revealed statistically significant traces of conservation in these species, suggesting that a proto-MHC region existed at the origin of all bilaterian species. We also propose a new approach to reconstruct ancestral genomes, which combines both stringent statistical testing and phylogenetic analysis.     

A comparative study of clustering methods for molecular data

The research aim is to use three clustering technologies for establishing molecular data model of large size sets by comparison between low energy samples (LES) and local molecular samples (LMS). Hierarchical cluster of multi-level tree distance relation, competitive learning network of similar inputs falling into the same cluster and topological SOM are used to analyze 6,242 LES and 5,000 LMS. Our experiments show that in SOM, there are 24 to 25 Davies-Boulding clustering index and color map cluster units in the LES more than 10 to 12 in the LMS, which is consistent with the results of hierarchical cluster and competitive learning network in the rough. The hierarchical cluster reflects the biggest inter-cluster distance about 30 for the LES is far larger than that of LMS about 10. The intra-cluster distance of LES about 15 is also far bigger than that of LMS about 3. In SOM, there are more cluster borders of high values (black) reflecting large distance and more clusters in the D-matrix and U-matrix of LES than that of LMS, due to the biggest standard deviation range from -8 to 10 of samples feature of the LES is bigger than that of LMS from -2.5 to 2.5.     

A comparative study of the purine- and pyrimidine-metabolising enzymes of a range of trypanosomatids

A range of trypanosomatids (amastigotes and cultured promastigotes of Leishmania mexicana mexicana, cultured promastigotes of L. m. amazonensis, L. donovani and L. tarentolae, culture forms of Crithidia fasciculata, Herpetomonas muscarum muscarum and H. m. ingenoplastis and procyclic trypomastigotes of Trypanosoma brucei brucei) have been surveyed for the presence of purine- and pyrimidine-metabolising enzymes. Several common features were observed, including the presence of nucleosidases, catabolic phosphorylases, phosphoribosyltransferases, kinases and cytidine deaminase and the apparent absence of AMP deaminase, anabolic purine phosphorylase and cytosine deaminase. Significant differences between species were discovered, notably in adenine and adenosine metabolism. Nucleoside phosphotransferase active on inosine was detected in insect trypanosomatids but not in L. m. mexicana.     

Aeroallergens: a comparative study of two monitoring methods

Olive and grass pollen grains are the major causes of hay fever in the Mediterranean region. A number of samplers and methods have been developed in recent years in order to obtain reliable data regarding airborne allergen concentrations. This paper reports on a detailed comparison of two samplers—Cyclone and ChemVol—and on the parameters that could influence their efficiency. Airborne concentrations of two key olive and grass allergens, Ole e 1 and Phl p 5, respectively, were monitored over two years with different weather patterns, 2012 and 2014. Allergenic particles were quantified by ELISA assay, and results were compared with pollen concentrations monitored using a Hirst-type volumetric spore trap over the same study periods. The influence of weather-related parameters on local airborne pollen and allergen concentrations was also analysed. Although a positive correlation was detected between results obtained using the two samplers during the pollen season, results for the cumulative annual Allergen Index varied considerably. The two samplers revealed a positive correlation between pollen concentrations and both minimum temperature during the warmer year (2012) and maximum temperature during the cooler year (2014); a negative significant correlation was observed in both cases with rainfall and relative humidity. In summary, although some differences were observed between the two samplers studied, both may be regarded as suitable for allergen detection.     

A comparative study of laboratory methods for the preparation of arabic acid

Different methods of precipitation of arabic acid from natural gum arabic are compared in terms of yield and molecular weight derived from gel chromatography experiments. All of the precipitation methods used gave products which were closely similar in terms of $\text{M}$_n, but precipitation with HCl/acetone and HAc/ethanol gave low yields (25 and 3%, respectively).     

Estimating the number of ancestral lineages using a maximum-likelihood method based on rejection sampling

Estimating the number of ancestral lineages of a sample of DNA sequences at time t in the past can be viewed as a variation on the problem of estimating the time to the most recent common ancestor. To estimate the number of ancestral lineages, we develop a maximum-likelihood approach that takes advantage of a prior model of population demography, in addition to the molecular data summarized by the pattern of polymorphic sites. The method relies on a rejection sampling algorithm that is introduced for simulating conditional coalescent trees given a fixed number of ancestral lineages at time t. Computer simulations show that the number of ancestral lineages can be estimated accurately, provided that the number of mutations that occurred since time t is sufficiently large. The method is applied to 986 present-day human sequences located in hypervariable region 1 of the mitochondrion to estimate the number of ancestral lineages of modern humans at the time of potential admixture with the Neanderthal population. Our estimates support a view that the proportion of the modern population consisting of Neanderthal contributions must be relatively small, less than approximately 5%, if the admixture happened as recently as 30,000 years ago.     

Four methods for general anaesthesia in the rabbit: a comparative study

The efficacy and safety of pentobarbitone, ketamine/xylazine, fentanyl/fluanisone/diazepam, and halothane/nitrous oxide anaesthesia were compared in 4 groups of six New Zealand White rabbits. Heart and respiratory rates, body temperature, reflexes, blood pressure and blood gases were measured. Pentobarbitone appeared to be unsuitable for anaesthesia in rabbits, as 5 of the 6 rabbits to whom it was administered, required artificial respiration or died. The combinations of ketamine/xylazine and fentanyl-fluanisone/diazepam both produced unpredictable levels of anaesthesia together with a substantial decline in arterial blood pressure and PO2. Despite a severe drop in blood pressure (up to 37.5%), anaesthesia with halothane and nitrous oxide was found to be superior to the other anaesthetic agents.     

Estimating ancestral distributions of lineages with uncertain sister groups： a statistical approach to Dispersal-Vicariance Analysis and a case using Aesculus L. （Sapindaceae） including fossils

We propose a simple statistical approach for using Dispersal-Vicariance Analysis （DIVA） software to infer biogeographic histories without fully bifurcating trees. In this approach, ancestral ranges are first optimized for a sample of Bayesian trees. The probability P of an ancestral range r at a node is then calculated as P（rY） = ∑t^n=1 F（rY）t Pt where Y is a node, and F（rY） is the frequency of range r among all the optimal solutions resulting from DIVA optimization at node Y, t is one of n topologies optimized, and Pt is the probability of topology t. Node Y is a hypothesized ancestor shared by a specific crown lineage and the sister of that lineage ＂x＂, where x may vary due to phylogenetic uncertainty （polytomies and nodes with posterior probability 〈 100%）. Using this method, the ancestral distribution at Y can be estimated to provide inference of the geographic origins of the specific crown group of interest. This approach takes into account phylogenetic uncertainty as well as uncertainty from DIVA optimization. It is an extension of the previously described method called Bayes-DIVA, which pairs Bayesian phylogenetic analysis with biogeographic analysis using DIVA. Further, we show that the probability P of an ancestral range at Y calculated using this method does not equate to pp＊F（rY） on the Bayesian consensus tree when both variables are 〈 100%, where pp is the posterior probability and F（rY） is the frequency of range r for the node containing the specific crown group. We tested our DIVA-Bayes approach using Aesculus L., which has major lineages unresolved as a polytomy. We inferred the most probable geographic origins of the five traditional sections of Aesculus and ofAesculus californica Nutt. and examined range subdivisions at parental nodes of these lineages. Additionally, we used the DIVA-Bayes data from Aesculus to quantify the effects on biogeographic inference of including two wildcard fossil taxa in phylogenetic analysis. Our analysis resolved the geographic     

Estimating primate densities using home range and line transect methods: A comparative test with the black colobus monkeyColobus satanas

The line transect method is one of the main methods used to estimate primate densities. Several protocols have been proposed to analyze the data recorded under this method but none of them have been widely accepted since there is a considerable controversy about their respective accuracy. In this study, densities of the black colobus monkeyColobus satanas calculated using eight different protocols were compared with the actual density given by the home range method. Rates of polyspecific associations were also compared. The two most accurate estimates of group density (under- or overestimation <10%) were yielded by the protocol that used the maximum transect-to-animal distance and by that of using a fixed distance of 100 m. These protocols, however, underestimated individual density because counts performed from transects underestimated by 23% the average group size. The six other protocols overestimated group density by 20–195%. Factors that could explain these overestimation were discussed. Because histogram of sighting frequency showed several classes of distances with no records and because groups have been detected as far as 160 m, we suggested that the uneven topography of the study site increased the variability of the sighting distances. Combined with a relatively low number of sightings (n=23), this did not allow to identify a sharp detection distance. Rates of polyspecific association found with the two methods were similar. We recommend to investigate the influence of the topography for bias in density estimates when using the line transect method.     

Abundance, distribution and life histories of grassland plants: a comparative study of 81 species

1 This study examines the abundance and distribution of grassland plant species in particular relation to features affecting colonization. Seed production (inversely related to seed size) and recruitment success (positively related) affect colonization ability, suggesting that seed size can be used as a key trait.
2 Data on seed size, dispersal mode, life form, geographical range size and abundance were gathered for 81 grassland plant species in a field study area in Sweden. Seed production and plant size were estimated for 69 of these species. Analyses were performed both across species, with species treated as independent data points, and for 43 'phylogenetically independent contrasts'.
3 The cross-species analyses suggested that local abundance was related to life forms but not dispersal or plant size. Perennials were generally most abundant, as were clonal species. If abundance reflects colonization we predicted that species with intermediately sized seeds (or intermediate seed production) would be most abundant, and this was supported by the phylogenetic contrast but not by cross-species analyses. In the former analysis, a high abundance of species was significantly associated with a small seed size deviation (and seed number deviation) from the median values of these traits in the community.
4 Local abundance, seed production and seed size deviation from the community median value were positively related to geographical range size in the cross-species analysis, but no relationships were seen in the phylogenetic contrast analysis.
5 We conclude that colonization processes do have a significant influence on abundance patterns in grasslands. Seed size is a key trait for colonizing ability, and the effects of the trade-off of seed size vs. seed number must be considered. No single mechanism can be identified that influences both abundance and geographical distribution range.     

Reconstructing the ancestral female gametophyte of angiosperms: Insights from Amborella and other ancient lineages of flowering plants

For more than a century, the common ancestor of flowering plants was thought to have had a seven-celled, eight-nucleate Polygonum-type female gametophyte. It is now evident that not one, but in fact three, patterns of female gametophyte development and mature structure characterize the common ancestors of the four most ancient clades of extant angiosperms: Amborella-type, Nuphar/Schisandra-type and Polygonum-type. The Amborella-type female gametophyte is restricted to a single extant species, Amborella trichopoda, and at maturity consists of eight cells and nine nuclei. Development of the Amborella-type gametophyte is essentially identical to the Polygonum-type except that there is an additional and asynchronous cell division at the micropylar pole prior to maturation that produces a third synergid and the egg cell. The Nuphar/Schisandra-type female gametophyte is four-nucleate and four-celled and at maturity contains a typical three-celled egg apparatus and a central cell with a single haploid polar nucleus. This type of gametophyte appears to be universal among extant members of the Nymphaeales (including Hydatellaceae) and Austrobaileyales. Based on explicit reconstruction of character distribution and evolution, the Polygonum-type female gametophyte is certain to be representative of the common ancestors of monocots, eudicots, magnoliids, Ceratophyllaceae, and Chloranthaceae. There are compelling biological reasons to suggest that the four-celled, four-nucleate female gametophyte (as found in Nymphaeales and Austrobaileyales) is ancestral among angiosperms, with transitions to Polygonum-type female gametophytes separately in the Amborellales and in the ancient angiosperm clade that includes all angiosperms except Amborella, Nymphaeales, and Austrobaileyales. Subsequent to the evolution of a seven-celled, eight-nucleate Polygonum-type female gametophyte in the Amborellales, we hypothesize that a peramorphic increase in egg apparatus cell number took place and led to the unique situation in which there are three synergids in Amborella trichopoda.     

Optimization of transfection methods for Huh-7 and Vero cells: A comparative study

Availability of an efficient transfection protocol is the first determinant in success of gene transferring studies in mammalian cells which is accomplished experimentally for every single cell type. Herein, we provide data of a comparative study on optimization of transfection condition by electroporation and chemical methods for Huh-7 and Vero cells. Different cell confluencies, DNA/reagent ratios and total transfection volumes were optimized for two chemical reagents including jetPEI? and Lipofectamine? 2000. Besides, the effects of electric field strength and pulse length were investigated to improve electroporation efficiency. Transfection of cells by pEGFP-N1 vector and tracking the expression of GFP by FACS and Fluorescence Microscopy analysis were the employed methods to evaluate transfection efficiencies. Optimized electroporation protocols yielded 63.73 ± 2.36 and 73.9 ± 1.6% of transfection in Huh-7 and Vero cells respectively, while maximum achieved level of transfection by jetPEI? was 14.2 ± 0.69 and 28 ± 1.11% Huh-7 and Vero cells, respectively. Post transfectional chilling of the cells did not improve electrotransfection efficiency of Huh-7 cells. Compared to chemical based reagents, electroporation showed superior levels of transfection in both cell lines. The presented protocols should satisfy most of the experimental applications requiring high transfection efficiencies of these two cell lines.