Mass mortality in Pacific oysters is associated with a specific gene expression signature

Mass mortality events occur in natural and cultured communities of bivalve molluscs. The Pacific oyster, Crassostrea gigas, is a dominant species in many intertidal locations as well as an important aquacultured bivalve species, and for the last 50 years, adult oysters have suffered frequent and extreme mass mortality events during summer months. To investigate the molecular changes that precede these mortality events, we employed a novel nonlethal sampling approach to collect haemolymph samples from individual oysters during the period that preceded a mortality event. Microarray-based gene expression screening of the collected haemolymph was used to identify a mortality gene expression signature that distinguished oysters that survived the mortality event from those individuals that died during the event. The signature was cross-validated by comparing two separate episodes of mortality. Here, we report that near-mortality oysters can be distinguished from longer-lived oysters by the elevated expression of genes associated with cell death, lysosomal proteolysis, and cellular assembly and organization. These results show the potential utility of nonlethal sampling approaches for investigating the environmental causes of mortality in natural populations in the field, and for predicting when such events could occur and which individuals will be affected.     

Groupwise sampling: a strategy to sample core entries from RAPD marker data with application to mulberry

Key message

A strategy for effective utilization of RAPD marker data for sampling diverse entries was suggested and utilized for the development of mulberry core collection.

Abstract

Mulberry (Morus spp.) is a perennial tree cultivated mainly for its foliage in sericulture industry and also known for its edible fruits, fodder, and valued timber. In recent years, mulberry cultivation is confronted with several abiotic and biotic stresses due to inimical climatic factors and this has necessitated the genetic improvement of the crop. Core collection is an efficient way of harnessing the trait variation and novel genes available in a natural gene pool for the development of improved elite lines. In this study, we analyzed 850 mulberry accessions assembled from 23 countries with separate sets of polymorphic RAPD markers along with a limited number of ISSR, SSR, and phenotypic markers. A total of 75 accessions were duplicated in 20 clusters among five natural groups. The limitations of the RAPD marker system like problem in cross gel comparison were tackled by adopting a novel “Groupwise sampling” approach. A mulberry core collection with 100 diverse entries was selected using maximization method implemented in MSTRAT software. The mean Dice dissimilarity coefficient computed from marker data was 0.308 among core entries. Indigenous and exotic entries were not discriminated in cluster and principal component analysis supporting the spread of mulberry far from the place of origin. Accessions belonging to two wild mulberry species from Andaman Islands and Himalayan region formed separate clusters indicating the geographical, reproductive, and taxonomic distinction. The identified core collection will be available for researchers for intensive mining of desirable alleles in mulberry improvement as well as in genome resequencing program.     

Dietary factors associated with dental erosion: a meta-analysis

BackgroundSome diet factors are risk factors for dental erosion.MethodsWe performed computer searches of PubMed, Cochrane Library, EBSCO, CALIS, et al., to search for studies investigating risk factors for dental erosion. For risk factors investigated in a comparative way, we computed pooled odds ratios (ORs) using the Mantel and Haenszel method.ResultsA total of 9 studies met the inclusion criteria, and 6 risk factors were considered, including soft drinks, sports drinks, juice, vitamin C, milk, and yoghourt. The following associations were found for soft drinks (OR = 2.41, 95%CI = 2.03–2.85) and vitamin C (OR = 1.16, 95%CI = 1.10–1.22). While juice (OR = 0.90, 95%CI = 0.25–3.24), sports drinks (OR = 1.58, 95%CI = 0.88–2.85), milk (OR = 0.67, 95%CI = 0.11–4.01), and yoghourt products (OR = 1.05, 95%CI = 0.28–3.96) were not associated with dental erosion.ConclusionsThis meta-analysis provides comprehensive evidence-based assessment of diet-related factors for dental erosion. Preventive strategies should be taken to reduce dental erosion.     

Al NMR: a novel NMR data processing program optimized for sparse sampling

Sparse sampling in biomolecular multidimensional NMR offers increased acquisition speed and resolution and, if appropriate conditions are met, an increase in sensitivity. Sparse sampling of indirectly detected time domains combined with the direct truly multidimensional Fourier transform has elicited particular attention because of the ability to generate a final spectrum amenable to traditional analysis techniques. A number of sparse sampling schemes have been described including radial sampling, random sampling, concentric sampling and variations thereof. A fundamental feature of these sampling schemes is that the resulting time domain data array is not amenable to traditional Fourier transform based processing and phasing correction techniques. In addition, radial sampling approaches offer a number of advantages and capabilities that are also not accessible using standard NMR processing techniques. These include sensitivity enhancement, sub-matrix processing and determination of minimal sets of sampling angles. Here we describe a new software package (Al NMR) that enables these capabilities in the context of a general NMR data processing environment.     

A computer programme for the calculation of radioactivity data from liquid-scintillation counters fitted with external standards

1. A method for transferring data from liquid-scintillation counters to automatic punched-card read-out is described. 2. A method of calibration of an external standard is presented that supplies sufficient information for the correction of quenched data by computer. 3. A computer programme in FORTRAN IV is described that calculates the data from one isotope, or two isotopes counted simultaneously, and that incorporates features for examining the reproducibility of the input data. 4. With the methods described, quench correction of samples containing either (3)H or (14)C was accurate until samples were quenched 70%. When the two isotopes were both present in one sample and counted simultaneously, the correction was accurate until the samples were quenched 60%. When quenching was greater than either 70 or 60% respectively, its correction was still possible but with slightly diminished accuracy and with greater variability.     

A blocking Gibbs sampling method to detect major genes with phenotypic data from a diallel mating

Diallel mating is a frequently used design for estimating the additive and dominance genetic (polygenic) effects involved in quantitative traits observed in the half- and full-sib progenies generated in plant breeding programmes. Gibbs sampling has been used for making statistical inferences for a mixed-inheritance model (MIM) that includes both major genes and polygenes. However, using this approach it has not been possible to incorporate the genetic properties of major genes with the additive and dominance polygenic effects in a diallel mating population. A parent block Gibbs sampling method was developed in this study to make statistical inferences about the major gene and polygenic effects on quantitative traits for progenies derived from a half-diallel mating design. Using simulated data sets with different major and polygenic effects, the proposed method accurately estimated the major and polygenic effects of quantitative traits, and possible genotypes of parents and progenies. The impact of specifying different prior distributions was examined and was found to have little effect on inference on the posterior distribution. This approach was applied to an experimental data set of Loblolly pine (Pinus taeda L.) derived from a 6-parent half-diallel mating. The result indicated that there might be a recessive major gene affecting height growth in this diallel population.     

Fossil biogeography: a new model to infer dispersal,extinction and sampling from palaeontological data

Methods in historical biogeography have revolutionized our ability to infer the evolution of ancestral geographical ranges from phylogenies of extant taxa, the rates of dispersals, and biotic connectivity among areas. However, extant taxa are likely to provide limited and potentially biased information about past biogeographic processes, due to extinction, asymmetrical dispersals and variable connectivity among areas. Fossil data hold considerable information about past distribution of lineages, but suffer from largely incomplete sampling. Here we present a new dispersal–extinction–sampling (DES) model, which estimates biogeographic parameters using fossil occurrences instead of phylogenetic trees. The model estimates dispersal and extinction rates while explicitly accounting for the incompleteness of the fossil record. Rates can vary between areas and through time, thus providing the opportunity to assess complex scenarios of biogeographic evolution. We implement the DES model in a Bayesian framework and demonstrate through simulations that it can accurately infer all the relevant parameters. We demonstrate the use of our model by analysing the Cenozoic fossil record of land plants and inferring dispersal and extinction rates across Eurasia and North America. Our results show that biogeographic range evolution is not a time-homogeneous process, as assumed in most phylogenetic analyses, but varies through time and between areas. In our empirical assessment, this is shown by the striking predominance of plant dispersals from Eurasia into North America during the Eocene climatic cooling, followed by a shift in the opposite direction, and finally, a balance in biotic interchange since the middle Miocene. We conclude by discussing the potential of fossil-based analyses to test biogeographic hypotheses and improve phylogenetic methods in historical biogeography.     

Protoceratium reticulatum in northern Japan: environmental factors associated with seasonal occurrence and related contamination of yessotoxin in scallops

In 2003, an occurrence of the yessotoxin (YTX)-producing dinoflagellate,Protoceratium reticulatum, and resultant toxin concentrationin scallops was monitored in Okkirai Bay, northern Japan. Theoccurrence peaked after 1 July and reached a maximum density(400 cells L^–1) on 16 July. It occurred over a wide rangeof water temperature and inorganic nutrient concentrations andwas tolerant of a broad range of environmental conditions. Hydrologicalparameters were monitored, and it was obvious that P. reticulatumflourished under low salinity (30.59–32.60) and occurredat highest density in the surface layer (0–5 m depth)where effects from rainfall were greatest. In addition, dinoflagellatedensity increase and decrease was well correlated with inflowsof oceanic water into the bay. Thus, it can be assumed thatthe oceanic inflows may cause initial population increases (e.g.excystment or input of a ‘seed population’), withresultant growth in rain-affected waters and subsequent spreadthroughout the entire bay via water movement. YTX and 45-OHYTXconcentrations in scallops reached maximum levels (0.79 µgg^–1 and 0.44 µg g^–1 of digestive gland, respectively)2 weeks after the maximum cell density of P. reticulatum, andhigh levels of the toxin continued for a month. Low levels ofthe toxin were detected even during periods when cells werenot observed.     

M-Finder: Uncovering functionally associated proteins from interactome data integrated with GO annotations

Background

Protein-protein interactions (PPIs) play a key role in understanding the mechanisms of cellular processes. The availability of interactome data has catalyzed the development of computational approaches to elucidate functional behaviors of proteins on a system level. Gene Ontology (GO) and its annotations are a significant resource for functional characterization of proteins. Because of wide coverage, GO data have often been adopted as a benchmark for protein function prediction on the genomic scale.

Results

We propose a computational approach, called M-Finder, for functional association pattern mining. This method employs semantic analytics to integrate the genome-wide PPIs with GO data. We also introduce an interactive web application tool that visualizes a functional association network linked to a protein specified by a user. The proposed approach comprises two major components. First, the PPIs that have been generated by high-throughput methods are weighted in terms of their functional consistency using GO and its annotations. We assess two advanced semantic similarity metrics which quantify the functional association level of each interacting protein pair. We demonstrate that these measures outperform the other existing methods by evaluating their agreement to other biological features, such as sequence similarity, the presence of common Pfam domains, and core PPIs. Second, the information flow-based algorithm is employed to discover a set of proteins functionally associated with the protein in a query and their links efficiently. This algorithm reconstructs a functional association network of the query protein. The output network size can be flexibly determined by parameters.

Conclusions

M-Finder provides a useful framework to investigate functional association patterns with any protein. This software will also allow users to perform further systematic analysis of a set of proteins for any specific function. It is available online at http://bionet.ecs.baylor.edu/mfinder

     

Some examples of a method for determining key factors from life table data

Summary The method of Manly (1977) for determining key factors in the life cycle of animal populations is illustrated on several sets of published data.     

A Monte Carlo study of tests on data originating from quadrat sampling. I: Data from a Poisson distribution

Computer simulations are used to examine the significance levels and powers of several tests which have been employed to compare the means of Poisson distributions. In particular, attention is focused on the behaviour of the tests when the means are small, as is often the case in ecological studies when populations of organisms are sampled using quadrats. Two approaches to testing are considered. The first assumes a log linear model for the Poisson data and leads to tests based on the deviance. The second employs standard analysis of variance tests following data transformations, including the often used logarithmic and square root transformations. For very small means it is found that a deviance-based test has the most favourable characteristics, generally outperforming analysis of variance tests on transformed data; none of the latter appears consistently better than any other. For larger means the standard analysis of variance on untransformed data performs well.     

Epizoanthidae (Hexacorallia: Zoantharia) associated with Granulifusus gastropods (Neogastropoda: Fasciolariidae) from the Indo-West Pacific

Organisms Diversity & Evolution - There have been few detailed studies on the associations between cnidarians and gastropod mollusks. Several hypotheses have been suggested to explain the...     

Large gryphaeid oysters as habitats for numerous sclerobionts: a case study from the northern Red Sea

The shell of a living specimen of the Indo-Pacific gryphaeid giant oyster Hyotissa hyotis was colonized by numerous encrusting, boring, nestling and baffling taxa which show characteristic distribution patterns. On the upper valve, sponge-induced bioerosion predominates. On the lower valve intergrowth of chamid bivalves and thick encrusting associations—consisting mostly of squamariacean and corallinacean red algae, acervulinid foraminifera, and scleractinian corals—provides numerous microhabitats for nestling arcid and mytilid bivalves as well as for encrusting bryozoans and serpulids. Such differences between exposed and cryptic surfaces are typical for many marine hard substrata and result from the long-term stable position of the oyster on the seafloor. The cryptic habitats support a species assemblage of crustose algae and foraminifera that, on exposed surfaces, would occur in much deeper water.     

Patterns of differential introgression in a salamander hybrid zone: inferences from genetic data and ecological niche modelling

Hybrid zones have yielded considerable insight into many evolutionary processes, including speciation and the maintenance of species boundaries. Presented here are analyses from a hybrid zone that occurs among three salamanders –Plethodon jordani, Plethodon metcalfi and Plethodon teyahalee– from the southern Appalachian Mountains. Using a novel statistical approach for analysis of non‐clinal, multispecies hybrid zones, we examined spatial patterns of variation at four markers: single‐nucleotide polymorphisms (SNPs) located in the mtDNA ND2 gene and the nuclear DNA ILF3 gene, and the morphological markers of red cheek pigmentation and white flecks. Concordance of the ILF3 marker and both morphological markers across four transects is observed. In three of the four transects, however, the pattern of mtDNA is discordant from all other markers, with a higher representation of P. metcalfi mtDNA in the northern and lower elevation localities than is expected given the ILF3 marker and morphology. To explore whether climate plays a role in the position of the hybrid zone, we created ecological niche models for P. jordani and P. metcalfi. Modelling results suggest that hybrid zone position is not determined by steep gradients in climatic suitability for either species. Instead, the hybrid zone lies in a climatically homogenous region that is broadly suitable for both P. jordani and P. metcalfi. We discuss various selective (natural selection associated with climate) and behavioural processes (sex‐biased dispersal, asymmetric reproductive isolation) that might explain the discordance in the extent to which mtDNA and nuclear DNA and colour‐pattern traits have moved across this hybrid zone.     

Environmental factors influencing the gobiid assemblage of a Mediterranean Lagoon: Empirical evidence from a long-term study

A severe freshwater inflow during our long-term ichthyological study of the brackish Vaccarès lagoon (1993–1998) helped us to assess the impact of sudden environmental changes on the specific biomass composition of the gobiid population and the catches per unit effort of the black goby Gobius niger, the common goby Pomatoschistus microps and the sand goby P. minutus. In 1993, the composition of the Gobiid fish assemblage of the Vaccarès lagoon was dominated by the black goby (63%) and finally evolved to an assemblage dominated by the common goby (80%). The black goby disappeared from the Vaccarès lagoon 2 years after the inflow, whereas catches of the common goby increased significantly after the environmental changes and reached maximum values in 1998. Catches of sand goby did not seem to be affected by environmental changes and depended on the communication between sea and lagoon. This study showed that evolution of an ecosystem after environmental changes is linked to the reaction that species developed to face perturbations.     

CoagVDb: a comprehensive database for coagulation factors and their associated SAPs

The current state of the art in medical genetics is to identify and classify the functional (deleterious) or non-functional (neutral) single amino acid substitutions (SAPs), also known as non-synonymous SNPs (nsSNPs). The primary goal is to elucidate the mechanisms through which functional SAPs exert their effects, and ultimately interrogating this information for association with complex phenotypes. This work focuses on coagulation factors involved in the coagulation cascade pathway which plays a vital role in the maintenance of homeostasis in the human system. We developed an integrated coagulation variation database, CoagVDb, which makes use of the biological information from various public databases such as NCBI, OMIM, UniProt, PDB and SAPs (rsIDs/variant). CoagVDb enriched with computational prediction scores classify SAPs as either deleterious or tolerated. Also, various other properties are incorporated such as amino acid composition, secondary structure elements, solvent accessibility, ordered/disordered regions, conservation, and the presence of disulfide bonds. This specialized database provides integration of various prediction scores from different computational methods along with gene, protein, and disease information. We hope our database will act as a useful reference resource for hematologists to reveal protein structure–function relationship and disease genotype–phenotype correlation.

Electronic supplementary material

The online version of this article (doi:10.1186/s40659-015-0028-5) contains supplementary material, which is available to authorized users.     

Limited sampling of conformational space by the distance geometry algorithm: implications for structures generated from NMR data

Calculations with a metric matrix distance geometry algorithm were performed that show that the standard implementation of the algorithm generally samples a very limited region of conformational space. This problem is most severe when only a small amount of distance information is used as input for the algorithm. Control calculations were performed on linear peptides, disulfide-linked peptides, and a double-stranded DNA decamer where only distances defining the covalent structures of the molecules (as well as the hydrogen bonds for the base pairs in the DNA) were included as input. Since the distance geometry algorithm is commonly used to generate structures of biopolymers from distance data obtained from NMR experiments, simulations were performed on the small globular protein basic pancreatic trypsin inhibitor (BPTI) that mimic calculations performed with actual NMR data. The results on BPTI and on the control peptides indicate that the standard implementation of the algorithm has two main problems: first, that it generates extended structures; second, that it has a tendency to consistently produce similar structures instead of sampling all structures consistent with the input distance information. These results also show that use of a simple root-mean-square deviation for evaluating the quality of the structures generated from NMR data may not be generally appropriate. The main sources of these problems are identified, and our results indicate that the problems are not a fundamental property of the distance geometry algorithm but arise from the implementations presently used to generate structures from NMR data. Several possible methods for alleviating these problems are discussed.