Mitochondrial metagenomics: letting the genes out of the bottle

‘Mitochondrial metagenomics’ (MMG) is a methodology for shotgun sequencing of total DNA from specimen mixtures and subsequent bioinformatic extraction of mitochondrial sequences. The approach can be applied to phylogenetic analysis of taxonomically selected taxa, as an economical alternative to mitogenome sequencing from individual species, or to environmental samples of mixed specimens, such as from mass trapping of invertebrates. The routine generation of mitochondrial genome sequences has great potential both for systematics and community phylogenetics. Mapping of reads from low-coverage shotgun sequencing of environmental samples also makes it possible to obtain data on spatial and temporal turnover in whole-community phylogenetic and species composition, even in complex ecosystems where species-level taxonomy and biodiversity patterns are poorly known. In addition, read mapping can produce information on species biomass, and potentially allows quantification of within-species genetic variation. The success of MMG relies on the formation of numerous mitochondrial genome contigs, achievable with standard genome assemblers, but various challenges for the efficiency of assembly remain, particularly in the face of variable relative species abundance and intra-specific genetic variation. Nevertheless, several studies have demonstrated the power of mitogenomes from MMG for accurate phylogenetic placement, evolutionary analysis of species traits, biodiversity discovery and the establishment of species distribution patterns; it offers a promising avenue for unifying the ecological and evolutionary understanding of species diversity

Multi-field representations of KP hierarchies and multi-matrix models

We discuss the integrable hierarchies that appear in multi--matrix models. They can be envisaged as multi--field representations of the KP hierarchy. We then study the possible reductions of this systems via the Dirac reduction method by suppressing successively one by one part of the fields. We find in this way new integrable hierarchies, of which we are able to write the Lax pair representations by means of suitable Drinfeld--Sokolov linear systems. At the bottom of each reduction procedure we find an $N$--th KdV hierarchy. We discuss in detail the case which leads to the KdV hierarchy and to the Boussinesque hierarchy, as well as the general case in the dispersionless limit.Comment: 14 pages, LaTeX, SISSA 53/93/EP, ASITP 93-2

De novo prediction of PTBP1 binding and splicing targets reveals unexpected features of its RNA recognition and function.

The splicing regulator Polypyrimidine Tract Binding Protein (PTBP1) has four RNA binding domains that each binds a short pyrimidine element, allowing recognition of diverse pyrimidine-rich sequences. This variation makes it difficult to evaluate PTBP1 binding to particular sites based on sequence alone and thus to identify target RNAs. Conversely, transcriptome-wide binding assays such as CLIP identify many in vivo targets, but do not provide a quantitative assessment of binding and are informative only for the cells where the analysis is performed. A general method of predicting PTBP1 binding and possible targets in any cell type is needed. We developed computational models that predict the binding and splicing targets of PTBP1. A Hidden Markov Model (HMM), trained on CLIP-seq data, was used to score probable PTBP1 binding sites. Scores from this model are highly correlated (ρ = -0.9) with experimentally determined dissociation constants. Notably, we find that the protein is not strictly pyrimidine specific, as interspersed Guanosine residues are well tolerated within PTBP1 binding sites. This model identifies many previously unrecognized PTBP1 binding sites, and can score PTBP1 binding across the transcriptome in the absence of CLIP data. Using this model to examine the placement of PTBP1 binding sites in controlling splicing, we trained a multinomial logistic model on sets of PTBP1 regulated and unregulated exons. Applying this model to rank exons across the mouse transcriptome identifies known PTBP1 targets and many new exons that were confirmed as PTBP1-repressed by RT-PCR and RNA-seq after PTBP1 depletion. We find that PTBP1 dependent exons are diverse in structure and do not all fit previous descriptions of the placement of PTBP1 binding sites. Our study uncovers new features of RNA recognition and splicing regulation by PTBP1. This approach can be applied to other multi-RRM domain proteins to assess binding site degeneracy and multifactorial splicing regulation

Ultrahigh energy neutrino scattering: an update

We update our estimates of charged and neutral current neutrino total cross sections on isoscalar nucleons at ultrahigh energies using a global (x, Q^2) fit, motivated by the Froissart bound, to the F_2 (electron-proton) structure function utilizing the most recent analysis of the complete ZEUS and H1 data sets from HERA I. Using the large Q^2, small Bjorken-x limits of the "wee" parton model, we connect the ultrahigh energy neutrino cross sections directly to the large Q^2, small-x extrapolation of our new fit, which we assume saturates the Froissart bound. We compare both to our previous work, which utilized only the smaller ZEUS data set, as well as to recent results of a calculation using the ZEUS-S based global perturbative QCD parton distributions using the combined HERA I results as input. Our new results substantiate our previous conclusions, again predicting significantly smaller cross sections than those predicted by extrapolating pQCD calculations to neutrino energies above 10^9 GeV.Comment: 8 pages, 1 figure, 3 table

The role of culture and diversity in the prevention of falls among older Chinese people

Original article can be found at : http://journals.cambridge.org/ Copyright Canadian Association on GerontologyThis grounded-theory study explored the perceptions of Chinese older people, living in England, on falls and fear of falling, and identified facilitators and barriers to fall prevention interventions. With a sample of 30 Chinese older people, we conducted two focus groups and 10 in-depth interviews in Mandarin or Cantonese. Interview transcripts, back translated, were analyzed using N6. Constant comparative analysis highlighted a range of health-seeking behaviors after a fall: Chinese older people were reluctant to use formal health services; talking about falls was avoided; older people hid falls from their adult children to avoid worrying them; and fatalistic views about falls and poor knowledge about availability and content of interventions were prevalent. Cost of interventions was important. Chinese older adults valued their independence, and cultural intergenerational relations had an impact on taking action to prevent falls. Cultural diversity affects older adults’ acceptance of fall prevention interventions.Peer reviewe

Experimental studies of species-specificity in cecropia-ant relationships

Journal ArticleStrict coevolution requires that interactions among organisms be speciesspecific. We assessed the relative roles of host- and habitat-specificity in determining the match between a genus of myrmecophytic trees and a guild of obligate plant-ants in the moist tropical forests of Madre de Dios, Peru. Four locally coexisting but habitat-restricted Cecropia species were cultivated in screen tents until all plants had developed myrmecophytic traits. Saplings were then placed within replicate blocks of each of two habitat types: riversides and small forest light gaps. Colonization events were recorded every 3 d between June and August of 1992, and queens were later removed from stem internodes for identification and brood censuses. A similar experiment, conducted in September through November of 1993, included just two species of Cecropia hosts. Effects of host species and habitat on queen colonization rates were evaluated by log-likelihood goodness-of-fit tests and contingency table tests. For three ant species, we also conducted queen preference experiments to compare queen behaviors across a range of host plants. Differences among ants in the extent of habitat-specificity vs. host-specificity provide evidence for multiple evolutionary routes to obligate association with Cecropia. Habitat- specificity exceeded host-specificity in Azteca ovaticeps (Dolichoderinae), for which queen preference experiments revealed no significant discrimination among hosts. This extreme riverside specialist is thought to have descended from generalist live-stem nesters in secondgrowth habitats. In Azteca australis, host-specificity was strong, and in this species only, directed toward hosts where brood production was most successful. Conflicting habitat associations in the two experiments indicated the weakness or absence of a consistent habitat affiliation in Azteca australis and suggested that colonization frequencies were influenced instead by proximity to foundress sources. Close relatives of A. australis live in exposed carton nests, which may have been positioned ancestrally on key resource plants, e.g., those producing lipid- and amino-acid-rich pearl bodies. Pachycondyla luteola (Ponerinae) exhibited both strong habitat and host associations and may have undergone pairwise coevolution with its forest-gap-dwelling primary host. Queens of Camponotus balzani (Formicinae), possibly a recent and secondary associate of Cecropia, were overrepresented in forest gap habitat but were host generalists, underrepresented only on a host with extremely small internodes. Apparently greater host-specificity in C. balzani at later stages of colony establishment may be due to differential post colonization mortality on the various hosts. Attack of ant queens by parasitoid wasps was strongly concentrated in the linear riverside habitat and weak to absent in the patchily distributed forest gap habitat. Due to lower rates of either parasitoid attack or other forms of queen mortality, Camponotus balzani experienced greater success in the forest gap habitat, where it was overrepresented in colonization experiments. Historical coincidences and preadaptations appear to have strongly influenced pairings between Cecropia species and their obligate plant-ants and account for much of the "apparent" niche partitioning observed in the system. Species-specificity seems to be determined mainly by coincident habitat affiliations of ants and plants ("coordinated dispersal") and by preadapted capacities of ants to distinguish among host-plant species. Multiple mechanisms for species-specificity may be characteristic of relationships in which associates disperse separately from one another (i.e., show horizontal transmission). Our results are consistent with the view that coadaptation and co-cladogenesis are more likely in systems where dispersal of associates is tightly coupled