Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples

Background

To understand the relationship between our bacterial microbiome and health, it is essential to define the microbiome in the absence of disease. The digestive tract includes diverse habitats and hosts the human body's greatest bacterial density. We describe the bacterial community composition of ten digestive tract sites from more than 200 normal adults enrolled in the Human Microbiome Project, and metagenomically determined metabolic potentials of four representative sites.

Results

The microbiota of these diverse habitats formed four groups based on similar community compositions: buccal mucosa, keratinized gingiva, hard palate; saliva, tongue, tonsils, throat; sub- and supra-gingival plaques; and stool. Phyla initially identified from environmental samples were detected throughout this population, primarily TM7, SR1, and Synergistetes. Genera with pathogenic members were well-represented among this disease-free cohort. Tooth-associated communities were distinct, but not entirely dissimilar, from other oral surfaces. The Porphyromonadaceae, Veillonellaceae and Lachnospiraceae families were common to all sites, but the distributions of their genera varied significantly. Most metabolic processes were distributed widely throughout the digestive tract microbiota, with variations in metagenomic abundance between body habitats. These included shifts in sugar transporter types between the supragingival plaque, other oral surfaces, and stool; hydrogen and hydrogen sulfide production were also differentially distributed.

Conclusions

The microbiomes of ten digestive tract sites separated into four types based on composition. A core set of metabolic pathways was present across these diverse digestive tract habitats. These data provide a critical baseline for future studies investigating local and systemic diseases affecting human health.     

Delimitation of lymphatic filariasis transmission risk areas: a geo-environmental approach

Background

The Global Programme to Eliminate Lymphatic Filariasis (GPELF) depends upon Mass Drug Administration (MDA) to interrupt transmission. Therefore, delimitation of transmission risk areas is an important step, and hence we attempted to define a geo-environmental risk model (GERM) for determining the areas of potential transmission of lymphatic filariasis.

Methods

A range of geo-environmental variables has been selected, and customized on GIS platform to develop GERM for identifying the areas of filariasis transmission in terms of "risk" and "non-risk". The model was validated through a 'ground truth study' following standard procedure using GIS tools for sampling and Immuno-chromotographic Test (ICT) for screening the individuals.

Results

A map for filariasis transmission was created and stratified into different spatial entities, "risk' and "non-risk", depending on Filariasis Transmission Risk Index (FTRI). The model estimation corroborated well with the ground (observed) data.

Conclusion

The geo-environmental risk model developed on GIS platform is useful for spatial delimitation purpose on a macro scale.     

Surprising complexity of the ancestral apoptosis network

Background

Apoptosis, one of the main types of programmed cell death, is regulated and performed by a complex protein network. Studies in model organisms, mostly in the nematode Caenorhabditis elegans, identified a relatively simple apoptotic network consisting of only a few proteins. However, analysis of several recently sequenced invertebrate genomes, ranging from the cnidarian sea anemone Nematostella vectensis, representing one of the morphologically simplest metazoans, to the deuterostomes sea urchin and amphioxus, contradicts the current paradigm of a simple ancestral network that expanded in vertebrates.

Results

Here we show that the apoptosome-forming CED-4/Apaf-1 protein, present in single copy in vertebrate, nematode, and insect genomes, had multiple paralogs in the cnidarian-bilaterian ancestor. Different members of this ancestral Apaf-1 family led to the extant proteins in nematodes/insects and in deuterostomes, explaining significant functional differences between proteins that until now were believed to be orthologous. Similarly, the evolution of the Bcl-2 and caspase protein families appears surprisingly complex and apparently included significant gene loss in nematodes and insects and expansions in deuterostomes.

Conclusion

The emerging picture of the evolution of the apoptosis network is one of a succession of lineage-specific expansions and losses, which combined with the limited number of 'apoptotic' protein families, resulted in apparent similarities between networks in different organisms that mask an underlying complex evolutionary history. Similar results are beginning to surface for other regulatory networks, contradicting the intuitive notion that regulatory networks evolved in a linear way, from simple to complex.     

Contribution of arbuscular mycorrhizal symbiosis to the survival of psammophilic plants after sea water flooding

Aims

Plants on coastal sand dunes are subjected to strong environmental fluctuations which affect their growth and survival. Sea water invasion of the dunar zone caused by storms is an important factor that determines the persistence of a plant community. In the present study, the benefits of arbuscular mycorrhiza on psammophilic plant species subjected to sea water flooding episodes were evaluated under controlled conditions and the effect of sea water on in vitro spore production was determined.

Methods

In a greenhouse experiment, the growth response of nine plant species to inoculation with Glomus intraradices in beach sand was evaluated. A second experiment was designed in order to test if plant survival under sea water flooding was influenced by the symbiosis. A third experiment was conducted in vitro to quantify the effect of sea water on the production of G. intraradices spores.

Results

Glomus intraradices was effective in promoting plant growth and survival in beach sand and promoted the survival of some species subjected to flooding events. Spore production was inhibited by 50% of sea water in the growth media, but not by 10% sea water.

Conclusions

Results obtained under controlled conditions indicated that arbuscular mycorrhiza can improve the establishment of certain dune plant species in beach sand as the symbiosis contributes to enhanced plant tolerance against occasional sea water flooding.     

From the Western Alps across Central Europe: Postglacial recolonisation of the tufa stream specialist Rhyacophila pubescens (Insecta,Trichoptera)

Background

Hybridization can have complex effects on evolutionary dynamics in ants because of the combination of haplodiploid sex-determination and eusociality. While hybrid non-reproductive workers have been found in a range of species, examples of gene-flow via hybrid queens and males are rare. We studied hybridization in East African army ants (Dorylus subgenus Anomma) using morphology, mitochondrial DNA sequences, and nuclear microsatellites.

Results

While the mitochondrial phylogeny had a strong geographic signal, different species were not recovered as monophyletic. At our main study site at Kakamega Forest, a mitochondrial haplotype was shared between a "Dorylus molestus-like" and a "Dorylus wilverthi-like" form. This pattern is best explained by introgression following hybridization between D. molestus and D. wilverthi. Microsatellite data from workers showed that the two morphological forms correspond to two distinct genetic clusters, with a significant proportion of individuals being classified as hybrids.

Conclusions

We conclude that hybridization and gene-flow between the two army ant species D. molestus and D. wilverthi has occurred, and that mating between the two forms continues to regularly produce hybrid workers. Hybridization is particularly surprising in army ants because workers have control over which males are allowed to mate with a young virgin queen inside the colony.     

Transcriptional profiling of Actinobacillus pleuropneumoniae under iron-restricted conditions

Background

Toll-like receptors (TLRs) play a central role in innate immunity. TLRs are membrane glycoproteins and contain leucine rich repeat (LRR) motif in the ectodomain. TLRs recognize and respond to molecules such as lipopolysaccharide, peptidoglycan, flagellin, and RNA from bacteria or viruses. The LRR domains in TLRs have been inferred to be responsible for molecular recognition. All LRRs include the highly conserved segment, LxxLxLxxNxL, in which "L" is Leu, Ile, Val, or Phe and "N" is Asn, Thr, Ser, or Cys and "x" is any amino acid. There are seven classes of LRRs including "typical" ("T") and "bacterial" ("S"). All known domain structures adopt an arc or horseshoe shape. Vertebrate TLRs form six major families. The repeat numbers of LRRs and their "phasing" in TLRs differ with isoforms and species; they are aligned differently in various databases. We identified and aligned LRRs in TLRs by a new method described here.

Results

The new method utilizes known LRR structures to recognize and align new LRR motifs in TLRs and incorporates multiple sequence alignments and secondary structure predictions. TLRs from thirty-four vertebrate were analyzed. The repeat numbers of the LRRs ranges from 16 to 28. The LRRs found in TLRs frequently consists of LxxLxLxxNxLxxLxxxxF/LxxLxx ("T") and sometimes short motifs including LxxLxLxxNxLxxLPx(x)LPxx ("S"). The TLR7 family (TLR7, TLR8, and TLR9) contain 27 LRRs. The LRRs at the N-terminal part have a super-motif of STT with about 80 residues. The super-repeat is represented by STTSTTSTT or _TTSTTSTT. The LRRs in TLRs form one or two horseshoe domains and are mostly flanked by two cysteine clusters including two or four cysteine residue.

Conclusion

Each of the six major TLR families is characterized by their constituent LRR motifs, their repeat numbers, and their patterns of cysteine clusters. The central parts of the TLR1 and TLR7 families and of TLR4 have more irregular or longer LRR motifs. These central parts are inferred to play a key role in the structure and/or function of their TLRs. Furthermore, the super-repeat in the TLR7 family suggests strongly that "bacterial" and "typical" LRRs evolved from a common precursor.     

Can molecular cell biology explain chromosome motions?

Background

Mitotic chromosome motions have recently been correlated with electrostatic forces, but a lingering "molecular cell biology" paradigm persists, proposing binding and release proteins or molecular geometries for force generation.

Results

Pole-facing kinetochore plates manifest positive charges and interact with negatively charged microtubule ends providing the motive force for poleward chromosome motions by classical electrostatics. This conceptual scheme explains dynamic tracking/coupling of kinetochores to microtubules and the simultaneous depolymerization of kinetochore microtubules as poleward force is generated.

Conclusion

We question here why cells would prefer complex molecular mechanisms to move chromosomes when direct electrostatic interactions between known bound charge distributions can accomplish the same task much more simply.     

Optimized submerged batch fermentation strategy for systems scale studies of metabolic switching in Streptomyces coelicolor A3(2)

Background

Given the complex mechanisms underlying biochemical processes systems biology researchers tend to build ever increasing computational models. However, dealing with complex systems entails a variety of problems, e.g. difficult intuitive understanding, variety of time scales or non-identifiable parameters. Therefore, methods are needed that, at least semi-automatically, help to elucidate how the complexity of a model can be reduced such that important behavior is maintained and the predictive capacity of the model is increased. The results should be easily accessible and interpretable. In the best case such methods may also provide insight into fundamental biochemical mechanisms.

Results

We have developed a strategy based on the Computational Singular Perturbation (CSP) method which can be used to perform a "biochemically-driven" model reduction of even large and complex kinetic ODE systems. We provide an implementation of the original CSP algorithm in COPASI (a COmplex PAthway SImulator) and applied the strategy to two example models of different degree of complexity - a simple one-enzyme system and a full-scale model of yeast glycolysis.

Conclusion

The results show the usefulness of the method for model simplification purposes as well as for analyzing fundamental biochemical mechanisms. COPASI is freely available at http://www.copasi.org.     

Origin and evolutionary plasticity of the gastric caecum in sea urchins (Echinodermata: Echinoidea)

Background  

The digestive tract of many metazoan invertebrates is characterized by the presence of caeca or diverticula that serve secretory and/or absorptive functions. With the development of various feeding habits, distinctive digestive organs may be present in certain taxa. This also holds true for sea urchins (Echinodermata: Echinoidea), in which a highly specialized gastric caecum can be found in members of a derived subgroup, the Irregularia (cake urchins, sea biscuits, sand dollars, heart urchins, and related forms). As such a specialized caecum has not been reported from "regular" sea urchin taxa, the aim of this study was to elucidate its evolutionary origin.     

Adolescent idiopathic scoliosis: natural history and long term treatment effects

Objective

To quantify and compare the forces exerted by scoliosis patients in fiberglass braces during exercises usually prescribed in departments where casts are made. The exercises are intended to increase corrective forces, activate muscles, stimulate ventilation and help the patient psychologically.

Setting

Outpatient care.

Patients

17 consecutive adolescent patients wearing fiberglass brace for idiopathic scoliosis.

Interventions

Exercises (kyphotization, rotation, "escape from the pad") in different positions (sitting, supine, on all fours).

Main outcome measure

Pressure detected by the F-Socket System between the rib hump and the pad of the brace.

Results

In static and dynamic conditions, the position adopted did not alter the total pressure exerted by the brace, although the part of the sensor stimulated did vary. Kyphotization and rotation exercises produced a significant increase of pressure (+ 58.9% and +29.8%, respectively); however, the "escape from the pad" exercise, despite its name, did not produce any significant variation of pressure.

Conclusion

Exercises in the brace allow adjunctive forces to be applied on soft tissues and through them, presumably on the spine. Different exercises can be chosen to obtain different actions. Physical exercises and sporting activities are useful in mechanical terms, although other important actions should not be overlooked.     

A general pipeline for the development of anchor markers for comparative genomics in plants

Background

The massive scale of microarray derived gene expression data allows for a global view of cellular function. Thus far, comparative studies of gene expression between species have been based on the level of expression of the gene across corresponding tissues, or on the co-expression of the gene with another gene.

Results

To compare gene expression between distant species on a global scale, we introduce the "expression context". The expression context of a gene is based on the co-expression with all other genes that have unambiguous counterparts in both genomes. Employing this new measure, we show 1) that the expression context is largely conserved between orthologs, and 2) that sequence identity shows little correlation with expression context conservation after gene duplication and speciation.

Conclusion

This means that the degree of sequence identity has a limited predictive quality for differential expression context conservation between orthologs, and thus presumably also for other facets of gene function.     

High Molecular Weight Mucin-like Glycoprotein in Bovine Milk

We purified an enzyme hydrolyzing 2-sulfo-α-L-fucopyranose pyridylaminated 2-sulfo-α-L-fucopyranosyl-(1→2)-fucose from the acetone powder of the digestive tract of a sea urchin. The enzyme was purified 307-fold with an overall recovery of 1.63% by ammonium sulfate precipitation, cation exchange chromatography, and gel filtration chromatography. The enzyme is useful for the structural analysis of sulfated fucan.     

Two or more enteropathogens are associated with diarrhoea in Mexican children

Background

The Apicomplexa are a diverse group of obligate protozoan parasites infesting a wide range of invertebrate and vertebrate hosts including humans. These parasites are notoriously difficult to control and many species continue to evolve resistance to commercial antibiotics. In this study, we sought to find an effective chemotherapeutic treatment against arthropod gregarines (Apicomplexa), and to identify candidate compounds for testing against other groups of protozoan parasites.

Methods

We tested eleven commercial antibiotics against a gregarine parasite of Romalea microptera grasshoppers. Infected insects were fed daily, lettuce containing known amounts of specific antibiotics. On Days 15 or 20, we measured the number of gregarines remaining in the digestive tract of each grasshopper.

Results

Treatment with metronidazole and griseofulvin in host insects significantly reduced gregarine counts, whereas, gregarine counts of insects fed, albendazole, ampicillin, chloramphenicol, fumagillin, quinine, streptomycin, sulfadimethoxine, thiabendazole or tetracycline, were not significantly different from the controls. However, albendazole produced a strong, but non-significant reduction in gregarine count, and streptomycin exhibited a non-significant antagonistic trend.

Conclusion

Our results confirm that gregarine infections are difficult to control and suggest the possibility that streptomycin might aggravate gregarine infection. In addition, the insect system described here, provides a simple, inexpensive, and effective method for screening antibiotics.     

Capture and commercialization of blue land crabs ("guaiamum") Cardisoma guanhumi (Lattreille, 1825) along the coast of Bahia State, Brazil: an ethnoecological approach

Background

Blue Land Crab (Cardisoma guanhumi) is one of the most important crustacean species captured and commercialized in Brazil. Although this species is not considered to be threatened with extinction, populations of C. guanhumi are known to be rapidly diminishing due to heavy harvesting pressures and degradation of their natural habitats, highlighting the necessity of developing and implanting management and protection strategies for their populations. There have been no ethnozoological publications that have focused specifically on C. guanhumi, in spite of importance of this type of information for developing efficient management plans of resource utilization. So, the present work describes the ethnoecological aspects of the capture and commercialization of C. guanhumi by a fishing community in northeastern Brazil.

Methods

Field work was carried out in the municipality of Mucuri, Bahia in Brazil, between the months of January and March/2011 through the use of open semi-structured interviews with all of the crustacean harvesters in city who acknowledged their work in capturing this species, totaling 12 interviewees. The informants were identified through the use of the "snowball" sampling technique. In addition to the interviews themselves, the "guided tour" technique and direct observations was employed.

Results

According all the interviewees, the C. guanhumi is popularly called "guaiamum" and is collected in "apicum" zones. They recognize sexual dimorphism in the species based on three morphological characteristics and the harvesters also pointed two stages in the reproductive cycle during the year and another phase mentioned by the interviewees was ecdysis. All of the interviewed affirmed that the size and the quantities C. guanhumi stocks in Mucuri have been diminishing. All of the interviewees agreed that the species and other mangrove resources constituted their principal source of income. The harvesters dedicated three to five days a week to collect Blue Land Crabs and the principal technique utilized for capturing is a trap called a "ratoeira" (rat-trap).

Conclusions

The results of the present work demonstrated that the community retains a vast and important volume of knowledge about C. guanhumi that could subsidize both scientific studies and the elaboration of viable management and conservation strategies for this species.     

The action of <Emphasis Type="Italic">Laminaria japonica</Emphasis> extractives on 1,3-β-D-glucanase,a digestive enzyme of the <Emphasis Type="Italic">Strongylocentrotus intermedius</Emphasis> sea urchin

Nutritional attractiveness of the brown alga Laminaria japonica for the sea urchin Strongylocentrotus intermedius was studied. The composition of L. japonica was analyzed after one and two years of its life under natural conditions, in its seedlings, and in the alga partially degraded by natural factors. Substances extracted with various solvents were tested for the presence of inhibitors and activators of 1,3-β-D-glucanase, a digestive enzyme of the sea urchin. Ethanolic extract of freshly harvested L. japonica was found to suppress the enzyme activity. Substances present in ethanolic extracts of the alga after one or two years of its life cycle and in the alga, partly degraded by natural factors, activated the sea urchin enzyme. This fact is in agreement with earlier natural observations concerning the nutritional attractiveness of such L. japonica samples for Strongylocentrotus intermedius.     

Two novel missense mutations in the myelin protein zero gene causes Charcot-Marie-Tooth type 2 and Déjérine-Sottas syndrome

Background

Gene-list annotations are critical for researchers to explore the complex relationships between genes and functionalities. Currently, the annotations of a gene list are usually summarized by a table or a barplot. As such, potentially biologically important complexities such as one gene belonging to multiple annotation categories are difficult to extract. We have devised explicit and efficient visualization methods that provide intuitive methods for interrogating the intrinsic connections between biological categories and genes.

Findings

We have constructed a data model and now present two novel methods in a Bioconductor package, "GeneAnswers", to simultaneously visualize genes, concepts (a.k.a. annotation categories), and concept-gene connections (a.k.a. annotations): the "Concept-and-Gene Network" and the "Concept-and-Gene Cross Tabulation". These methods have been tested and validated with microarray-derived gene lists.

Conclusions

These new visualization methods can effectively present annotations using Gene Ontology, Disease Ontology, or any other user-defined gene annotations that have been pre-associated with an organism's genome by human curation, automated pipelines, or a combination of the two. The gene-annotation data model and associated methods are available in the Bioconductor package called "GeneAnswers " described in this publication.     

Gitksan medicinal plants-cultural choice and efficacy

Background

The use of plants for healing by any cultural group is integrally related to local concepts of the nature of disease, the nature of plants, and the world view of the culture. The physical and chemical properties of the plants themselves also bear on their selection by people for medicines, as does the array of plants available for people to choose from. I examine use of medicinal plants from a "biobehavioral" perspective to illuminate cultural selection of plants used for medicine by the Gitksan of northwestern British Columbia, Canada.

Methods

Consultant consensus, "intercultural consensus", independent use of the same plants by other cultural groups, and phytochemistry and bioassay results from the literature, were employed in analysis of probable empirical efficacy of plant uses.

Results

70% of 37 Gitksan medicinal plants were used similarly by other cultures where direct diffusion is not known to have occurred; eleven plants, including the eight most frequently mentioned medicinal plants, also show active phytochemicals or bioassays indicating probable physiologically based therapeutic effects.

Conclusion

Analysis of intercultural consensus revealed that the majority of cultures in the British Columbia region within the plant ranges use the same plants, or closely related species, in similar ways. The rigor of this analysis is effected by the lack of consistent data on all taxa of interest for all cultures within the region.     

Which strategy is better for linkage analysis: single-nucleotide polymorphisms or microsatellites? Evaluation by identity-by-state – identity-by-descent transformation affected sib-pair method on GAW14 data

Background

The genetics of plumage of Japanese quail is of interest both from a biological standpoint, for comparative studies between avian species, and from a zootechnical standpoint, for identifying commercial selection lines or crosses. There are only few plumage mutations reported in quail, and the present work describes a new color variant "rusty" and a new feather structure "curly", and their heredity from an F1 and F2 segregation experiment.

Results

Curly feathers result from abnormal early growth caused by transient joining of follicle walls of adjacent feathers around 10 days of age, but the expression of the trait is variable. Rusty plumage color results from the replacement of the wild-type plumage pattern on the tip of the feather by a reddish coloration, but the pigmentation of the bottom part of the feather is not affected. Two lines breeding true for the curly or the rusty phenotype were developed. Both characters are determined by autosomal recessive mutations which are independent. The curly mutation has also a positive effect on body weight at 5 weeks of age.

Conclusion

The curly line is a new model which may be used for further work on the growth of the feather, and the rusty mutation is a new addition to the panel of plumage mutations available for comparative studies in poultry, and more generally among avian species.