Towards online multiresolution community detection in large-scale networks

The investigation of community structure in networks has aroused great interest in multiple disciplines. One of the challenges is to find local communities from a starting vertex in a network without global information about the entire network. Many existing methods tend to be accurate depending on a priori assumptions of network properties and predefined parameters. In this paper, we introduce a new quality function of local community and present a fast local expansion algorithm for uncovering communities in large-scale networks. The proposed algorithm can detect multiresolution community from a source vertex or communities covering the whole network. Experimental results show that the proposed algorithm is efficient and well-behaved in both real-world and synthetic networks.     

Future hotspots of terrestrial mammal loss

Current levels of endangerment and historical trends of species and habitats are the main criteria used to direct conservation efforts globally. Estimates of future declines, which might indicate different priorities than past declines, have been limited by the lack of appropriate data and models. Given that much of conservation is about anticipating and responding to future threats, our inability to look forward at a global scale has been a major constraint on effective action. Here, we assess the geography and extent of projected future changes in suitable habitat for terrestrial mammals within their present ranges. We used a global earth-system model, IMAGE, coupled with fine-scale habitat suitability models and parametrized according to four global scenarios of human development. We identified the most affected countries by 2050 for each scenario, assuming that no additional conservation actions other than those described in the scenarios take place. We found that, with some exceptions, most of the countries with the largest predicted losses of suitable habitat for mammals are in Africa and the Americas. African and North American countries were also predicted to host the most species with large proportional global declines. Most of the countries we identified as future hotspots of terrestrial mammal loss have little or no overlap with the present global conservation priorities, thus confirming the need for forward-looking analyses in conservation priority setting. The expected growth in human populations and consumption in hotspots of future mammal loss mean that local conservation actions such as protected areas might not be sufficient to mitigate losses. Other policies, directed towards the root causes of biodiversity loss, are required, both in Africa and other parts of the world.     

Towards more robust methods of alien gene detection

Because the properties of horizontally-transferred genes will reflect the mutational proclivities of their donor genomes, they often show atypical compositional properties relative to native genes. Parametric methods use these discrepancies to identify bacterial genes recently acquired by horizontal transfer. However, compositional patterns of native genes vary stochastically, leaving no clear boundary between typical and atypical genes. As a result, while strongly atypical genes are readily identified as alien, genes of ambiguous character are poorly classified when a single threshold separates typical and atypical genes. This limitation affects all parametric methods that examine genes independently, and escaping it requires the use of additional genomic information. We propose that the performance of all parametric methods can be improved by using a multiple-threshold approach. First, strongly atypical alien genes and strongly typical native genes would be identified using conservative thresholds. Genes with ambiguous compositional features would then be classified by examining gene context, including the class (native or alien) of flanking genes. By including additional genomic information in a multiple-threshold framework, we observed a remarkable improvement in the performance of several popular, but algorithmically distinct, methods for alien gene detection.     

A ribosomal DNA-based framework for the detection and quantification of stress-sensitive nematode families in terrestrial habitats

Indigenous communities of soil‐resident nematodes have a high potential for soil health assessment as nematodes are diverse, abundant, trophically heterogeneous and easily extractable from soil. The conserved morphology of nematodes is the main operational reason for their under‐exploitation as soil health indicators, and a user‐friendly biosensor system should preferably be based on nonmorphological traits. More than 80% of the most environmental stress‐sensitive nematode families belong to the orders Mononchida and Dorylaimida. The phylogenetic resolution offered by full‐length small subunit ribosomal DNA (SSU rDNA) sequences within these two orders is highly different. Notwithstanding several discrepancies between morphology and SSU rDNA‐based systematics, Mononchida families (indicated here as M1–M5) are relatively well‐supported and, consequently, family‐specific DNA sequences signatures could be defined. Apart from Nygolaimidae and Longidoridae, the resolution among Dorylaimida families was poor. Therefore, a part of the more variable large subunit rDNA (≈ 1000 bp from the 5′‐end) was sequenced for 72 Dorylaimida species. Sequence analysis revealed a subclade division among Dorylaimida (here defined as D1–D9, PP1–PP3) that shows only distant similarity with ‘classical’ Dorylaimid systematics. Most subclades were trophically homogeneous, and — in most cases — specific morphological characteristics could be pinpointed that support the proposed division. To illustrate the practicability of the proposed molecular framework, we designed primers for the detection of individual subclades within the order Mononchida in a complex DNA background (viz. in terrestrial or freshwater nematode communities) and tested them in quantitative assays (real‐time polymerase chain reaction). Our results constitute proof‐of‐principle for the concept of DNA sequence signatures‐based monitoring of stress sensitive nematode families in environmental samples.     

Non-invasive multi-species monitoring: real-time PCR detection of small mammal and squirrel prey DNA in pine marten (Martes martes) scats

DNA identification of mammal species occurring in the diet of a predator is potentially a useful approach to remotely monitor the distribution of multiple species. This is important in Ireland, where it has been shown that the combined presence of the introduced bank vole and greater white-toothed shrew impact the distribution of the indigenous small mammals, the wood mouse and pygmy shrew. Direct monitoring of these species and their interactions requires trapping, a labour-intensive and costly approach. In this study, we applied an indirect method by genetically testing the presence of small mammals in pine marten scats collected during the National Pine Marten Survey (2005–2007) to map their distribution. We also included additional scats to investigate if less common prey items, the red squirrel and grey squirrel, could also be detected. This study demonstrates that all target species were genetically detected from pine marten scats. This strategy could be implemented as a monitoring programme for indigenous and introduced mammal species.     

Towards more accurate detection of pathogenic Gram-positive bacteria in waters

Medically important bacteria can persist in surface waters longer than was previously thought, by activating specific survival strategies and, thus, may represent a further threat to human health, in that they are non-detectable by the traditional culture methods currently used for the evaluation of microbiological quality. Combining microbial physiology, microbial biochemistry, microbial genetics, microbial ecology and molecular biology techniques allow us to achieve more accurate detection of human pathogens located in natural environments external to the human body.     

Using scats of a generalist carnivore as a tool to monitor small mammal communities in Mediterranean habitats

Owl pellets have long been used to analyze communities of small mammals, while analogous analyses of faeces of mammal carnivores are not available. We demonstrate that common genet (Genetta genetta) scats can be used as a reliable method to sample small mammal communities and to monitor their variations. We have compiled data on 6350 small mammal remains of 18 species found in scats from 51 different latrines in a 1200 km² area of northeastern Spain. Genet scats sampled effectively 95.6% of the small mammal species ranging in size from 2.7 to 385 g. Spatial patterns of diet composition along environmental gradients of elevation, climate and land-use matched expected changes in small mammal communities along these gradients according to ecological requirements of prey species. Frequencies of occurrence of prey in genet scats were strongly correlated with frequencies of occurrence in barn owl (Tyto alba) pellets. Genet scats included two forest species not preyed upon by owls, whereas only one species was not preyed upon by genets. Forests species were more frequent in genet than in barn owl diets after correcting for environmental effects, whereas the opposite was true for open-habitat and synanthropic species. Scats of generalist carnivores can be used to estimate the spatial patterns of distribution and abundance of small mammal communities. Genet scats in fact overcome some of the limitations of more traditional sampling methods (live-trapping and owl diets), as genets were less selective and their diets reflect more accurately changes in community composition.     

Inventory of terrestrial alien arthropod predators and parasites established in Europe

There are currently 1590 terrestrial arthropod species identified as alien to Europe. Of these, 513 are predators or parasites. The largest group is the insects (409 species), followed by spiders (47 species), myriapods (34 species) and mites (23 species). The species within these alien groupings are extremely diverse, as highlighted by the large number of families represented (115 families). The majority (66.1%) of alien arthropod predator and parasite species arrived unintentionally, but at least 174 (33.9%) have been introduced intentionally, mainly for biological control purposes. Assessment of the major invasion pathways is difficult due to the lack of comprehensive information but it is likely that the majority of predatory or parasitic alien arthropods arrive through leading-edge dispersal or as contaminants and stowaways. The number of new species arriving in Europe has progressively increased since 1500, with the increase in global trade over the last century accelerating this rate of increase. Only a small number of alien predatory and parasitic arthropods in Europe have been shown to cause either an ecological or economical impact, yet knowledge is severely limited by a paucity of data.     

Towards large-scale synthetic applications of Baeyer-Villiger monooxygenases

Biocatalysis is coming of age, with an increasing number of reactions being scaled-up and developed. The diversity of reactions is also increasing and oxidation reactions have recently been considered for scale-up to commercial processes. One important chemical conversion, which is difficult to achieve enantio- or enantiotopo- selectively, is the Baeyer-Villiger (BV) oxidation of ketones. Using cyclohexanone monooxygenase to catalyse the reaction produces optically pure esters and lactones with exquisite enantiomeric excess values. Recently, these enzymes and their many applications in synthetic chemistry have been explored. The scale-up of these conversions has been examined with the idea of implementing the first commercial Baeyer-Villiger monooxygenase-based process. Here, we review the state-of-the-art situation for the scale-up and exploitation of these enzymes.     

Towards large-scale purification of natural CSF-1 from human placenta tissue extracts

The monocyte-macrophage colony-stimulating factor (colony-stimulating factor 1) is characterized and partially purified from industrially processed human tissues for the first time. A five-step purification procedure using placenta tissue extracts furnished a 13,620-fold enrichment of biological activity. This procedure includes a "pilot" scale anion-exchange chromatography at pH 4.5, gel permeation, and lectin affinity separation followed by HPLC steps (hydrophobic interaction and C18 reverse-phase chromatographies). The purified bioactive material, which stimulates only monocyte-macrophage progenitors and mature cells, showed an Mr of 58,000-62,000 (gel filtration) and an isoelectric point of 3.8-4.0. The hydrophobicity of the molecule was low, and the biological activity was eluted at 50% acetonitrile on a C18 reverse-phase HPLC column. It was totally inactivated by 2-beta-mercaptoethanol reduction and heat treatment. Immunoprecipitation and neutralization of biological activity with specific anti-CSF-1 antibodies (not shown) demonstrated that this material was CSF-1. Step 5 of this protocol yielded two silver-stained bands on 12.5% SDS-PAGE: a major 55-kDa band (96%) and a minor 33-kDa band (4%). CSF-1 was detected exclusively in a band of 52-62 kDa by both Western immunoblotting and bioassays. Immunoaffinity techniques using antibodies directed against selective epitopes on the placental CSF-1 are now considered to purify this material to homogeneity. This approach to the mass production of natural CSF-1 from human tissue has advantages with respect to both the difficulty of post-translational processing of bioactive material in procaryotes and the cost of eucaryotic cell cultures.     

DNA-based detection of the fungal pathogen Geomyces destructans in soils from bat hibernacula

White-nose syndrome (WNS) is an emerging disease causing unprecedented morbidity and mortality among bats in eastern North America. The disease is characterized by cutaneous infection of hibernating bats by the psychrophilic fungus Geomyces destructans. Detection of G. destructans in environments occupied by bats will be critical for WNS surveillance, management and characterization of the fungal lifecycle. We initiated an rRNA gene region-based molecular survey to characterize the distribution of G. destructans in soil samples collected from bat hibernacula in the eastern United States with an existing PCR test. Although this test did not specifically detect G. destructans in soil samples based on a presence/absence metric, it did favor amplification of DNA from putative Geomyces species. Cloning and sequencing of PCR products amplified from 24 soil samples revealed 74 unique sequence variants representing 12 clades. Clones with exact sequence matches to G. destructans were identified in three of 19 soil samples from hibernacula in states where WNS is known to occur. Geomyces destructans was not identified in an additional five samples collected outside the region where WNS has been documented. This study highlights the diversity of putative Geomyces spp. in soil from bat hibernacula and indicates that further research is needed to better define the taxonomy of this genus and to develop enhanced diagnostic tests for rapid and specific detection of G. destructans in environmental samples.     

Towards an efficient and robust foot classification from pedobarographic images

This paper presents a new computational framework for automatic foot classification from digital plantar pressure images. It classifies the foot as left or right and simultaneously calculates two well-known footprint indices: the Cavanagh's arch index (AI) and the modified AI. The accuracy of the framework was evaluated using a set of plantar pressure images from two common pedobarographic devices. The results were outstanding, as all feet under analysis were correctly classified as left or right and no significant differences were observed between the footprint indices calculated using the computational solution and the traditional manual method. The robustness of the proposed framework to arbitrary foot orientations and to the acquisition device was also tested and confirmed.     

Towards an efficient and robust foot classification from pedobarographic images

This paper presents a new computational framework for automatic foot classification from digital plantar pressure images. It classifies the foot as left or right and simultaneously calculates two well-known footprint indices: the Cavanagh's arch index (AI) and the modified AI. The accuracy of the framework was evaluated using a set of plantar pressure images from two common pedobarographic devices. The results were outstanding, as all feet under analysis were correctly classified as left or right and no significant differences were observed between the footprint indices calculated using the computational solution and the traditional manual method. The robustness of the proposed framework to arbitrary foot orientations and to the acquisition device was also tested and confirmed.     

Comparative study of Spanish and Italian terrestrial small mammal coenoses from different biotopes in Mediterranean peninsular tip regions

A comparison of terrestrial small mammal coenoses belonging to nine different biotopes in the tips of the Iberian and Italian peninsulas was carried out using the pitfall trapping method. The influence of both habitat type and peninsular effect on composition of small mammal coenoses was analysed. In Southern Italy, 203 specimens belonging to seven species were trapped: Suncus etruscus (Savi, 1822), Crocidura suaveolens (Pallas, 1811), C. leucodon (Hermann, 1780), Microtus savii (de Sélys-Longchamps, 1838), Apodemus sylvaticus (L., 1758), A. flavicollis (Melchior, 1834) and Mus musculus domesticus Schwarz & Schwarz, 1943. In Southern Spain 428 specimens belonging to five species were trapped: Suncus etruscus, Crocidura russula (Hermann, 1780), Microtus duodecimcostatus (de Sélys-Longchamps, 1839), Apodemus sylvaticus and Mus spretus Lataste, 1883. The relative density of small mammals occurring in the nine Spanish sampling stations was twice that recorded in the Italian stations; however the number of species recorded in the different biotopes show similar mean values, ranging from three to five in Andalusia and from three to six in Calabria. Apodemus sylvaticus was the dominant species in the Calabrian stations, whereas Crocidura russula prevailed in Andalusia. The biotic diversity values are very similar in the Calabrian and Andalusian biotopes. By contrast, the Insectivora/Rodentia ratio was always higher in Andalusia. The more xerophytic biotopes showed greater similarities between the communities in Southern Spain and Southern Italy, while the cooler biotopes differed between these two peninsulas.     

Towards more efficient longline fisheries: fish feeding behaviour,bait characteristics and development of alternative baits

Better knowledge of food search behaviour in fish is essential for studies that aim to improve longline fishing, particularly through bait development. This review provides an overview of our understanding of how fish detect and locate sources of food odour, focusing on the stimuli and sensory modalities involved, and on factors that affect feeding activity. Studies that identify feeding attractants and efforts to develop alternative longline baits are presented. The review reveals that such studies are few in number, and that to date there are no alternatives to traditional baits in commercial longlining despite the growing demand for these resources, which are also used for human consumption. The chemical compounds that elicit food search behaviour differ from species to species, and species selectivity could be improved by incorporating specific feeding attractants in manufactured baits. The unique properties of chemical stimuli and odour dispersal form the basis for improving longline efficiency through the development of a long-lasting bait. Vision is important in prey capture, and manufactured baits can be made more visible than natural baits by increasing the contrast (e.g. via fluorescent or polarising coatings) and creating motion through buoyancy. Physical properties such as size, shape, texture and strength can also be manipulated in a manufactured bait to improve catch efficiency. Knowledge obtained from studies of various aspects of food search behaviour is of paramount importance for future research aimed at alternative bait development and improving longline fishing.     

When more is less: the fitness consequences of predators attacking more unpalatable prey when more are presented

In 1879, Fritz Müller hypothesized that mimetic resemblance in which defended prey display the same warning signal would share the costs of predator education. Although Müller argued that predators would need to ingest a fixed number of prey with a given visual signal when learning to avoid unpalatable prey, this assumption lacks empirical support. We report an experiment which shows that, as the number of unpalatable prey presented to them increased, avian predators attacked higher numbers of those prey. We calculated that, when predators increase attacks, the fitness costs incurred by unpalatable prey can be substantial. This suggests that the survival benefits of mimicry could be lower than Müller proposed. An important finding is, however, that these costs decline in importance as the total number of available prey increases.     

DNA-based detection of Bt resistance alleles in pink bollworm

Evolution of resistance by pests is the main threat to long-term insect control by transgenic crops that produce Bacillus thuringiensis (Bt) toxins. We previously identified three mutant alleles (r1, r2, r3) of a cadherin gene in pink bollworm (Pectinophora gossypiella) linked with recessive resistance to Bt toxin Cry1Ac and survival on transgenic Bt cotton. Here we describe a polymerase chain reaction (PCR)-based method that detects the mutation in genomic DNA of each of the three resistant alleles. Using primers that distinguish between resistant and susceptible (s) alleles, this method enables identification of 10 genotypes (r1r1, r1r2, r1r3, r2r2, r2r3, r3r3, r1s, r2s, r3s, and ss) at the cadherin locus. For each of the three resistant alleles, the method detected the resistance allele in a single heterozygote (r1s, r2s, or r3s) pooled with DNA from the equivalent of 19 susceptible (ss) individuals. The results suggest that the DNA-based detection method described here could greatly increase the efficiency of monitoring for resistance to Cry1Ac compared to bioassays that detect rare individuals with homozygous resistance.     

Multiplexed detection of pathogen DNA with DNA-based fluorescence nanobarcodes

Rapid, multiplexed, sensitive and specific molecular detection is of great demand in gene profiling, drug screening, clinical diagnostics and environmental analysis. One of the major challenges in multiplexed analysis is to identify each specific reaction with a distinct label or 'code'. Two encoding strategies are currently used: positional encoding, in which every potential reaction is preassigned a particular position on a solid-phase support such as a DNA microarray, and reaction encoding, where every possible reaction is uniquely tagged with a code that is most often optical or particle based. The micrometer size, polydispersity, complex fabrication process and nonbiocompatibility of current codes limit their usability. Here we demonstrate the synthesis of dendrimer-like DNA-based, fluorescence-intensity-coded nanobarcodes, which contain a built-in code and a probe for molecular recognition. Their application to multiplexed detection of the DNA of several pathogens is first shown using fluorescence microscopy and dot blotting, and further demonstrated using flow cytometry that resulted in detection that was sensitive (attomole) and rapid.