Expression cartography of human tissues using self organizing maps

Background

Although homology-based methods are among the most widely used methods for predicting the structure and function of proteins, the question as to whether interface sequence conservation can be effectively exploited in predicting protein-protein interfaces has been a subject of debate.

Results

We studied more than 300,000 pair-wise alignments of protein sequences from structurally characterized protein complexes, including both obligate and transient complexes. We identified sequence similarity criteria required for accurate homology-based inference of interface residues in a query protein sequence. Based on these analyses, we developed HomPPI, a class of sequence homology-based methods for predicting protein-protein interface residues. We present two variants of HomPPI: (i) NPS-HomPPI (Non partner-specific HomPPI), which can be used to predict interface residues of a query protein in the absence of knowledge of the interaction partner; and (ii) PS-HomPPI (Partner-specific HomPPI), which can be used to predict the interface residues of a query protein with a specific target protein. Our experiments on a benchmark dataset of obligate homodimeric complexes show that NPS-HomPPI can reliably predict protein-protein interface residues in a given protein, with an average correlation coefficient (CC) of 0.76, sensitivity of 0.83, and specificity of 0.78, when sequence homologs of the query protein can be reliably identified. NPS-HomPPI also reliably predicts the interface residues of intrinsically disordered proteins. Our experiments suggest that NPS-HomPPI is competitive with several state-of-the-art interface prediction servers including those that exploit the structure of the query proteins. The partner-specific classifier, PS-HomPPI can, on a large dataset of transient complexes, predict the interface residues of a query protein with a specific target, with a CC of 0.65, sensitivity of 0.69, and specificity of 0.70, when homologs of both the query and the target can be reliably identified. The HomPPI web server is available at http://homppi.cs.iastate.edu/.

Conclusions

Sequence homology-based methods offer a class of computationally efficient and reliable approaches for predicting the protein-protein interface residues that participate in either obligate or transient interactions. For query proteins involved in transient interactions, the reliability of interface residue prediction can be improved by exploiting knowledge of putative interaction partners.     

Constructing linkage maps in autotetraploid species using simulated annealing

In this paper we demonstrate how molecular markers segregating in a full-sib autotetraploid mapping population can be ordered to form a linkage map using simulated annealing. This approach facilitates the examination of orders close to the optimum to see which marker placings are fixed and identify the markers whose position is less certain. A simulation study investigates the effects of population size, marker spacing, ratio of dominant to codominant markers, typing errors and missing values. The method is applied to map 30 amplified fragment length polymorphism and microsatellite markers on linkage group IV of potato.     

Cost-effectiveness of habitat-suitability maps using low-detailed data for elusive bat species

European bat species are strictly protected by law, and the Member States of the European Union are obliged to record species condition and to contribute to their conservation. Habitat-suitability models are an essential aid in assessing the conservation status and distribution of a species. However, model performance depends on the data quality. This study compares habitat-suitability models that were generated from two data sets that differ in the degree of details included. The first model used data that were low in detail but freely available and the second used data that were very detailed but costly. Three hypotheses were addressed: (1) that the model using low-detailed data is sufficient in its performance to aid the assessment of species distribution and infrastructural planning; (2) the visualisation of actual species distribution is more accurate in the high-detailed model; and (3) habitat-suitability maps can depict species distribution better than species occurrence data alone. To develop models, climate, geographic and roosting data of Myotis bechsteinii were used. Models allowed very good spatial predictions of suitable habitats. However, the model using low-detailed data overestimated suitable habitat. The high-detailed model was more able to predict actual species distribution. These findings were supported by field evaluation where M. bechsteinii could only be detected in areas where both models predicted high habitat suitability. This framework is promising as it resulted in spatially explicit habitat-suitability maps and suggests that similar models may be used to improve the understanding of bat distribution and factors endangering other species of bats.     

Clustering of ant communities and indicator species analysis using self-organizing maps

To understand the complex relationships that exist between ant assemblages and their habitats, we performed a self-organizing map (SOM) analysis to clarify the interactions among ant diversity, spatial distribution, and land use types in Fukuoka City, Japan. A total of 52 species from 12 study sites with nine land use types were collected from 1998 to 2012. A SOM was used to classify the collected data into three clusters based on the similarities between the ant communities. Consequently, each cluster reflected both the species composition and habitat characteristics in the study area. A detrended correspondence analysis (DCA) corroborated these findings, but removal of unique and duplicate species from the dataset in order to avoid sampling errors had a marked effect on the results; specifically, the clusters produced by DCA before and after the exclusion of specific data points were very different, while the clusters produced by the SOM were consistent. In addition, while the indicator value associated with SOMs clearly illustrated the importance of individual species in each cluster, the DCA scatterplot generated for species was not clear. The results suggested that SOM analysis was better suited for understanding the relationships between ant communities and species and habitat characteristics.     

Construction of genetic maps for some Eurasian coniferous species using allozyme genes

In an analysis of allozyme genes in three pine and one spruce species distributed in Eurasia, 45 of 87 loci were mapped. Four linkage groups inPinus sylvestris andPicea abies, three inPinus pallasiana, and two inPinus pumila were determined. The order and the locations of homologous genes in the linkage groups in the different species were similar. The data suggest that during the separate development of thePinus andPicea genera that has lasted for millions of years, there was not any large inversion, translocation, or other significant chromosomal change, at least in the gene blocks analyzed.     

Non-invasive assessment of parasitic nematode species diversity in wild Soay sheep using molecular markers

Considerable effort has been put into detecting and identifying parasitic nematodes in live ruminants, but to date most studies are limited to a small group of nematodes and/or to experimentally infected sheep. In this study, a PCR-based assay using species-specific primer pairs, located in the second internal transcribed spacer ribosomal DNA, was developed to identify nine different species from six different families of parasitic nematodes in a wild, unmanaged and naturally infected population of sheep. Each primer pair was tested for its specificity and sensitivity and it exclusively amplified the species it was designed for and exhibited a high degree of sensitivity. The method was applied to eggs and cultured larvae to identify the parasitic nematodes present in a pooled faecal sample from several host individuals with unknown parasite burden. To test detection reliability, a faecal sample from an individual with known parasite burden (through post-mortem analysis) was also examined. All species present could be correctly identified by PCR, but detecting very low levels and/or early stages of infection proved to be difficult. The method was also tested for its applicability to high through-put screening of faecal samples.     

A QTL for broad-spectrum resistance to cyst nematode species (Globodera spp.) maps to a resistance gene cluster in potato

 Broad-spectrum resistance in potato to the potato cyst nematode (PCN) species Globodera rostochiensis and G. pallida is commonly regarded as a polygenically inherited trait. Yet, by use of QTL analysis and a selected set of PCN populations, resistance to both PCN species could be ascribed to the action of locus Grp1. Grp1 confers major resistance to G. rostochiensis line Ro₅-22 and G. pallida population Pa₂-D383 and partial resistance to G. pallida population Pa₃-Rookmaker. Grp1 was mapped on chromosome 5 using previously characterized AFLP markers. Cleaved amplified polymorphic sequence (CAPS) markers available for RFLP loci GP21 and GP179 revealed that Grp1 maps on a genomic region harboring other resistance factors to viral, fungal and nematodal pathogens. The present data indicate that Grp1 is a compound locus which contains multiple genes involved in PCN resistance. Received: 10 September 1997 / Accepted: 6 October 1997     

An experimental protocol to select nematode species from an entire community using progressive sedimentary enrichment

The purpose of this study was to introduce free-living marine nematodes to the ‘world of biomarkers’. Biomarkers are still not used in the monitoring and assessment of this highly diverse phylum, because the technique needs to be applied at the single species level. This incurs high costs and involves time-consuming procedures, which are currently the main pitfalls when it comes to the application of these techniques to marine nematodes. Consequently, this work proposes an innovative protocol for selecting a single species from an entire community of nematodes using two independent selection processes whereby the sediment of the microcosms is progressively and separately enriched with fine and coarse sediment fractions. During our experiment, the abundance and number of nematode species decreased discernibly with exposure to both finer and coarser sediment. Multivariate analyses revealed that deposit- and epigrowth-feeders were the most tolerant feeding guilds, probably due to their deposit-feeding and microvore behaviours. At the end of the experiment, Terschellingia longicaudata and Ptycholaimellus ponticus became the unique members of the community when the sediment was enriched with fine and coarse sediment particles, respectively. After the complete alteration of the community, and when the mono-species level had been achieved, it was possible to maintain these two species alive, and without any drop in numbers, under the same laboratory conditions considered during the selection process. Accordingly, the protocol adopted here lays new foundations for the study of nematodes in the biomarker field.     

The risks of using molecular biodiversity data for incidental detection of species of concern

Incidental detection of species of concern (e.g., invasive species, pathogens, threatened and endangered species) during biodiversity assessments based on high‐throughput DNA sequencing holds significant risks in the absence of rigorous, fit‐for‐purpose data quality and reporting standards. Molecular biodiversity data are predominantly collected for ecological studies and thus are generated to common quality assurance standards. However, the detection of certain species of concern in these data would likely elicit interest from end users working in biosecurity or other surveillance contexts (e.g., pathogen detection in health‐related fields), for which more stringent quality control standards are essential to ensure that data are suitable for informing decision‐making and can withstand legal or political challenges. We suggest here that data quality and reporting criteria are urgently needed to enable clear identification of those studies that may be appropriately applied to surveillance contexts. In the interim, more pointed disclaimers on uncertainties associated with the detection and identification of species of concern may be warranted in published studies. This is not only to ensure the utility of molecular biodiversity data for consumers, but also to protect data generators from uncritical and potentially ill‐advised application of their science in decision‐making.     

A comparison of the rate of drying of four nematode species using a liquid paraffin technique

A technique of immersion refractometry has been employed to compare the rates at which four species of nematodes lose water during desiccation at 0% r.h. Panagrellus redivivus and Ditylenchus myceliophagus showed little ability to control water loss, although in the latter species coiling helped slow the rate of drying. Ditylenchus dipsaci and Anguina tritici exhibited a much greater degree of control over water loss during desiccation, A. tritici being more successful. D. dipsaci revived from ‘wool’ showed a marked decrease in ability to control water loss when compared with freshly extracted worms. The results obtained have been compared with those from work using interference microscopy, and a critical assessment of the liquid paraffin technique is presented.     

Development of a polymerase chain reaction-based denaturing gradient gel electrophoresis technique to study nematode species biodiversity using the 18s rDNA gene

A polymerase chain reaction (PCR)-based denaturing gradient gel electrophoresis (DGGE) technique was developed to evaluate nematode biodiversity. Amplified fragments (approximately 630 bp) of nematode 18S rDNA could be separated by DGGE at 60 °C for 5.5 h using a gradient of 30–55% denaturant. No DNA from the nematodes’ food source was observed on the gels. The sensitivity of the system was tested using DNA from six species of Steinernema. The system clearly separated PCR fragments from all species except S. tami and S. carpocapsae, which had similar melting behaviour despite being widely separated on the phylogenetic tree.     

South African mouse shrews (<Emphasis Type="Italic">Myosorex</Emphasis>) feel the heat: using species distribution models (SDMs) and IUCN Red List criteria to flag extinction risks due to climate change

Five species of mouse or forest shrews (Myosorex) are endemic to South Africa, Lesotho and Swaziland, four of which (Myosorex varius, Myosorex cafer, Myosorex longicaudatus and Myosorex cf. tenuis) are associated with montane or temperate grassland, fynbos and/or forest habitats while a fifth (Myosorex sclateri) is associated with lowland subtropical forests. Due to their small size, specialised habitat, low dispersal capacity, high metabolism and sensitivity to temperature extremes, we predicted that, particularly for montane species, future climate change should have a negative impact on area of occupancy (AOO) and ultimately extinction risks. Species distribution models (SDMs) indicated general declines in AOO of three species by 2050 under the A1b and A2 climate change scenarios (M. cafer, M. varius, M. longicaudatus) while two species (M. sclateri and M. cf. tenuis) remained unchanged (assuming no dispersal) or increased their AOO (assuming dispersal). While temperate species such as M. varius appear to be limited by temperature maxima (preferring cooler temperatures), the subtropical species M. sclateri appears to be limited by temperature minima (preferring warmer temperatures). Evidence for declines in AOO informed the uplisting (to a higher category of threat) of the Red List status of four Myosorex species to either vulnerable or endangered as part of a separate regional International Union for Conservation of Nature (IUCN) Red List assessment.