A Functional Analysis on the Interspecies Interaction between Mouse LFA-1 and Human Intercellular Adhesion Molecule-1 at the Cell Level.

PubMed

Núñez, David; Comas, Laura; Lanuza, Pilar M; Sánchez-Martinez, Diego; Pérez-Hernández, Marta; Catalán, Elena; Domingo, María Pilar; Velázquez-Campoy, Adrián; Pardo, Julián; Gálvez, Eva M

2017-01-01

The interaction between intercellular adhesion molecules (ICAM) and the integrin leukocyte function-associated antigen-1 (LFA-1) is crucial for the regulation of several physiological and pathophysiological processes like cell-mediated elimination of tumor or virus infected cells, cancer metastasis, or inflammatory and autoimmune processes. Using purified proteins it was reported a species restriction for the interaction of ICAM-1 and LFA-1, being mouse ICAM-1 able to interact with human LFA-1 but not human ICAM-1 with mouse LFA-1. However, in vivo results employing tumor cells transfected with human ICAM-1 suggest that functionally mouse LFA-1 can recognize human ICAM-1. In order to clarify the interspecies cross-reactivity of the ICAM-1/LFA-1 interaction, we have performed functional studies analyzing the ability of human soluble ICAM-1 and human/mouse LFA-1 derived peptides to inhibit cell aggregation and adhesion as well as cell-mediated cytotoxicity in both mouse and human systems. In parallel, the affinity of the interaction between mouse LFA-1-derived peptides and human ICAM-1 was determined by calorimetry assays. According to the results obtained, it seems that human ICAM-1 is able to interact with mouse LFA-1 on intact cells, which should be taking into account when using humanized mice and xenograft models for the study of immune-related processes.

Postdoctoral Fellow | Center for Cancer Research

Cancer.gov

The Khare lab in the Laboratory of Molecular Biology, NCI Center for Cancer Research, NIH, is looking to recruit highly motivated researchers interested in a postdoctoral fellowship to study the molecular and genetic basis of complex microbial behaviors. Our lab is focused on multiple research avenues including interspecies interactions, antibiotic persistence, and adaptation

Interspecies interactions that result in Bacillus subtilis forming biofilms are mediated mainly by members of its own genus.

PubMed

Shank, Elizabeth A; Klepac-Ceraj, Vanja; Collado-Torres, Leonardo; Powers, Gordon E; Losick, Richard; Kolter, Roberto

2011-11-29

Many different systems of bacterial interactions have been described. However, relatively few studies have explored how interactions between different microorganisms might influence bacterial development. To explore such interspecies interactions, we focused on Bacillus subtilis, which characteristically develops into matrix-producing cannibals before entering sporulation. We investigated whether organisms from the natural environment of B. subtilis--the soil--were able to alter the development of B. subtilis. To test this possibility, we developed a coculture microcolony screen in which we used fluorescent reporters to identify soil bacteria able to induce matrix production in B. subtilis. Most of the bacteria that influence matrix production in B. subtilis are members of the genus Bacillus, suggesting that such interactions may be predominantly with close relatives. The interactions we observed were mediated via two different mechanisms. One resulted in increased expression of matrix genes via the activation of a sensor histidine kinase, KinD. The second was kinase independent and conceivably functions by altering the relative subpopulations of B. subtilis cell types by preferentially killing noncannibals. These two mechanisms were grouped according to the inducing strain's relatedness to B. subtilis. Our results suggest that bacteria preferentially alter their development in response to secreted molecules from closely related bacteria and do so using mechanisms that depend on the phylogenetic relatedness of the interacting bacteria.

Stringent homology-based prediction of H. sapiens-M. tuberculosis H37Rv protein-protein interactions.

PubMed

Zhou, Hufeng; Gao, Shangzhi; Nguyen, Nam Ninh; Fan, Mengyuan; Jin, Jingjing; Liu, Bing; Zhao, Liang; Xiong, Geng; Tan, Min; Li, Shijun; Wong, Limsoon

2014-04-08

H. sapiens-M. tuberculosis H37Rv protein-protein interaction (PPI) data are essential for understanding the infection mechanism of the formidable pathogen M. tuberculosis H37Rv. Computational prediction is an important strategy to fill the gap in experimental H. sapiens-M. tuberculosis H37Rv PPI data. Homology-based prediction is frequently used in predicting both intra-species and inter-species PPIs. However, some limitations are not properly resolved in several published works that predict eukaryote-prokaryote inter-species PPIs using intra-species template PPIs. We develop a stringent homology-based prediction approach by taking into account (i) differences between eukaryotic and prokaryotic proteins and (ii) differences between inter-species and intra-species PPI interfaces. We compare our stringent homology-based approach to a conventional homology-based approach for predicting host-pathogen PPIs, based on cellular compartment distribution analysis, disease gene list enrichment analysis, pathway enrichment analysis and functional category enrichment analysis. These analyses support the validity of our prediction result, and clearly show that our approach has better performance in predicting H. sapiens-M. tuberculosis H37Rv PPIs. Using our stringent homology-based approach, we have predicted a set of highly plausible H. sapiens-M. tuberculosis H37Rv PPIs which might be useful for many of related studies. Based on our analysis of the H. sapiens-M. tuberculosis H37Rv PPI network predicted by our stringent homology-based approach, we have discovered several interesting properties which are reported here for the first time. We find that both host proteins and pathogen proteins involved in the host-pathogen PPIs tend to be hubs in their own intra-species PPI network. Also, both host and pathogen proteins involved in host-pathogen PPIs tend to have longer primary sequence, tend to have more domains, tend to be more hydrophilic, etc. And the protein domains from both host and pathogen proteins involved in host-pathogen PPIs tend to have lower charge, and tend to be more hydrophilic. Our stringent homology-based prediction approach provides a better strategy in predicting PPIs between eukaryotic hosts and prokaryotic pathogens than a conventional homology-based approach. The properties we have observed from the predicted H. sapiens-M. tuberculosis H37Rv PPI network are useful for understanding inter-species host-pathogen PPI networks and provide novel insights for host-pathogen interaction studies.

Morphological plasticity in watermelon in response to interspecific competition in a low-resource intercropping system

USDA-ARS?s Scientific Manuscript database

Interspecies specific interactions are generally regarded as drivers of plant productivity in multispecies agroecosystems. Positive interactions such as facilitation can dominate over competition under high abiotic stress conditions. Furthermore, complementary use of resource in diverse communities ...

Observation of a Degenerate Fermi Gas Trapped by a Bose-Einstein Condensate

NASA Astrophysics Data System (ADS)

DeSalvo, B. J.; Patel, Krutik; Johansen, Jacob; Chin, Cheng

2017-12-01

We report on the formation of a stable quantum degenerate mixture of fermionic 6Li and bosonic 133Cs in an optical trap by sympathetic cooling near an interspecies Feshbach resonance. New regimes of quantum degenerate Bose-Fermi mixtures are identified. With moderate attractive interspecies interactions, we show that a degenerate Fermi gas of Li can be fully confined in a Cs Bose-Einstein condensate without external potentials. For stronger attraction where mean-field collapse is expected, no such instability is observed. Potential mechanisms to explain this phenomenon are discussed.

Hardwiring microbes via direct interspecies electron transfer: mechanisms and applications.

PubMed

Cheng, Qiwen; Call, Douglas F

2016-08-10

Multicellular microbial communities are important catalysts in engineered systems designed to treat wastewater, remediate contaminated sediments, and produce energy from biomass. Understanding the interspecies interactions within them is therefore essential to design effective processes. The flow of electrons within these communities is especially important in the determination of reaction possibilities (thermodynamics) and rates (kinetics). Conventional models of electron transfer incorporate the diffusion of metabolites generated by one organism and consumed by a second, frequently referred to as mediated interspecies electron transfer (MIET). Evidence has emerged in the last decade that another method, called direct interspecies electron transfer (DIET), may occur between organisms or in conjunction with electrically conductive materials. Recent research has suggested that DIET can be stimulated in engineered systems to improve desired treatment goals and energy recovery in systems such as anaerobic digesters and microbial electrochemical technologies. In this review, we summarize the latest understanding of DIET mechanisms, the associated microorganisms, and the underlying thermodynamics. We also critically examine approaches to stimulate DIET in engineered systems and assess their effectiveness. We find that in most cases attempts to promote DIET in mixed culture systems do not yield the improvements expected based on defined culture studies. Uncertainties of other processes that may be co-occurring in real systems, such as contaminant sorption and biofilm promotion, need to be further investigated. We conclude by identifying areas of future research related to DIET and its application in biological treatment processes.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rawle, Rachel A.; Hamerly, Timothy; Tripet, Brian P.

Studies of interspecies interactions are inherently difficult due to the complex mechanisms which enable these relationships. A model system for studying interspecies interactions is the marine hyperthermophiles Ignicoccus hospitalis and Nanoarchaeum equitans. Recent independently-conducted ‘omics’ analyses have generated insights into the molecular factors modulating this association. However, significant questions remain about the nature of the interactions between these archaea. We jointly analyzed multiple levels of omics datasets obtained from published, independent transcriptomics, proteomics, and metabolomics analyses. DAVID identified functionally-related groups enriched when I. hospitalis is grown alone or in co-culture with N. equitans. Enriched molecular pathways were subsequently visualized usingmore » interaction maps generated using STRING. Key findings of our multi-level omics analysis indicated that I. hospitalis provides precursors to N. equitans for energy metabolism. Analysis indicated an overall reduction in diversity of metabolic precursors in the I. hospitalis–N. equitans co-culture, which has been connected to the differential use of ribosomal subunits and was previously unnoticed. We also identified differences in precursors linked to amino acid metabolism, NADH metabolism, and carbon fixation, providing new insights into the metabolic adaptions of I. hospitalis enabling the growth of N. equitans. In conclusion, this multi-omics analysis builds upon previously identified cellular patterns while offering new insights into mechanisms that enable the I. hospitalis–N. equitans association. This study applies statistical and visualization techniques to a mixed-source omics dataset to yield a more global insight into a complex system, that was not readily discernable from separate omics studies.« less

Interspecies Systems Biology Uncovers Metabolites Affecting C. elegans Gene Expression and Life History Traits

PubMed Central

Watson, Emma; MacNeil, Lesley T.; Ritter, Ashlyn D.; Yilmaz, L. Safak; Rosebrock, Adam P.; Caudy, Amy A.; Walhout, Albertha J. M.

2014-01-01

SUMMARY Diet greatly influences gene expression and physiology. In mammals, elucidating the effects and mechanisms of individual nutrients is challenging due to the complexity of both the animal and its diet. Here we used an interspecies systems biology approach with Caenorhabditis elegans and two if its bacterial diets, Escherichia coli and Comamonas aquatica, to identify metabolites that affect the animal’s gene expression and physiology. We identify vitamin B12 as the major dilutable metabolite provided by Comamonas aq. that regulates gene expression, accelerates development and reduces fertility, but does not affect lifespan. We find that vitamin B12 has a dual role in the animal: it affects development and fertility via the methionine/S-Adenosylmethionine (SAM) cycle and breaks down the short-chain fatty acid propionic acid preventing its toxic buildup. Our interspecies systems biology approach provides a paradigm for understanding complex interactions between diet and physiology. PMID:24529378

Evolutionary Role of Interspecies Hybridization and Genetic Exchanges in Yeasts

PubMed Central

Dujon, Bernard

2012-01-01

Summary: Forced interspecific hybridization has been used in yeasts for many years to study speciation or to construct artificial strains with novel fermentative and metabolic properties. Recent genome analyses indicate that natural hybrids are also generated spontaneously between yeasts belonging to distinct species, creating lineages with novel phenotypes, varied genetic stability, or altered virulence in the case of pathogens. Large segmental introgressions from evolutionarily distant species are also visible in some yeast genomes, suggesting that interspecific genetic exchanges occur during evolution. The origin of this phenomenon remains unclear, but it is likely based on weak prezygotic barriers, limited Dobzhansky-Muller (DM) incompatibilities, and rapid clonal expansions. Newly formed interspecies hybrids suffer rapid changes in the genetic contribution of each parent, including chromosome loss or aneuploidy, translocations, and loss of heterozygosity, that, except in a few recently studied cases, remain to be characterized more precisely at the genomic level by use of modern technologies. We review here known cases of natural or artificially formed interspecies hybrids between yeasts and discuss their potential importance in terms of genome evolution. Problems of meiotic fertility, ploidy constraint, gene and gene product compatibility, and nucleomitochondrial interactions are discussed and placed in the context of other known mechanisms of yeast genome evolution as a model for eukaryotes. PMID:23204364

Networks of energetic and metabolic interactions define dynamics in microbial communities.

PubMed

Embree, Mallory; Liu, Joanne K; Al-Bassam, Mahmoud M; Zengler, Karsten

2015-12-15

Microorganisms form diverse communities that have a profound impact on the environment and human health. Recent technological advances have enabled elucidation of community diversity at high resolution. Investigation of microbial communities has revealed that they often contain multiple members with complementing and seemingly redundant metabolic capabilities. An understanding of the communal impacts of redundant metabolic capabilities is currently lacking; specifically, it is not known whether metabolic redundancy will foster competition or motivate cooperation. By investigating methanogenic populations, we identified the multidimensional interspecies interactions that define composition and dynamics within syntrophic communities that play a key role in the global carbon cycle. Species-specific genomes were extracted from metagenomic data using differential coverage binning. We used metabolic modeling leveraging metatranscriptomic information to reveal and quantify a complex intertwined system of syntrophic relationships. Our results show that amino acid auxotrophies create additional interdependencies that define community composition and control carbon and energy flux through the system while simultaneously contributing to overall community robustness. Strategic use of antimicrobials further reinforces this intricate interspecies network. Collectively, our study reveals the multidimensional interactions in syntrophic communities that promote high species richness and bolster community stability during environmental perturbations.

Phenotypic responses to interspecies competition and commensalism in a naturally-derived microbial co-culture.

PubMed

Khan, Nymul; Maezato, Yukari; McClure, Ryan S; Brislawn, Colin J; Mobberley, Jennifer M; Isern, Nancy; Chrisler, William B; Markillie, Lye Meng; Barney, Brett M; Song, Hyun-Seob; Nelson, William C; Bernstein, Hans C

2018-01-10

The fundamental question of whether different microbial species will co-exist or compete in a given environment depends on context, composition and environmental constraints. Model microbial systems can yield some general principles related to this question. In this study we employed a naturally occurring co-culture composed of heterotrophic bacteria, Halomonas sp. HL-48 and Marinobacter sp. HL-58, to ask two fundamental scientific questions: 1) how do the phenotypes of two naturally co-existing species respond to partnership as compared to axenic growth? and 2) how do growth and molecular phenotypes of these species change with respect to competitive and commensal interactions? We hypothesized - and confirmed - that co-cultivation under glucose as the sole carbon source would result in competitive interactions. Similarly, when glucose was swapped with xylose, the interactions became commensal because Marinobacter HL-58 was supported by metabolites derived from Halomonas HL-48. Each species responded to partnership by changing both its growth and molecular phenotype as assayed via batch growth kinetics and global transcriptomics. These phenotypic responses depended on nutrient availability and so the environment ultimately controlled how they responded to each other. This simplified model community revealed that microbial interactions are context-specific and different environmental conditions dictate how interspecies partnerships will unfold.

Phenotypic responses to interspecies competition and commensalism in a naturally-derived microbial co-culture

DOE Office of Scientific and Technical Information (OSTI.GOV)

Khan, Nymul; Maezato, Yukari; McClure, Ryan S.

The fundamental question of whether different microbial species will co-exist or compete in a given environment depends on context, composition and environmental constraints. Model microbial systems can yield some general principles related to this question. In this study we employed a naturally occurring co-culture composed of heterotrophic bacteria, Halomonas sp. HL-48 and Marinobacter sp. HL-58, to ask two fundamental scientific questions: 1) how do the phenotypes of two naturally co-existing species respond to partnership as compared to axenic growth? and 2) how do growth and molecular phenotypes of these species change with respect to competitive and commensal interactions? We hypothesizedmore » – and confirmed – that co-cultivation under glucose as the sole carbon source would result in a competitive interactions. Similarly, when glucose was swapped with xylose, the interactions became commensal because Marinobacter HL-58 was supported by metabolites derived from Halomonas HL-48. Each species responded to partnership by changing both its growth and molecular phenotype as assayed via batch growth kinetics and global transcriptomics. These phenotypic responses depended nutrient availability and so the environment ultimately controlled how they responded to each other. This simplified model community revealed that microbial interactions are context-specific and different environmental conditions dictate how interspecies partnerships will unfold.« less

Eating For Two: How Metabolism Establishes Interspecies Interactions in the Gut

PubMed Central

Fischbach, Michael A.; Sonnenburg, Justin L.

2011-01-01

In bacterial communities, ‘tight economic times’ are the norm. Of the many challenges bacteria face in making a living, perhaps none are more important than generating energy, maintaining redox balance, and acquiring carbon and nitrogen to synthesize primary metabolites. The ability of bacteria to meet these challenges depends heavily on the rest of their community. Indeed, the most fundamental way in which bacteria communicate is by importing the substrates for metabolism and exporting metabolic end products. As an illustration of this principle, we will travel down a carbohydrate catabolic pathway common to many species of Bacteroides, highlighting the interspecies interactions established (often inevitably) at its key steps. We also discuss the metabolic considerations in maintaining the stability of host-associated microbial communities. PMID:22018234

The effects of arbuscular mycorrhizal fungi and root interaction on the competition between Trifolium repens and Lolium perenne.

PubMed

Ren, Haiyan; Gao, Tao; Hu, Jian; Yang, Gaowen

2017-01-01

Understanding the factors that alter competitive interactions and coexistence between plants is a key issue in ecological research. A pot experiment was conducted to test the effects of root interaction and arbuscular mycorrhizal fungi (AMF) inoculation on the interspecies competition between Trifolium repens and Lolium perenne under different proportions of mixed sowing by the combination treatment of two levels of AMF inoculation (inoculation and non-inoculation) and two levels of root interaction (root interaction and non-root interaction). Overall, the aboveground and belowground biomass of T. repens and L. perenne were not altered by AMF inoculation across planting ratios, probably because the fertile soil reduced the positive effect of AMF on plant growth. Both inter- and intraspecies root interaction significantly decreased the aboveground biomass of T. repens , but tended to increase the aboveground biomass of L. perenne across planting ratios, and thus peaked at the 4:4 polyculture. These results showed that T. repens competed poorly with L. perenne because of inter and intraspecies root interaction. Our results indicate that interspecies root interaction regulates the competitive ability of grass L. perenne and legume T. repens in mixtures and further makes great contribution for overyielding. Furthermore, AMF may not be involved in plant-plant interaction in fertile condition.

Selective distillation phenomenon in two-species Bose-Einstein condensates in open boundary optical lattices.

PubMed

Bai, Xiao-Dong; Zhang, Mei; Xiong, Jun; Yang, Guo-Jian; Deng, Fu-Guo

2015-11-24

We investigate the formation of discrete breathers (DBs) and the dynamics of the mixture of two-species Bose-Einstein condensates (BECs) in open boundary optical lattices using the discrete nonlinear Schrödinger equations. The results show that the coupling of intra- and interspecies interaction can lead to the existence of pure single-species DBs and symbiotic DBs (i.e., two-species DBs). Furthermore, we find that there is a selective distillation phenomenon in the dynamics of the mixture of two-species BECs. One can selectively distil one species from the mixture of two-species BECs and can even control dominant species fraction by adjusting the intra- and interspecies interaction in optical lattices. Our selective distillation mechanism may find potential application in quantum information storage and quantum information processing based on multi-species atoms.

Selective distillation phenomenon in two-species Bose-Einstein condensates in open boundary optical lattices

PubMed Central

Bai, Xiao-Dong; Zhang, Mei; Xiong, Jun; Yang, Guo-Jian; Deng, Fu-Guo

2015-01-01

We investigate the formation of discrete breathers (DBs) and the dynamics of the mixture of two-species Bose-Einstein condensates (BECs) in open boundary optical lattices using the discrete nonlinear Schrödinger equations. The results show that the coupling of intra- and interspecies interaction can lead to the existence of pure single-species DBs and symbiotic DBs (i.e., two-species DBs). Furthermore, we find that there is a selective distillation phenomenon in the dynamics of the mixture of two-species BECs. One can selectively distil one species from the mixture of two-species BECs and can even control dominant species fraction by adjusting the intra- and interspecies interaction in optical lattices. Our selective distillation mechanism may find potential application in quantum information storage and quantum information processing based on multi-species atoms. PMID:26597592

Phylo-VISTA: Interactive visualization of multiple DNA sequence alignments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shah, Nameeta; Couronne, Olivier; Pennacchio, Len A.

The power of multi-sequence comparison for biological discovery is well established. The need for new capabilities to visualize and compare cross-species alignment data is intensified by the growing number of genomic sequence datasets being generated for an ever-increasing number of organisms. To be efficient these visualization algorithms must support the ability to accommodate consistently a wide range of evolutionary distances in a comparison framework based upon phylogenetic relationships. Results: We have developed Phylo-VISTA, an interactive tool for analyzing multiple alignments by visualizing a similarity measure for multiple DNA sequences. The complexity of visual presentation is effectively organized using a frameworkmore » based upon interspecies phylogenetic relationships. The phylogenetic organization supports rapid, user-guided interspecies comparison. To aid in navigation through large sequence datasets, Phylo-VISTA leverages concepts from VISTA that provide a user with the ability to select and view data at varying resolutions. The combination of multiresolution data visualization and analysis, combined with the phylogenetic framework for interspecies comparison, produces a highly flexible and powerful tool for visual data analysis of multiple sequence alignments. Availability: Phylo-VISTA is available at http://www-gsd.lbl. gov/phylovista. It requires an Internet browser with Java Plugin 1.4.2 and it is integrated into the global alignment program LAGAN at http://lagan.stanford.edu« less

Multi-omics analysis provides insight to the Ignicoccus hospitalis - Nanoarchaeum equitans association

DOE PAGES

Rawle, Rachel A.; Hamerly, Timothy; Tripet, Brian P.; ...

2017-06-04

Studies of interspecies interactions are inherently difficult due to the complex mechanisms which enable these relationships. A model system for studying interspecies interactions is the marine hyperthermophiles Ignicoccus hospitalis and Nanoarchaeum equitans. Recent independently-conducted ‘omics’ analyses have generated insights into the molecular factors modulating this association. However, significant questions remain about the nature of the interactions between these archaea. We jointly analyzed multiple levels of omics datasets obtained from published, independent transcriptomics, proteomics, and metabolomics analyses. DAVID identified functionally-related groups enriched when I. hospitalis is grown alone or in co-culture with N. equitans. Enriched molecular pathways were subsequently visualized usingmore » interaction maps generated using STRING. Key findings of our multi-level omics analysis indicated that I. hospitalis provides precursors to N. equitans for energy metabolism. Analysis indicated an overall reduction in diversity of metabolic precursors in the I. hospitalis–N. equitans co-culture, which has been connected to the differential use of ribosomal subunits and was previously unnoticed. We also identified differences in precursors linked to amino acid metabolism, NADH metabolism, and carbon fixation, providing new insights into the metabolic adaptions of I. hospitalis enabling the growth of N. equitans. In conclusion, this multi-omics analysis builds upon previously identified cellular patterns while offering new insights into mechanisms that enable the I. hospitalis–N. equitans association. This study applies statistical and visualization techniques to a mixed-source omics dataset to yield a more global insight into a complex system, that was not readily discernable from separate omics studies.« less

Multi-omics analysis provides insight to the Ignicoccus hospitalis-Nanoarchaeum equitans association.

PubMed

Rawle, Rachel A; Hamerly, Timothy; Tripet, Brian P; Giannone, Richard J; Wurch, Louie; Hettich, Robert L; Podar, Mircea; Copié, Valerie; Bothner, Brian

2017-09-01

Studies of interspecies interactions are inherently difficult due to the complex mechanisms which enable these relationships. A model system for studying interspecies interactions is the marine hyperthermophiles Ignicoccus hospitalis and Nanoarchaeum equitans. Recent independently-conducted 'omics' analyses have generated insights into the molecular factors modulating this association. However, significant questions remain about the nature of the interactions between these archaea. We jointly analyzed multiple levels of omics datasets obtained from published, independent transcriptomics, proteomics, and metabolomics analyses. DAVID identified functionally-related groups enriched when I. hospitalis is grown alone or in co-culture with N. equitans. Enriched molecular pathways were subsequently visualized using interaction maps generated using STRING. Key findings of our multi-level omics analysis indicated that I. hospitalis provides precursors to N. equitans for energy metabolism. Analysis indicated an overall reduction in diversity of metabolic precursors in the I. hospitalis-N. equitans co-culture, which has been connected to the differential use of ribosomal subunits and was previously unnoticed. We also identified differences in precursors linked to amino acid metabolism, NADH metabolism, and carbon fixation, providing new insights into the metabolic adaptions of I. hospitalis enabling the growth of N. equitans. This multi-omics analysis builds upon previously identified cellular patterns while offering new insights into mechanisms that enable the I. hospitalis-N. equitans association. Our study applies statistical and visualization techniques to a mixed-source omics dataset to yield a more global insight into a complex system, that was not readily discernable from separate omics studies. Copyright © 2017 Elsevier B.V. All rights reserved.

Stringent homology-based prediction of H. sapiens-M. tuberculosis H37Rv protein-protein interactions

PubMed Central

2014-01-01

Background H. sapiens-M. tuberculosis H37Rv protein-protein interaction (PPI) data are essential for understanding the infection mechanism of the formidable pathogen M. tuberculosis H37Rv. Computational prediction is an important strategy to fill the gap in experimental H. sapiens-M. tuberculosis H37Rv PPI data. Homology-based prediction is frequently used in predicting both intra-species and inter-species PPIs. However, some limitations are not properly resolved in several published works that predict eukaryote-prokaryote inter-species PPIs using intra-species template PPIs. Results We develop a stringent homology-based prediction approach by taking into account (i) differences between eukaryotic and prokaryotic proteins and (ii) differences between inter-species and intra-species PPI interfaces. We compare our stringent homology-based approach to a conventional homology-based approach for predicting host-pathogen PPIs, based on cellular compartment distribution analysis, disease gene list enrichment analysis, pathway enrichment analysis and functional category enrichment analysis. These analyses support the validity of our prediction result, and clearly show that our approach has better performance in predicting H. sapiens-M. tuberculosis H37Rv PPIs. Using our stringent homology-based approach, we have predicted a set of highly plausible H. sapiens-M. tuberculosis H37Rv PPIs which might be useful for many of related studies. Based on our analysis of the H. sapiens-M. tuberculosis H37Rv PPI network predicted by our stringent homology-based approach, we have discovered several interesting properties which are reported here for the first time. We find that both host proteins and pathogen proteins involved in the host-pathogen PPIs tend to be hubs in their own intra-species PPI network. Also, both host and pathogen proteins involved in host-pathogen PPIs tend to have longer primary sequence, tend to have more domains, tend to be more hydrophilic, etc. And the protein domains from both host and pathogen proteins involved in host-pathogen PPIs tend to have lower charge, and tend to be more hydrophilic. Conclusions Our stringent homology-based prediction approach provides a better strategy in predicting PPIs between eukaryotic hosts and prokaryotic pathogens than a conventional homology-based approach. The properties we have observed from the predicted H. sapiens-M. tuberculosis H37Rv PPI network are useful for understanding inter-species host-pathogen PPI networks and provide novel insights for host-pathogen interaction studies. Reviewers This article was reviewed by Michael Gromiha, Narayanaswamy Srinivasan and Thomas Dandekar. PMID:24708540

In Search of the E. coli Compounds that Change the Antibiotic Production Pattern of Streptomyces coelicolor During Inter-species Interaction.

PubMed

Mavituna, Ferda; Luti, Khalid Jaber Kadhum; Gu, Lixing

2016-08-01

The aim of this work was to investigate the interaction between E.coli and Streptomyces coelicolor A3 (2) for the increased production of undecylprodigiosin and identify the E. coli actives mediating this inter-species interaction. The antibiotics of interest were the red-pigmented undecylprodigiosin and blue-pigmented actinorhodin. Pure cultures of S. coelicolor in a defined medium produced higher concentrations of actinorhodin compared to those of undecylprodigiosin. The latter however, is more important due to its immunosuppressive and antitumor properties. As a strategy to increase undecylprodigiosin production, we added separately, live cells and heat-killed cells of E. coli C600, and the cell-free supernatant of E. coli culture to S. coelicolor cultures in shake flasks. The interaction with live cells of E. coli altered the antibiotic production pattern and undecylprodigiosin production was enhanced by 3.5-fold compared to the pure cultures of S. coelicolor and actinorhodin decreased by 15-fold. The heat-killed cells of E. coli however, had no effect on antibiotic production. In all cases, growth and glucose consumption of S. coelicolor remained almost the same as those observed in the pure culture indicating that the changes in antibiotic production were not due to nutritional stress. Results with cell-free supernatant of E. coli culture indicated that the interaction between S. coelicolor and E. coli was mediated via diffusible molecule(s). Using a set of extraction procedures and agar-well diffusion bioassays, we isolated and preliminarily identified a class of compounds. For the preliminary verification, we added the compound which was the common chemical structural moiety in this class of compounds to the pure S. coelicolor cultures. We observed similar effects on antibiotic production as with the live E. coli cells and their supernatant indicating that this class of compounds secreted by E. coli indeed could act as actives during interspecies interaction and increase the production of undecylprodigiosin. Copyright © 2016 Elsevier Inc. All rights reserved.

Draft Genome Sequence of Pedobacter sp. Strain V48, Isolated from a Coastal Sand Dune in the Netherlands

PubMed Central

Bitzer, Adam S.; Garbeva, Paolina

2014-01-01

Pedobacter sp. strain V48 participates in an interaction with Pseudomonas fluorescens which elicits interaction-induced phenotypes. We report the draft genome sequence of Pedobacter sp. V48, consisting of 6.46 Mbp. The sequence will contribute to improved understanding of the genus and facilitate genomic analysis of the model interspecies interaction with P. fluorescens. PMID:24578271

Streptococcus mutans SpaP binds to RadD of Fusobacterium nucleatum ssp. polymorphum.

PubMed

Guo, Lihong; Shokeen, Bhumika; He, Xuesong; Shi, Wenyuan; Lux, Renate

2017-10-01

Adhesin-mediated bacterial interspecies interactions are important elements in oral biofilm formation. They often occur on a species-specific level, which could determine health or disease association of a biofilm community. Among the key players involved in these processes are the ubiquitous fusobacteria that have been recognized for their ability to interact with numerous different binding partners. Fusobacterial interactions with Streptococcus mutans, an important oral cariogenic pathogen, have previously been described but most studies focused on binding to non-mutans streptococci and specific cognate adhesin pairs remain to be identified. Here, we demonstrated differential binding of oral fusobacteria to S. mutans. Screening of existing mutant derivatives indicated SpaP as the major S. mutans adhesin specific for binding to Fusobacterium nucleatum ssp. polymorphum but none of the other oral fusobacteria tested. We inactivated RadD, a known adhesin of F. nucleatum ssp. nucleatum for interaction with a number of gram-positive species, in F. nucleatum ssp. polymorphum and used a Lactococcus lactis heterologous SpaP expression system to demonstrate SpaP interaction with RadD of F. nucleatum ssp. polymorphum. This is a novel function for SpaP, which has mainly been characterized as an adhesin for binding to host proteins including salivary glycoproteins. In conclusion, we describe an additional role for SpaP as adhesin in interspecies adherence with RadD-SpaP as the interacting adhesin pair for binding between S. mutans and F. nucleatum ssp. polymorphum. Furthermore, S. mutans attachment to oral fusobacteria appears to involve species- and subspecies-dependent adhesin interactions. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Interplay between the gut microbiota and immune responses of ayu (Plecoglossus altivelis) during Vibrio anguillarum infection.

PubMed

Nie, Li; Zhou, Qian-Jin; Qiao, Yan; Chen, Jiong

2017-09-01

Gut microbiota plays fundamental roles in protection against pathogen invasion. However, the mechanism and extent of responses of gut microbiota to pathogenic infection are poorly understood. This study investigated the gut bacterial communities and immune responses of ayu (Plecoglossus altivelis) upon exposure to Vibrio anguillarum. The succession of V. anguillarum infection was evidenced by increased expression of immune genes and bacterial loads in ayu tissues, which in turn altered the composition and predicted functions of gut bacterial community. The dynamics of gut bacterial diversity and evenness were temporally stable in control ayu but were reduced in infected subjects, particularly at the late stages of infection. Variations in the gut microbiota were significantly associated with the expression levels of TNF-α (P = 0.019) and IL-1 β (P = 0.013). The profiles of certain gut bacterial taxa were indicative of V. anguillarum infection. Compared with healthy controls, the ayu infected with V. anguillarum possessed less complex, fewer connected, and lower cooperative gut bacterial interspecies interaction, coinciding with significant shifts in keystone species. These findings imply that V. anguillarum infection substantially disrupted the compositions and interspecies interaction of ayu gut bacterial community, thereby altering gut microbial-mediated functions and inducing host immune responses. This study provides an integrated overview on the interaction between the gut microbiota and host immune responses to pathogen infection from an ecological perspective. Copyright © 2017 Elsevier Ltd. All rights reserved.

Biofilm development and enhanced stress resistance of a model, mixed-species community biofilm.

PubMed

Lee, Kai Wei Kelvin; Periasamy, Saravanan; Mukherjee, Manisha; Xie, Chao; Kjelleberg, Staffan; Rice, Scott A

2014-04-01

Most studies of biofilm biology have taken a reductionist approach, where single-species biofilms have been extensively investigated. However, biofilms in nature mostly comprise multiple species, where interspecies interactions can shape the development, structure and function of these communities differently from biofilm populations. Hence, a reproducible mixed-species biofilm comprising Pseudomonas aeruginosa, Pseudomonas protegens and Klebsiella pneumoniae was adapted to study how interspecies interactions affect biofilm development, structure and stress responses. Each species was fluorescently tagged to determine its abundance and spatial localization within the biofilm. The mixed-species biofilm exhibited distinct structures that were not observed in comparable single-species biofilms. In addition, development of the mixed-species biofilm was delayed 1-2 days compared with the single-species biofilms. Composition and spatial organization of the mixed-species biofilm also changed along the flow cell channel, where nutrient conditions and growth rate of each species could have a part in community assembly. Intriguingly, the mixed-species biofilm was more resistant to the antimicrobials sodium dodecyl sulfate and tobramycin than the single-species biofilms. Crucially, such community level resilience was found to be a protection offered by the resistant species to the whole community rather than selection for the resistant species. In contrast, community-level resilience was not observed for mixed-species planktonic cultures. These findings suggest that community-level interactions, such as sharing of public goods, are unique to the structured biofilm community, where the members are closely associated with each other.

Interspecies Interactions Reverse the Hazard of Antibiotics Exposure: A Plankton Community Study on Responses to Ciprofloxacin hydrochloride.

PubMed

Wang, Changyou; Wang, Ziyang; Zhang, Yong; Su, Rongguo

2017-05-24

The ecotoxicological effects of Ciprofloxacin hydrochloride (CIP) were tested on population densities of plankton assemblages consisting of two algae (Isochrysis galbana and Platymonas subcordiformis) and a rotifer (Brachionus plicatilis). The I. galbana showed a significant decrease in densities when concentrations of CIP were above 2.0 mg L -1 in single-species tests, while P. subcordiformis and B. plicatilis were stable in densities when CIP were less than10.0 mg L -1 . The equilibrium densities of I. galbana in community test increased with CIP concentrations after falling to a trough at 5.0 mg L -1 , showed a completely different pattern of P. subcordiformis which decreased with CIP concentrations after reaching a peak at 30.0 mg L -1 . The observed beneficial effect was a result of interspecies interactions of trophic cascade that buffered for more severe direct effects of toxicants. The community test-based NOEC of CIP (2.0 mg L -1 ), embodying the indirect effects, was different from the extrapolated one derived by single-species tests (0.5 mg L -1 ), but all lacked confidence interval. A CIP threshold concentration of obvious relevance to ecological interaction was calculated with a simplified plankton ecological model, achieving a value of 1.26 mg L -1 with a 95% bootstrapping confidence interval from 1.18 to 1.31 mg L -1 .

Propionibacterium-Produced Coproporphyrin III Induces Staphylococcus aureus Aggregation and Biofilm Formation

PubMed Central

Wollenberg, Michael S.; Claesen, Jan; Escapa, Isabel F.; Aldridge, Kelly L.; Fischbach, Michael A.

2014-01-01

ABSTRACT The majority of bacteria detected in the nostril microbiota of most healthy adults belong to three genera: Propionibacterium, Corynebacterium, and Staphylococcus. Among these staphylococci is the medically important bacterium Staphylococcus aureus. Almost nothing is known about interspecies interactions among bacteria in the nostrils. We observed that crude extracts of cell-free conditioned medium from Propionibacterium spp. induce S. aureus aggregation in culture. Bioassay-guided fractionation implicated coproporphyrin III (CIII), the most abundant extracellular porphyrin produced by human-associated Propionibacterium spp., as a cause of S. aureus aggregation. This aggregation response depended on the CIII dose and occurred during early stationary-phase growth, and a low pH (~4 to 6) was necessary but was not sufficient for its induction. Additionally, CIII induced plasma-independent S. aureus biofilm development on an abiotic surface in multiple S. aureus strains. In strain UAMS-1, CIII stimulation of biofilm depended on sarA, a key biofilm regulator. This study is one of the first demonstrations of a small-molecule-mediated interaction among medically relevant members of the nostril microbiota and the first description of a role for CIII in bacterial interspecies interactions. Our results indicate that CIII may be an important mediator of S. aureus aggregation and/or biofilm formation in the nostril or other sites inhabited by Propionibacterium spp. and S. aureus. PMID:25053784

Intra- and inter-species interactions within biofilms of important foodborne bacterial pathogens

PubMed Central

Giaouris, Efstathios; Heir, Even; Desvaux, Mickaël; Hébraud, Michel; Møretrø, Trond; Langsrud, Solveig; Doulgeraki, Agapi; Nychas, George-John; Kačániová, Miroslava; Czaczyk, Katarzyna; Ölmez, Hülya; Simões, Manuel

2015-01-01

A community-based sessile life style is the normal mode of growth and survival for many bacterial species. Under such conditions, cell-to-cell interactions are inevitable and ultimately lead to the establishment of dense, complex and highly structured biofilm populations encapsulated in a self-produced extracellular matrix and capable of coordinated and collective behavior. Remarkably, in food processing environments, a variety of different bacteria may attach to surfaces, survive, grow, and form biofilms. Salmonella enterica, Listeria monocytogenes, Escherichia coli, and Staphylococcus aureus are important bacterial pathogens commonly implicated in outbreaks of foodborne diseases, while all are known to be able to create biofilms on both abiotic and biotic surfaces. Particularly challenging is the attempt to understand the complexity of inter-bacterial interactions that can be encountered in such unwanted consortia, such as competitive and cooperative ones, together with their impact on the final outcome of these communities (e.g., maturation, physiology, antimicrobial resistance, virulence, dispersal). In this review, up-to-date data on both the intra- and inter-species interactions encountered in biofilms of these pathogens are presented. A better understanding of these interactions, both at molecular and biophysical levels, could lead to novel intervention strategies for controlling pathogenic biofilm formation in food processing environments and thus improve food safety. PMID:26347727

Symbiosis-inspired approaches to antibiotic discovery.

PubMed

Adnani, Navid; Rajski, Scott R; Bugni, Tim S

2017-07-06

Covering: 2010 up to 2017Life on Earth is characterized by a remarkable abundance of symbiotic and highly refined relationships among life forms. Defined as any kind of close, long-term association between two organisms, symbioses can be mutualistic, commensalistic or parasitic. Historically speaking, selective pressures have shaped symbioses in which one organism (typically a bacterium or fungus) generates bioactive small molecules that impact the host (and possibly other symbionts); the symbiosis is driven fundamentally by the genetic machineries available to the small molecule producer. The human microbiome is now integral to the most recent chapter in animal-microbe symbiosis studies and plant-microbe symbioses have significantly advanced our understanding of natural products biosynthesis; this also is the case for studies of fungal-microbe symbioses. However, much less is known about microbe-microbe systems involving interspecies interactions. Microbe-derived small molecules (i.e. antibiotics and quorum sensing molecules, etc.) have been shown to regulate transcription in microbes within the same environmental niche, suggesting interspecies interactions whereas, intraspecies interactions, such as those that exploit autoinducing small molecules, also modulate gene expression based on environmental cues. We, and others, contend that symbioses provide almost unlimited opportunities for the discovery of new bioactive compounds whose activities and applications have been evolutionarily optimized. Particularly intriguing is the possibility that environmental effectors can guide laboratory expression of secondary metabolites from "orphan", or silent, biosynthetic gene clusters (BGCs). Notably, many of the studies summarized here result from advances in "omics" technologies and highlight how symbioses have given rise to new anti-bacterial and antifungal natural products now being discovered.

Maintenance of genetic diversity through plant-herbivore interactions

PubMed Central

Gloss, Andrew D.; Dittrich, Anna C. Nelson; Goldman-Huertas, Benjamin; Whiteman, Noah K.

2013-01-01

Identifying the factors governing the maintenance of genetic variation is a central challenge in evolutionary biology. New genomic data, methods and conceptual advances provide increasing evidence that balancing selection, mediated by antagonistic species interactions, maintains functionally-important genetic variation within species and natural populations. Because diverse interactions between plants and herbivorous insects dominate terrestrial communities, they provide excellent systems to address this hypothesis. Population genomic studies of Arabidopsis thaliana and its relatives suggest spatial variation in herbivory maintains adaptive genetic variation controlling defense phenotypes, both within and among populations. Conversely, inter-species variation in plant defenses promotes adaptive genetic variation in herbivores. Emerging genomic model herbivores of Arabidopsis could illuminate how genetic variation in herbivores and plants interact simultaneously. PMID:23834766

Development of Interspecies Correlation Models for Petroleum Hydrocarbons

EPA Science Inventory

Estimating the consequences of petroleum products to water column organisms has commonly been hampered by limited acute toxicity data, which exists only for a relatively small number of test species. In this study, we developed petroleum-specific Interspecies Correlation Estimati...

Convergent targeting of a common host protein-network by pathogen effectors from three kingdoms of life

PubMed Central

Weßling, Ralf; Epple, Petra; Altmann, Stefan; He, Yijian; Yang, Li; Henz, Stefan R.; McDonald, Nathan; Wiley, Kristin; Bader, Kai Christian; Gläßer, Christine; Mukhtar, M. Shahid; Haigis, Sabine; Ghamsari, Lila; Stephens, Amber E.; Ecker, Joseph R.; Vidal, Marc; Jones, Jonathan D. G.; Mayer, Klaus F. X.; van Themaat, Emiel Ver Loren; Weigel, Detlef; Schulze-Lefert, Paul; Dangl, Jeffery L.; Panstruga, Ralph; Braun, Pascal

2014-01-01

SUMMARY While conceptual principles governing plant immunity are becoming clear, its systems-level organization and the evolutionary dynamic of the host-pathogen interface are still obscure. We generated a systematic protein-protein interaction network of virulence effectors from the ascomycete pathogen Golovinomyces orontii and Arabidopsis thaliana host proteins. We combined this dataset with corresponding data for the eubacterial pathogen Pseudomonas syringae and the oomycete pathogen Hyaloperonospora arabidopsidis. The resulting network identifies host proteins onto which intraspecies and interspecies pathogen effectors converge. Phenotyping of 124 Arabidopsis effector-interactor mutants revealed a correlation between intra- and interspecies convergence and several altered immune response phenotypes. The effectors and most heavily targeted host protein co-localized in sub-nuclear foci. Products of adaptively selected Arabidopsis genes are enriched for interactions with effector targets. Our data suggest the existence of a molecular host-pathogen interface that is conserved across Arabidopsis accessions, while evolutionary adaptation occurs in the immediate network neighborhood of effector targets. PMID:25211078

Superfluid Boson-Fermion Mixture: Structure Formation and Collective Periodic Motion

NASA Astrophysics Data System (ADS)

Mitra, A.

2018-01-01

Multiple periodic domain formation due to a modulation instability in a boson-fermion mixture superfluid in the unitary regime has been studied. The periodicity of the structure evolves with time. At the early stage of evolution, bosonic domains show the periodic nature, whereas the periodicity in the fermionic (Cooper pair) domains appears at the late stage of evolution. The nature of interatomic interspecies interactions affects the domain formation. In a harmonic trap, the mixture executes an undamped oscillation. The frequency of the oscillation depends on the relative coupling strength between boson-fermion and fermion-fermion. The repulsive boson-fermion interaction reduces the oscillation frequency, whereas the attractive interaction enhances the frequency significantly.

Function of the Pyruvate Oxidase-Lactate Oxidase Cascade in Interspecies Competition between Streptococcus oligofermentans and Streptococcus mutans

PubMed Central

Liu, Lei

2012-01-01

Complex interspecies interactions occur constantly between oral commensals and the opportunistic pathogen Streptococcus mutans in dental plaque. Previously, we showed that oral commensal Streptococcus oligofermentans possesses multiple enzymes for H2O2 production, especially lactate oxidase (Lox), allowing it to out-compete S. mutans. In this study, through extensive biochemical and genetic studies, we identified a pyruvate oxidase (pox) gene in S. oligofermentans. A pox deletion mutant completely lost Pox activity, while ectopically expressed pox restored activity. Pox was determined to produce most of the H2O2 in the earlier growth phase and log phase, while Lox mainly contributed to H2O2 production in stationary phase. Both pox and lox were expressed throughout the growth phase, while expression of the lox gene increased by about 2.5-fold when cells entered stationary phase. Since lactate accumulation occurred to a large degree in stationary phase, the differential Pox- and Lox-generated H2O2 can be attributed to differential gene expression and substrate availability. Interestingly, inactivation of pox causes a dramatic reduction in H2O2 production from lactate, suggesting a synergistic action of the two oxidases in converting lactate into H2O2. In an in vitro two-species biofilm experiment, the pox mutant of S. oligofermentans failed to inhibit S. mutans even though lox was active. In summary, S. oligofermentans develops a Pox-Lox synergy strategy to maximize its H2O2 formation so as to win the interspecies competition. PMID:22287002

Signaling in host-associated microbial communities

PubMed Central

Fischbach, Michael A.; Segre, Julia A.

2016-01-01

Human-associated microbiota form and stabilize communities based on interspecies interactions. We review how these microbe-microbe and microbe-host interactions are communicated to shape communities over a human’s lifespan, including periods of health and disease. Modeling and dissecting signaling in host-associated communities is crucial to understand their function, and will open the door to therapies that prevent or correct microbial community dysfunction to promote health and treat disease. PMID:26967294

Metabolic Network Modeling for Computer-Aided Design of Microbial Interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Song, Hyun-Seob; Nelson, William C.; Lee, Joon-Yong

Interest in applying microbial communities to biotechnology continues to increase. Successful engineering of microbial communities requires a fundamental shift in focus from enhancing metabolic capabilities in individual organisms to promoting synergistic interspecies interactions. This goal necessitates in silico tools that provide a predictive understanding of how microorganisms interact with each other and their environments. In this regard, we highlight a need for a new concept that we have termed biological computer-aided design of interactions (BioCADi). We ground this discussion within the context of metabolic network modeling.

Alanine racemase is essential for the growth and interspecies competitiveness of Streptococcus mutans.

PubMed

Wei, Yuan; Qiu, Wei; Zhou, Xue-Dong; Zheng, Xin; Zhang, Ke-Ke; Wang, Shi-Da; Li, Yu-Qing; Cheng, Lei; Li, Ji-Yao; Xu, Xin; Li, Ming-Yun

2016-12-16

D-alanine (D-Ala) is an essential amino acid that has a key role in bacterial cell wall synthesis. Alanine racemase (Alr) is a unique enzyme that interconverts L-alanine and D-alanine in most bacteria, making this enzyme a potential target for antimicrobial drug development. Streptococcus mutans is a major causative factor of dental caries. The factors involved in the survival, virulence and interspecies interactions of S. mutans could be exploited as potential targets for caries control. The current study aimed to investigate the physiological role of Alr in S. mutans. We constructed alr mutant strain of S. mutans and evaluated its phenotypic traits and interspecies competitiveness compared with the wild-type strain. We found that alr deletion was lethal to S. mutans. A minimal supplement of D-Ala (150 μg·mL -1 ) was required for the optimal growth of the alr mutant. The depletion of D-alanine in the growth medium resulted in cell wall perforation and cell lysis in the alr mutant strain. We also determined the compromised competitiveness of the alr mutant strain relative to the wild-type S. mutans against other oral streptococci (S. sanguinis or S. gordonii), demonstrated using either conditioned medium assays or dual-species fluorescent in situ hybridization analysis. Given the importance and necessity of alr to the growth and competitiveness of S. mutans, Alr may represent a promising target to modulate the cariogenicity of oral biofilms and to benefit the management of dental caries.

A Network Approach of Gene Co-expression in the Zea mays/Aspergillus flavus Pathosystem to Map Host/Pathogen Interaction Pathways.

PubMed

Musungu, Bryan M; Bhatnagar, Deepak; Brown, Robert L; Payne, Gary A; OBrian, Greg; Fakhoury, Ahmad M; Geisler, Matt

2016-01-01

A gene co-expression network (GEN) was generated using a dual RNA-seq study with the fungal pathogen Aspergillus flavus and its plant host Zea mays during the initial 3 days of infection. The analysis deciphered novel pathways and mapped genes of interest in both organisms during the infection. This network revealed a high degree of connectivity in many of the previously recognized pathways in Z. mays such as jasmonic acid, ethylene, and reactive oxygen species (ROS). For the pathogen A. flavus , a link between aflatoxin production and vesicular transport was identified within the network. There was significant interspecies correlation of expression between Z. mays and A. flavus for a subset of 104 Z. mays , and 1942 A. flavus genes. This resulted in an interspecies subnetwork enriched in multiple Z. mays genes involved in the production of ROS. In addition to the ROS from Z. mays , there was enrichment in the vesicular transport pathways and the aflatoxin pathway for A. flavus . Included in these genes, a key aflatoxin cluster regulator, AflS, was found to be co-regulated with multiple Z. mays ROS producing genes within the network, suggesting AflS may be monitoring host ROS levels. The entire GEN for both host and pathogen, and the subset of interspecies correlations, is presented as a tool for hypothesis generation and discovery for events in the early stages of fungal infection of Z. mays by A. flavus .

A Network Approach of Gene Co-expression in the Zea mays/Aspergillus flavus Pathosystem to Map Host/Pathogen Interaction Pathways

PubMed Central

Musungu, Bryan M.; Bhatnagar, Deepak; Brown, Robert L.; Payne, Gary A.; OBrian, Greg; Fakhoury, Ahmad M.; Geisler, Matt

2016-01-01

A gene co-expression network (GEN) was generated using a dual RNA-seq study with the fungal pathogen Aspergillus flavus and its plant host Zea mays during the initial 3 days of infection. The analysis deciphered novel pathways and mapped genes of interest in both organisms during the infection. This network revealed a high degree of connectivity in many of the previously recognized pathways in Z. mays such as jasmonic acid, ethylene, and reactive oxygen species (ROS). For the pathogen A. flavus, a link between aflatoxin production and vesicular transport was identified within the network. There was significant interspecies correlation of expression between Z. mays and A. flavus for a subset of 104 Z. mays, and 1942 A. flavus genes. This resulted in an interspecies subnetwork enriched in multiple Z. mays genes involved in the production of ROS. In addition to the ROS from Z. mays, there was enrichment in the vesicular transport pathways and the aflatoxin pathway for A. flavus. Included in these genes, a key aflatoxin cluster regulator, AflS, was found to be co-regulated with multiple Z. mays ROS producing genes within the network, suggesting AflS may be monitoring host ROS levels. The entire GEN for both host and pathogen, and the subset of interspecies correlations, is presented as a tool for hypothesis generation and discovery for events in the early stages of fungal infection of Z. mays by A. flavus. PMID:27917194

INTERSPECIES EXTRAPOLATION AND IN VITRO SCREENING BASED UPON RECOMBINANT AR AND ER PROTEINS

EPA Science Inventory

While EDCs have the potential to act via several mechanisms of action, one of the most widely accepted is the ability of environmental chemicals to interact directly with either the estrogen (ER) or androgen receptor (AR). Although we know that the steroid receptors of the lower...

Pirated Siderophores Promote Sporulation in Bacillus subtilis.

PubMed

Grandchamp, Gabrielle M; Caro, Lews; Shank, Elizabeth A

2017-05-15

In microbial communities, bacteria chemically and physically interact with one another. Some of these interactions are mediated by secreted specialized metabolites that act as either intraspecies or interspecies signals to alter gene expression and to change cell physiology. Bacillus subtilis is a well-characterized soil microbe that can differentiate into multiple cell types, including metabolically dormant endospores. We were interested in identifying microbial interactions that affected sporulation in B. subtilis Using a fluorescent transcriptional reporter, we observed that coculturing B. subtilis with Escherichia coli promoted sporulation gene expression via a secreted metabolite. To identify the active compound, we screened the E. coli Keio Collection and identified the sporulation-accelerating cue as the siderophore enterobactin. B. subtilis has multiple iron acquisition systems that are used to take up the B. subtilis- produced siderophore bacillibactin, as well as to pirate exogenous siderophores such as enterobactin. While B. subtilis uses a single substrate binding protein (FeuA) to take up both bacillibactin and enterobactin, we discovered that it requires two distinct genes to sporulate in response to these siderophores (the esterase gene besA for bacillibactin and a putative esterase gene, ybbA , for enterobactin). In addition, we found that siderophores from a variety of other microbial species also promote sporulation in B. subtilis Our results thus demonstrate that siderophores can act not only as bacterial iron acquisition systems but also as interspecies cues that alter cellular development and accelerate sporulation in B. subtilis IMPORTANCE While much is known about the genetic regulation of Bacillus subtilis sporulation, little is understood about how other bacteria influence this process. This work describes an interaction between Escherichia coli and B. subtilis that accelerates sporulation in B. subtilis The interaction is mediated by the E. coli siderophore enterobactin; we show that other species' siderophores also promote sporulation gene expression in B. subtilis These results suggest that siderophores not only may supply bacteria with the mineral nutrient iron but also may play a role in bacterial interspecies signaling, providing a cue for sporulation. Siderophores are produced by many bacterial species and thus potentially play important roles in altering bacterial cell physiology in diverse environments. Copyright © 2017 Grandchamp et al.

Pirated Siderophores Promote Sporulation in Bacillus subtilis

PubMed Central

Grandchamp, Gabrielle M.; Caro, Lews

2017-01-01

ABSTRACT In microbial communities, bacteria chemically and physically interact with one another. Some of these interactions are mediated by secreted specialized metabolites that act as either intraspecies or interspecies signals to alter gene expression and to change cell physiology. Bacillus subtilis is a well-characterized soil microbe that can differentiate into multiple cell types, including metabolically dormant endospores. We were interested in identifying microbial interactions that affected sporulation in B. subtilis. Using a fluorescent transcriptional reporter, we observed that coculturing B. subtilis with Escherichia coli promoted sporulation gene expression via a secreted metabolite. To identify the active compound, we screened the E. coli Keio Collection and identified the sporulation-accelerating cue as the siderophore enterobactin. B. subtilis has multiple iron acquisition systems that are used to take up the B. subtilis-produced siderophore bacillibactin, as well as to pirate exogenous siderophores such as enterobactin. While B. subtilis uses a single substrate binding protein (FeuA) to take up both bacillibactin and enterobactin, we discovered that it requires two distinct genes to sporulate in response to these siderophores (the esterase gene besA for bacillibactin and a putative esterase gene, ybbA, for enterobactin). In addition, we found that siderophores from a variety of other microbial species also promote sporulation in B. subtilis. Our results thus demonstrate that siderophores can act not only as bacterial iron acquisition systems but also as interspecies cues that alter cellular development and accelerate sporulation in B. subtilis. IMPORTANCE While much is known about the genetic regulation of Bacillus subtilis sporulation, little is understood about how other bacteria influence this process. This work describes an interaction between Escherichia coli and B. subtilis that accelerates sporulation in B. subtilis. The interaction is mediated by the E. coli siderophore enterobactin; we show that other species' siderophores also promote sporulation gene expression in B. subtilis. These results suggest that siderophores not only may supply bacteria with the mineral nutrient iron but also may play a role in bacterial interspecies signaling, providing a cue for sporulation. Siderophores are produced by many bacterial species and thus potentially play important roles in altering bacterial cell physiology in diverse environments. PMID:28283524

Nicotine Enhances Interspecies Relationship between Streptococcus mutans and Candida albicans.

PubMed

Liu, Shiyu; Qiu, Wei; Zhang, Keke; Zhou, Xuedong; Ren, Biao; He, Jinzhi; Xu, Xin; Cheng, Lei; Li, Mingyun

2017-01-01

Streptococcus mutans and Candida albicans are common microorganisms in the human oral cavity. The synergistic relationship between these two species has been deeply explored in many studies. In the present study, the effect of alkaloid nicotine on the interspecies between S. mutans and C. albicans is explored. We developed a dual-species biofilm model and studied biofilm biomass, biofilm structure, synthesis of extracellular polysaccharides (EPS), and expression of glucosyltransferases (Gtfs). Biofilm formation and bacterial and fungal cell numbers in dual-species biofilms increased in the presence of nicotine. More C. albicans cells were present in the dual-species biofilms in the nicotine-treated groups as determined by scanning electron microscopy. The synthesis of EPS was increased by 1 mg/ml of nicotine as detected by confocal laser scanning microscopy. The result of qRT-PCR showed gtfs expression was upregulated when 1 mg/ml of nicotine was used. We speculate that nicotine promoted the growth of S. mutans , and more S. mutans cells attracted more C. albicans cells due to the interaction between two species. Since S. mutans and C. albicans are putative pathogens for dental caries, the enhancement of the synergistic relationship by nicotine may contribute to caries development in smokers.

Aqueous and Tissue Residue-Based Interspecies Correlation Estimation Models Provide Conservative Hazard Estimates for Aromatic Compounds

EPA Science Inventory

Interspecies correlation estimation (ICE) models were developed for 30 nonpolar aromatic compounds to allow comparison of prediction accuracy between 2 data compilation approaches. Type 1 models used data combined across studies, and type 2 models used data combined only within s...

Simple waves in a two-component Bose-Einstein condensate

NASA Astrophysics Data System (ADS)

Ivanov, S. K.; Kamchatnov, A. M.

2018-04-01

We study the dynamics of so-called simple waves in a two-component Bose-Einstein condensate. The evolution of the condensate is described by Gross-Pitaevskii equations which can be reduced for these simple wave solutions to a system of ordinary differential equations which coincide with those derived by Ovsyannikov for the two-layer fluid dynamics. We solve the Ovsyannikov system for two typical situations of large and small difference between interspecies and intraspecies nonlinear interaction constants. Our analytic results are confirmed by numerical simulations.

Interspecies Interactions and Potential Influenza A Virus Risk in Small Swine Farms in Peru

DTIC Science & Technology

2012-03-15

or ducks was observed in 36% of all farms. Human-avian interactions were less frequent overall. Use of adequate biosecurity and hygiene practices by...Wild, aquatic birds—especially ducks and geese—are widely recognized to be reservoirs of IAVs [1]. Numerous avian influenza strains have been...combination of avian and human influenza strains [22,23]. Increased human consumption of meat , more efficient animal husbandry practices and the

Metabolic Characterization of the Common Marmoset (Callithrix jacchus)

PubMed Central

Go, Young-Mi; Liang, Yongliang; Uppal, Karan; Soltow, Quinlyn A.; Promislow, Daniel E. L.; Wachtman, Lynn M.; Jones, Dean P.

2015-01-01

High-resolution metabolomics has created opportunity to integrate nutrition and metabolism into genetic studies to improve understanding of the diverse radiation of primate species. At present, however, there is very little information to help guide experimental design for study of wild populations. In a previous non-targeted metabolomics study of common marmosets (Callithrix jacchus), Rhesus macaques, humans, and four non-primate mammalian species, we found that essential amino acids (AA) and other central metabolites had interspecies variation similar to intraspecies variation while non-essential AA, environmental chemicals and catabolic waste products had greater interspecies variation. The present study was designed to test whether 55 plasma metabolites, including both nutritionally essential and non-essential metabolites and catabolic products, differ in concentration in common marmosets and humans. Significant differences were present for more than half of the metabolites analyzed and included AA, vitamins and central lipid metabolites, as well as for catabolic products of AA, nucleotides, energy metabolism and heme. Three environmental chemicals were present at low nanomolar concentrations but did not differ between species. Sex and age differences in marmosets were present for AA and nucleotide metabolism and warrant additional study. Overall, the results suggest that quantitative, targeted metabolomics can provide a useful complement to non-targeted metabolomics for studies of diet and environment interactions in primate evolution. PMID:26581102

Assessing the role of spatial structure on cell-specific activity and interactions within uncultured methane-oxidizing syntrophic consortia (Invited)

NASA Astrophysics Data System (ADS)

Orphan, V. J.; McGlynn, S.; Chadwick, G.; Dekas, A.; Green-Saxena, A.

2013-12-01

Sulfate-coupled anaerobic oxidation of methane is catalysed through symbiotic associations between archaea and sulphate-reducing bacteria and represents the dominant sink for methane in the oceans. These methane-oxidizing symbiotic consortia form well-structured multi-celled aggregations in marine methane seeps, where close spatial proximity is believed to be essential for efficient exchange of substrates between syntrophic partners. The nature of this interspecies metabolic relationship is still unknown however there are a number of hypotheses regarding the electron carrying intermediate and ecophysiology of the partners, each of which should be affected by, and influence, the spatial arrangement of archaeal and bacterial cells within aggregates. To advance our understanding of the role of spatial structure within naturally occurring environmental consortia, we are using spatial statistical methods combined with fluorescence in situ hybridization and high-resolution nanoscale secondary ion mass spectrometry (FISH-nanoSIMS) to quantify the effect of spatial organization and intra- and inter-species interactions on cell-specific microbial activity within these diverse archaeal-bacterial partnerships.

Numerical modeling of pulsed laser-material interaction and of laser plume dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, Qiang; Shi, Yina

2015-03-10

We have developed two-dimensional Arbitrary Lagrangian Eulerian (ALE) code which is used to study the physical processes, the plasma absorption, the crater profile, and the temperature distribution on metallic target and below the surface. The ALE method overcomes problems with Lagrangian moving mesh distortion by mesh smoothing and conservative quantities remapping from Lagrangian mesh to smoothed one. A new second order accurate diffusion solver has been implemented for the thermal conduction and radiation transport on distorted mesh. The results of numerical simulation of pulsed laser ablation are presented. The influences of different processes, such as time evolution of the surfacemore » temperature, interspecies interactions (elastic collisions, recombination-dissociation reaction), interaction with an ambient gas are examined. The study presents particular interest for the analysis of experimental results obtained during pulsed laser ablation.« less

The anaerobic digestion process

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rivard, C.J.; Boone, D.R.

1996-01-01

The microbial process of converting organic matter into methane and carbon dioxide is so complex that anaerobic digesters have long been treated as {open_quotes}black boxes.{close_quotes} Research into this process during the past few decades has gradually unraveled this complexity, but many questions remain. The major biochemical reactions for forming methane by methanogens are largely understood, and evolutionary studies indicate that these microbes are as different from bacteria as they are from plants and animals. In anaerobic digesters, methanogens are at the terminus of a metabolic web, in which the reactions of myriads of other microbes produce a very limited rangemore » of compounds - mainly acetate, hydrogen, and formate - on which the methanogens grow and from which they form methane. {open_quotes}Interspecies hydrogen-transfer{close_quotes} and {open_quotes}interspecies formate-transfer{close_quotes} are major mechanisms by which methanogens obtain their substrates and by which volatile fatty acids are degraded. Present understanding of these reactions and other complex interactions among the bacteria involved in anaerobic digestion is only now to the point where anaerobic digesters need no longer be treated as black boxes.« less

Differential Biofilm Formation and Chemical Disinfection Resistance of Sessile Cells of Listeria monocytogenes Strains under Monospecies and Dual-Species (with Salmonella enterica) Conditions

PubMed Central

Kostaki, Maria; Chorianopoulos, Nikos; Braxou, Elli; Nychas, George-John

2012-01-01

This study aimed to investigate the possible influence of bacterial intra- and interspecies interactions on the ability of Listeria monocytogenes and Salmonella enterica to develop mixed-culture biofilms on an abiotic substratum, as well as on the subsequent resistance of sessile cells to chemical disinfection. Initially, three strains from each species were selected and left to attach and form biofilms on stainless steel (SS) coupons incubated at 15°C for 144 h, in periodically renewable tryptone soy broth (TSB), under either monoculture or mixed-culture (mono-/dual-species) conditions. Following biofilm formation, mixed-culture sessile communities were subjected to 6-min disinfection treatments with (i) benzalkonium chloride (50 ppm), (ii) sodium hypochlorite (10 ppm), (iii) peracetic acid (10 ppm), and (iv) a mixture of hydrogen peroxide (5 ppm) and peracetic acid (5 ppm). Results revealed that both species reached similar biofilm counts (ca. 105 CFU cm−2) and that, in general, interspecies interactions did not have any significant effect either on the biofilm-forming ability (as this was assessed by agar plating enumeration of the mechanically detached biofilm bacteria) or on the antimicrobial resistance of each individual species. Interestingly, pulsed-field gel electrophoresis (PFGE) analysis clearly showed that the three L. monocytogenes strains did not contribute at the same level either to the formation of mixed-culture sessile communities (mono-/dual species) or to their antimicrobial recalcitrance. Additionally, the simultaneous existence inside the biofilm structure of S. enterica cells seemed to influence the occurrence and resistance pattern of L. monocytogenes strains. In sum, this study highlights the impact of microbial interactions taking place inside a mixed-culture sessile community on both its population dynamics and disinfection resistance. PMID:22307304

Interspecies hormonal control of host root morphology by parasitic plants

PubMed Central

Melnyk, Charles W.; Wakatake, Takanori; Zhang, Jing; Sakamoto, Yuki; Kiba, Takatoshi; Yoshida, Satoko; Matsunaga, Sachihiro; Sakakibara, Hitoshi

2017-01-01

Parasitic plants share a common anatomical feature, the haustorium. Haustoria enable both infection and nutrient transfer, which often leads to growth penalties for host plants and yield reduction in crop species. Haustoria also reciprocally transfer substances, such as RNA and proteins, from parasite to host, but the biological relevance for such movement remains unknown. Here, we studied such interspecies transport by using the hemiparasitic plant Phtheirospermum japonicum during infection of Arabidopsis thaliana. Tracer experiments revealed a rapid and efficient transfer of carboxyfluorescein diacetate (CFDA) from host to parasite upon formation of vascular connections. In addition, Phtheirospermum induced hypertrophy in host roots at the site of infection, a form of enhanced secondary growth that is commonly observed during various parasitic plant–host interactions. The plant hormone cytokinin is important for secondary growth, and we observed increases in cytokinin and its response during infection in both host and parasite. Phtheirospermum-induced host hypertrophy required cytokinin signaling genes (AHK3,4) but not cytokinin biosynthesis genes (IPT1,3,5,7) in the host. Furthermore, expression of a cytokinin-degrading enzyme in Phtheirospermum prevented host hypertrophy. Wild-type hosts with hypertrophy were smaller than ahk3,4 mutant hosts resistant to hypertrophy, suggesting hypertrophy improves the efficiency of parasitism. Taken together, these results demonstrate that the interspecies movement of a parasite-derived hormone modified both host root morphology and fitness. Several microbial and animal plant pathogens use cytokinins during infections, highlighting the central role of this growth hormone during the establishment of plant diseases and revealing a common strategy for parasite infections of plants. PMID:28461500

Interspecies hormonal control of host root morphology by parasitic plants.

PubMed

Spallek, Thomas; Melnyk, Charles W; Wakatake, Takanori; Zhang, Jing; Sakamoto, Yuki; Kiba, Takatoshi; Yoshida, Satoko; Matsunaga, Sachihiro; Sakakibara, Hitoshi; Shirasu, Ken

2017-05-16

Parasitic plants share a common anatomical feature, the haustorium. Haustoria enable both infection and nutrient transfer, which often leads to growth penalties for host plants and yield reduction in crop species. Haustoria also reciprocally transfer substances, such as RNA and proteins, from parasite to host, but the biological relevance for such movement remains unknown. Here, we studied such interspecies transport by using the hemiparasitic plant Phtheirospermum japonicum during infection of Arabidopsis thaliana Tracer experiments revealed a rapid and efficient transfer of carboxyfluorescein diacetate (CFDA) from host to parasite upon formation of vascular connections. In addition, Phtheirospermum induced hypertrophy in host roots at the site of infection, a form of enhanced secondary growth that is commonly observed during various parasitic plant-host interactions. The plant hormone cytokinin is important for secondary growth, and we observed increases in cytokinin and its response during infection in both host and parasite. Phtheirospermum -induced host hypertrophy required cytokinin signaling genes ( AHK3,4 ) but not cytokinin biosynthesis genes ( IPT1,3,5,7) in the host. Furthermore, expression of a cytokinin-degrading enzyme in Phtheirospermum prevented host hypertrophy. Wild-type hosts with hypertrophy were smaller than ahk3,4 mutant hosts resistant to hypertrophy, suggesting hypertrophy improves the efficiency of parasitism. Taken together, these results demonstrate that the interspecies movement of a parasite-derived hormone modified both host root morphology and fitness. Several microbial and animal plant pathogens use cytokinins during infections, highlighting the central role of this growth hormone during the establishment of plant diseases and revealing a common strategy for parasite infections of plants.

Analyses of Coronavirus Assembly Interactions with Interspecies Membrane and Nucleocapsid Protein Chimeras

PubMed Central

Kuo, Lili; Hurst-Hess, Kelley R.; Koetzner, Cheri A.

2016-01-01

ABSTRACT The coronavirus membrane (M) protein is the central actor in virion morphogenesis. M organizes the components of the viral membrane, and interactions of M with itself and with the nucleocapsid (N) protein drive virus assembly and budding. In order to further define M-M and M-N interactions, we constructed mutants of the model coronavirus mouse hepatitis virus (MHV) in which all or part of the M protein was replaced by its phylogenetically divergent counterpart from severe acute respiratory syndrome coronavirus (SARS-CoV). We were able to obtain viable chimeras containing the entire SARS-CoV M protein as well as mutants with intramolecular substitutions that partitioned M protein at the boundaries between the ectodomain, transmembrane domains, or endodomain. Our results show that the carboxy-terminal domain of N protein, N3, is necessary and sufficient for interaction with M protein. However, despite some previous genetic and biochemical evidence that mapped interactions with N to the carboxy terminus of M, it was not possible to define a short linear region of M protein sufficient for assembly with N. Thus, interactions with N protein likely involve multiple linearly discontiguous regions of the M endodomain. The SARS-CoV M chimera exhibited a conditional growth defect that was partially suppressed by mutations in the envelope (E) protein. Moreover, virions of the M chimera were markedly deficient in spike (S) protein incorporation. These findings suggest that the interactions of M protein with both E and S protein are more complex than previously thought. IMPORTANCE The assembly of coronavirus virions entails concerted interactions among the viral structural proteins and the RNA genome. One strategy to study this process is through construction of interspecies chimeras that preserve or disrupt particular inter- or intramolecular associations. In this work, we replaced the membrane (M) protein of the model coronavirus mouse hepatitis virus with its counterpart from a heterologous coronavirus. The results clarify our understanding of the interaction between the coronavirus M protein and the nucleocapsid protein. At the same time, they reveal unanticipated complexities in the interactions of M with the viral spike and envelope proteins. PMID:26889024

Molecular Markers for Interspecies Transmission of Avian Influenza Viruses in Mammalian Hosts

PubMed Central

Lee, Taehyung

2017-01-01

In the last decade, a wide range of avian influenza viruses (AIVs) have infected various mammalian hosts and continuously threaten both human and animal health. It is a result of overcoming the inter-species barrier which is mostly associated with gene reassortment and accumulation of mutations in their gene segments. Several recent studies have shed insights into the phenotypic and genetic changes that are involved in the interspecies transmission of AIVs. These studies have a major focus on transmission from avian to mammalian species due to the high zoonotic potential of the viruses. As more mammalian species have been infected with these viruses, there is higher risk of genetic evolution of these viruses that may lead to the next human pandemic which represents and raises public health concern. Thus, understanding the mechanism of interspecies transmission and molecular determinants through which the emerging AIVs can acquire the ability to transmit to humans and other mammals is an important key in evaluating the potential risk caused by AIVs among humans. Here, we summarize previous and recent studies on molecular markers that are specifically involved in the transmission of avian-derived influenza viruses to various mammalian hosts including humans, pigs, horses, dogs, and marine mammals. PMID:29236050

Coordination and Collective Decision Making

DTIC Science & Technology

2015-08-21

Fisheries , (06 2014): 1. doi: 10.1111/faf.12084 L. Giuggioli, J. R. Potts, D. I. Rubenstein, S. A. Levin. Stigmergy, collective actions, and animal ...terrestrial and marine food webs, as well as enabling interspecies interactions such as reproduction. Eulerian models describe aggregations of animals in...achieved in decision-making. Animal groups frequently display highly coordinated movements, and provide an excellent vehicle by which to understand

The oxidative environment: a mediator of interspecies communication that drives symbiosis evolution.

PubMed

Moné, Yves; Monnin, David; Kremer, Natacha

2014-06-22

Symbiotic interactions are ubiquitous in nature and play a major role in driving the evolution of life. Interactions between partners are often mediated by shared signalling pathways, which strongly influence both partners' biology and the evolution of the association in various environments. As an example of 'common language', the regulation of the oxidative environment plays an important role in driving the evolution of symbiotic associations. Such processes have been occurring for billions of years, including the increase in Earth's atmospheric oxygen and the subsequent evolution of mitochondria. The effect of reactive oxygen species and reactive nitrogen species (RONS) has been characterized functionally, but the molecular dialogue between partners has not been integrated within a broader evolutionary context yet. Given the pleiotropic role of RONS in cell-cell communication, development and immunity, but also their associated physiological costs, we discuss here how their regulation can influence the establishment, the maintenance and the breakdown of various symbiotic associations. By synthesizing recent developments in redox biology, we aim to provide an interdisciplinary understanding of the influence of such mediators of interspecies communication on the evolution and stability of symbioses, which in turn can shape ecosystems and play a role in health and disease.

Genome-driven evolutionary game theory helps understand the rise of metabolic interdependencies in microbial communities.

PubMed

Zomorrodi, Ali R; Segrè, Daniel

2017-11-16

Metabolite exchanges in microbial communities give rise to ecological interactions that govern ecosystem diversity and stability. It is unclear, however, how the rise of these interactions varies across metabolites and organisms. Here we address this question by integrating genome-scale models of metabolism with evolutionary game theory. Specifically, we use microbial fitness values estimated by metabolic models to infer evolutionarily stable interactions in multi-species microbial "games". We first validate our approach using a well-characterized yeast cheater-cooperator system. We next perform over 80,000 in silico experiments to infer how metabolic interdependencies mediated by amino acid leakage in Escherichia coli vary across 189 amino acid pairs. While most pairs display shared patterns of inter-species interactions, multiple deviations are caused by pleiotropy and epistasis in metabolism. Furthermore, simulated invasion experiments reveal possible paths to obligate cross-feeding. Our study provides genomically driven insight into the rise of ecological interactions, with implications for microbiome research and synthetic ecology.

Influence of bacterial interactions on pneumococcal colonization of the nasopharynx

PubMed Central

Shak, Joshua R.; Vidal, Jorge E.; Klugman, Keith P.

2013-01-01

Streptococcus pneumoniae (the pneumococcus) is a common commensal inhabitant of the nasopharynx and a frequent etiologic agent in serious diseases such as pneumonia, otitis media, bacteremia, and meningitis. Multiple pneumococcal strains can colonize the nasopharynx, which is also home to many other bacterial species. Intraspecies and interspecies interactions influence pneumococcal carriage in important ways. Co-colonization by two or more pneumococcal strains has implications for vaccine serotype replacement, carriage detection, and pneumonia diagnostics. Interactions between the pneumococcus and other bacterial species alter carriage prevalence, modulate virulence, and affect biofilm formation. By examining these interactions, this review highlights how the bacterial ecosystem of the nasopharynx changes the nature and course of pneumococcal carriage. PMID:23273566

Fig volatile compounds--a first comparative study.

PubMed

Grison-Pigé, Laure; Hossaert-McKey, Martine; Greeff, Jaco M; Bessière, Jean-Marie

2002-09-01

We analysed the compounds of volatile blends released by receptive figs of twenty Ficus species to attract their specific pollinating wasps. In all, 99 different compounds were identified. The compounds are mainly terpenoids, aliphatic compounds and products from the shikimic acid pathway. In each species blend, there are few major compounds, which are generally common among floral fragrances. Most species blends also include rare compounds, but generally their proportion in the blend is low. A possible basis for species-specificity of Ficus-wasp interactions is discussed in relation to the patterns of volatiles found in this interspecies comparison. Copyright 2002 Elsevier Science Ltd.

Recent Transmission of a Novel Alphacoronavirus, Bat Coronavirus HKU10, from Leschenault's Rousettes to Pomona Leaf-Nosed Bats: First Evidence of Interspecies Transmission of Coronavirus between Bats of Different Suborders

PubMed Central

Lau, Susanna K. P.; Li, Kenneth S. M.; Tsang, Alan K. L.; Shek, Chung-Tong; Wang, Ming; Choi, Garnet K. Y.; Guo, Rongtong; Wong, Beatrice H. L.; Poon, Rosana W. S.; Lam, Carol S. F.; Wang, Sylvia Y. H.; Fan, Rachel Y. Y.; Chan, Kwok-Hung; Zheng, Bo-Jian

2012-01-01

Although coronaviruses are known to infect various animals by adapting to new hosts, interspecies transmission events are still poorly understood. During a surveillance study from 2005 to 2010, a novel alphacoronavirus, BatCoV HKU10, was detected in two very different bat species, Ro-BatCoV HKU10 in Leschenault's rousettes (Rousettus leschenaulti) (fruit bats in the suborder Megachiroptera) in Guangdong and Hi-BatCoV HKU10 in Pomona leaf-nosed bats (Hipposideros pomona) (insectivorous bats in the suborder Microchiroptera) in Hong Kong. Although infected bats appeared to be healthy, Pomona leaf-nosed bats carrying Hi-BatCoV HKU10 had lower body weights than uninfected bats. To investigate possible interspecies transmission between the two bat species, the complete genomes of two Ro-BatCoV HKU10 and six Hi-BatCoV HKU10 strains were sequenced. Genome and phylogenetic analyses showed that Ro-BatCoV HKU10 and Hi-BatCoV HKU10 represented a novel alphacoronavirus species, sharing highly similar genomes except in the genes encoding spike proteins, which had only 60.5% amino acid identities. Evolution of the spike protein was also rapid in Hi-BatCoV HKU10 strains from 2005 to 2006 but stabilized thereafter. Molecular-clock analysis dated the most recent common ancestor of all BatCoV HKU10 strains to 1959 (highest posterior density regions at 95% [HPDs], 1886 to 2002) and that of Hi-BatCoV HKU10 to 1986 (HPDs, 1956 to 2004). The data suggested recent interspecies transmission from Leschenault's rousettes to Pomona leaf-nosed bats in southern China. Notably, the rapid adaptive genetic change in BatCoV HKU10 spike protein by ∼40% amino acid divergence after recent interspecies transmission was even greater than the ∼20% amino acid divergence between spike proteins of severe acute respiratory syndrome-related Rhinolophus bat coronavirus (SARSr-CoV) in bats and civets. This study provided the first evidence for interspecies transmission of coronavirus between bats of different suborders. PMID:22933277

Highly trabeculated structure of the human endocardium underlies asymmetrical response to low-energy monophasic shocks

NASA Astrophysics Data System (ADS)

Connolly, Adam; Robson, Matthew D.; Schneider, Jürgen; Burton, Rebecca; Plank, Gernot; Bishop, Martin J.

2017-09-01

Novel low-energy defibrillation therapies are thought to be driven by virtual-electrodes (VEs), due to the interaction of applied monophasic electric shocks with fine-scale anatomical structures within the heart. Significant inter-species differences in the cardiac (micro)-anatomy exist, however, particularly with respect to the degree of endocardial trabeculations, which may underlie important differences in response to low-energy defibrillation protocols. Understanding the interaction of monophasic electric fields with the specific human micro-anatomy is therefore imperative in facilitating the translation and optimisation of these promising experimental therapies to the clinic. In this study, we sought to investigate how electric fields from implanted devices interact with the highly trabeculated human endocardial surface to better understand shock success in order to help optimise future clinical protocols. A bi-ventricular human computational model was constructed from high resolution (350 μm) ex-vivo MR data, including anatomically accurate endocardial structures. Monophasic shocks were applied between a basal right ventricular catheter and an exterior ground. Shocks of varying strengths were applied with both anodal [positive right ventricle (RV) electrode] and cathodal (negative RV electrode) polarities at different states of tissue refractoriness and during induced arrhythmias. Anodal shocks induced isolated positive VEs at the distal side of "detached" trabeculations, which rapidly spread into hyperpolarised tissue on the surrounding endocardial surfaces following the shock. Anodal shocks thus depolarised more tissue 10 ms after the shock than cathodal shocks where the propagation of activation from VEs induced on the proximal side of "detached" trabeculations was prevented due to refractory endocardium. Anodal shocks increased arrhythmia complexity more than cathodal shocks during failed anti-arrhythmia shocks. In conclusion, multiple detached trabeculations in the human ventricle interact with anodal stimuli to induce multiple secondary sources from VEs, facilitating more rapid shock-induced ventricular excitation compared to cathodal shocks. Such a mechanism may help explain inter-species differences in response to shocks and help to develop novel defibrillation strategies.

A review on the bioenergetics of anaerobic microbial metabolism close to the thermodynamic limits and its implications for digestion applications.

PubMed

Leng, Ling; Yang, Peixian; Singh, Shubham; Zhuang, Huichuan; Xu, Linji; Chen, Wen-Hsing; Dolfing, Jan; Li, Dong; Zhang, Yan; Zeng, Huiping; Chu, Wei; Lee, Po-Heng

2018-01-01

The exploration of the energetics of anaerobic digestion systems can reveal how microorganisms cooperate efficiently for cell growth and methane production, especially under low-substrate conditions. The establishment of a thermodynamically interdependent partnership, called anaerobic syntrophy, allows unfavorable reactions to proceed. Interspecies electron transfer and the concentrations of electron carriers are crucial for maintaining this mutualistic activity. This critical review summarizes the functional microorganisms and syntroph partners, particularly in the metabolic pathways and energy conservation of syntrophs. The kinetics and thermodynamics of propionate degradation to methane, reversibility of the acetate oxidation process, and estimation of microbial growth are summarized. The various routes of interspecies electron transfer, reverse electron transfer, and Poly-β-hydroxyalkanoate formation in the syntrophic community are also reviewed. Finally, promising and critical directions of future research are proposed. Fundamental insight in the activities and interactions involved in AD systems could serve as a guidance for engineered systems optimization and upgrade. Copyright © 2017 Elsevier Ltd. All rights reserved.

Cysteine-Accelerated Methanogenic Propionate Degradation in Paddy Soil Enrichment.

PubMed

Zhuang, Li; Ma, Jinlian; Tang, Jia; Tang, Ziyang; Zhou, Shungui

2017-05-01

Propionate degradation is a critical step during the conversion of complex organic matter under methanogenic conditions, and it requires a syntrophic cooperation between propionate-oxidizing bacteria and methanogenic archaea. Increasing evidences suggest that interspecies electron transfer for syntrophic metabolism is not limited to the reducing equivalents of hydrogen and formate. This study tested the ability of an electron shuttle to mediate interspecies electron transfer in syntrophic methanogenesis. We found that cysteine supplementation (100, 400, and 800 μM) accelerated CH 4 production from propionate in paddy soil enrichments. Of the concentrations tested, 100 μM cysteine was the most effective at enhancing propionate degradation to CH 4 , and the rates of CH 4 production and propionate degradation were increased by 109 and 79%, respectively, compared with the cysteine-free control incubations. We eliminated the possibility that the stimulatory effect of cysteine on methanogenesis was attributable to the function of cysteine as a methanogenic substrate in the presence of propionate. The potential catalytic effect involved cysteine serving as an electron carrier to mediate interspecies electron transfer in syntrophic propionate oxidization. The redox potential of cystine/cysteine, which is dependent on the concentration, might be more suitable to facilitate interspecies electron transfer between syntrophic partners at a concentration of 100 μM. Pelotomaculum, obligately syntrophic, propionate-oxidizing bacteria, and hydrogenotrophic methanogens of the family Methanobacteriaceae are predominant in cysteine-mediated methanogenic propionate degradation. The stimulatory effect of cysteine on syntrophic methanogenesis offers remarkable potential for improving the performance of anaerobic digestion and conceptually broaden strategies for interspecies electron transfer in syntrophic metabolism.

In vitro development and cytological quality of inter-species (porcine→bovine) cloned embryos are affected by trichostatin A-dependent epigenomic modulation of adult mesenchymal stem cells.

PubMed

Opiela, J; Samiec, M; Romanek, J

2017-07-15

Artificial epigenomic modulation of in vitro cultured mesenchymal stem cells (MSCs) by applying a non-selective HDAC inhibitor, termed TSA, can facilitate more epigenetic reprogramming of transcriptional activity of the somatic cell-descended nuclear genome in NT pig embryos. The results of the present investigation showed that TSA-dependent epigenomic modulation of nuclear donor MSCs highly affects both the in vitro developmental capability and the cytological quality of inter-species (porcine→bovine) cloned embryos. The developmental competences to reach the blastocyst stage among hybrid (porcine→bovine) nuclear-transferred embryos that had been reconstructed with bovine ooplasts and epigenetically modulated porcine MSCs were maintained at a relatively high level. These competences were higher than those noted in studies by other authors, but they were still decreased compared to those of intra-species (porcine) cloned embryos that had been reconstituted with porcine ooplasts and either the cell nuclei of epigenetically transformed MSCs or the cell nuclei of epigenetically non-transformed MSCs. In conclusion, MSCs undergoing TSA-dependent epigenetic transformation were used for the first time as a source of nuclear donor cells not only for inter-species somatic cell cloning in pigs but also for inter-species somatic cell cloning in other livestock species. Moreover, as a result of the current research, efficient sequential physicochemical activation of inter-species nuclear-transferred clonal cybrids derived from bovine ooplasm and porcine MSC nuclei was developed. Copyright © 2017 Elsevier Inc. All rights reserved.

The role of multispecies social interactions in shaping Pseudomonas aeruginosa pathogenicity in the cystic fibrosis lung.

PubMed

O'Brien, Siobhán; Fothergill, Joanne L

2017-08-15

Pseudomonas aeruginosa is a major pathogen in the lungs of cystic fibrosis (CF) patients. However, it is now recognised that a diverse microbial community exists in the airways comprising aerobic and anaerobic bacteria as well as fungi and viruses. This rich soup of microorganisms provides ample opportunity for interspecies interactions, particularly when considering secreted compounds. Here, we discuss how P. aeruginosa-secreted products can have community-wide effects, with the potential to ultimately shape microbial community dynamics within the lung. We focus on three well-studied traits associated with worsening clinical outcome in CF: phenazines, siderophores and biofilm formation, and discuss how secretions can shape interactions between P. aeruginosa and other commonly encountered members of the lung microbiome: Staphylococcus aureus, the Burkholderia cepacia complex, Candida albicans and Aspergillus fumigatus. These interactions may shape the evolutionary trajectory of P. aeruginosa while providing new opportunities for therapeutic exploitation of the CF lung microbiome. © FEMS 2017.

The role of multispecies social interactions in shaping Pseudomonas aeruginosa pathogenicity in the cystic fibrosis lung

PubMed Central

Fothergill, Joanne L.

2017-01-01

Abstract Pseudomonas aeruginosa is a major pathogen in the lungs of cystic fibrosis (CF) patients. However, it is now recognised that a diverse microbial community exists in the airways comprising aerobic and anaerobic bacteria as well as fungi and viruses. This rich soup of microorganisms provides ample opportunity for interspecies interactions, particularly when considering secreted compounds. Here, we discuss how P. aeruginosa-secreted products can have community-wide effects, with the potential to ultimately shape microbial community dynamics within the lung. We focus on three well-studied traits associated with worsening clinical outcome in CF: phenazines, siderophores and biofilm formation, and discuss how secretions can shape interactions between P. aeruginosa and other commonly encountered members of the lung microbiome: Staphylococcus aureus, the Burkholderia cepacia complex, Candida albicans and Aspergillus fumigatus. These interactions may shape the evolutionary trajectory of P. aeruginosa while providing new opportunities for therapeutic exploitation of the CF lung microbiome. PMID:28859314

A novel approach identifying hybrid sterility QTL on the autosomes of Drosophila simulans and D. mauritiana.

PubMed

Dickman, Christopher T D; Moehring, Amanda J

2013-01-01

When species interbreed, the hybrid offspring that are produced are often sterile. If only one hybrid sex is sterile, it is almost always the heterogametic (XY or ZW) sex. Taking this trend into account, the predominant model used to explain the genetic basis of F1 sterility involves a deleterious interaction between recessive sex-linked loci from one species and dominant autosomal loci from the other species. This model is difficult to evaluate, however, as only a handful of loci influencing interspecies hybrid sterility have been identified, and their autosomal genetic interactors have remained elusive. One hindrance to their identification has been the overwhelming effect of the sex chromosome in mapping studies, which could 'mask' the ability to accurately map autosomal factors. Here, we use a novel approach employing attached-X chromosomes to create reciprocal backcross interspecies hybrid males that have a non-recombinant sex chromosome and recombinant autosomes. The heritable variation in phenotype is thus solely caused by differences in the autosomes, thereby allowing us to accurately identify the number and location of autosomal sterility loci. In one direction of backcross, all males were sterile, indicating that sterility could be entirely induced by the sex chromosome complement in these males. In the other direction, we identified nine quantitative trait loci that account for a surprisingly large amount (56%) of the autosome-induced phenotypic variance in sterility, with a large contribution of autosome-autosome epistatic interactions. These loci are capable of acting dominantly, and thus could contribute to F1 hybrid sterility.

Influence of bacterial interactions on pneumococcal colonization of the nasopharynx.

PubMed

Shak, Joshua R; Vidal, Jorge E; Klugman, Keith P

2013-03-01

Streptococcus pneumoniae (the pneumococcus) is a common commensal inhabitant of the nasopharynx and a frequent etiologic agent in serious diseases such as pneumonia, otitis media, bacteremia, and meningitis. Multiple pneumococcal strains can colonize the nasopharynx, which is also home to many other bacterial species. Intraspecies and interspecies interactions influence pneumococcal carriage in important ways. Co-colonization by two or more pneumococcal strains has implications for vaccine serotype replacement, carriage detection, and pneumonia diagnostics. Interactions between the pneumococcus and other bacterial species alter carriage prevalence, modulate virulence, and affect biofilm formation. By examining these interactions, this review highlights how the bacterial ecosystem of the nasopharynx changes the nature and course of pneumococcal carriage. Copyright © 2012 Elsevier Ltd. All rights reserved.

Canine distemper outbreak in raccoons suggests pathogen interspecies transmission amongst alien and native carnivores in urban areas from Germany.

PubMed

Rentería-Solís, Zaida; Förster, Christine; Aue, Angelika; Wittstatt, Ulrich; Wibbelt, Gudrun; König, Matthias

2014-11-07

From December 2012 to May 2013, an outbreak occurred among urban wild carnivores from Berlin. We collected 97 free-ranging raccoons from the city area. PCR assays, histopathology and immunohistochemistry confirmed canine distemper virus (CDV) infection in 74 raccoons. Phylogenetic analysis of haemagglutinin gene fragments (1767 nucleotides) of CDV isolated from four raccoons showed close relation to CDV isolates from foxes from Germany and a domestic dog from Hungary; all belonging to the "Europe" lineage of CDV. These study results suggest an inter-species transmission of CDV as the origin for the outbreak among the raccoon population. Implications for domestic pets and suggested interspecies transmission between urban wildlife and raccoons are discussed. This is the first major outbreak of CDV amongst free-ranging raccoons in Europe. Copyright © 2014 Elsevier B.V. All rights reserved.

Mechanisms Underlying Mammalian Hybrid Sterility in Two Feline Interspecies Models

PubMed Central

Davis, Brian W.; Seabury, Christopher M.; Brashear, Wesley A.; Li, Gang; Roelke-Parker, Melody; Murphy, William J.

2015-01-01

The phenomenon of male sterility in interspecies hybrids has been observed for over a century, however, few genes influencing this recurrent phenotype have been identified. Genetic investigations have been primarily limited to a small number of model organisms, thus limiting our understanding of the underlying molecular basis of this well-documented “rule of speciation.” We utilized two interspecies hybrid cat breeds in a genome-wide association study employing the Illumina 63 K single-nucleotide polymorphism array. Collectively, we identified eight autosomal genes/gene regions underlying associations with hybrid male sterility (HMS) involved in the function of the blood-testis barrier, gamete structural development, and transcriptional regulation. We also identified several candidate hybrid sterility regions on the X chromosome, with most residing in close proximity to complex duplicated regions. Differential gene expression analyses revealed significant chromosome-wide upregulation of X chromosome transcripts in testes of sterile hybrids, which were enriched for genes involved in chromatin regulation of gene expression. Our expression results parallel those reported in Mus hybrids, supporting the “Large X-Effect” in mammalian HMS and the potential epigenetic basis for this phenomenon. These results support the value of the interspecies feline model as a powerful tool for comparison to rodent models of HMS, demonstrating unique aspects and potential commonalities that underpin mammalian reproductive isolation. PMID:26006188

Binary mixtures of condensates in generic confining potentials

NASA Astrophysics Data System (ADS)

Facchi, P.; Florio, G.; Pascazio, S.; Pepe, F. V.

2011-12-01

We study a binary mixture of Bose-Einstein condensates, confined in a generic potential, in the Thomas-Fermi approximation. We search for the zero-temperature ground state of the system, both in the case of fixed numbers of particles and fixed chemical potentials. For generic potentials, we analyze the transition from mixed to separated ground-state configurations as the inter-species interaction increases. We derive a simple formula that enables one to determine the location of the domain walls. Finally, we find criteria for the energetic stability of separated configurations, depending on the number and the position of the domain walls separating the two species.

Proinflammatory Cytokines as Regulators of Vaginal Microbiota.

PubMed

Kremleva, E A; Sgibnev, A V

2016-11-01

It was shown that IL-1β, IL-8, and IL-6 in concentrations similar to those in the vagina of healthy women stimulated the growth of normal microflora (Lactobacillus spp.) and suppressed the growth and biofilm production by S. aureus and E. coli. On the contrary, these cytokines in higher concentrations typical of vaginal dysbiosis suppressed normal microflora and stimulated the growth of opportunistic microorganisms. TGF-β1 in both doses produced a stimulating effects on study vaginal microsymbionts. It is hypothesized that pro-inflammatory cytokines serve as the molecules of interspecies communication coordinating the interactions of all components of the vaginal symbiotic system.

Interspecies Extrapolation

EPA Science Inventory

Interspecies extrapolation encompasses two related but distinct topic areas that are germane to quantitative extrapolation and hence computational toxicology-dose scaling and parameter scaling. Dose scaling is the process of converting a dose determined in an experimental animal ...

Interspecies interactions stimulate diversification of the Streptomyces coelicolor secreted metabolome.

PubMed

Traxler, Matthew F; Watrous, Jeramie D; Alexandrov, Theodore; Dorrestein, Pieter C; Kolter, Roberto

2013-08-20

Soils host diverse microbial communities that include filamentous actinobacteria (actinomycetes). These bacteria have been a rich source of useful metabolites, including antimicrobials, antifungals, anticancer agents, siderophores, and immunosuppressants. While humans have long exploited these compounds for therapeutic purposes, the role these natural products may play in mediating interactions between actinomycetes has been difficult to ascertain. As an initial step toward understanding these chemical interactions at a systems level, we employed the emerging techniques of nanospray desorption electrospray ionization (NanoDESI) and matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) imaging mass spectrometry to gain a global chemical view of the model bacterium Streptomyces coelicolor interacting with five other actinomycetes. In each interaction, the majority of secreted compounds associated with S. coelicolor colonies were unique, suggesting an idiosyncratic response from S. coelicolor. Spectral networking revealed a family of unknown compounds produced by S. coelicolor during several interactions. These compounds constitute an extended suite of at least 12 different desferrioxamines with acyl side chains of various lengths; their production was triggered by siderophores made by neighboring strains. Taken together, these results illustrate that chemical interactions between actinomycete bacteria exhibit high complexity and specificity and can drive differential secondary metabolite production. Actinomycetes, filamentous actinobacteria from the soil, are the deepest natural source of useful medicinal compounds, including antibiotics, antifungals, and anticancer agents. There is great interest in developing new strategies that increase the diversity of metabolites secreted by actinomycetes in the laboratory. Here we used several metabolomic approaches to examine the chemicals made by these bacteria when grown in pairwise coculture. We found that these interspecies interactions stimulated production of numerous chemical compounds that were not made when they grew alone. Among these compounds were at least 12 different versions of a molecule called desferrioxamine, a siderophore used by the bacteria to gather iron. Many other compounds of unknown identity were also observed, and the pattern of compound production varied greatly among the interaction sets. These findings suggest that chemical interactions between actinomycetes are surprisingly complex and that coculture may be a promising strategy for finding new molecules from actinomycetes.

INTERSPECIES DOSIMETRY MODELS FOR PULMONARY PHARMACOLOGY

EPA Science Inventory

Interspecies Dosimetry Models for Pulmonary Pharmacology

Ted B. Martonen, Jeffry D. Schroeter, and John S. Fleming

Experimental Toxicology Division, National Health and Environmental Effects Research Laboratory, U.S. Environmental Protection Agency, Research Triangl...

Successful cloning of coyotes through interspecies somatic cell nuclear transfer using domestic dog oocytes.

PubMed

Hwang, Insung; Jeong, Yeon Woo; Kim, Joung Joo; Lee, Hyo Jeong; Kang, Mina; Park, Kang Bae; Park, Jung Hwan; Kim, Yeun Wook; Kim, Woo Tae; Shin, Taeyoung; Hyun, Sang Hwan; Jeung, Eui-Bae; Hwang, Woo Suk

2013-01-01

Interspecies somatic cell nuclear transfer (iSCNT) is an emerging assisted reproductive technology (ART) for preserving Nature's diversity. The scarcity of oocytes from some species makes utilisation of readily available oocytes inevitable. In the present study, we describe the successful cloning of coyotes (Canis latrans) through iSCNT using oocytes from domestic dogs (Canis lupus familiaris or dingo). Transfer of 320 interspecies-reconstructed embryos into 22 domestic dog recipients resulted in six pregnancies, from which eight viable offspring were delivered. Fusion rate and cloning efficiency during iSCNT cloning of coyotes were not significantly different from those observed during intraspecies cloning of domestic dogs. Using neonatal fibroblasts as donor cells significantly improved the cloning efficiency compared with cloning using adult fibroblast donor cells (P<0.05). The use of domestic dog oocytes in the cloning of coyotes in the present study holds promise for cloning other endangered species in the Canidae family using similar techniques. However, there are still limitations of the iSCNT technology, as demonstrated by births of morphologically abnormal coyotes and the clones' inheritance of maternal domestic dog mitochondrial DNA.

Observation of interspecies ion separation in inertial-confinement-fusion implosions

DOE PAGES

Hsu, Scott C.; Joshi, Tirtha Raj; Hakel, Peter; ...

2016-10-24

Here we report direct experimental evidence of interspecies ion separation in direct-drive, inertial-confinement-fusion experiments on the OMEGA laser facility. These experiments, which used plastic capsules with D 2/Ar gas fill (1% Ar by atom), were designed specifically to reveal interspecies ion separation by exploiting the predicted, strong ion thermo-diffusion between ion species of large mass and charge difference. Via detailed analyses of imaging x-ray-spectroscopy data, we extract Ar-atom-fraction radial profiles at different times, and observe both enhancement and depletion compared to the initial 1%-Ar gas fill. The experimental results are interpreted with radiation-hydrodynamic simulations that include recently implemented, first-principles modelsmore » of interspecies ion diffusion. Finally, the experimentally inferred Ar-atom-fraction profiles agree reasonably, but not exactly, with calculated profiles associated with the incoming and rebounding first shock.« less

Blow-up behavior of ground states for a nonlinear Schrödinger system with attractive and repulsive interactions

NASA Astrophysics Data System (ADS)

Guo, Yujin; Zeng, Xiaoyu; Zhou, Huan-Song

2018-01-01

We consider a nonlinear Schrödinger system arising in a two-component Bose-Einstein condensate (BEC) with attractive intraspecies interactions and repulsive interspecies interactions in R2. We get ground states of this system by solving a constrained minimization problem. For some kinds of trapping potentials, we prove that the minimization problem has a minimizer if and only if the attractive interaction strength ai (i = 1 , 2) of each component of the BEC system is strictly less than a threshold a*. Furthermore, as (a1 ,a2) ↗ (a* ,a*), the asymptotical behavior for the minimizers of the minimization problem is discussed. Our results show that each component of the BEC system concentrates at a global minimum of the associated trapping potential.

Evolutionary Analysis of Heterochromatin Protein Compatibility by Interspecies Complementation in Saccharomyces

PubMed Central

Zill, Oliver A.; Scannell, Devin R.; Kuei, Jeffrey; Sadhu, Meru; Rine, Jasper

2012-01-01

The genetic bases for species-specific traits are widely sought, but reliable experimental methods with which to identify functionally divergent genes are lacking. In the Saccharomyces genus, interspecies complementation tests can be used to evaluate functional conservation and divergence of biological pathways or networks. Silent information regulator (SIR) proteins in S. bayanus provide an ideal test case for this approach because they show remarkable divergence in sequence and paralog number from those found in the closely related S. cerevisiae. We identified genes required for silencing in S. bayanus using a genetic screen for silencing-defective mutants. Complementation tests in interspecies hybrids identified an evolutionarily conserved Sir-protein-based silencing machinery, as defined by two interspecies complementation groups (SIR2 and SIR3). However, recessive mutations in S. bayanus SIR4 isolated from this screen could not be complemented by S. cerevisiae SIR4, revealing species-specific functional divergence in the Sir4 protein despite conservation of the overall function of the Sir2/3/4 complex. A cladistic complementation series localized the occurrence of functional changes in SIR4 to the S. cerevisiae and S. paradoxus branches of the Saccharomyces phylogeny. Most of this functional divergence mapped to sequence changes in the Sir4 PAD. Finally, a hemizygosity modifier screen in the interspecies hybrids identified additional genes involved in S. bayanus silencing. Thus, interspecies complementation tests can be used to identify (1) mutations in genetically underexplored organisms, (2) loci that have functionally diverged between species, and (3) evolutionary events of functional consequence within a genus. PMID:22923378

MECHANISTIC DOSIMETRY MODELS OF NANOMATERIAL DEPOSITION IN THE RESPIRATORY TRACT

EPA Science Inventory

Accurate health risk assessments of inhalation exposure to nanomaterials will require dosimetry models that account for interspecies differences in dose delivered to the respiratory tract. Mechanistic models offer the advantage to interspecies extrapolation that physicochemica...

INTER-SPECIES MODELS FOR ACUTE AQUATIC TOXICITY BASED ON MECHANISM OF ACTION

EPA Science Inventory

This presentation will provide interspecies QSARs for acute toxicity to 17 aquatic species, such as fish, snail, tadpole, hydrozoan, crustacean, insect larvae, and bacteria developed using 5,000 toxic effect results for approximately 2400 chemicals.

Assessing Uncertainty of Interspecies Correlation Estimation Models for Aromatic Compounds

EPA Science Inventory

We developed Interspecies Correlation Estimation (ICE) models for aromatic compounds containing 1 to 4 benzene rings to assess uncertainty in toxicity extrapolation in two data compilation approaches. ICE models are mathematical relationships between surrogate and predicted test ...

The Fusobacterium nucleatum Outer Membrane Protein RadD Is an Arginine-Inhibitable Adhesin Required for Inter-Species Adherence and the Structured Architecture of Multi-Species Biofilm

PubMed Central

Kaplan, Christopher W.; Lux, Renate; Haake, Susan Kinder; Shi, Wenyuan

2009-01-01

Summary A defining characteristic of the suspected periodontal pathogen Fusobacterium nucleatum is its ability to adhere to a plethora of oral bacteria. This distinguishing feature is suggested to play an important role in oral biofilm formation and pathogenesis, with fusobacteria proposed to serve as central “bridging organisms” in the architecture of the oral biofilm bringing together species which would not interact otherwise. Previous studies indicate that these bacterial interactions are mediated by galactose- or arginine-inhibitable adhesins although genetic evidence for the role and nature of these proposed adhesins remains elusive. To characterize these adhesins at the molecular level, the genetically transformable F. nucleatum strain ATCC 23726 was screened for adherence properties, and arginine inhibitable adhesion was evident, while galactose-inhibitable adhesion was not detected. Six potential arginine binding proteins were isolated from the membrane fraction of F. nucleatum ATCC 23726 and identified via mass spectroscopy as members of the outer membrane family of proteins in F. nucleatum. Inactivation of the genes encoding these six candidates for arginine-inhibitable adhesion and two additional homologues revealed that only a mutant derivative carrying an insertion in Fn1526 (now designated as radD) demonstrated significantly decreased co-aggregation with representatives of the Gram-positive “early oral colonizers”. Lack of the 350 kDa outer membrane protein encoded by radD resulted in the failure to form the extensive structured biofilm observed with the parent strain when grown in the presence of Streptococcus sanguinis ATCC 10556. These findings indicate that radD is responsible for arginine-inhibitable adherence of F. nucleatum and provides definitive molecular evidence that F. nucleatum adhesins play a vital role in inter-species adherence and multispecies biofilm formation. PMID:19007407

Inter-species chimeras of leukaemia inhibitory factor define a major human receptor-binding determinant.

PubMed Central

Owczarek, C M; Layton, M J; Metcalf, D; Lock, P; Willson, T A; Gough, N M; Nicola, N A

1993-01-01

Human leukaemia inhibitory factor (hLIF) binds to both human and mouse LIF receptors (LIF-R), while mouse LIF (mLIF) binds only to mouse LIF-R. Moreover, hLIF binds with higher affinity to the mLIF-R than does mLIF. In order to define the regions of the hLIF molecule responsible for species-specific interaction with the hLIF-R and for the unusual high-affinity binding to the mLIF-R, a series of 15 mouse/human LIF hybrids has been generated. Perhaps surprisingly, both of these properties mapped to the same region of the hLIF molecule. The predominant contribution was from residues in the loop linking the third and fourth helices, with lesser contributions from residues in the third helix and the loop connecting the second and third helices in the predicted three-dimensional structure. Since all chimeras retained full biological activity and receptor-binding activity on mouse cells, and there was little variation in the specific biological activity of the purified proteins, it can be concluded that the overall secondary and tertiary structures of each chimera were intact. This observation also implied that the primary binding sites on mLIF and hLIF for the mLIF-R were unaltered by inter-species domain swapping. Consequently, the site on the hLIF molecule that confers species-specific binding to the hLIF-R and higher affinity binding to the mLIF-R, must constitute an additional interaction site to that used by both mLIF and hLIF to bind to the mLIF-R. These studies define a maximum of 15 amino acid differences between hLIF and mLIF that are responsible for the different properties of these proteins. Images PMID:8253075

Development of Species Sensitivity Distributions for Wildlife Using Interspecies Toxicity Correlation Models

EPA Science Inventory

Species sensitivity distributions (SSD) are cumulative distributions of chemical toxicity of multiple species and have had limited application in wildlife risk assessment because of relatively small datasets of wildlife toxicity values. Interspecies correlation estimation (ICE) m...

Interspecies chimeras.

PubMed

Suchy, Fabian; Nakauchi, Hiromitsu

2018-05-30

By probing early embryogenesis and regeneration, interspecies chimeras provide a unique platform for discovery and clinical use. Although efficient generation of human:animal chimeric embryos remains elusive, recent advancements attempt to overcome incompatibilities in xenogeneic development and transplantation. Copyright © 2018 Elsevier Ltd. All rights reserved.

Role of interspecies interactions in dual-species biofilms developed in vitro by uropathogens isolated from polymicrobial urinary catheter-associated bacteriuria.

PubMed

Galván, E M; Mateyca, C; Ielpi, L

2016-10-01

Most catheter-associated urinary tract infections are polymicrobial. Here, uropathogen interactions in dual-species biofilms were studied. The dual-species associations selected based on their prevalence in clinical settings were Klebsiella pneumoniae-Escherichia coli, E. coli-Enterococcus faecalis, K. pneumoniae-E. faecalis, and K. pneumoniae-Proteus mirabilis. All species developed single-species biofilms in artificial urine. The ability of K. pneumoniae to form biofilms was not affected by E. coli or E. faecalis co-inoculation, but was impaired by P. mirabilis. Conversely, P. mirabilis established a biofilm when co-inoculated with K. pneumoniae. Additionally, E. coli persistence in biofilms was hampered by K. pneumoniae but not by E. faecalis. Interestingly, E. coli, but not K. pneumoniae, partially inhibited E. faecalis attachment to the surface and retarded biofilm development. The findings reveal bacterial interactions between uropathogens in dual-species biofilms ranged from affecting initial adhesion to outcompeting one bacterial species, depending on the identity of the partners involved.

Microbial Herd Protection Mediated by Antagonistic Interaction in Polymicrobial Communities

PubMed Central

Wong, Megan J. Q.; Liang, Xiaoye; Smart, Matt; Tang, Le; Moore, Richard; Ingalls, Brian

2016-01-01

ABSTRACT In host and natural environments, microbes often exist in complex multispecies communities. The molecular mechanisms through which such communities develop and persist, despite significant antagonistic interactions between species, are not well understood. The type VI secretion system (T6SS) is a lethal weapon commonly employed by Gram-negative bacteria to inhibit neighboring species through the delivery of toxic effectors. It is well established that intraspecies protection is conferred by immunity proteins that neutralize effector toxicities. In contrast, the mechanisms for interspecies protection are not clear. Here we use two T6SS-active antagonistic bacterial species, Aeromonas hydrophila and Vibrio cholerae, to demonstrate that interspecies protection is dependent on effectors. A. hydrophila and V. cholerae do not share conserved immunity genes but could coexist equally in a mixture. However, mutants lacking the T6SS or effectors were effectively eliminated by the competing wild-type strain. Time-lapse microscopic analyses showed that mutually lethal interactions drive the segregation of mixed species into distinct single-species clusters by eliminating interspersed single cells. Cluster formation provides herd protection by abolishing lethal interactions inside each cluster and restricting the interactions to the boundary. Using an agent-based modeling approach, we simulated the antagonistic interactions of two hypothetical species. The resulting simulations recapitulated our experimental observations. These results provide mechanistic insights regarding the general role of microbial weapons in determining the structures of complex multispecies communities. IMPORTANCE Investigating the warfare of microbes allows us to better understand the ecological relationships in complex microbial communities such as the human microbiota. Here we use the T6SS, a deadly bacterial weapon, as a model to demonstrate the importance of lethal interactions in determining community structures and the exchange of genetic materials. This simplified model elucidates a mechanism of microbial herd protection by which competing antagonistic species can coexist in the same niche, despite their diverse mutually destructive activities. Our results also suggest that antagonistic interactions impose strong selection that could promote multicellular organism-like social behaviors and contribute to the transition to multicellularity during evolution. PMID:27637882

ESTIMATION OF CHEMICAL TOXICITY TO WILDLIFE SPECIES USING INTERSPECIES CORRELATION MODELS

EPA Science Inventory

Ecological risks to wildlife are typically assessed using toxicity data for relataively few species and with limited understanding of differences in species sensitivity to contaminants. Empirical interspecies correlation models were derived from LD50 values for 49 wildlife speci...

Domain wall suppression in trapped mixtures of Bose-Einstein condensates

NASA Astrophysics Data System (ADS)

Pepe, Francesco V.; Facchi, Paolo; Florio, Giuseppe; Pascazio, Saverio

2012-08-01

The ground-state energy of a binary mixture of Bose-Einstein condensates can be estimated for large atomic samples by making use of suitably regularized Thomas-Fermi density profiles. By exploiting a variational method on the trial densities the energy can be computed by explicitly taking into account the normalization condition. This yields analytical results and provides the basis for further improvement of the approximation. As a case study, we consider a binary mixture of 87Rb atoms in two different hyperfine states in a double-well potential and discuss the energy crossing between density profiles with different numbers of domain walls, as the number of particles and the interspecies interaction vary.

Discovery of antimicrobial lipodepsipeptides produced by a Serratia sp. within mosquito microbiomes.

PubMed

Ganley, Jack; Carr, Gavin; Ioerger, Thomas; Sacchettini, James; Clardy, Jon; Derbyshire, Emily

2018-04-26

The Anopheles mosquito that harbors the Plasmodium parasite contains a microbiota that can influence both the vector and parasite. In recent years, insect-associated microbes have highlighted the untapped potential of exploiting interspecies interactions to discover bioactive compounds. In this study, we report the discovery of nonribosomal lipodepsipeptides that are produced by a Serratia sp. within the midgut and salivary glands of A. stephensi mosquitoes. The lipodepsipeptides, stephensiolides A-K, have antibiotic activity and facilitate bacterial surface motility. Bioinformatic analyses indicate that the stephensiolides are ubiquitous in nature and are likely important for Serratia spp. colonization within mosquitoes, humans, and other ecological niches. Our results demonstrate the usefulness of probing insect-microbiome interactions, enhance our understanding of the chemical ecology within Anopheles mosquitoes, and provide a secondary metabolite scaffold to further investigate this complex relationship. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Augmenting Species Diversity in Water Quality Criteria Derivation using Interspecies Correlation Models

EPA Science Inventory

The specific requirements for taxa diversity of the 1985 guidelines have limited the number of ambient water quality criteria (AWQC) developed for aquatic life protection. The EPA developed the Web-based Interspecies Correlation Estimation (Web-ICE) tool to allow extrapolation of...

Acute toxicity prediction to threatened and endangered species using Interspecies Correlation Estimation (ICE) models

EPA Science Inventory

Evaluating contaminant sensitivity of threatened and endangered (listed) species and protectiveness of chemical regulations often depends on toxicity data for commonly tested surrogate species. The U.S. EPA’s Internet application Web-ICE is a suite of Interspecies Correlati...

ESTIMATION OF AQUATIC SPECIES SENSITIVITY USING INTERSPECIES CORRELATION AND ACUTE TO CHRONIC TOXICITY MODELS

EPA Science Inventory

Abstract for presentation

Estimation of aquatic species sensitivity using interspecies correlation and acute to chronic toxicity models

Determining species sensitivity of aquatic organisms to contaminants is a critical component of criteria development and ecolog...

Demonstration of the Web-based Interspecies Correlation Estimation (Web-ICE) modeling application

EPA Science Inventory

The Web-based Interspecies Correlation Estimation (Web-ICE) modeling application is available to the risk assessment community through a user-friendly internet platform (http://epa.gov/ceampubl/fchain/webice/). ICE models are log-linear least square regressions that predict acute...

Habitat interaction between two species of chipmunk in the Basin and Range Province of Nevada

USGS Publications Warehouse

Lowrey, Christopher; Longshore, Kathleen M.

2013-01-01

Interspecies interactions can affect how species are distributed, put constraints on habitat expansion, and reduce the fundamental niche of the affected species. Using logistic regression, we analyzed and compared 174 Tamias palmeri and 94 Tamias panamintinus within an isolated mountain range of the Basin and Range Province of southern Nevada. Tamias panamintinus was more likely to use pinyon/ponderosa/fir mixed forests than pinyon alone, compared to random sites. In the presence of T palmeri, however, interaction analyses indicated T. panamintinus was less likely to occupy the mixed forests and more likely near large rocks on southern aspects. This specie s-by-habitat interaction data suggest that T. palmeri excludes T panamintinus from areas of potentially suitable habitat. Climate change may adversely affect species of restricted distribution. Habitat isolation and species interactions in this region may thus increase survival risks as climate temperatures rise.

Potential for direct interspecies electron transfer in an electric-anaerobic system to increase methane production from sludge digestion.

PubMed

Zhao, Zhiqiang; Zhang, Yaobin; Wang, Liying; Quan, Xie

2015-06-09

Direct interspecies electron transfer (DIET) between Geobacter species and Methanosaeta species is an alternative to interspecies hydrogen transfer (IHT) in anaerobic digester, which however has not been established in anaerobic sludge digestion as well as in bioelectrochemical systems yet. In this study, it was found that over 50% of methane production of an electric-anaerobic sludge digester was resulted from unknown pathway. Pyrosequencing analysis revealed that Geobacter species were significantly enriched with electrodes. Fluorescence in situ hybridization (FISH) further confirmed that the dominant Geobacter species enriched belonged to Geobacter metallireducens. Together with Methanosaeta species prevailing in the microbial communities, the direct electron exchange between Geobacter species and Methanosaeta species might be an important reason for the "unknown" increase of methane production. Conductivity of the sludge in this electric-anaerobic digester was about 30% higher than that of the sludge in a control digester without electrodes. This study not only revealed for the first time that DIET might be the important mechanism on the methanogenesis of bioelectrochemical system, but also provided a new method to enhance DIET by means of bioelectric enrichment of Geobacter species.

Potential for direct interspecies electron transfer in an electric-anaerobic system to increase methane production from sludge digestion

PubMed Central

Zhao, Zhiqiang; Zhang, Yaobin; Wang, Liying; Quan, Xie

2015-01-01

Direct interspecies electron transfer (DIET) between Geobacter species and Methanosaeta species is an alternative to interspecies hydrogen transfer (IHT) in anaerobic digester, which however has not been established in anaerobic sludge digestion as well as in bioelectrochemical systems yet. In this study, it was found that over 50% of methane production of an electric-anaerobic sludge digester was resulted from unknown pathway. Pyrosequencing analysis revealed that Geobacter species were significantly enriched with electrodes. Fluorescence in situ hybridization (FISH) further confirmed that the dominant Geobacter species enriched belonged to Geobacter metallireducens. Together with Methanosaeta species prevailing in the microbial communities, the direct electron exchange between Geobacter species and Methanosaeta species might be an important reason for the “unknown” increase of methane production. Conductivity of the sludge in this electric-anaerobic digester was about 30% higher than that of the sludge in a control digester without electrodes. This study not only revealed for the first time that DIET might be the important mechanism on the methanogenesis of bioelectrochemical system, but also provided a new method to enhance DIET by means of bioelectric enrichment of Geobacter species. PMID:26057581

Influence of Taxonomic Relatedness and Chemical Mode of Action in Acute Interspecies Estimation Models for Aquatic species

EPA Science Inventory

Ecological risks to aquatic organisms are typically assessed using toxicity data for relatively few species and with limited understanding of relative species sensitivity. We developed a comprehensive set of interspecies correlation estimation (ICE) models for aquatic organisms a...

Lessons from Interspecies Mammalian Chimeras.

PubMed

Suchy, Fabian; Nakauchi, Hiromitsu

2017-10-06

As chimeras transform from beasts of Greek mythology into tools of contemporary bioscience, secrets of developmental biology and evolutionary divergence are being revealed. Recent advances in stem cell biology and interspecies chimerism have generated new models with extensive basic and translational applications, including generation of transplantable, patient-specific organs.

Comparison of Species Sensitivity Distributions Derived from Interspecies Correlation Models to Distributions used to Derive Water Quality Criteria

EPA Science Inventory

Species sensitivity distributions (SSD) require a large number of measured toxicity values to define a chemical’s toxicity to multiple species. This investigation comprehensively evaluated the accuracy of SSDs generated from toxicity values predicted from interspecies correlation...

Microbial herd protection mediated by antagonistic interaction in polymicrobial communities.

PubMed

Wong, Megan; Liang, Xiaoye; Smart, Matt; Tang, Le; Moore, Richard; Ingalls, Brian; Dong, Tao G

2016-09-16

In the host and natural environments, microbes often exist in complex multispecies communities. The molecular mechanisms through which such communities develop and persist - despite significant antagonistic interactions between species - are not well understood. The type VI secretion system (T6SS) is a lethal weapon commonly employed by Gram-negative bacteria to inhibit neighboring species through delivery of toxic effectors. It is well established that intra-species protection is conferred by immunity proteins that neutralize effector toxicities. By contrast, the mechanisms for interspecies protection are not clear. Here we use two T6SS active antagonistic bacteria, Aeromonas hydrophila (AH) and Vibrio cholerae (VC), to demonstrate that interspecies protection is dependent on effectors. AH and VC do not share conserved immunity genes but could equally co-exist in a mixture. However, mutants lacking the T6SS or effectors were effectively eliminated by the other competing wild type. Time-lapse microscopy analyses show that mutually lethal interactions drive the segregation of mixed species into distinct single-species clusters by eliminating interspersed single cells. Cluster formation provides herd protection by abolishing lethal interaction inside each cluster and restricting it to the boundary. Using an agent-based modeling approach, we simulated the antagonistic interactions of two hypothetical species. The resulting simulations recapitulate our experimental observation. These results provide mechanistic insights for the general role of microbial weapons in determining the structures of complex multispecies communities. Investigating the warfare of microbes allows us to better understand the ecological relationships in complex microbial communities such as the human microbiota. Here we use the T6SS, a deadly bacterial weapon, as a model to demonstrate the importance of lethal interactions in determining community structures and exchange of genetic materials. This simplified model elucidates a mechanism of microbial herd protection by which competing antagonistic species coexist in the same niche despite their diverse mutually destructive activities. Our results also suggest that antagonistic interaction imposes a strong selection that could promote multicellular like social behaviors and contribute to the transition to multicellularity during evolution. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Mechanisms Underlying Mammalian Hybrid Sterility in Two Feline Interspecies Models.

PubMed

Davis, Brian W; Seabury, Christopher M; Brashear, Wesley A; Li, Gang; Roelke-Parker, Melody; Murphy, William J

2015-10-01

The phenomenon of male sterility in interspecies hybrids has been observed for over a century, however, few genes influencing this recurrent phenotype have been identified. Genetic investigations have been primarily limited to a small number of model organisms, thus limiting our understanding of the underlying molecular basis of this well-documented "rule of speciation." We utilized two interspecies hybrid cat breeds in a genome-wide association study employing the Illumina 63 K single-nucleotide polymorphism array. Collectively, we identified eight autosomal genes/gene regions underlying associations with hybrid male sterility (HMS) involved in the function of the blood-testis barrier, gamete structural development, and transcriptional regulation. We also identified several candidate hybrid sterility regions on the X chromosome, with most residing in close proximity to complex duplicated regions. Differential gene expression analyses revealed significant chromosome-wide upregulation of X chromosome transcripts in testes of sterile hybrids, which were enriched for genes involved in chromatin regulation of gene expression. Our expression results parallel those reported in Mus hybrids, supporting the "Large X-Effect" in mammalian HMS and the potential epigenetic basis for this phenomenon. These results support the value of the interspecies feline model as a powerful tool for comparison to rodent models of HMS, demonstrating unique aspects and potential commonalities that underpin mammalian reproductive isolation. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Antagonistic interactions amongst bacteriocin-producing enteric bacteria in dual species biofilms.

PubMed

Tait, K; Sutherland, I W

2002-01-01

The objective of this study was to investigate the antagonistic interactions between bacteriocin-producing enteric bacteria in dual species biofilms and the interspecies interactions correlated with sensitivity to biocides. When compared with their single species counterparts, the dual species biofilms formed by bacteriocin-producing strains exhibited a decrease in biofilm size and an increase in sensitivity to the antimicrobial agents hypochlorite, triclosan and benzalkonium chloride. The five dual species biofilms studied all resulted in biofilms containing a mixture of the two strains. This was attributed to the spatial distribution of cells within the biofilm, with each strain forming its own microcolonies. The production of a bacteriocin also gave a strain a competitive advantage when interacting with a bacteriocin-sensitive strain within a biofilm, both in gaining a foothold in a new environment and in preventing the colonization of a potential competitor into a pre-established biofilm. It was concluded that bacteriocins might be used specifically for interacting with competing strains within a biofilm, as opposed to a planktonic, environment. Unlike planktonically grown bacteriocin-producing populations, where one strain will always be out-competed, bacteriocin-producing and bacteriocin-sensitive strains can coexist in biofilm communities, clearly demonstrating major differences between biofilm and planktonic competition. This paper highlights the importance of bacteriocin production in the development of biofilm communities.

Using Web-based Interspecies Correlation Estimation (Web-ICE) models as a tool for acute toxicity prediction

EPA Science Inventory

In order to assess risk of contaminants to taxa with limited or no toxicity data available, Interspecies Correlation Estimation (ICE) models have been developed by the U.S. Environmental Protection Agency to extrapolate contaminant sensitivity predictions based on data from commo...

Development of Algal Interspecies Correlation Estimation Models for Chemical Hazard Assessment

EPA Science Inventory

Web-based Interspecies Correlation Estimation (ICE) is an application developed to predict the acute toxicity of a chemical from 1 species to another taxon. Web-ICE models use the acute toxicity value for a surrogate species to predict effect values for other species, thus potent...

Human and Rat ABC Transporter Efflux of Bisphenol A and Bisphenol A Glucuronide: Interspecies Comparison and Implications for Pharmacokinetic Assessment

EPA Science Inventory

Significant interspecies differences exist between human and rodent with respect to absorption, distribution, and excretion of bisphenol A (BPA) and its primary metabolite, BPA-glucuronide (BPA-G). ATP-Binding Cassette (ABC) transporter enzymes play important roles in these physi...

INTERSPECIES CORRELATION ESTIMATION (ICE) FOR ACUTE TOXICITY TO AQUATIC ORGANISMS AND WILDLIFE. II. USER MANUAL AND SOFTWARE

EPA Science Inventory

Asfaw, Amha, Mark R. Ellersieck and Foster L. Mayer. 2003. Interspecies Correlation Estimations (ICE) for Acute Toxicity to Aquatic Organisms and Wildlife. II. User Manual and Software. EPA/600/R-03/106. U.S. Environmental Protection Agency, National Health and Environmental Effe...

76 FR 33752 - Notice of Availability of the External Review Draft of the Guidance for Applying Quantitative...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-09

... External Review Draft of the Guidance for Applying Quantitative Data To Develop Data-Derived Extrapolation... Applying Quantitative Data to Develop Data-Derived Extrapolation Factors for Interspecies and Intraspecies... Applying Quantitative Data to Develop Data-Derived Extrapolation Factors for Interspecies and Intraspecies...

Web-based Interspecies Correlation Estimation (Web-ICE) for Acute Toxicity: User Manual Version 3.1

EPA Science Inventory

Predictive toxicological models are integral to ecological risk assessment because data for most species are limited. Web-based Interspecies Correlation Estimation (Web-ICE) models are least square regressions that predict acute toxicity (LC50/LD50) of a chemical to a species, ge...

WEB-BASED INTERSPECIES CORRELATION ESTIMATION (WEB-ICE) FOR ACUTE TOXICITY: USER MANUAL V2

EPA Science Inventory

Predictive toxicological models are integral to environmental risk Assessment where data for most species are limited. Web-based Interspecies Correlation Estimation (Web-ICE) models are least square regressions that predict acute toxicity (LC50/LD50) of a chemical to a species, ...

INTERSPIA: a web application for exploring the dynamics of protein-protein interactions among multiple species.

PubMed

Kwon, Daehong; Lee, Daehwan; Kim, Juyeon; Lee, Jongin; Sim, Mikang; Kim, Jaebum

2018-05-09

Proteins perform biological functions through cascading interactions with each other by forming protein complexes. As a result, interactions among proteins, called protein-protein interactions (PPIs) are not completely free from selection constraint during evolution. Therefore, the identification and analysis of PPI changes during evolution can give us new insight into the evolution of functions. Although many algorithms, databases and websites have been developed to help the study of PPIs, most of them are limited to visualize the structure and features of PPIs in a chosen single species with limited functions in the visualization perspective. This leads to difficulties in the identification of different patterns of PPIs in different species and their functional consequences. To resolve these issues, we developed a web application, called INTER-Species Protein Interaction Analysis (INTERSPIA). Given a set of proteins of user's interest, INTERSPIA first discovers additional proteins that are functionally associated with the input proteins and searches for different patterns of PPIs in multiple species through a server-side pipeline, and second visualizes the dynamics of PPIs in multiple species using an easy-to-use web interface. INTERSPIA is freely available at http://bioinfo.konkuk.ac.kr/INTERSPIA/.

ISAAC - InterSpecies Analysing Application using Containers.

PubMed

Baier, Herbert; Schultz, Jörg

2014-01-15

Information about genes, transcripts and proteins is spread over a wide variety of databases. Different tools have been developed using these databases to identify biological signals in gene lists from large scale analysis. Mostly, they search for enrichments of specific features. But, these tools do not allow an explorative walk through different views and to change the gene lists according to newly upcoming stories. To fill this niche, we have developed ISAAC, the InterSpecies Analysing Application using Containers. The central idea of this web based tool is to enable the analysis of sets of genes, transcripts and proteins under different biological viewpoints and to interactively modify these sets at any point of the analysis. Detailed history and snapshot information allows tracing each action. Furthermore, one can easily switch back to previous states and perform new analyses. Currently, sets can be viewed in the context of genomes, protein functions, protein interactions, pathways, regulation, diseases and drugs. Additionally, users can switch between species with an automatic, orthology based translation of existing gene sets. As todays research usually is performed in larger teams and consortia, ISAAC provides group based functionalities. Here, sets as well as results of analyses can be exchanged between members of groups. ISAAC fills the gap between primary databases and tools for the analysis of large gene lists. With its highly modular, JavaEE based design, the implementation of new modules is straight forward. Furthermore, ISAAC comes with an extensive web-based administration interface including tools for the integration of third party data. Thus, a local installation is easily feasible. In summary, ISAAC is tailor made for highly explorative interactive analyses of gene, transcript and protein sets in a collaborative environment.

A modeling approach to direct interspecies electron transfer process in anaerobic transformation of ethanol to methane.

PubMed

Liu, Yiwen; Zhang, Yaobin; Zhao, Zhiqiang; Ngo, Huu Hao; Guo, Wenshan; Zhou, Junliang; Peng, Lai; Ni, Bing-Jie

2017-01-01

Recent studies have shown that direct interspecies electron transfer (DIET) plays an important part in contributing to methane production from anaerobic digestion. However, so far anaerobic digestion models that have been proposed only consider two pathways for methane production, namely, acetoclastic methanogenesis and hydrogenotrophic methanogenesis, via indirect interspecies hydrogen transfer, which lacks an effective way for incorporating DIET into this paradigm. In this work, a new mathematical model is specifically developed to describe DIET process in anaerobic digestion through introducing extracellular electron transfer as a new pathway for methane production, taking anaerobic transformation of ethanol to methane as an example. The developed model was able to successfully predict experimental data on methane dynamics under different experimental conditions, supporting the validity of the developed model. Modeling predictions clearly demonstrated that DIET plays an important role in contributing to overall methane production (up to 33 %) and conductive material (i.e., carbon cloth) addition would significantly promote DIET through increasing ethanol conversion rate and methane production rate. The model developed in this work will potentially enhance our current understanding on syntrophic metabolism via DIET.

Metazoa Ludens: Mixed Reality Interaction and Play Between Humans and Animals

NASA Astrophysics Data System (ADS)

Cheok, Adrian David

Although animals and pets are so important for families and society, in modern urban lifestyles we can spend little time with our animal friends. Interactive media should be aimed to enhance not only human-to-human communication, but also human-to-animal communication. Thus, we promote a new type of inter-species media interaction which allows human users to interact and play with their small pet friends (in this case hamsters) remotely via the Internet through a mixed reality based game system “Metazoa Ludens”. We scientifically examined the effectiveness of this system in a two-pronged approach. Firstly and most importantly, the positive effects to the hamsters were ensured using Body Condition Score study. Secondly, the method of Duncan was used to assess the strength of preference of the hamsters towards Metazoa Ludens. Lastly, the effectiveness of this remote interaction with respect to the human users as a interactive gaming system with their pets/friends (hamsters) was examined based on Csikszentmihalyi's (Beyond boredom and anxiety, 1975) Flow theory. The results of both studies inform of positive remote interaction between human users and their pet friends using our research system. This research is not aimed just at providing specific experimental results on the implemented research system, but is aimed as a wider lesson for human-to-animal interactive media. Thus also the lessons learned are extrapolated and detailed in this chapter as a framework in general for human-to-animal interaction systems.

USE OF INTERSPECIES CORRELATION ESTIMATIONS TO PREDICT HC5'S BASED ON QSAR

EPA Science Inventory

Dyer, S.D., S. Belanger, J. Chaney, D. Versteeg and F. Mayer. In press. Use of Interspecies Correlation Estimations to predict HC5's Based on QSARs (Abstract). To be presented at the SETAC Europe 14th Annual Meeting: Environmental Science Solution: A Pan-European Perspective, 18-...

Application of the Web-based Interspecies Correlation Estimation (Web-ICE) tool to assess risks of national pesticide registrations to federally listed (threatened and endangered) species

EPA Science Inventory

The National Academy of Science (NAS) recently recommended exploration of predictive tools, such as interspecies correlation estimation (ICE), to estimate acute toxicity values for listed species and support development of species sensitivity distributions (SSDs). We explored the...

Trichostatin A (TSA) improves the development of rabbit-rabbit intraspecies cloned embryos, but not rabbit-human interspecies cloned embryos.

PubMed

Shi, Li-Hong; Miao, Yi-Liang; Ouyang, Ying-Chun; Huang, Jun-Cheng; Lei, Zi-Li; Yang, Ji-Wen; Han, Zhi-Ming; Song, Xiang-Fen; Sun, Qing-Yuan; Chen, Da-Yuan

2008-03-01

The interspecies somatic cell nuclear transfer (iSCNT) technique for therapeutic cloning gives great promise for treatment of many human diseases. However, the incomplete nuclear reprogramming and the low blastocyst rate of iSCNT are still big problems. Herein, we observed the effect of TSA on the development of rabbit-rabbit intraspecies and rabbit-human interspecies cloned embryos. After treatment with TSA for 6 hr during activation, we found that the blastocyst rate of rabbit-rabbit cloned embryos was more than two times higher than that of untreated embryos; however, the blastocyst rate of TSA-treated rabbit-human interspecies cloned embryos decreased. We also found evident time-dependent histone deacetylation-reacetylation changes in rabbit-rabbit cloned embryos, but not in rabbit-human cloned embryos from fusion to 6 hr after activation. Our results suggest that TSA-treatment does not improve blastocyst development of rabbit-human iSCNT embryos and that abnormal histone deacetylation-reacetylation changes in iSCNT embryos may account for their poor blastocyst development. (c) 2008 Wiley-Liss, Inc.

PCPPI: a comprehensive database for the prediction of Penicillium-crop protein-protein interactions.

PubMed

Yue, Junyang; Zhang, Danfeng; Ban, Rongjun; Ma, Xiaojing; Chen, Danyang; Li, Guangwei; Liu, Jia; Wisniewski, Michael; Droby, Samir; Liu, Yongsheng

2017-01-01

Penicillium expansum , the causal agent of blue mold, is one of the most prevalent post-harvest pathogens, infecting a wide range of crops after harvest. In response, crops have evolved various defense systems to protect themselves against this and other pathogens. Penicillium -crop interaction is a multifaceted process and mediated by pathogen- and host-derived proteins. Identification and characterization of the inter-species protein-protein interactions (PPIs) are fundamental to elucidating the molecular mechanisms underlying infection processes between P. expansum and plant crops. Here, we have developed PCPPI, the Penicillium -Crop Protein-Protein Interactions database, which is constructed based on the experimentally determined orthologous interactions in pathogen-plant systems and available domain-domain interactions (DDIs) in each PPI. Thus far, it stores information on 9911 proteins, 439 904 interactions and seven host species, including apple, kiwifruit, maize, pear, rice, strawberry and tomato. Further analysis through the gene ontology (GO) annotation indicated that proteins with more interacting partners tend to execute the essential function. Significantly, semantic statistics of the GO terms also provided strong support for the accuracy of our predicted interactions in PCPPI. We believe that all the PCPPI datasets are helpful to facilitate the study of pathogen-crop interactions and freely available to the research community. : http://bdg.hfut.edu.cn/pcppi/index.html. © The Author(s) 2017. Published by Oxford University Press.

Microbial interspecies electron transfer via electric currents through conductive minerals

PubMed Central

Kato, Souichiro; Hashimoto, Kazuhito; Watanabe, Kazuya

2012-01-01

In anaerobic biota, reducing equivalents (electrons) are transferred between different species of microbes [interspecies electron transfer (IET)], establishing the basis of cooperative behaviors and community functions. IET mechanisms described so far are based on diffusion of redox chemical species and/or direct contact in cell aggregates. Here, we show another possibility that IET also occurs via electric currents through natural conductive minerals. Our investigation revealed that electrically conductive magnetite nanoparticles facilitated IET from Geobacter sulfurreducens to Thiobacillus denitrificans, accomplishing acetate oxidation coupled to nitrate reduction. This two-species cooperative catabolism also occurred, albeit one order of magnitude slower, in the presence of Fe ions that worked as diffusive redox species. Semiconductive and insulating iron-oxide nanoparticles did not accelerate the cooperative catabolism. Our results suggest that microbes use conductive mineral particles as conduits of electrons, resulting in efficient IET and cooperative catabolism. Furthermore, such natural mineral conduits are considered to provide ecological advantages for users, because their investments in IET can be reduced. Given that conductive minerals are ubiquitously and abundantly present in nature, electric interactions between microbes and conductive minerals may contribute greatly to the coupling of biogeochemical reactions. PMID:22665802

From genomes to metabolomes: Understanding mechanisms of symbiosis and cell-cell signaling using the archaeal system Ignicoccus-Nanoarchaeum

DOE Office of Scientific and Technical Information (OSTI.GOV)

Podar, Mircea; Hettich, Robert; Copie, Valerie

The main objective of this project was to use symbiotic Nanoarchaeaota, a group of thermophilic Archaea that are obligate symbionts/parasites on other Archaea, to develop an integrated multi-omic approach to study inter-species interactions as well as to understand fundamental mechanism that enable such relationships. As part of this grant we have achieved a number of important milestone on both technical and scientific levels. On the technical side, we developed immunofluorescence labeling and tracking methods to follow Nanoarchaeota in cultures and in environmental samples, we applied such methods in conjunction with flow cytometry to quantify and isolate uncultured representatives from themore » environment and characterized them by single cell genomics. On the proteomics side, we developed a more efficient and sensitive method to recover and semi-quantitatively measure membrane proteins, while achieving high total cellular proteome coverage (70-80% of the predicted proteome). Metabolomic analyses used complementary NMR and LC/GC mass spectrometry and led to the identification of novel lipids in these organisms as well as quantification of some of the major metabolites. Importantly, using several informatics approaches we were also able to integrate the transcriptomic, proteomic and metabolomic datasets, revealing aspects of the interspecies interaction that were not evident in the single omic analyses (manuscript in review). On the science side we determined that N. equitans and I. hospitalis are metabolically coupled and that N. equitans is strictly dependent on its host both for metabolic precursors and energetic needs. The actual mechanism by which small molecules move across the cell membrane remains unknown. The Ignicoccus host responds to the metabolic and energetic burned by upregulating of key primary metabolism steps and ATP synthesis. The two species have co-evolved, aspect that we determined by comparative genomics with other species of Ignicoccus (manuscript in preparation) and by characterizing other similar Nanoarchaeota systems. Using a single cell genomics approach we characterized the first terrestrial geothermal Nanoarchaeota system, from Yellowstone National Park. That nanoarchaeon uses a different host, a species of Sulfolobales, and comparative genomics with N. equitans-Ignicoccus allowed us to come up with an evolutionary model for the evolution of this group of organisms across marine and terrestrial ecosystems. Based on metabolic inferences we were also able to isolate in culture the first such terrestrial nanoarchaeal system, also from Yellowstone, which involves a species of Acidilobus. The novel nanoarchaeal system was characterized using proteomics and it helped us better understand the metabolic capabilities of these organisms as well as how co-evolution shapes the genomes of interacting species. It was also one of the very few cases in which prior genomic data was used to successfully design an approach to culture an organism, which remains the gold standard in microbiology research. As a better understanding of interspecies interaction requires multiple model systems, we have pursued identification and genomic characterization or isolation of additional nanoarchaeal systems from geographically and geochemically distinct environments. Two additional nanoarchaeal systems are presently being characterized from hot springs in Yellowstone and Iceland and will be the subject to future publications.« less

Saccharomyces interspecies hybrids as model organisms for studying yeast adaptation to stressful environments.

PubMed

Lopandic, Ksenija

2018-01-01

The strong development of molecular biology techniques and next-generation sequencing technologies in the last two decades has significantly improved our understanding of the evolutionary history of Saccharomyces yeasts. It has been shown that many strains isolated from man-made environments are not pure genetic lines, but contain genetic materials from different species that substantially increase their genome complexity. A number of strains have been described as interspecies hybrids, implying different yeast species that under specific circumstances exchange and recombine their genomes. Such fusing usually results in a wide variety of alterations at the genetic and chromosomal levels. The observed changes have suggested a high genome plasticity and a significant role of interspecies hybridization in the adaptation of yeasts to environmental stresses and industrial processes. There is a high probability that harsh wine and beer fermentation environments, from which the majority of interspecies hybrids have been isolated so far, influence their selection and stabilization as well as their genomic and phenotypic heterogeneity. The lessons we have learned about geno- and phenotype plasticity and the diversity of natural and commercial yeast hybrids have already had a strong impact on the development of artificial hybrids that can be successfully used in the fermentation-based food and beverage industry. The creation of artificial hybrids through the crossing of strains with desired attributes is a possibility to obtain a vast variety of new, but not genetically modified yeasts with a range of improved and beneficial traits. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

[In vitro development and chimeric efficiency of mouse-porcine interspecies chimeric embryos in different culture systems].

PubMed

Wang, Ying; Ren, Jilong; Song, Yuran; Hai, Tang; Zhou, Qi; Liu, Zhonghua

2016-07-25

With the advancements of stem cells and regenerative medicine, interspecies chimera has become a hot topic and will pave a new way of providing donor sources in organ transplantation. However, the interspecies chimera is confronted with a number of scientific questions and technical obstacles, including selections of appropriate embryonic stage and appropriate culture medium; those factors will deeply influence the developmental balance between donor cells and receptor embryos. Due to its relatively rapid reproductive cycle and similar organ size to human's, porcine is a very potential donor candidate to study these questions. To compare the development and chimeric efficiency of interspecies embryos, we tested and evaluated three different culture systems, PZM-3 (Porcine zygotic medium), culture medium for iPSCs (N2B27) and 3.5 h of N2B27 before PZM-3 (N2B27(3.5 h)), and two different embryonic stages, 8-cell and blastocyst in mouse-porcine chimeric embryos using parthenogenetically activated porcine embryos and mouse induced pluripotent stem cells (miPS). The results showed that, PZM-3 was beneficial for both development of chimeric embryos and miPSCs proliferation in porcine embryos in the 8-cell injection group. After early blastocyst injection, the chimeric efficiency did not appear significantly different among the three culture systems but was lower than 8-cell injection. In summary, the results suggest that 8-cell injection and PZM-3 culture medium are more beneficial to the in vitro development and chimeric efficiency of mouse-porcine chimeric embryos.

Comprehensive mollusk acute toxicity database improves the use of Interspecies Correlation Estimation (ICE) models to predict toxicity of untested freshwater and endangered mussel species

EPA Science Inventory

Interspecies correlation estimation (ICE) models extrapolate acute toxicity data from surrogate test species to untested taxa. A suite of ICE models developed from a comprehensive database is available on the US Environmental Protection Agency’s web-based application, Web-I...

SPECIES DIFFERENCES IN ANDROGEN AND ESTROGEN RECEPTOR STRUCTURE AND FUNCTION AMONG VERTEBRATES AND INVERTEBRATES: INTERSPECIES EXTRAPOLATIONS REGARDING ENDOCRINE DISRUPTING CHEMICALS

EPA Science Inventory

Species Differences in Androgen and Estrogen Receptor Structure and Function Among Vertebrates and Invertebrates: Interspecies Extrapolations regarding Endocrine Disrupting Chemicals
VS Wilson1, GT Ankley2, M Gooding 1,3, PD Reynolds 1,4, NC Noriega 1, M Cardon 1, P Hartig1,...

USE OF INTERSPECIES CORRELATION ESTIMATIONS TO PREDICT HC5'S BASED ON MINIMAL DATA

EPA Science Inventory

Dyer, S., S. Belanger, J. Chaney, D. Versteeg and F. Mayer. In press. Use of Interspecies Correlation Estimations to Predict HC5's Based on Minimal Data (Abstract). To be presented at the SETAC Fourth World Congress, 14-18 November 2004, Portland, OR. 1 p. (ERL,GB R1013).

Metabolite exchange between microbiome members produces compounds that influence Drosophila behavior

PubMed Central

Fischer, Caleb N; Trautman, Eric P; Crawford, Jason M; Stabb, Eric V; Handelsman, Jo; Broderick, Nichole A

2017-01-01

Animals host multi-species microbial communities (microbiomes) whose properties may result from inter-species interactions; however, current understanding of host-microbiome interactions derives mostly from studies in which elucidation of microbe-microbe interactions is difficult. In exploring how Drosophila melanogaster acquires its microbiome, we found that a microbial community influences Drosophila olfactory and egg-laying behaviors differently than individual members. Drosophila prefers a Saccharomyces-Acetobacter co-culture to the same microorganisms grown individually and then mixed, a response mainly due to the conserved olfactory receptor, Or42b. Acetobacter metabolism of Saccharomyces-derived ethanol was necessary, and acetate and its metabolic derivatives were sufficient, for co-culture preference. Preference correlated with three emergent co-culture properties: ethanol catabolism, a distinct volatile profile, and yeast population decline. Egg-laying preference provided a context-dependent fitness benefit to larvae. We describe a molecular mechanism by which a microbial community affects animal behavior. Our results support a model whereby emergent metabolites signal a beneficial multispecies microbiome. DOI: http://dx.doi.org/10.7554/eLife.18855.001 PMID:28068220

Two-component quantum Hall effects in topological flat bands

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zeng, Tian-Sheng; Zhu, Wei; Sheng, D. N.

2017-03-27

Here in this paper, we study quantum Hall states for two-component particles (hardcore bosons and fermions) loading in topological lattice models. By tuning the interplay of interspecies and intraspecies interactions, we demonstrate that two-component fractional quantum Hall states emerge at certain fractional filling factors ν = 1/2 for fermions (ν = 2/3 for bosons) in the lowest Chern band, classified by features from ground states including the unique Chern number matrix (inverse of the K matrix), the fractional charge and spin pumpings, and two parallel propagating edge modes. Moreover, we also apply our strategy to two-component fermions at integer fillingmore » factor ν = 2 , where a possible topological Neel antiferromagnetic phase is under intense debate very recently. For the typical π -flux checkerboard lattice, by tuning the onsite Hubbard repulsion, we establish a first-order phase transition directly from a two-component fermionic ν = 2 quantum Hall state at weak interaction to a topologically trivial antiferromagnetic insulator at strong interaction, and therefore exclude the possibility of an intermediate topological phase for our system.« less

Diffusion of multiple species with excluded-volume effects.

PubMed

Bruna, Maria; Chapman, S Jonathan

2012-11-28

Stochastic models of diffusion with excluded-volume effects are used to model many biological and physical systems at a discrete level. The average properties of the population may be described by a continuum model based on partial differential equations. In this paper we consider multiple interacting subpopulations/species and study how the inter-species competition emerges at the population level. Each individual is described as a finite-size hard core interacting particle undergoing brownian motion. The link between the discrete stochastic equations of motion and the continuum model is considered systematically using the method of matched asymptotic expansions. The system for two species leads to a nonlinear cross-diffusion system for each subpopulation, which captures the enhancement of the effective diffusion rate due to excluded-volume interactions between particles of the same species, and the diminishment due to particles of the other species. This model can explain two alternative notions of the diffusion coefficient that are often confounded, namely collective diffusion and self-diffusion. Simulations of the discrete system show good agreement with the analytic results.

Global and quantitative proteomic analysis of dogs infected by avian-like H3N2 canine influenza virus

PubMed Central

Su, Shuo; Tian, Jin; Hong, Malin; Zhou, Pei; Lu, Gang; Zhu, Huachen; Zhang, Guihong; Lai, Alexander; Li, Shoujun

2015-01-01

Canine influenza virus A (H3N2) is a newly emerged etiological agent for respiratory infections in dogs. The mechanism of interspecies transmission from avian to canine species and the development of diseases in this new host remain to be explored. To investigate this, we conducted a differential proteomics study in 2-month-old beagles inoculated intranasally with 106 TCID50 of A/canine/Guangdong/01/2006 (H3N2) virus. Lung sections excised at 12 h post-inoculation (hpi), 4 days, and 7 days post-inoculation (dpi) were processed for global and quantitative analysis of differentially expressed proteins. A total of 17,796 proteins were identified at different time points. About 1.6% was differentially expressed between normal and infected samples. Of these, 23, 27, and 136 polypeptides were up-regulated, and 14, 18, and 123 polypeptides were down-regulated, at 12 hpi, 4 dpi, and 7 dpi, respectively. Vann diagram analysis indicated that 17 proteins were up-regulated and one was down-regulated at all three time points. Selected proteins were validated by real-time PCR and by Western blot. Our results show that apoptosis and cytoskeleton-associated proteins expression was suppressed, whereas interferon-induced proteins plus other innate immunity proteins were induced after the infection. Understanding of the interactions between virus and the host will provide insights into the basis of interspecies transmission, adaptation, and virus pathogenicity. PMID:25883591

Volatile Compounds Emitted by Pseudomonas aeruginosa Stimulate Growth of the Fungal Pathogen Aspergillus fumigatus.

PubMed

Briard, Benoit; Heddergott, Christoph; Latgé, Jean-Paul

2016-03-15

Chronic lung infections with opportunistic bacterial and fungal pathogens are a major cause of morbidity and mortality especially in patients with cystic fibrosis. Pseudomonas aeruginosa is the most frequently colonizing bacterium in these patients, and it is often found in association with the filamentous fungus Aspergillus fumigatus. P. aeruginosa is known to inhibit the growth of A. fumigatus in situations of direct contact, suggesting the existence of interspecies communication that may influence disease outcome. Our study shows that the lung pathogens P. aeruginosa and A. fumigatus can interact at a distance via volatile-mediated communication and expands our understanding of interspecific signaling in microbial communities. Microbiota studies have shown that pathogens cannot be studied individually anymore and that the establishment and progression of a specific disease are due not to a single microbial species but are the result of the activity of many species living together. To date, the interaction between members of the human microbiota has been analyzed in situations of direct contact or liquid-mediated contact between organisms. This study showed unexpectedly that human opportunistic pathogens can interact at a distance after sensing volatiles emitted by another microbial species. This finding will open a new research avenue for the understanding of microbial communities. Copyright © 2016 Briard et al.

Enabling interspecies epigenomic comparison with CEpBrowser.

PubMed

Cao, Xiaoyi; Zhong, Sheng

2013-05-01

We developed the Comparative Epigenome Browser (CEpBrowser) to allow the public to perform multi-species epigenomic analysis. The web-based CEpBrowser integrates, manages and visualizes sequencing-based epigenomic datasets. Five key features were developed to maximize the efficiency of interspecies epigenomic comparisons. CEpBrowser is a web application implemented with PHP, MySQL, C and Apache. URL: http://www.cepbrowser.org/.

Performance of Proximity Loggers in Recording Intra- and Inter-Species Interactions: A Laboratory and Field-Based Validation Study

PubMed Central

Carter, Stephen P.; Bearhop, Stuart; Harrison, Xavier A.; Dall, Sasha R. X.; McDonald, Robbie A.; Delahay, Richard J.

2012-01-01

Knowledge of the way in which animals interact through social networks can help to address questions surrounding the ecological and evolutionary consequences of social organisation, and to understand and manage the spread of infectious diseases. Automated proximity loggers are increasingly being used to record interactions between animals, but the accuracy and reliability of the collected data remain largely un-assessed. Here we use laboratory and observational field data to assess the performance of these devices fitted to a herd of 32 beef cattle (Bos taurus) and nine groups of badgers (Meles meles, n  = 77) living in the surrounding woods. The distances at which loggers detected each other were found to decrease over time, potentially related to diminishing battery power that may be a function of temperature. Loggers were highly accurate in recording the identification of contacted conspecifics, but less reliable at determining contact duration. There was a tendency for extended interactions to be recorded as a series of shorter contacts. We show how data can be manipulated to correct this discrepancy and accurately reflect observed interaction patterns by combining records between any two loggers that occur within a 1 to 2 minute amalgamation window, and then removing any remaining 1 second records. We make universally applicable recommendations for the effective use of proximity loggers, to improve the validity of data arising from future studies. PMID:22745704

Inhibitory role of acyl homoserine lactones in hemolytic activity and viability of Streptococcus pyogenes M6 S165

PubMed Central

Saroj, Sunil D.; Holmer, Linda; Berengueras, Júlia M.; Jonsson, Ann-Beth

2017-01-01

Streptococcus pyogenes an adapted human pathogen asymptomatically colonizes the nasopharynx, among other polymicrobial communities. However, information on the events leading to the colonization and expression of virulence markers subject to interspecies and host-bacteria interactions are limited. The interference of acyl homoserine lactones (AHLs) with the hemolytic activity and viability of S. pyogenes M6 S165 was examined. AHLs, with fatty acid side chains ≥12 carbon atoms, inhibited hemolytic activity by downregulating the expression of the sag operon involved in the production of streptolysin S. Inhibitory AHLs upregulated the expression of transcriptional regulator LuxR. Electrophoretic mobility shift assays revealed the interaction of LuxR with the region upstream of sagA. AHL-mediated bactericidal activity observed at higher concentrations (mM range) was an energy-dependent process, constrained by the requirement of glucose and iron. Ferrichrome transporter FtsABCD facilitated transport of AHLs across the streptococcal membrane. The study demonstrates a previously unreported role for AHLs in S. pyogenes virulence. PMID:28303956

Inhibitory role of acyl homoserine lactones in hemolytic activity and viability of Streptococcus pyogenes M6 S165.

PubMed

Saroj, Sunil D; Holmer, Linda; Berengueras, Júlia M; Jonsson, Ann-Beth

2017-03-17

Streptococcus pyogenes an adapted human pathogen asymptomatically colonizes the nasopharynx, among other polymicrobial communities. However, information on the events leading to the colonization and expression of virulence markers subject to interspecies and host-bacteria interactions are limited. The interference of acyl homoserine lactones (AHLs) with the hemolytic activity and viability of S. pyogenes M6 S165 was examined. AHLs, with fatty acid side chains ≥12 carbon atoms, inhibited hemolytic activity by downregulating the expression of the sag operon involved in the production of streptolysin S. Inhibitory AHLs upregulated the expression of transcriptional regulator LuxR. Electrophoretic mobility shift assays revealed the interaction of LuxR with the region upstream of sagA. AHL-mediated bactericidal activity observed at higher concentrations (mM range) was an energy-dependent process, constrained by the requirement of glucose and iron. Ferrichrome transporter FtsABCD facilitated transport of AHLs across the streptococcal membrane. The study demonstrates a previously unreported role for AHLs in S. pyogenes virulence.

SARS-CoV and Emergent Coronaviruses: Viral Determinants of Interspecies Transmission

PubMed Central

Bolles, Meagan; Donaldson, Eric; Baric, Ralph

2011-01-01

Most new emerging viruses are derived from strains circulating in zoonotic reservoirs. Coronaviruses, which had an established potential for cross-species transmission within domesticated animals, suddenly became relevant with the unexpected emergence of the highly pathogenic human SARS-CoV strain from zoonotic reservoirs in 2002. SARS-CoV infected approximately 8000 people worldwide before public health measures halted the epidemic. Supported by robust time-ordered sequence variation, structural biology, well-characterized patient pools, and biological data, the emergence of SARS-CoV represents one of the best studied natural models of viral disease emergence from zoonotic sources. This review article summarizes previous and more recent advances into the molecular and structural characteristics, with particular emphasis on host-receptor interactions, that drove this remarkable virus disease outbreak in human populations. PMID:22180768

Species and interspecies radioimmunoassays for rat type C virus p30: interviral comparisons and assay of human tumor extracts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Charman, H.P.; White, M.H.; Rahman, R.

1976-01-01

The major internal protein, p30, of rat type C virus (RaLV) was purified and utilized to establish intra- and interspecies radioimmunoassays. Three rat viruses were compared in homologous and heterologous intraspecies assays with no evidence of type specificity. The only heterologous viruses to give inhibition in these species assays were the feline (FeLV) and hamster (HaLV) type C viruses; these reactions were incomplete and required high virus concentrations. An interspecies assay using a goat antiserum prepared after sequentially immunizing with FeLV, RD 114, and woolly monkey virus p30's and labeled RaLV p30 was inhibited by all mammalian type C viruses,more » although preferentially by RaLV, FeLV, and HaLV. Thus, as in a previously reported assay developed with HaLV p30, rat, hamster, and cat p30's seem more closely related to each other than to mouse type C virus p30. High levels of specific antigen were found in all cell lines producing rat virus, whereas embryonic tissues from several rat strains and cell lines considered virus-free based on other tests were negative for p30. Rats bearing tumors containing Moloney murine sarcoma virus (RaLV) did not contain free circulating antibody to RaLV p30. Fifty-one human tumor extracts (including two tumor cell lines) were tested for activity in the RaLV species and 47 in the interspecies assays after Sephadex gel filtration and pooling of material in the 15,000- to 40,000-molecular-weight range. At a sensitivity level of 7 ng/ml (0.7 ng/assay) in the interspecies assay, all human tissues, with one exception, were negative. The one positive result is considered nonspecific based on proteolysis of the labeled antigen. Input tissue protein of the purified tumor extracts averaged 1.9 mg/ml with a range of less than 0.025 to 22 mg/ml. Tissues from NIH Swiss mice processed in the same manner were positive in the interspecies assay but negative in the intraspecies RaLV assay. (auth)« less

Linearmycins Activate a Two-Component Signaling System Involved in Bacterial Competition and Biofilm Morphology

PubMed Central

2017-01-01

ABSTRACT Bacteria use two-component signaling systems to adapt and respond to their competitors and changing environments. For instance, competitor bacteria may produce antibiotics and other bioactive metabolites and sequester nutrients. To survive, some species of bacteria escape competition through antibiotic production, biofilm formation, or motility. Specialized metabolite production and biofilm formation are relatively well understood for bacterial species in isolation. How bacteria control these functions when competitors are present is not well studied. To address fundamental questions relating to the competitive mechanisms of different species, we have developed a model system using two species of soil bacteria, Bacillus subtilis and Streptomyces sp. strain Mg1. Using this model, we previously found that linearmycins produced by Streptomyces sp. strain Mg1 cause lysis of B. subtilis cells and degradation of colony matrix. We identified strains of B. subtilis with mutations in the two-component signaling system yfiJK operon that confer dual phenotypes of specific linearmycin resistance and biofilm morphology. We determined that expression of the ATP-binding cassette (ABC) transporter yfiLMN operon, particularly yfiM and yfiN, is necessary for biofilm morphology. Using transposon mutagenesis, we identified genes that are required for YfiLMN-mediated biofilm morphology, including several chaperones. Using transcriptional fusions, we found that YfiJ signaling is activated by linearmycins and other polyene metabolites. Finally, using a truncated YfiJ, we show that YfiJ requires its transmembrane domain to activate downstream signaling. Taken together, these results suggest coordinated dual antibiotic resistance and biofilm morphology by a single multifunctional ABC transporter promotes competitive fitness of B. subtilis. IMPORTANCE DNA sequencing approaches have revealed hitherto unexplored diversity of bacterial species in a wide variety of environments that includes the gastrointestinal tract of animals and the rhizosphere of plants. Interactions between different species in bacterial communities have impacts on our health and industry. However, many approaches currently used to study whole bacterial communities do not resolve mechanistic details of interspecies interactions, including how bacteria sense and respond to their competitors. Using a competition model, we have uncovered dual functions for a previously uncharacterized two-component signaling system involved in specific antibiotic resistance and biofilm morphology. Insights gleaned from signaling within interspecies interaction models build a more complete understanding of gene functions important for bacterial communities and will enhance community-level analytical approaches. PMID:28461449

Interspecies communication between plant and mouse gut host cells through edible plant derived exosome-like nanoparticles.

PubMed

Mu, Jingyao; Zhuang, Xiaoying; Wang, Qilong; Jiang, Hong; Deng, Zhong-Bin; Wang, Baomei; Zhang, Lifeng; Kakar, Sham; Jun, Yan; Miller, Donald; Zhang, Huang-Ge

2014-07-01

Exosomes, small vesicles participating in intercellular communication, have been extensively studied recently; however, the role of edible plant derived exosomes in interspecies communication has not been investigated. Here, we investigate the biological effects of edible plant derived exosome-like nanoparticles (EPDENs) on mammalian cells. In this study, exosome-like nanoparticles from four edible plants were isolated and characterized. We show that these EPDENs contain proteins, lipids, and microRNA. EPDENs are taken up by intestinal macrophages and stem cells. The results generated from EPDEN-transfected macrophages indicate that ginger EPDENs preferentially induce the expression of the antioxidation gene, heme oxygenase-1 and the anti-inflammatory cytokine, IL-10; whereas grapefruit, ginger, and carrot EPDENs promote activation of nuclear factor like (erythroid-derived 2). Furthermore, analysis of the intestines of canonical Wnt-reporter mice, i.e. B6.Cg-Tg(BAT-lacZ)3Picc/J mice, revealed that the numbers of β-galactosidase(+) (β-Gal) intestinal crypts are increased, suggesting that EPDEN treatment of mice leads to Wnt-mediated activation of the TCF4 transcription machinery in the crypts. The data suggest a role for EPDEN-mediated interspecies communication by inducing expression of genes for anti-inflammation cytokines, antioxidation, and activation of Wnt signaling, which are crucial for maintaining intestinal homeostasis. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Fibroblast cell line establishment, cryopreservation and interspecies embryos reconstruction in red panda ( Ailurus fulgens).

PubMed

Tao, Yong; Liu, Jianming; Zhang, Yunhai; Zhang, Meiling; Fang, Junshun; Han, Wei; Zhang, Zhizhong; Liu, Ya; Ding, Jianping; Zhang, Xiaorong

2009-05-01

In evolution, the red panda (Ailurus fulgens) plays a pivotal role in the higher level phylogeny of arctoides carnivore mammals. The red panda inhabits certain Asian countries only and its numbers are decreasing. Therefore, the development of feasible ways to preserve this species is necessary. Genetic resource cryopreservation and somatic cell nuclear transfer (SCNT) have been used extensively to rescue this endangered species. The present study describes the establishment, for the first time, of a red panda ear fibroblast cell line, which was then cryopreserved, thawed and cultured. Through micromanipulation, interspecies embryos were reconstructed using the cryopreserved-thawed fibroblasts of the red panda as the donor and rabbit oocytes as recipients. A total of 194 enucleated rabbit oocytes were reconstructed with red panda ear fibroblasts; enucleated oocytes were activated without fusion as the control. The results show that the fibroblast cell line was established successfully by tissue culture and then cryopreserved in liquid nitrogen. Supplementation with 20% fetal bovine serum and 8% dimethyl sulphoxide in basic medium facilitated the cryopreservation. The interspecies embryos were successfully reconstructed. The cleavage, morulae and blastocyst rates after in vitro culture were 71, 47 and 23% (31/194), respectively. This study indicated that a somatic cell line could be established and cryopreserved from red panda and that rabbit cytoplast supports mitotic cleavage of the red panda karyoplasts and is capable of reprogramming the nucleus to achieve blastocysts.

Interspecies communication between plant and mouse gut host cells through edible plant derived exosome-like nanoparticles

PubMed Central

Mu, Jingyao; Zhuang, Xiaoying; Wang, Qilong; Jiang, Hong; Deng, Zhong-Bin; Wang, Baomei; Zhang, Lifeng; Kakar, Sham; Jun, Yan; Miller, Donald; Zhang, Huang-Ge

2015-01-01

Scope Exosomes, small vesicles participating in intercellular communication have been extensively studied recently; however, the role of edible plant derived exosomes in interspecies communication has not been investigated. Here, we investigate the biological effects of edible plant derived exosome-like nanoparticles (EPDEN) on mammalian cells. Methods and results In this study, exosome-like nanoparticles from four edible plants were isolated and characterized. We show that these EPDENs contain proteins, lipids and microRNA. EPDENs are taken up by intestinal macrophages and stem cells. The results generated from EPDEN transfected macrophages indicate that ginger EPDENs preferentially induce the expression of the anti-oxidation gene, heme oxygenase-1 (HO-1) and the anti-inflammatory cytokine, IL-10; whereas grapefruit, ginger, and carrot EPDENs promote activation of nuclear factor (erythroid-derived 2)-like 2 (Nrf2). Furthermore, analysis of the intestines of canonical Wnt reporter mice, i.e., B6.Cg-Tg(BAT-lacZ)3Picc/J mice, revealed that the numbers of β-galactosidase+ (β-Gal) intestinal crypts are increased, suggesting that EPDEN treatment of mice leads to Wnt mediated activation of the Tcf4 transcription machinery in the crypts. Conclusion The data suggest a role for EPDEN mediated interspecies communication by inducing expression of genes for anti-inflammation cytokines, anti-oxidation and activation of Wnt signaling, which are crucial for maintaining intestinal homeostasis. PMID:24842810

Acute oral toxicity: variability, reliability, relevance and interspecies comparison of rodent LD50 data from literature surveyed for the ACuteTox project.

PubMed

Hoffmann, Sebastian; Kinsner-Ovaskainen, Agnieszka; Prieto, Pilar; Mangelsdorf, Inge; Bieler, Christian; Cole, Thomas

2010-12-01

The ACuteTox project has aimed to optimise and prevalidate an in vitro testing strategy for predicting human acute toxicity. Ninety-seven reference substances were selected and an in vivo acute toxicity database was compiled. Comprehensive statistical analyses of the in vivo LD50 data to evaluate variability and reliability, interspecies correlation, predictive capacities with regard to EU and GHS toxicity categories, and deduction of performance criteria for in vitro methods is presented. For the majority of substances variability among rodent data followed a log normal distribution where good reproducibility was found. Rat and mouse interspecies comparison of LD50 studies by ordinary regression showed high correlation, with coefficients of determination, ranging between 0.8 and 0.9. Substance specific differences were only significant for warfarin and cycloheximide. No correlation of compound LD50 range with presumed study quality rank (by assigning Klimisch reliability scores) was found. Modelling based on LD50 variability showed that with at least 90% probability ∼54% of the substances would fall into only one GHS category and ∼44% would fall within two adjacent categories. These results could form the basis for deriving a predictive capacity that should be expected from alternative approaches to the conventional in vivo acute oral toxicity test. Copyright © 2010 Elsevier Inc. All rights reserved.

Observation of Interspecies Ion Separation in Inertial-Confinement-Fusion Implosions via Imaging X-ray spectroscopy

NASA Astrophysics Data System (ADS)

Joshi, Tirtha Raj

2016-10-01

Interspecies ion separation has been proposed as a yield-degradation mechanism in inertial-confinement-fusion (ICF) experiments. We present direct experimental evidence of interspecies ion separation in direct-drive ICF experiments performed at the OMEGA laser facility. These experiments were designed based on the fact that interspecies ion thermo-diffusion would be strongest for species with large mass and charge difference. The targets were spherical plastic shells filled with D2 and Ar (1% by atom). Ar K-shell spectral features were observed primarily between the time of first-shock convergence and slightly before neutron bang time, using a time- and space-integrated spectrometer, streaked crystal spectrometer, and two gated multi-monochromatic X-ray imagers fielded along quasi-orthogonal lines-of-sight. Detailed spectroscopic analyses of spatially resolved Ar K-shell lines reveal deviation from the initial 1%-Ar gas fill and show both Ar-concentration enhancement and depletion at different times and radial positions of the implosion. The experimental results are interpreted with radiation-hydrodynamic simulations that include recently implemented, first-principles models of interspecies ion diffusion. The experimentally inferred Ar-atom-fraction profiles agree gently with calculated profiles associated with the incoming and rebounding first shock. This work was done in collaboration with P. Hakel, S. C. Hsu, E. L. Vold, M. J. Schmitt, N. M. Hoffman, R. M. Rauenzahn, G. Kagan, X.-Z. Tang, Y. Kim, and H. W. Herrmann of LANL, and R. C. Mancini of UNR. LA-UR-16-24804. Supported by the LANL ICF and ASC Programs under US-DoE contract no. DE-AC52-06NA25396.

Broad Feshbach resonance in the 6Li-40K mixture.

PubMed

Tiecke, T G; Goosen, M R; Ludewig, A; Gensemer, S D; Kraft, S; Kokkelmans, S J J M F; Walraven, J T M

2010-02-05

We study the widths of interspecies Feshbach resonances in a mixture of the fermionic quantum gases 6Li and 40K. We develop a model to calculate the width and position of all available Feshbach resonances for a system. Using the model, we select the optimal resonance to study the {6}Li/{40}K mixture. Experimentally, we obtain the asymmetric Fano line shape of the interspecies elastic cross section by measuring the distillation rate of 6Li atoms from a potassium-rich 6Li/{40}K mixture as a function of magnetic field. This provides us with the first experimental determination of the width of a resonance in this mixture, DeltaB=1.5(5) G. Our results offer good perspectives for the observation of universal crossover physics using this mass-imbalanced fermionic mixture.

Predicting the impact of biocorona formation kinetics on interspecies extrapolations of nanoparticle biodistribution modeling.

PubMed

Sahneh, Faryad Darabi; Scoglio, Caterina M; Monteiro-Riviere, Nancy A; Riviere, Jim E

2015-01-01

To assess the impact of biocorona kinetics on expected tissue distribution of nanoparticles (NPs) across species. The potential fate of NPs in vivo is described through a simple and descriptive pharmacokinetic model using rate processes dependent upon basal metabolic rate coupled to dynamics of protein corona. Mismatch of time scales between interspecies allometric scaling and the kinetics of corona formation is potentially a fundamental issue with interspecies extrapolations of NP biodistribution. The impact of corona evolution on NP biodistribution across two species is maximal when corona transition half-life is close to the geometric mean of NP half-lives of the two species. While engineered NPs can successfully reach target cells in rodent models, the results may be different in humans due to the fact that the longer circulation time allows for further biocorona evolution.

Inter-species competition-facilitation in stochastic riparian vegetation dynamics.

PubMed

Tealdi, Stefano; Camporeale, Carlo; Ridolfi, Luca

2013-02-07

Riparian vegetation is a highly dynamic community that lives on river banks and which depends to a great extent on the fluvial hydrology. The stochasticity of the discharge and erosion/deposition processes in fact play a key role in determining the distribution of vegetation along a riparian transect. These abiotic processes interact with biotic competition/facilitation mechanisms, such as plant competition for light, water, and nutrients. In this work, we focus on the dynamics of plants characterized by three components: (1) stochastic forcing due to river discharges, (2) competition for resources, and (3) inter-species facilitation due to the interplay between vegetation and fluid dynamics processes. A minimalist stochastic bio-hydrological model is proposed for the dynamics of the biomass of two vegetation species: one species is assumed dominant and slow-growing, the other is subdominant, but fast-growing. The stochastic model is solved analytically and the probability density function of the plant biomasses is obtained as a function of both the hydrologic and biologic parameters. The impact of the competition/facilitation processes on the distribution of vegetation species along the riparian transect is investigated and remarkable effects are observed. Finally, a good qualitative agreement is found between the model results and field data. Copyright © 2012 Elsevier Ltd. All rights reserved.

Validation and Application of Pharmacokinetic Models for Interspecies Extrapolations in Toxicity Risk Assessments of Volatile Organics

DTIC Science & Technology

1988-08-30

Ai _.. ;:: -- I. OVERALL OBJECTIVE AND STATEMENT OF WORK The overall objective of the proposed project is to investigate the scientific basis...development and inter-species correlations with toxicity. A second series of tissue disposition experiments will be conducted to determine what ...elimination of halocarbons is hepatic metabolism. If metabolism plays a significant role in the disposition and subsequent neurobehavioral effects of

Nasal microenvironments and interspecific interactions influence nasal microbiota complexity and S. aureus carriage.

PubMed

Yan, Miling; Pamp, Sünje J; Fukuyama, Julia; Hwang, Peter H; Cho, Do-Yeon; Holmes, Susan; Relman, David A

2013-12-11

The indigenous microbiota of the nasal cavity plays important roles in human health and disease. Patterns of spatial variation in microbiota composition may help explain Staphylococcus aureus colonization and reveal interspecies and species-host interactions. To assess the biogeography of the nasal microbiota, we sampled healthy subjects, representing both S. aureus carriers and noncarriers at three nasal sites (anterior naris, middle meatus, and sphenoethmoidal recess). Phylogenetic compositional and sparse linear discriminant analyses revealed communities that differed according to site epithelium type and S. aureus culture-based carriage status. Corynebacterium accolens and C. pseudodiphtheriticum were identified as the most important microbial community determinants of S. aureus carriage, and competitive interactions were only evident at sites with ciliated pseudostratified columnar epithelium. In vitro cocultivation experiments provided supporting evidence of interactions among these species. These results highlight spatial variation in nasal microbial communities and differences in community composition between S. aureus carriers and noncarriers. Copyright © 2013 Elsevier Inc. All rights reserved.

Nasal microenvironments and interspecific interactions influence nasal microbiota complexity and S. aureus carriage

PubMed Central

Yan, Miling; Pamp, Sünje J.; Fukuyama, Julia; Hwang, Peter H.; Cho, Do-Yeon; Holmes, Susan; Relman, David A.

2013-01-01

Summary The indigenous microbiota of the nasal cavity plays important roles in human health and disease. Patterns of spatial variation in microbiota composition may help explain Staphylococcus aureus colonization, and reveal interspecies and species-host interactions. To assess the biogeography of the nasal microbiota, we sampled healthy subjects, representing both S. aureus carriers and non-carriers, at 3 nasal sites (anterior naris, middle meatus, and sphenoethmoidal recess). Phylogenetic compositional and sparse linear discriminant analyses revealed communities that differed according to site epithelium type and S. aureus culture-based carriage status. Corynebacterium accolens and C. pseudodiphtheriticum were identified as the most important microbial community determinants of S. aureus carriage, with competitive interactions evident only at sites with ciliated pseudostratified columnar epithelium. In vitro co-cultivation experiments provided supporting evidence of interactions among these species. These results highlight spatial variation in nasal microbial communities and differences in community composition between S. aureus carriers and non-carriers. PMID:24331461

Ultracold Realization of AntiFerromagenteic Order

NASA Astrophysics Data System (ADS)

Shrestha, Uttam

2011-03-01

We investigate numerically the experimental feasibility of observing the antiferromagnetic (AF) order in the bosonic mixtures of rubidium (87 Rb) and potassium (41 K) in a two-dimensional optical lattice with external trapping potential. Within the mean-field approximation we have found the ground states which, for a specific range of parameters such as inter-species interactions and lattice height, interpolate from phase separation to the AF order. For the moderate lattice heights the coexistence of the Mott and AF phase is possible for rubidium atoms while the potassium atoms remain superfluid with overlapped AF phase. In our view there has not been any study on AF order in two-component systems when one component remains in the superfluid phase while the other is in the Mott phase. Therefore, this observation may provide a novel regime for studying quantum magnetism in ultracold systems. This work was supported by the EU Contract EU STREP NAMEQUAM.

Few-body resonances of unequal-mass systems with infinite interspecies two-body s-wave scattering length

DOE Office of Scientific and Technical Information (OSTI.GOV)

Blume, D.; Daily, K. M.

Two-component Fermi and Bose gases with infinitely large interspecies s-wave scattering length a{sub s} exhibit a variety of intriguing properties. Among these are the scale invariance of two-component Fermi gases with equal masses, and the favorable scaling of Efimov features for two-component Bose gases and Bose-Fermi mixtures with unequal masses. This paper builds on our earlier work [Phys. Rev. Lett. 105, 170403 (2010)] and presents a detailed discussion of our studies of small unequal-mass two-component systems with infinite a{sub s} in the regime where three-body Efimov physics is absent. We report on nonuniversal few-body resonances. Just like with two-body systemsmore » on resonance, few-body systems have a zero-energy bound state in free space and a diverging generalized scattering length. Our calculations are performed within a nonperturbative microscopic framework and investigate the energetics and structural properties of small unequal-mass two-component systems as functions of the mass ratio {kappa}, and the numbers N{sub 1} and N{sub 2} of heavy and light atoms. For purely attractive Gaussian two-body interactions, we find that the (N{sub 1},N{sub 2})=(2,1) and (3,1) systems exhibit three-body and four-body resonances at mass ratios {kappa}=12.314(2) and 10.4(2), respectively. The three- and four-particle systems on resonance are found to be large. It seems feasible that the features discussed in this paper can be probed experimentally with present-day technology.« less

Modelling of groundwater-vegetation interactions in a tidal marsh

NASA Astrophysics Data System (ADS)

Xin, Pei; Kong, Jun; Li, Ling; Barry, D. A.

2013-07-01

Wetting and drying due to tidal fluctuations affect soil conditions and hence plant growth in tidal marshes. Here, a coupled one-dimensional model was developed to simulate interacting groundwater flow and plant growth in these wetlands. The simulation results revealed three characteristic zones of soil conditions for plant growth along a cross-creek section subjected to the combined influences of spring-neap tides and evapotranspiration: (1) a near-creek zone affected by semi-diurnal tides over the whole spring-neap cycle, where the soil is well aerated although the plant growth could be slightly limited by the local water content dropping periodically below the wilting point on the ebb tide; (2) a less well-drained zone where drainage occurs only during neap tides (for which the daily inundation is absent) and plant growth is aeration-limited; and (3) an interior zone where evapotranspiration determines the soil-water saturation. Plant growth dynamics, which depend on these soil conditions, lead to spatial biomass distributions that are consistent with the characteristic zonation. The simulations shed light on the feedback mechanism for groundwater-vegetation interactions in the marsh system. It was demonstrated that the growth of pioneer plants can improve the soil aeration condition as a result of transpiration. The strength of this feedback varies spatially in accordance with the three characteristic zones of soil-water saturation. However, the development of another species in the marsh system is likely to be more complicated than suggested by the "positive feedback" mechanism proposed previously, due to the influence of inter-species competition. The feedback effects are generally more complex, involving both plant growth enhancement and inhibition depending on the combined influence of the intra- and inter-species competition, the ecosystem's carrying capacity and plant transpiration. These findings demonstrate the interplay of ecological and hydrological processes in tidal marshes, and provide guidance for future research, including field investigations that aim to establish the principle relationship between marsh morphology and plant zonation.

Morphological and molecular characterization of yellow oyster mushroom, Pleurotus citrinopileatus, hybrids obtained by interspecies mating.

PubMed

Rosnina, A G; Tan, Yee Shin; Abdullah, Noorlidah; Vikineswary, S

2016-02-01

Pleurotus citrinopileatus (yellow oyster mushroom) has an attractive shape and yellow colour but the fragile texture complicates packaging, and its strong aroma is unappealing to consumers. This study aimed to improve the characteristics and yield of P. citrinopileatus by interspecies mating between monokaryotic cultures of P. citrinopileatus and P. pulmonarius. Ten monokaryon cultures of the parental lines were crossed in all combinations to obtain hybrids. Eleven compatible mating pairs were obtained and cultivated to observe their sporophore morphology and yield. The selected hybrid, i.e. P1xC9, was beige in colour while hybrid P3xC8 was yellow in colour. Their sporophores had less offensive aroma, improved texture and higher yield. The DNA sequences of these hybrids were found to be in the same clade as the P. citrinopileatus parent with a bootstrap value of 99%. High bootstrap values indicate high genetic homology between hybrids and the P. citrinopileatus parent. The biological efficiencies of these hybrids P1xC9 (70.97%) and P3xC8 (52.14%) were also higher than the P. citrinopileatus parent (35.63%). Interspecies hybrids obtained by this mating technique can lead to better strains of mushrooms for genetic improvement of the Pleurotus species.

Leishmania infantum: Lipophosphoglycan intraspecific variation and interaction with vertebrate and invertebrate hosts.

PubMed

Coelho-Finamore, J M; Freitas, V C; Assis, R R; Melo, M N; Novozhilova, N; Secundino, N F; Pimenta, P F; Turco, S J; Soares, R P

2011-03-01

Interspecies variations in lipophosphoglycan (LPG) have been the focus of intense study over the years due its role in specificity during sand fly-Leishmania interaction. This cell surface glycoconjugate is highly polymorphic among species with variations in sugars that branch off the conserved Gal(β1,4)Man(α1)-PO(4) backbone of repeat units. However, the degree of intraspecies polymorphism in LPG of Leishmania infantum (syn. Leishmania chagasi) is not known. In this study, intraspecific variation in the repeat units of LPG was evaluated in 16 strains of L. infantum from Brazil, France, Algeria and Tunisia. The structural polymorphism in the L. infantum LPG repeat units was relatively slight and consisted of three types: type I does not have side chains; type II has one β-glucose residue that branches off the disaccharide-phosphate repeat units and type III has up to three glucose residues (oligo-glucosylated). The significance of these modifications was investigated during in vivo interaction of L. infantum with Lutzomyia longipalpis, and in vitro interaction of the parasites and respective LPGs with murine macrophages. There were no consequential differences in the parasite densities in sand fly midguts infected with Leishmania strains exhibiting type I, II and III LPGs. However, higher nitric oxide production was observed in macrophages exposed to glucosylated type II LPG. Copyright © 2010 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.

Host Genotype and Microbiota Contribute Asymmetrically to Transcriptional Variation in the Threespine Stickleback Gut

PubMed Central

Small, Clayton M.; Milligan-Myhre, Kathryn; Bassham, Susan; Guillemin, Karen

2017-01-01

Recent studies of interactions between hosts and their resident microbes have revealed important ecological and evolutionary consequences that emerge from these complex interspecies relationships, including diseases that occur when the interactions go awry. Given the preponderance of these interactions, we hypothesized that effects of the microbiota on gene expression in the developing gut—an important aspect of host biology—would be pervasive, and that these effects would be both comparable in magnitude to and contingent on effects of the host genetic background. To evaluate the effects of the microbiota, host genotype, and their interaction on gene expression in the gut of a genetically diverse, gnotobiotic host model, the threespine stickleback (Gasterosteus aculeatus), we compared RNA-seq data among 84 larval fish. Surprisingly, we found that stickleback population and family differences explained substantially more gene expression variation than the presence of microbes. Expression levels of 72 genes, however, were affected by our microbiota treatment. These genes, including many associated with innate immunity, comprise a tractable subset of host genetic factors for precise, systems-level study of host–microbe interactions in the future. Importantly, our data also suggest subtle signatures of a statistical interaction between host genotype and the microbiota on expression patterns of genetic pathways associated with innate immunity, coagulation and complement cascades, focal adhesion, cancer, and peroxisomes. These genotype-by-environment interactions may prove to be important leads to the understanding of host genetic mechanisms commonly at the root of sometimes complex molecular relationships between hosts and their resident microbes. PMID:28391321

Assembly of bipolar microtubule structures by passive cross-linkers and molecular motors

NASA Astrophysics Data System (ADS)

Johann, D.; Goswami, D.; Kruse, K.

2016-06-01

During cell division, sister chromatids are segregated by the mitotic spindle, a bipolar assembly of interdigitating antiparallel polar filaments called microtubules. The spindle contains the midzone, a stable region of overlapping antiparallel microtubules, that is essential for maintaining bipolarity. Although a lot is known about the molecular players involved, the mechanism underlying midzone formation and maintenance is still poorly understood. We study the interaction of polar filaments that are cross-linked by molecular motors moving directionally and by passive cross-linkers diffusing along microtubules. Using a particle-based stochastic model, we find that the interplay of motors and passive cross-linkers can generate a stable finite overlap between a pair of antiparallel polar filaments. We develop a mean-field theory to study this mechanism in detail and investigate the influence of steric interactions between motors and passive cross-linkers on the overlap dynamics. In the presence of interspecies steric interactions, passive cross-linkers mimic the behavior of molecular motors and stable finite overlaps are generated even for non-cross-linking motors. Finally, we develop a mean-field theory for a bundle of aligned polar filaments and show that they can self-organize into a spindlelike pattern. Our work suggests possible ways as to how cells can generate spindle midzones and control their extensions.

A novel small molecule methyltransferase is important for virulence in Candida albicans.

PubMed

Lissina, Elena; Weiss, David; Young, Brian; Rella, Antonella; Cheung-Ong, Kahlin; Del Poeta, Maurizio; Clarke, Steven G; Giaever, Guri; Nislow, Corey

2013-12-20

Candida albicans is an opportunistic pathogen capable of causing life-threatening infections in immunocompromised individuals. Despite its significant health impact, our understanding of C. albicans pathogenicity is limited, particularly at the molecular level. One of the largely understudied enzyme families in C. albicans are small molecule AdoMet-dependent methyltransferases (smMTases), which are important for maintenance of cellular homeostasis by clearing toxic chemicals, generating novel cellular intermediates, and regulating intra- and interspecies interactions. In this study, we demonstrated that C. albicans Crg1 (CaCrg1) is a bona fide smMTase that interacts with the toxin in vitro and in vivo. We report that CaCrg1 is important for virulence-related processes such as adhesion, hyphal elongation, and membrane trafficking. Biochemical and genetic analyses showed that CaCrg1 plays a role in the complex sphingolipid pathway: it binds to exogenous short-chain ceramides in vitro and interacts genetically with genes of glucosylceramide pathway, and the deletion of CaCRG1 leads to significant changes in the abundance of phytoceramides. Finally we found that this novel lipid-related smMTase is required for virulence in the waxmoth Galleria mellonella, a model of infection.

Structural basis of the interspecies interaction between the chaperone DnaK(Hsp70) and the co-chaperone GrpE of archaea and bacteria.

PubMed

Zmijewski, Michał A; Skórko-Glonek, Joanna; Tanfani, Fabio; Banecki, Bogdan; Kotlarz, Agnieszka; Macario, Alberto J L; Lipińska, Barbara

2007-01-01

Hsp70s are chaperone proteins that are conserved in evolution and present in all prokaryotic and eukaryotic organisms. In the archaea, which form a distinct kingdom, the Hsp70 chaperones have been found in some species only, including Methanosarcina mazei. Both the bacterial and archaeal Hsp70(DnaK) chaperones cooperate with a GrpE co-chaperone which stimulates the ATPase activity of the DnaK protein. It is currently believed that the archaeal Hsp70 system was obtained by the lateral transfer of chaperone genes from bacteria. Our previous finding that the DnaK and GrpE proteins of M. mazei can functionally cooperate with the Escherichia coli GrpE and DnaK supported this hypothesis. However, the cooperation was surprising, considering the very low identity of the GrpE proteins (26%) and the relatively low identity of the DnaK proteins (56%). The aim of this work was to investigate the molecular basis of the observed interspecies chaperone interaction. Infrared resolution-enhanced spectra of the M. mazei and E. coli DnaK proteins were almost identical, indicating high similarity of their secondary structures, however, some small differences in band position and in the intensity of amide I' band components were observed and discussed. Profiles of thermal denaturation of both proteins were similar, although they indicated a higher thermostability of the M. mazei DnaK compared to the E. coli DnaK. Electrophoresis under non-denaturing conditions demonstrated that purified DnaK and GrpE of E. coli and M. mazei formed mixed complexes. Protein modeling revealed high similarity of the 3-dimensional structures of the archaeal and bacterial DnaK and GrpE proteins.

White-Tailed Deer Susceptible to Scrapie by Natural Route of Infection

USDA-ARS?s Scientific Manuscript database

Interspecies transmission studies afford the opportunity to better understand the potential host range and origins of prion diseases. Previous experiments demonstrated that white-tailed deer are susceptible to sheep-derived scrapie by intracranial inoculation. The purpose of this study was to determ...

White-Tailed Deer Susceptible to Scrapie by Natural Route of Infection

USDA-ARS?s Scientific Manuscript database

Interspecies transmission studies afford the opportunity to better understand the potential host range and origins of prion diseases. Previous experiments demonstrated that white-tailed deer are susceptible to sheep-derived scrapie by intracranial inoculation. The purpose of an ongoing study is to...

Epidemiological Study of Paratuberculosis in Wild Rabbits in Scotland

PubMed Central

Greig, Alastair; Stevenson, Karen; Henderson, Dennis; Perez, Valentin; Hughes, Valerie; Pavlik, Ivo; Hines, Murray E.; McKendrick, Iain; Sharp, J. Michael

1999-01-01

A survey of 22 farms confirmed the presence of paratuberculosis in wild rabbits in Scotland. Regional differences were apparent in the prevalence of the disease in rabbits, with a significantly higher incidence occurring in the Tayside region. Statistical analysis showed a significant relationship between a previous history or current problem of paratuberculosis in cattle and the presence of paratuberculosis in rabbits on the farms. Molecular genetic typing techniques could not discriminate between selected rabbit and cattle isolates from the same or different farms, suggesting that the same strain may infect and cause disease in both species and that interspecies transmission may occur. The possibility of interspecies transmission and the involvement of wildlife in the epidemiology of paratuberculosis have important implications for the control of the disease. PMID:10325318

Marine crude-oil biodegradation: a central role for interspecies interactions

PubMed Central

2012-01-01

The marine environment is highly susceptible to pollution by petroleum, and so it is important to understand how microorganisms degrade hydrocarbons, and thereby mitigate ecosystem damage. Our understanding about the ecology, physiology, biochemistry and genetics of oil-degrading bacteria and fungi has increased greatly in recent decades; however, individual populations of microbes do not function alone in nature. The diverse array of hydrocarbons present in crude oil requires resource partitioning by microbial populations, and microbial modification of oil components and the surrounding environment will lead to temporal succession. But even when just one type of hydrocarbon is present, a network of direct and indirect interactions within and between species is observed. In this review we consider competition for resources, but focus on some of the key cooperative interactions: consumption of metabolites, biosurfactant production, provision of oxygen and fixed nitrogen. The emphasis is largely on aerobic processes, and especially interactions between bacteria, fungi and microalgae. The self-construction of a functioning community is central to microbial success, and learning how such “microbial modules” interact will be pivotal to enhancing biotechnological processes, including the bioremediation of hydrocarbons. PMID:22591596

Burkholderia Diffusible Signal Factor Signals to Francisella novicida To Disperse Biofilm and Increase Siderophore Production

PubMed Central

Dean, Scott N.; Chung, Myung-Chul

2015-01-01

In many bacteria, the ability to modulate biofilm production relies on specific signaling molecules that are either self-produced or made by neighboring microbes within the ecological niche. We analyzed the potential interspecies signaling effect of the Burkholderia diffusible signal factor (BDSF) on Francisella novicida, a model organism for Francisella tularensis, and demonstrated that BDSF both inhibits the formation and causes the dispersion of Francisella biofilm. Specificity was demonstrated for the cis versus the trans form of BDSF. Using transcriptome sequencing, quantitative reverse transcription-PCR, and activity assays, we found that BDSF altered the expression of many F. novicida genes, including genes involved in biofilm formation, such as chitinases. Using a chitinase inhibitor, the antibiofilm activity of BDSF was also shown to be chitinase dependent. In addition, BDSF caused an increase in RelA expression and increased levels of (p)ppGpp, leading to decreased biofilm production. These results support our observation that exposure of F. novicida to BDSF causes biofilm dispersal. Furthermore, BDSF upregulated the genes involved in iron acquisition (figABCD), increasing siderophore production. Thus, this study provides evidence for a potential role and mechanism of diffusible signal factor (DSF) signaling in the genus Francisella and suggests the possibility of interspecies signaling between Francisella and other bacteria. Overall, this study suggests that in response to the interspecies DSF signal, F. novicida can alter its gene expression and regulate its biofilm formation. PMID:26231649

Observation and modeling of interspecies ion separation in inertial confinement fusion implosions via imaging x-ray spectroscopy

DOE PAGES

Joshi, Tirtha Raj; Hakel, Peter; Hsu, Scott C.; ...

2017-03-22

In this article, we report the first direct experimental evidence of interspecies ion separation in direct-drive inertial confinement fusion experiments performed at the OMEGA laser facility via spectrally, temporally, and spatially resolved imaging x-ray-spectroscopy data [S. C. Hsu et al., Europhys. Lett. 115, 65001 (2016)]. These experiments were designed based on the expectation that interspecies ion thermo-diffusion would be the strongest for species with a large mass and charge difference. The targets were spherical plastic shells filled with D2 and a trace amount of Ar (0.1% or 1% by atom). Ar K-shell spectral features were observed primarily between the timemore » of first-shock convergence and slightly before the neutron bang time, using a time- and space-integrated spectrometer, a streaked crystal spectrometer, and two gated multi-monochromatic x-ray imagers fielded along quasi-orthogonal lines of sight. Detailed spectroscopic analyses of spatially resolved Ar K-shell lines reveal the deviation from the initial 1% Ar gas fill and show both Ar-concentration enhancement and depletion at different times and radial positions of the implosion. The experimental results are interpreted using radiation-hydrodynamic simulations that include recently implemented, first-principles models of interspecies ion diffusion. Lastly, the experimentally inferred Ar-atom fraction profiles agree reasonably with calculated profiles associated with the incoming and rebounding first shock.« less

Male sex interspecies divergence and down regulation of expression of spermatogenesis genes in Drosophila sterile hybrids.

PubMed

Sundararajan, Vignesh; Civetta, Alberto

2011-01-01

Male sex genes have shown a pattern of rapid interspecies divergence at both the coding and gene expression level. A common outcome from crosses between closely-related species is hybrid male sterility. Phenotypic and genetic studies in Drosophila sterile hybrid males have shown that spermatogenesis arrest is postmeiotic with few exceptions, and that most misregulated genes are involved in late stages of spermatogenesis. Comparative studies of gene regulation in sterile hybrids and parental species have mainly used microarrays providing a whole genome representation of regulatory problems in sterile hybrids. Real-time PCR studies can reject or reveal differences not observed in microarray assays. Moreover, differences in gene expression between samples can be dependant on the source of RNA (e.g., whole body vs. tissue). Here we survey expression in D. simulans, D. mauritiana and both intra and interspecies hybrids using a real-time PCR approach for eight genes expressed at the four main stages of sperm development. We find that all genes show a trend toward under expression in the testes of sterile hybrids relative to parental species with only the two proliferation genes (bam and bgcn) and the two meiotic class genes (can and sa) showing significant down regulation. The observed pattern of down regulation for the genes tested can not fully explain hybrid male sterility. We discuss the down regulation of spermatogenesis genes in hybrids between closely-related species within the contest of rapid divergence experienced by the male genome, hybrid sterility and possible allometric changes due to subtle testes-specific developmental abnormalities.

General two-species interacting Lotka-Volterra system: Population dynamics and wave propagation

NASA Astrophysics Data System (ADS)

Zhu, Haoqi; Wang, Mao-Xiang; Lai, Pik-Yin

2018-05-01

The population dynamics of two interacting species modeled by the Lotka-Volterra (LV) model with general parameters that can promote or suppress the other species is studied. It is found that the properties of the two species' isoclines determine the interaction of species, leading to six regimes in the phase diagram of interspecies interaction; i.e., there are six different interspecific relationships described by the LV model. Four regimes allow for nontrivial species coexistence, among which it is found that three of them are stable, namely, weak competition, mutualism, and predator-prey scenarios can lead to win-win coexistence situations. The Lyapunov function for general nontrivial two-species coexistence is also constructed. Furthermore, in the presence of spatial diffusion of the species, the dynamics can lead to steady wavefront propagation and can alter the population map. Propagating wavefront solutions in one dimension are investigated analytically and by numerical solutions. The steady wavefront speeds are obtained analytically via nonlinear dynamics analysis and verified by numerical solutions. In addition to the inter- and intraspecific interaction parameters, the intrinsic speed parameters of each species play a decisive role in species populations and wave properties. In some regimes, both species can copropagate with the same wave speeds in a finite range of parameters. Our results are further discussed in the light of possible biological relevance and ecological implications.

Synergisms between microbial pathogens in plant disease complexes: a growing trend

PubMed Central

Lamichhane, Jay Ram; Venturi, Vittorio

2015-01-01

Plant diseases are often thought to be caused by one species or even by a specific strain. Microbes in nature, however, mostly occur as part of complex communities and this has been noted since the time of van Leeuwenhoek. Interestingly, most laboratory studies focus on single microbial strains grown in pure culture; we were therefore unaware of possible interspecies and/or inter-kingdom interactions of pathogenic microbes in the wild. In human and animal infections, it is now being recognized that many diseases are the result of multispecies synergistic interactions. This increases the complexity of the disease and has to be taken into consideration in the development of more effective control measures. On the other hand, there are only a few reports of synergistic pathogen–pathogen interactions in plant diseases and the mechanisms of interactions are currently unknown. Here we review some of these reports of synergism between different plant pathogens and their possible implications in crop health. Finally, we briefly highlight the recent technological advances in diagnostics as these are beginning to provide important insights into the microbial communities associated with complex plant diseases. These examples of synergistic interactions of plant pathogens that lead to disease complexes might prove to be more common than expected and understanding the underlying mechanisms might have important implications in plant disease epidemiology and management. PMID:26074945

INTER-SPECIES STEROID RECEPTOR EXTRAPOLATION STUDIES FOR ENDOCRINE DISRUPTING CHEMICALS

EPA Science Inventory

In: Environmental Sciences in the 21st Century: Paradigms, Opportunities, and Challenges: Abstract Book: SETAC 21st Annual Meeting, 12-16 November 2000, Nashville, TN. Society of Environmental Toxicology and Chemistry, Pensacola, FL. Pp. 117-118.

Phototrophic biofilm assembly in microbial-mat-derived unicyanobacterial consortia: model systems for the study of autotroph-heterotroph interactions

PubMed Central

Cole, Jessica K.; Hutchison, Janine R.; Renslow, Ryan S.; Kim, Young-Mo; Chrisler, William B.; Engelmann, Heather E.; Dohnalkova, Alice C.; Hu, Dehong; Metz, Thomas O.; Fredrickson, Jim K.; Lindemann, Stephen R.

2014-01-01

Microbial autotroph-heterotroph interactions influence biogeochemical cycles on a global scale, but the diversity and complexity of natural systems and their intractability to in situ manipulation make it challenging to elucidate the principles governing these interactions. The study of assembling phototrophic biofilm communities provides a robust means to identify such interactions and evaluate their contributions to the recruitment and maintenance of phylogenetic and functional diversity over time. To examine primary succession in phototrophic communities, we isolated two unicyanobacterial consortia from the microbial mat in Hot Lake, Washington, characterizing the membership and metabolic function of each consortium. We then analyzed the spatial structures and quantified the community compositions of their assembling biofilms. The consortia retained the same suite of heterotrophic species, identified as abundant members of the mat and assigned to Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes. Autotroph growth rates dominated early in assembly, yielding to increasing heterotroph growth rates late in succession. The two consortia exhibited similar assembly patterns, with increasing relative abundances of members from Bacteroidetes and Alphaproteobacteria concurrent with decreasing relative abundances of those from Gammaproteobacteria. Despite these similarities at higher taxonomic levels, the relative abundances of individual heterotrophic species were substantially different in the developing consortial biofilms. This suggests that, although similar niches are created by the cyanobacterial metabolisms, the resulting webs of autotroph-heterotroph and heterotroph-heterotroph interactions are specific to each primary producer. The relative simplicity and tractability of the Hot Lake unicyanobacterial consortia make them useful model systems for deciphering interspecies interactions and assembly principles relevant to natural microbial communities. PMID:24778628

Cloning Endangered Felids by Interspecies Somatic Cell Nuclear Transfer.

PubMed

Gómez, Martha C; Pope, C Earle

2015-01-01

In 2003, the first wild felid was produced by interspecies somatic cell nuclear transfer. Since then other wild felid clone offspring have been produced by using the same technique with minor modifications. This chapter describes detailed protocols used in our laboratory for (1) the isolation, culture, and preparation of fibroblast cells as donor nucleus, and (2) embryo reconstruction with domestic cat enucleated oocytes to produce cloned embryos that develop to the blastocyst stage in vitro and, after transfer into synchronized recipients, establish successful pregnancies.

Effect of epidemic spreading on species coexistence in spatial rock-paper-scissors games.

PubMed

Wang, Wen-Xu; Lai, Ying-Cheng; Grebogi, Celso

2010-04-01

A fundamental question in nonlinear science and evolutionary biology is how epidemic spreading may affect coexistence. We address this question in the framework of mobile species under cyclic competitions by investigating the roles of both intra- and interspecies spreading. A surprising finding is that intraspecies infection can strongly promote coexistence while interspecies spreading cannot. These results are quantified and a theoretical paradigm based on nonlinear partial differential equations is derived to explain the numerical results.

Interactions of Freshwater Cyanobacteria with Bacterial Antagonists

PubMed Central

Beier, Sara; Grabherr, Manfred

2017-01-01

ABSTRACT Cyanobacterial and algal mass development, or blooms, have severe effects on freshwater and marine systems around the world. Many of these phototrophs produce a variety of potent toxins, contribute to oxygen depletion, and affect water quality in several ways. Coexisting antagonists, such as cyanolytic bacteria, hold the potential to suppress, or even terminate, such blooms, yet the nature of this interaction is not well studied. We isolated 31 cyanolytic bacteria affiliated with the genera Pseudomonas, Stenotrophomonas, Acinetobacter, and Delftia from three eutrophic freshwater lakes in Sweden and selected four phylogenetically diverse bacterial strains with strong-to-moderate lytic activity. To characterize their functional responses to the presence of cyanobacteria, we performed RNA sequencing (RNA-Seq) experiments on coculture incubations, with an initial predator-prey ratio of 1:1. Genes involved in central cellular pathways, stress-related heat or cold shock proteins, and antitoxin genes were highly expressed in both heterotrophs and cyanobacteria. Heterotrophs in coculture expressed genes involved in cell motility, signal transduction, and putative lytic activity. l,d-Transpeptidase was the only significantly upregulated lytic gene in Stenotrophomonas rhizophila EK20. Heterotrophs also shifted their central metabolism from the tricarboxylic acid cycle to the glyoxylate shunt. Concurrently, cyanobacteria clearly show contrasting antagonistic interactions with the four tested heterotrophic strains, which is also reflected in the physical attachment to their cells. In conclusion, antagonistic interactions with cyanobacteria were initiated within 24 h, and expression profiles suggest varied responses for the different cyanobacteria and studied cyanolytes. IMPORTANCE Here, we present how gene expression profiles can be used to reveal interactions between bloom-forming freshwater cyanobacteria and antagonistic heterotrophic bacteria. Species-specific responses in both heterotrophs and cyanobacteria were identified. The study contributes to a better understanding of the interspecies cellular interactions underpinning the persistence and collapse of cyanobacterial blooms. PMID:28115385

Interactions of Freshwater Cyanobacteria with Bacterial Antagonists.

PubMed

Osman, Omneya Ahmed; Beier, Sara; Grabherr, Manfred; Bertilsson, Stefan

2017-04-01

Cyanobacterial and algal mass development, or blooms, have severe effects on freshwater and marine systems around the world. Many of these phototrophs produce a variety of potent toxins, contribute to oxygen depletion, and affect water quality in several ways. Coexisting antagonists, such as cyanolytic bacteria, hold the potential to suppress, or even terminate, such blooms, yet the nature of this interaction is not well studied. We isolated 31 cyanolytic bacteria affiliated with the genera Pseudomonas , Stenotrophomonas , Acinetobacter , and Delftia from three eutrophic freshwater lakes in Sweden and selected four phylogenetically diverse bacterial strains with strong-to-moderate lytic activity. To characterize their functional responses to the presence of cyanobacteria, we performed RNA sequencing (RNA-Seq) experiments on coculture incubations, with an initial predator-prey ratio of 1:1. Genes involved in central cellular pathways, stress-related heat or cold shock proteins, and antitoxin genes were highly expressed in both heterotrophs and cyanobacteria. Heterotrophs in coculture expressed genes involved in cell motility, signal transduction, and putative lytic activity. l,d-Transpeptidase was the only significantly upregulated lytic gene in Stenotrophomonas rhizophila EK20. Heterotrophs also shifted their central metabolism from the tricarboxylic acid cycle to the glyoxylate shunt. Concurrently, cyanobacteria clearly show contrasting antagonistic interactions with the four tested heterotrophic strains, which is also reflected in the physical attachment to their cells. In conclusion, antagonistic interactions with cyanobacteria were initiated within 24 h, and expression profiles suggest varied responses for the different cyanobacteria and studied cyanolytes. IMPORTANCE Here, we present how gene expression profiles can be used to reveal interactions between bloom-forming freshwater cyanobacteria and antagonistic heterotrophic bacteria. Species-specific responses in both heterotrophs and cyanobacteria were identified. The study contributes to a better understanding of the interspecies cellular interactions underpinning the persistence and collapse of cyanobacterial blooms. Copyright © 2017 Osman et al.

Spicing Up the N Gene: F. O. Holmes and Tobacco mosaic virus Resistance in Capsicum and Nicotiana Plants.

PubMed

Scholthof, Karen-Beth G

2017-02-01

One of the seminal events in plant pathology was the discovery by Francis O. Holmes that necrotic local lesions induced on certain species of Nicotiana following rub-inoculation of Tobacco mosaic virus (TMV) was due to a specific interaction involving a dominant host gene (N). From this, Holmes had an idea that if the N gene from N. glutinosa was introgressed into susceptible tobacco, the greatly reduced titer of TMV would, by extension, prevent subsequent infection of tomato and pepper plants by field workers whose hands were contaminated with TMV from their use of chewing and smoking tobacco. The ultimate outcome has many surprising twists and turns, including Holmes' failure to obtain fertile crosses of N. glutinosa × N. tabacum after 3 years of intensive work. Progress was made with N. digluta, a rare amphidiploid that was readily crossed with N. tabacum. And, importantly, the first demonstration by Holmes of the utility of interspecies hybridization for virus resistance was made with Capsicum (pepper) species with the identification of the L gene in Tabasco pepper, that he introgressed into commercial bell pepper varieties. Holmes' findings are important as they predate Flor's gene-for-gene hypothesis, show the use of interspecies hybridization for control of plant pathogens, and the use of the local lesion as a bioassay to monitor resistance events in crop plants.

Metagenomic insight into methanogenic reactors promoting direct interspecies electron transfer via granular activated carbon.

PubMed

Park, Jeong-Hoon; Park, Jong-Hun; Je Seong, Hoon; Sul, Woo Jun; Jin, Kang-Hyun; Park, Hee-Deung

2018-07-01

To provide insight into direct interspecies electron transfer via granular activated carbon (GAC), the effect of GAC supplementation on anaerobic digestion was evaluated. Compared to control samples, the GAC supplementation increased the total amount of methane production and its production rate by 31% and 72%, respectively. 16S rDNA sequencing analysis revealed a shift in the archaeal community composition; the Methanosarcina proportion decreased 17%, while the Methanosaeta proportion increased 5.6%. Metagenomic analyses based on shotgun sequencing demonstrated that the abundance of pilA and omcS genes belonging to Geobacter species decreased 69.4% and 29.4%, respectively. Furthermore, the analyses suggested a carbon dioxide reduction pathway rather than an acetate decarboxylation pathway for methane formation. Taken together, these results suggest that GAC improved methane production performance by shifting the microbial community and altering functional genes associated with direct interspecies electron transfer via conductive materials. Copyright © 2018 Elsevier Ltd. All rights reserved.

Interspecies Chimerism with Mammalian Pluripotent Stem Cells.

PubMed

Wu, Jun; Platero-Luengo, Aida; Sakurai, Masahiro; Sugawara, Atsushi; Gil, Maria Antonia; Yamauchi, Takayoshi; Suzuki, Keiichiro; Bogliotti, Yanina Soledad; Cuello, Cristina; Morales Valencia, Mariana; Okumura, Daiji; Luo, Jingping; Vilariño, Marcela; Parrilla, Inmaculada; Soto, Delia Alba; Martinez, Cristina A; Hishida, Tomoaki; Sánchez-Bautista, Sonia; Martinez-Martinez, M Llanos; Wang, Huili; Nohalez, Alicia; Aizawa, Emi; Martinez-Redondo, Paloma; Ocampo, Alejandro; Reddy, Pradeep; Roca, Jordi; Maga, Elizabeth A; Esteban, Concepcion Rodriguez; Berggren, W Travis; Nuñez Delicado, Estrella; Lajara, Jeronimo; Guillen, Isabel; Guillen, Pedro; Campistol, Josep M; Martinez, Emilio A; Ross, Pablo Juan; Izpisua Belmonte, Juan Carlos

2017-01-26

Interspecies blastocyst complementation enables organ-specific enrichment of xenogenic pluripotent stem cell (PSC) derivatives. Here, we establish a versatile blastocyst complementation platform based on CRISPR-Cas9-mediated zygote genome editing and show enrichment of rat PSC-derivatives in several tissues of gene-edited organogenesis-disabled mice. Besides gaining insights into species evolution, embryogenesis, and human disease, interspecies blastocyst complementation might allow human organ generation in animals whose organ size, anatomy, and physiology are closer to humans. To date, however, whether human PSCs (hPSCs) can contribute to chimera formation in non-rodent species remains unknown. We systematically evaluate the chimeric competency of several types of hPSCs using a more diversified clade of mammals, the ungulates. We find that naïve hPSCs robustly engraft in both pig and cattle pre-implantation blastocysts but show limited contribution to post-implantation pig embryos. Instead, an intermediate hPSC type exhibits higher degree of chimerism and is able to generate differentiated progenies in post-implantation pig embryos. Copyright © 2017 Elsevier Inc. All rights reserved.

Molecular Genetic Analysis of the Melanoma Regulatory locus in Xiphophorus Interspecies Hybrids

PubMed Central

Lu, Yuan; Boswell, Mikki; Boswell, William; Kneitz, Susanne; Hausmann, Michael; Klotz, Barbara; Regneri, Janine; Savage, Markita; Amores, Angel; Postlethwait, John; Warren, Wesley; Schartl, Manfred; Walter, Ronald

2018-01-01

Development of spontaneous melanoma in Xiphophorus interspecies backcross hybrid progeny, (X. hellerii × [X. maculatus Jp 163 A × X. hellerii]) is due to Mendelian segregation of a oncogene (xmrk) and a molecularly uncharacterized locus, called R(Diff), on LG5. R(Diff) is thought to suppresses the activity of xmrk in healthy X. maculatus Jp 163 A parental species that rarely develop melanoma. To better understand the molecular genetics of R(Diff), we utilized RNA-Seq to study allele-specific gene expression of spontaneous melanoma tumors and corresponding normal skin samples derived from 15 first generation backcross (BC1) hybrids and 13 fifth generation (BC5) hybrids. Allele-specific expression was determined for all genes and assigned to parental allele inheritance for each backcross hybrid individual. Results showed that genes residing in a 5.81 Mbp region on LG5 were exclusively expressed from the X. hellerii alleles in tumor-bearing BC1 hybrids. This observation indicates this region is consistently homozygous for X. hellerii alleles in tumor bearing animals, and therefore defines this region to be the R(Diff) locus. The R(Diff) locus harbors 164 gene models and includes the previously characterized R(Diff) candidate, cdkn2x. Twenty one genes in the R(Diff) region show differential expression in the tumor samples compared to normal skin tissue. These results further characterize the R(Diff) locus and suggest tumor suppression may require a multigenic region rather than a single gene variant. Differences in gene expression between tumor and normal skin tissue in this region may indicate interactions among several genes are required for backcross hybrid melanoma development. PMID:28345808

Ambient ionization mass spectrometry imaging for characterizing plant-microbe interactions using liquid extraction surface analysis (LESA)

NASA Astrophysics Data System (ADS)

Chu, R. K.; Anderton, C.; Weston, D. J.; Carrell, A. A.; Paša-Tolić, L.; Veličković, D.; Tfaily, M.

2017-12-01

The rhizosphere consists of a diverse community of plants, bacteria and fungi that are interacting with each other and with complex soil matrix they occupy. By studying the chemical signaling and processes that occur within this dynamic microenvironment, we will further our understanding of the symbiotic and competitive interaction within microbial communities. Field studies and bulk analyses shed light on the mechanisms by which environmental perturbations alter carbon and nitrogen cycling, but what is less clear are the intra- and interspecies molecular transformations and transactions between the different constituents within the rhizosphere. Chemical imaging by liquid extraction surface analysis mass spectrometry (LESA-MS) is a highly sensitive technique capable of providing both spatial and molecular information. Here, we examined the chemical interactions among a tripartite system of peat moss (Sphagnum fallax), cyanobacteria (Nostoc muscorium), and fungus (Trizdiaspa). We coupled LESA source to both a 15 Tesla Fourier transform ion cyclotron resonance mass spectrometer (FTICR-MS), for ultrahigh mass resolution and mass accuracy results, and a Thermo Velos-LTQ mass spectrometer, for tandem MS of selected molecules to increase confidence in molecular identifications. With LESA-MS approach we spatially probed the tripartite interactions and isolated cultures using a coordinate system that can be mapped back and overlaid onto the original image. Using this method, we mapped an array of metabolic distributions within the model sphagnum microbiome. For instance, we identified carbendazim, an anti-fungal agent, distributed within the interaction zone between the bacteria and fungi, while glyceropcholine and sucrose were localized within the sphagnum and fungus interaction zone. Further analysis will look into larger metabolites, lipids, and small proteins.

Dynamic remodeling of microbial biofilms by functionally distinct exopolysaccharides.

PubMed

Chew, Su Chuen; Kundukad, Binu; Seviour, Thomas; van der Maarel, Johan R C; Yang, Liang; Rice, Scott A; Doyle, Patrick; Kjelleberg, Staffan

2014-08-05

Biofilms are densely populated communities of microbial cells protected and held together by a matrix of extracellular polymeric substances. The structure and rheological properties of the matrix at the microscale influence the retention and transport of molecules and cells in the biofilm, thereby dictating population and community behavior. Despite its importance, quantitative descriptions of the matrix microstructure and microrheology are limited. Here, particle-tracking microrheology in combination with genetic approaches was used to spatially and temporally study the rheological contributions of the major exopolysaccharides Pel and Psl in Pseudomonas aeruginosa biofilms. Psl increased the elasticity and effective cross-linking within the matrix, which strengthened its scaffold and appeared to facilitate the formation of microcolonies. Conversely, Pel reduced effective cross-linking within the matrix. Without Psl, the matrix becomes more viscous, which facilitates biofilm spreading. The wild-type biofilm decreased in effective cross-linking over time, which would be advantageous for the spreading and colonization of new surfaces. This suggests that there are regulatory mechanisms to control production of the exopolysaccharides that serve to remodel the matrix of developing biofilms. The exopolysaccharides were also found to have profound effects on the spatial organization and integration of P. aeruginosa in a mixed-species biofilm model of P. aeruginosa-Staphylococcus aureus. Pel was required for close association of the two species in mixed-species microcolonies. In contrast, Psl was important for P. aeruginosa to form single-species biofilms on top of S. aureus biofilms. Our results demonstrate that Pel and Psl have distinct physical properties and functional roles during biofilm formation. Importance: Most bacteria grow as biofilms in the environment or in association with eukaryotic hosts. Removal of biofilms that form on surfaces is a challenge in clinical and industrial settings. One of the defining features of a biofilm is its extracellular matrix. The matrix has a heterogeneous structure and is formed from a secretion of various biopolymers, including proteins, extracellular DNA, and polysaccharides. It is generally known to interact with biofilm cells, thus affecting cell physiology and cell-cell communication. Despite the fact that the matrix may comprise up to 90% of the biofilm dry weight, how the matrix properties affect biofilm structure, maturation, and interspecies interactions remain largely unexplored. This study reveals that bacteria can use specific extracellular polymers to modulate the physical properties of their microenvironment. This in turn impacts biofilm structure, differentiation, and interspecies interactions. Copyright © 2014 Chew et al.

Periods and stages of the prenatal development of the domestic cat.

PubMed

Knospe, C

2002-02-01

Twenty-two stages of the prenatal development of the domestic cat are described for intraspecies comparison in embryological studies. These are assigned to the 15 embryonal periods based on the Nomina Embryologica Veterinaria to make the interspecies comparison possible.

Evaluation of missing value methods for predicting ambient BTEX concentrations in two neighbouring cities in Southwestern Ontario Canada

NASA Astrophysics Data System (ADS)

Miller, Lindsay; Xu, Xiaohong; Wheeler, Amanda; Zhang, Tianchu; Hamadani, Mariam; Ejaz, Unam

2018-05-01

High density air monitoring campaigns provide spatial patterns of pollutant concentrations which are integral in exposure assessment. Such analysis can assist with the determination of links between air quality and health outcomes, however, problems due to missing data can threaten to compromise these studies. This research evaluates four methods; mean value imputation, inverse distance weighting (IDW), inter-species ratios, and regression, to address missing spatial concentration data ranging from one missing data point up to 50% missing data. BTEX (benzene, toluene, ethylbenzene, and xylenes) concentrations were measured in Windsor and Sarnia, Ontario in the fall of 2005. Concentrations and inter-species ratios were generally similar between the two cities. Benzene (B) was observed to be higher in Sarnia, whereas toluene (T) and the T/B ratios were higher in Windsor. Using these urban, industrialized cities as case studies, this research demonstrates that using inter-species ratios or regression of the data for which there is complete information, along with one measured concentration (i.e. benzene) to predict for missing concentrations (i.e. TEX) results in good agreement between predicted and measured values. In both cities, the general trend remains that best agreement is observed for the leave-one-out scenario, followed by 10% and 25% missing, and the least agreement for the 50% missing cases. In the absence of any known concentrations IDW can provide reasonable agreement between observed and estimated concentrations for the BTEX species, and was superior over mean value imputation which was not able to preserve the spatial trend. The proposed methods can be used to fill in missing data, while preserving the general characteristics and rank order of the data which are sufficient for epidemiologic studies.

Superfluid-insulator transitions of two-species bosons in an optical lattice

DOE Office of Scientific and Technical Information (OSTI.GOV)

Isacsson, A.; Department of Physics, Yale University, P.O. Box 208120, New Haven, Connecticut 06520-8120; Cha, M.-C.

2005-11-01

We consider the two-species bosonic Hubbard model with variable interspecies interaction and hopping strength in the grand canonical ensemble with a common chemical potential. We analyze the superfluid-insulator (SI) transition for the relevant parameter regimes and compute the ground state phase diagram in the vicinity of odd filling Mott states. We find that the superfluid-insulator transition occurs with (a) simultaneous onset of superfluidity of both species or (b) coexistence of Mott insulating state of one species and superfluidity of the other or, in the case of unit filling (c) complete depopulation of one species. The superfluid-insulator transition can be firstmore » order in a large region of the phase diagram. We develop a variational mean-field method which takes into account the effect of second order quantum fluctuations on the superfluid-insulator transition and corroborate the mean-field phase diagram using a quantum Monte Carlo study.« less

Metaorganisms as the new frontier

PubMed Central

Bosch, Thomas C.G.; McFall-Ngai, Margaret J.

2014-01-01

Summary Because it appears that almost all organisms are part of an interdependent meta-organism, an understanding of the underlying host-microbe species associations, and of its evolution and molecular underpinnings, has become the new frontier in zoology. The availability of novel highthroughput sequencing methods together with the conceptual understanding that advances mostly originate at the intersection of traditional disciplinary boundaries, enable biologists to dissect the mechanisms that control the interdependent associations of species. In this perspective article, we outline some of the issues in interspecies interactions, present two case studies illuminating the necessity of interfacial research when addressing complex and fundamental zoological problems, and show that an interdisciplinary approach that seeks to understand co-evolved multi-species relationships will connect genomes, phenotypes, ecosystems and the evolutionary forces that have shaped them. We hope that this article inspires other collaborations of a similar nature on the diverse landscape commonly referred to as “zoology”. PMID:21737250

Metaorganisms as the new frontier.

PubMed

Bosch, Thomas C G; McFall-Ngai, Margaret J

2011-09-01

Because it appears that almost all organisms are part of an interdependent metaorganism, an understanding of the underlying host-microbe species associations, and of evolution and molecular underpinnings, has become the new frontier in zoology. The availability of novel high-throughput sequencing methods, together with the conceptual understanding that advances mostly originate at the intersection of traditional disciplinary boundaries, enable biologists to dissect the mechanisms that control the interdependent associations of species. In this review article, we outline some of the issues in inter-species interactions, present two case studies illuminating the necessity of interfacial research when addressing complex and fundamental zoological problems, and show that an interdisciplinary approach that seeks to understand co-evolved multi-species relationships will connect genomes, phenotypes, ecosystems and the evolutionary forces that have shaped them. We hope that this article inspires other collaborations of a similar nature on the diverse landscape commonly referred to as "zoology". Copyright © 2011 Elsevier GmbH. All rights reserved.

Ecosystem vulnerability to climate change in the southeastern United States

USGS Publications Warehouse

Cartwright, Jennifer M.; Costanza, Jennifer

2016-08-11

Two recent investigations of climate-change vulnerability for 19 terrestrial, aquatic, riparian, and coastal ecosystems of the southeastern United States have identified a number of important considerations, including potential for changes in hydrology, disturbance regimes, and interspecies interactions. Complementary approaches using geospatial analysis and literature synthesis integrated information on ecosystem biogeography and biodiversity, climate projections, vegetation dynamics, soil and water characteristics, anthropogenic threats, conservation status, sea-level rise, and coastal flooding impacts. Across a diverse set of ecosystems—ranging in size from dozens of square meters to thousands of square kilometers—quantitative and qualitative assessments identified types of climate-change exposure, evaluated sensitivity, and explored potential adaptive capacity. These analyses highlighted key gaps in scientific understanding and suggested priorities for future research. Together, these studies help create a foundation for ecosystem-level analysis of climate-change vulnerability to support effective biodiversity conservation in the southeastern United States.

Untargeted metabolomics studies employing NMR and LC-MS reveal metabolic coupling between Nanoarcheum equitans and its archaeal host Ignicoccus hospitalis.

PubMed

Hamerly, Timothy; Tripet, Brian P; Tigges, Michelle; Giannone, Richard J; Wurch, Louie; Hettich, Robert L; Podar, Mircea; Copié, Valerie; Bothner, Brian

2015-08-01

Interspecies interactions are the basis of microbial community formation and infectious diseases. Systems biology enables the construction of complex models describing such interactions, leading to a better understanding of disease states and communities. However, before interactions between complex organisms can be understood, metabolic and energetic implications of simpler real-world host-microbe systems must be worked out. To this effect, untargeted metabolomics experiments were conducted and integrated with proteomics data to characterize key molecular-level interactions between two hyperthermophilic microbial species, both of which have reduced genomes. Metabolic changes and transfer of metabolites between the archaea Ignicoccus hospitalis and Nanoarcheum equitans were investigated using integrated LC-MS and NMR metabolomics. The study of such a system is challenging, as no genetic tools are available, growth in the laboratory is challenging, and mechanisms by which they interact are unknown. Together with information about relative enzyme levels obtained from shotgun proteomics, the metabolomics data provided useful insights into metabolic pathways and cellular networks of I. hospitalis that are impacted by the presence of N. equitans , including arginine, isoleucine, and CTP biosynthesis. On the organismal level, the data indicate that N. equitans exploits metabolites generated by I. hospitalis to satisfy its own metabolic needs. This finding is based on N. equitans 's consumption of a significant fraction of the metabolite pool in I. hospitalis that cannot solely be attributed to increased biomass production for N. equitans . Combining LC-MS and NMR metabolomics datasets improved coverage of the metabolome and enhanced the identification and quantitation of cellular metabolites.

Untargeted metabolomics studies employing NMR and LC-MS reveal metabolic coupling between Nanoarcheum equitans and its archaeal host Ignicoccus hospitalis

PubMed Central

Hamerly, Timothy; Tripet, Brian P.; Tigges, Michelle; Giannone, Richard J.; Wurch, Louie; Hettich, Robert L.; Podar, Mircea; Copié, Valerie; Bothner, Brian

2014-01-01

Interspecies interactions are the basis of microbial community formation and infectious diseases. Systems biology enables the construction of complex models describing such interactions, leading to a better understanding of disease states and communities. However, before interactions between complex organisms can be understood, metabolic and energetic implications of simpler real-world host-microbe systems must be worked out. To this effect, untargeted metabolomics experiments were conducted and integrated with proteomics data to characterize key molecular-level interactions between two hyperthermophilic microbial species, both of which have reduced genomes. Metabolic changes and transfer of metabolites between the archaea Ignicoccus hospitalis and Nanoarcheum equitans were investigated using integrated LC-MS and NMR metabolomics. The study of such a system is challenging, as no genetic tools are available, growth in the laboratory is challenging, and mechanisms by which they interact are unknown. Together with information about relative enzyme levels obtained from shotgun proteomics, the metabolomics data provided useful insights into metabolic pathways and cellular networks of I. hospitalis that are impacted by the presence of N. equitans, including arginine, isoleucine, and CTP biosynthesis. On the organismal level, the data indicate that N. equitans exploits metabolites generated by I. hospitalis to satisfy its own metabolic needs. This finding is based on N. equitans’s consumption of a significant fraction of the metabolite pool in I. hospitalis that cannot solely be attributed to increased biomass production for N. equitans. Combining LC-MS and NMR metabolomics datasets improved coverage of the metabolome and enhanced the identification and quantitation of cellular metabolites. PMID:26273237

A Multifluid Numerical Algorithm for Interpenetrating Plasma Dynamics

NASA Astrophysics Data System (ADS)

Ghosh, Debojyoti; Kavouklis, Christos; Berger, Richard; Chapman, Thomas; Hittinger, Jeffrey

2017-10-01

Interpenetrating plasmas occur in situations including inertial confinement fusion experiments, where plasmas ablate off the hohlraum and capsule surfaces and interact with each other, and in high-energy density physics experiments that involve the collision of plasma streams ablating off discs irradiated by laser beams. Single-fluid, multi-species hydrodynamic models are not well-suited to study this interaction because they cannot support more than a single fluid velocity; this results in unphysical solutions. Though kinetic models yield accurate solutions for multi-fluid interactions, they are prohibitively expensive for at-scale three-dimensional (3D) simulations. In this study, we propose a multifluid approach where the compressible fluid equations are solved for each ion species and the electrons. Electrostatic forces and inter-species friction and thermal equilibration couple the species. A high-order finite-volume algorithm with explicit time integration is used to solve on a 3D Cartesian domain, and a high-order Poisson solver is used to compute the electrostatic potential. We present preliminary results for the interpenetration of two plasma streams in vacuum and in the presence of a gas fill. This work was performed under the auspices of the U.S. DOE by Lawrence Livermore National Laboratory under Contract No. DE-AC52- 07NA27344 and funded by the LDRD Program at LLNL under project tracking code 17-ERD-081.

Photographic evidence of interspecies mating in geckos of the Lepidodactylus lugubris unisexual-bisexual complex (Squamata: Gekkonidae)

USGS Publications Warehouse

Buden, Donald W.; Cianchini, Carlos; Taborosi, Danko; Fisher, Robert N.; Bauer, Aaron; Ineich, Ivan

2014-01-01

An interspecies mating between unisexual Lepidodactylus lugubris and a male of the bisexual Lepidodactylus moestus was photographed by Carlos Cianchini on Kosrae [Island], FSM, at 18:15 h on 22 August 2013 (Figure 1). The mating pair was on a window frame inside a house at Pukusruk Wan village (05°21'01" N, 163°00'41" E, elev. 28 m a.s.l.) on the northeastern side of the island. This is the first direct evidence of mating between these two species.

Stochastic ontogenetic growth model

NASA Astrophysics Data System (ADS)

West, B. J.; West, D.

2012-02-01

An ontogenetic growth model (OGM) for a thermodynamically closed system is generalized to satisfy both the first and second law of thermodynamics. The hypothesized stochastic ontogenetic growth model (SOGM) is shown to entail the interspecies allometry relation by explicitly averaging the basal metabolic rate and the total body mass over the steady-state probability density for the total body mass (TBM). This is the first derivation of the interspecies metabolic allometric relation from a dynamical model and the asymptotic steady-state distribution of the TBM is fit to data and shown to be inverse power law.

Interspecies chimeric complementation for the generation of functional human tissues and organs in large animal hosts.

PubMed

Wu, Jun; Izpisua Belmonte, Juan Carlos

2016-06-01

The past decade's rapid progress in human pluripotent stem cell (hPSC) research has generated hope for meeting the rising demand of organ donation, which remains the only effective cure for end-stage organ failure, a major cause of death worldwide. Despite the potential, generation of transplantable organs from hPSCs using in vitro differentiation is far-fetched. An in vivo interspecies chimeric complementation strategy relying on chimeric-competent hPSCs and zygote genome editing provides an auspicious alternative for providing unlimited organ source for transplantation.

Evaluation on direct interspecies electron transfer in anaerobic sludge digestion of microbial electrolysis cell.

PubMed

Zhao, Zisheng; Zhang, Yaobin; Quan, Xie; Zhao, Huimin

2016-01-01

Increase of methanogenesis in methane-producing microbial electrolysis cells (MECs) is frequently believed as a result of cathodic reduction of CO2. Recent studies indicated that this electromethanogenesis only accounted for a little part of methane production during anaerobic sludge digestion. Instead, direct interspecies electron transfer (DIET) possibly plays an important role in methane production. In this study, anaerobic digestion of sludge were investigated in a single-chamber MEC reactor, a carbon-felt supplemented reactor and a common anaerobic reactor to evaluate the effects of DIET on the sludge digestion. The results showed that adding carbon felt into the reactor increased 12.9% of methane production and 17.2% of sludge reduction. Imposing a voltage on the carbon felt further improved the digestion. Current calculation showed that the cathodic reduction only contributed to 27.5% of increased methane production. Microbial analysis indicated that DIET played an important role in the anaerobic sludge digestion in the MEC. Copyright © 2015 Elsevier Ltd. All rights reserved.

Mitochondrial DNA transmission and confounding mitochondrial influences in cloned cattle and pigs.

PubMed

Takeda, Kumiko

2013-04-01

Although somatic cell nuclear transfer (SCNT) is a powerful tool for production of cloned animals, SCNT embryos generally have low developmental competency and many abnormalities. The interaction between the donor nucleus and the enucleated ooplasm plays an important role in early embryonic development, but the underlying mechanisms that negatively impact developmental competency remain unclear. Mitochondria have a broad range of critical functions in cellular energy supply, cell signaling, and programmed cell death; thus, affect embryonic and fetal development. This review focuses on mitochondrial considerations influencing SCNT techniques in farm animals. Donor somatic cell mitochondrial DNA (mtDNA) can be transmitted through what has been considered a "bottleneck" in mitochondrial genetics via the SCNT maternal lineage. This indicates that donor somatic cell mitochondria have a role in the reconstructed cytoplasm. However, foreign somatic cell mitochondria may affect the early development of SCNT embryos. Nuclear-mitochondrial interactions in interspecies/intergeneric SCNT (iSCNT) result in severe problems. A major biological selective pressure exists against survival of exogenous mtDNA in iSCNT. Yet, mtDNA differences in SCNT animals did not reflect transfer of proteomic components following proteomic analysis. Further study of nuclear-cytoplasmic interactions is needed to illuminate key developmental characteristics of SCNT animals associated with mitochondrial biology.

Punctuated equilibrium as an emergent process and its modified thermodynamic characterization.

PubMed

Wosniack, M E; da Luz, M G E; Schulman, L S

2017-01-07

We address evolutionary dynamics and consider under which conditions the ecosystem interaction network allows punctuated equilibrium (i.e., alternation between hectic and quasi-stable phases). We focus on the links connecting various species and on the strength and sign of those links. For this study we consider the Tangled Nature model, which allows considerable flexibility and plasticity in the analysis of interspecies interactions. We find that it is necessary to have a proper balance of connectivity and interaction intensities so as to establish the kind of mutual cooperation and competition found in nature. It suggests evolutionary punctuated equilibrium as an emergent process, thus displaying features of complex systems. To explicitly demonstrate this fact we consider an extended form of thermodynamics, defining (for the present context) relevant out-of-equilibrium "collective" functions. We then show how to characterize the punctuated equilibrium through entropy-like and free energy-like quantities. Finally, from a close analogy to thermodynamic systems, we propose a protocol similar to simulated annealing. It is based on controlling the species' rate of mutation during the hectic periods, in this way enhancing the exploration of the genome space (similar to the known behavior of bacteria in stressful environments). This allows the system to more rapidly converge to long-duration quasi-stable phases. Copyright © 2016 Elsevier Ltd. All rights reserved.

Interspecies Interactions Stimulate Diversification of the Streptomyces coelicolor Secreted Metabolome

PubMed Central

Traxler, Matthew F.; Watrous, Jeramie D.; Alexandrov, Theodore; Dorrestein, Pieter C.; Kolter, Roberto

2013-01-01

ABSTRACT Soils host diverse microbial communities that include filamentous actinobacteria (actinomycetes). These bacteria have been a rich source of useful metabolites, including antimicrobials, antifungals, anticancer agents, siderophores, and immunosuppressants. While humans have long exploited these compounds for therapeutic purposes, the role these natural products may play in mediating interactions between actinomycetes has been difficult to ascertain. As an initial step toward understanding these chemical interactions at a systems level, we employed the emerging techniques of nanospray desorption electrospray ionization (NanoDESI) and matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) imaging mass spectrometry to gain a global chemical view of the model bacterium Streptomyces coelicolor interacting with five other actinomycetes. In each interaction, the majority of secreted compounds associated with S. coelicolor colonies were unique, suggesting an idiosyncratic response from S. coelicolor. Spectral networking revealed a family of unknown compounds produced by S. coelicolor during several interactions. These compounds constitute an extended suite of at least 12 different desferrioxamines with acyl side chains of various lengths; their production was triggered by siderophores made by neighboring strains. Taken together, these results illustrate that chemical interactions between actinomycete bacteria exhibit high complexity and specificity and can drive differential secondary metabolite production. PMID:23963177

Identifying Keystone Species in the Human Gut Microbiome from Metagenomic Timeseries Using Sparse Linear Regression

PubMed Central

Fisher, Charles K.; Mehta, Pankaj

2014-01-01

Human associated microbial communities exert tremendous influence over human health and disease. With modern metagenomic sequencing methods it is now possible to follow the relative abundance of microbes in a community over time. These microbial communities exhibit rich ecological dynamics and an important goal of microbial ecology is to infer the ecological interactions between species directly from sequence data. Any algorithm for inferring ecological interactions must overcome three major obstacles: 1) a correlation between the abundances of two species does not imply that those species are interacting, 2) the sum constraint on the relative abundances obtained from metagenomic studies makes it difficult to infer the parameters in timeseries models, and 3) errors due to experimental uncertainty, or mis-assignment of sequencing reads into operational taxonomic units, bias inferences of species interactions due to a statistical problem called “errors-in-variables”. Here we introduce an approach, Learning Interactions from MIcrobial Time Series (LIMITS), that overcomes these obstacles. LIMITS uses sparse linear regression with boostrap aggregation to infer a discrete-time Lotka-Volterra model for microbial dynamics. We tested LIMITS on synthetic data and showed that it could reliably infer the topology of the inter-species ecological interactions. We then used LIMITS to characterize the species interactions in the gut microbiomes of two individuals and found that the interaction networks varied significantly between individuals. Furthermore, we found that the interaction networks of the two individuals are dominated by distinct “keystone species”, Bacteroides fragilis and Bacteroided stercosis, that have a disproportionate influence on the structure of the gut microbiome even though they are only found in moderate abundance. Based on our results, we hypothesize that the abundances of certain keystone species may be responsible for individuality in the human gut microbiome. PMID:25054627

Trade-off between morphological convergence and opportunistic diet behavior in fish hybrid zone

PubMed Central

Corse, Emmanuel; Costedoat, Caroline; Pech, Nicolas; Chappaz, Rémi; Grey, Jonathan; Gilles, André

2009-01-01

Background The invasive Chondrostoma nasus nasus has colonized part of the distribution area of the protected endemic species Chondrostoma toxostoma toxostoma. This hybrid zone is a complex system where multiple effects such as inter-species competition, bi-directional introgression, strong environmental pressure and so on are combined. Why do sympatric Chondrostoma fish present a unidirectional change in body shape? Is this the result of inter-species interactions and/or a response to environmental effects or the result of trade-offs? Studies focusing on the understanding of a trade-off between multiple parameters are still rare. Although this has previously been done for Cichlid species flock and for Darwin finches, where mouth or beak morphology were coupled to diet and genetic identification, no similar studies have been done for a fish hybrid zone in a river. We tested the correlation between morphology (body and mouth morphology), diet (stable carbon and nitrogen isotopes) and genomic combinations in different allopatric and sympatric populations for a global data set of 1330 specimens. To separate the species interaction effect from the environmental effect in sympatry, we distinguished two data sets: the first one was obtained from a highly regulated part of the river and the second was obtained from specimens coming from the less regulated part. Results The distribution of the hybrid combinations was different in the two part of the sympatric zone, whereas all the specimens presented similar overall changes in body shape and in mouth morphology. Sympatric specimens were also characterized by a larger diet behavior variance than reference populations, characteristic of an opportunistic diet. No correlation was established between the body shape (or mouth deformation) and the stable isotope signature. Conclusion The Durance River is an untamed Mediterranean river despite the presence of numerous dams that split the river from upstream to downstream. The sympatric effect on morphology and the large diet behavior range can be explained by a tendency toward an opportunistic behavior of the sympatric specimens. Indeed, the similar response of the two species and their hybrids implied an adaptation that could be defined as an alternative trade-off that underline the importance of epigenetics mechanisms for potential success in a novel environment. PMID:19860907

Impaired Spatial Navigation in Pediatric Anxiety

ERIC Educational Resources Information Center

Mueller, Sven C.; Temple, Veronica; Cornwell, Brian; Grillon, Christian; Pine, Daniel S.; Ernst, Monique

2009-01-01

Background: Previous theories implicate hippocampal dysfunction in anxiety disorders. Most of the data supporting these theories stem from animal research, particularly lesion studies. The generalization of findings from rodent models to human function is hampered by fundamental inter-species differences. The present work uses a task of spatial…

White-tailed Deer are Susceptible to Sheep Scrapie by Intracerebral Inoculation

USDA-ARS?s Scientific Manuscript database

Interspecies transmission studies afford the opportunity to better understand the potential host range and origins of prion diseases. The purpose of this experiment was to determine susceptibility of white-tailed deer to scrapie after intracerebral inoculation and to compare clinical signs and lesi...

Dual-species Bose-Einstein condensate of {sup 87}Rb and {sup 133}Cs

DOE Office of Scientific and Technical Information (OSTI.GOV)

McCarron, D. J.; Cho, H. W.; Jenkin, D. L.

2011-07-15

We report the formation of a dual-species Bose-Einstein condensate of {sup 87}Rb and {sup 133}Cs in the same trapping potential. Our method exploits the efficient sympathetic cooling of {sup 133}Cs via elastic collisions with {sup 87}Rb, initially in a magnetic quadrupole trap and subsequently in a levitated optical trap. The two condensates each contain up to 2x10{sup 4} atoms and exhibit a striking phase separation, revealing the mixture to be immiscible due to strong repulsive interspecies interactions. Sacrificing all the {sup 87}Rb during the cooling, we create single-species {sup 133}Cs condensates of up to 6x10{sup 4} atoms.

Inhibition of Cell Differentiation in Bacillus subtilis by Pseudomonas protegens

PubMed Central

Powers, Matthew J.; Sanabria-Valentín, Edgardo; Bowers, Albert A.

2015-01-01

ABSTRACT Interspecies interactions have been described for numerous bacterial systems, leading to the identification of chemical compounds that impact bacterial physiology and differentiation for processes such as biofilm formation. Here, we identified soil microbes that inhibit biofilm formation and sporulation in the common soil bacterium Bacillus subtilis. We did so by creating a reporter strain that fluoresces when the transcription of a biofilm-specific gene is repressed. Using this reporter in a coculture screen, we identified Pseudomonas putida and Pseudomonas protegens as bacteria that secrete compounds that inhibit biofilm gene expression in B. subtilis. The active compound produced by P. protegens was identified as the antibiotic and antifungal molecule 2,4-diacetylphloroglucinol (DAPG). Colonies of B. subtilis grown adjacent to a DAPG-producing P. protegens strain had altered colony morphologies relative to B. subtilis colonies grown next to a DAPG-null P. protegens strain (phlD strain). Using a subinhibitory concentration of purified DAPG in a pellicle assay, we saw that biofilm-specific gene transcription was delayed relative to transcription in untreated samples. These transcriptional changes also corresponded to phenotypic alterations: both biofilm biomass and spore formation were reduced in B. subtilis liquid cultures treated with subinhibitory concentrations of DAPG. Our results add DAPG to the growing list of antibiotics that impact bacterial development and physiology at subinhibitory concentrations. These findings also demonstrate the utility of using coculture as a means to uncover chemically mediated interspecies interactions between bacteria. IMPORTANCE Biofilms are communities of bacteria adhered to surfaces by an extracellular matrix; such biofilms can have important effects in both clinical and agricultural settings. To identify chemical compounds that inhibited biofilm formation, we used a fluorescent reporter to screen for bacteria that inhibited biofilm gene expression in Bacillus subtilis. We identified Pseudomonas protegens as one such bacterium and found that the biofilm-inhibiting compound it produces was the antibiotic 2,4-diacetylphloroglucinol (DAPG). We showed that even at subinhibitory concentrations, DAPG inhibits biofilm formation and sporulation in B. subtilis. These findings have potential implications for understanding the interactions between these two microbes in the natural world and support the idea that many compounds considered antibiotics can impact bacterial development at subinhibitory concentrations. PMID:25825426

Use of comparative genomics approaches to characterize interspecies differences in response to environmental chemicals: Challenges, opportunities, and research needs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Burgess-Herbert, Sarah L., E-mail: sarah.burgess@alum.mit.edu; Euling, Susan Y.

A critical challenge for environmental chemical risk assessment is the characterization and reduction of uncertainties introduced when extrapolating inferences from one species to another. The purpose of this article is to explore the challenges, opportunities, and research needs surrounding the issue of how genomics data and computational and systems level approaches can be applied to inform differences in response to environmental chemical exposure across species. We propose that the data, tools, and evolutionary framework of comparative genomics be adapted to inform interspecies differences in chemical mechanisms of action. We compare and contrast existing approaches, from disciplines as varied as evolutionarymore » biology, systems biology, mathematics, and computer science, that can be used, modified, and combined in new ways to discover and characterize interspecies differences in chemical mechanism of action which, in turn, can be explored for application to risk assessment. We consider how genetic, protein, pathway, and network information can be interrogated from an evolutionary biology perspective to effectively characterize variations in biological processes of toxicological relevance among organisms. We conclude that comparative genomics approaches show promise for characterizing interspecies differences in mechanisms of action, and further, for improving our understanding of the uncertainties inherent in extrapolating inferences across species in both ecological and human health risk assessment. To achieve long-term relevance and consistent use in environmental chemical risk assessment, improved bioinformatics tools, computational methods robust to data gaps, and quantitative approaches for conducting extrapolations across species are critically needed. Specific areas ripe for research to address these needs are recommended.« less

Interspecies nuclear transfer using fibroblasts from leopard, tiger, and lion ear piece collected postmortem as donor cells and rabbit oocytes as recipients.

PubMed

Yelisetti, Uma Mahesh; Komjeti, Suman; Katari, Venu Charan; Sisinthy, Shivaji; Brahmasani, Sambasiva Rao

2016-06-01

Skin fibroblast cells were obtained from a small piece of an ear of leopard, lion, and tiger collected postmortem and attempts were made to synchronize the skin fibroblasts at G0/G1 of cell cycle using three different approaches. Efficiency of the approaches was tested following interspecies nuclear transfer with rabbit oocytes as recipient cytoplasm. Fluorescence-activated cell sorting revealed that the proportion of G0/G1 cells increased significantly (P < 0.05) when cells subjected to serum starvation, contact inhibition, and 3 mM sodium butyrate (NaBu) treatment when compared with cycling cells. However, 3 mM NaBu treatment caused alterations in cell morphology and increase in dead cells. Thus, interspecies nuclear transfer was carried out using fibroblast cells subjected to contact inhibition for 72 h, serum starvation for 48 h, and cells treated with 1.0 mM NaBu for 48 h. The fusion rates, the proportion of fused couplets that cleaved to two-cell and developed to blastocyst, were highest in all three species when the donor cells were treated with 1.0 mM NaBu for 48 h. But, the blastocyst percentage of interspecies nuclear embryos (5-6%) was significantly lower when compared with rabbit-rabbit nuclear transfer embryos (22.9%). In conclusion, fibroblast cells of leopard, lion, and tiger were successfully synchronized and used for the development of blastocysts using rabbit oocytes as recipient cytoplasm.

Human platelet lysate supplementation of mesenchymal stromal cell delivery: issues of xenogenicity and species variability.

PubMed

Allen, Ashley B; Butts, Emily B; Copland, Ian B; Stevens, Hazel Y; Guldberg, Robert E

2017-10-01

Immunogenicity of fetal bovine serum (FBS) poses a problem for its use in the propagation of autologous mesenchymal stromal cells (MSCs) for cell therapy. Human platelet lysate (hPL), an enriched growth factor solution containing mitogenic and angiogenic cues, has potential utility in replacing FBS for human MSC (hMSC) delivery strategies. Despite its potentiation of hMSC number in vitro, little is known concerning its capacity to supplement implanted hMSC-seeded constructs and promote tissue regeneration in vivo. In this study, we tested the effects of incorporating hPL in cell-seeded constructs implanted subcutaneously into immunocompromised rats, investigated in vitro interactions between hPL and rat MSCs (rMSCs) and determined interspecies variability in the PL product [hPL vs rat PL (rPL)] and its effect on cultured MSCs (hPL/hMSCs vs rPL/rMSCs). The overarching aim was to determine the utility of hPL to foster MSC survival in preclinical rodent models. Exposure to hPL-supplemented media resulted in rMSC death, by a process attributable to heat-labile proteins, but not membrane attack complex formation. In the in vitro syngeneic model, the rodent product proved fundamentally distinct from the human product, with rPL having substantially lower growth factor content than hPL. Moreover, contrary to the positive effects of hPL on hMSC expansion, rPL did not reduce rMSC doubling time for the serum concentrations examined. When tested in vivo, hPL did not improve cell survival within hydrogel constructs through 2 weeks postimplantation. In summary, this study highlights the many facets of xenogenicity and interspecies variability that must be considered in the preclinical evaluation of hPL. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Characterization of a bacterial tyrosine kinase in Porphyromonas gingivalis involved in polymicrobial synergy.

PubMed

Wright, Christopher J; Xue, Peng; Hirano, Takanori; Liu, Chengcheng; Whitmore, Sarah E; Hackett, Murray; Lamont, Richard J

2014-06-01

Interspecies communication between Porphyromonas gingivalis and Streptococcus gordonii underlies the development of synergistic dual species communities. Contact with S. gordonii initiates signal transduction within P. gingivalis that is based on protein tyrosine (de)phosphorylation. In this study, we characterize a bacterial tyrosine (BY) kinase (designated Ptk1) of P. gingivalis and demonstrate its involvement in interspecies signaling. Ptk1 can utilize ATP for autophosphorylation and is dephosphorylated by the P. gingivalis tyrosine phosphatase, Ltp1. Community development with S. gordonii is severely abrogated in a ptk1 mutant of P. gingivalis, indicating that tyrosine kinase activity is required for maximal polymicrobial synergy. Ptk1 controls the levels of the transcriptional regulator CdhR and the fimbrial adhesin Mfa1 which mediates binding to S. gordonii. The ptk1 gene is in an operon with two genes involved in exopolysaccharide synthesis, and similar to other BY kinases, Ptk1 is necessary for exopolysaccharide production in P. gingivalis. Ptk1 can phosphorylate the capsule related proteins PGN_0224, a UDP-acetyl-mannosamine dehydrogenase, and PGN_0613, a UDP-glucose dehydrogenase, in P. gingivalis. Knockout of ptk1 in an encapsulated strain of P. gingivalis resulted in loss of capsule production. Collectively these results demonstrate that the P. gingivalis Ptk1 BY kinase regulates interspecies communication and controls heterotypic community development with S. gordonii through adjusting the levels of the Mfa1 adhesin and exopolysaccharide. © 2014 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Feshbach spectroscopy and dual-species Bose-Einstein condensation of 23Na-39K mixtures

NASA Astrophysics Data System (ADS)

Schulze, Torben A.; Hartmann, Torsten; Voges, Kai K.; Gempel, Matthias W.; Tiemann, Eberhard; Zenesini, Alessandro; Ospelkaus, Silke

2018-02-01

We present measurements of interspecies Feshbach resonances and subsequent creation of dual-species Bose-Einstein condensates of 23Na and 39K. We prepare both optically trapped ensembles in the spin state |f =1 ,mf=-1 > and perform atom loss spectroscopy in a magnetic field range from 0 to 700 G . The observed features include several s -wave poles and a zero crossing of the interspecies scattering length as well as inelastic two-body contributions in the M =mNa+mK=-2 submanifold. We identify and discuss the suitability of different magnetic field regions for the purposes of sympathetic cooling of 39K and achieving dual-species degeneracy. Two condensates are created simultaneously by evaporation at a magnetic field of about 150 G , which provides sizable intra- and interspecies scattering rates needed for fast thermalization. The impact of the differential gravitational sag on the miscibility criterion for the mixture is discussed. Our results serve as a promising starting point for the magnetoassociation into quantum degenerate 23Na39K Feshbach molecules.

Improving toxicity extrapolation using molecular sequence similarity: A case study of pyrethroids and the sodium ion channel

EPA Science Inventory

A significant challenge in ecotoxicology has been determining chemical hazards to species with limited or no toxicity data. Currently, extrapolation tools like U.S. EPA’s Web-based Interspecies Correlation Estimation (Web-ICE; www3.epa.gov/webice) models categorize toxicity...

Bridging the Gap between the Human and Macaque Connectome: A Quantitative Comparison of Global Interspecies Structure-Function Relationships and Network Topology

PubMed Central

Miranda-Dominguez, Oscar; Mills, Brian D.; Grayson, David; Woodall, Andrew; Grant, Kathleen A.; Kroenke, Christopher D.

2014-01-01

Resting state functional connectivity MRI (rs-fcMRI) may provide a powerful and noninvasive “bridge” for comparing brain function between patients and experimental animal models; however, the relationship between human and macaque rs-fcMRI remains poorly understood. Here, using a novel surface deformation process for species comparisons in the same anatomical space (Van Essen, 2004, 2005), we found high correspondence, but also unique hub topology, between human and macaque functional connectomes. The global functional connectivity match between species was moderate to strong (r = 0.41) and increased when considering the top 15% strongest connections (r = 0.54). Analysis of the match between functional connectivity and the underlying anatomical connectivity, derived from a previous retrograde tracer study done in macaques (Markov et al., 2012), showed impressive structure–function correspondence in both the macaque and human. When examining the strongest structural connections, we found a 70–80% match between structural and functional connectivity matrices in both species. Finally, we compare species on two widely used metrics for studying hub topology: degree and betweenness centrality. The data showed topological agreement across the species, with nodes of the posterior cingulate showing high degree and betweenness centrality. In contrast, nodes in medial frontal and parietal cortices were identified as having high degree and betweenness in the human as opposed to the macaque. Our results provide: (1) a thorough examination and validation for a surface-based interspecies deformation process, (2) a strong theoretical foundation for making interspecies comparisons of rs-fcMRI, and (3) a unique look at topological distinctions between the species. PMID:24741045

High-performance metabolic profiling of plasma from seven mammalian species for simultaneous environmental chemical surveillance and bioeffect monitoring.

PubMed

Park, Youngja H; Lee, Kichun; Soltow, Quinlyn A; Strobel, Frederick H; Brigham, Kenneth L; Parker, Richard E; Wilson, Mark E; Sutliff, Roy L; Mansfield, Keith G; Wachtman, Lynn M; Ziegler, Thomas R; Jones, Dean P

2012-05-16

High-performance metabolic profiling (HPMP) by Fourier-transform mass spectrometry coupled to liquid chromatography gives relative quantification of thousands of chemicals in biologic samples but has had little development for use in toxicology research. In principle, the approach could be useful to detect complex metabolic response patterns to toxicologic exposures and to detect unusual abundances or patterns of potentially toxic chemicals. As an initial study to develop these possible uses, we applied HPMP and bioinformatics analysis to plasma of humans, rhesus macaques, marmosets, pigs, sheep, rats and mice to determine: (1) whether more chemicals are detected in humans living in a less controlled environment than captive species and (2) whether a subset of plasma chemicals with similar inter-species and intra-species variation could be identified for use in comparative toxicology. Results show that the number of chemicals detected was similar in humans (3221) and other species (range 2537-3373). Metabolite patterns were most similar within species and separated samples according to family and order. A total of 1485 chemicals were common to all species; 37% of these matched chemicals in human metabolomic databases and included chemicals in 137 out of 146 human metabolic pathways. Probability-based modularity clustering separated 644 chemicals, including many endogenous metabolites, with inter-species variation similar to intra-species variation. The remaining chemicals had greater inter-species variation and included environmental chemicals as well as GSH and methionine. Together, the data suggest that HPMP provides a platform that can be useful within human populations and controlled animal studies to simultaneously evaluate environmental exposures and biological responses to such exposures. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

[Mechanisms of viral emergence and interspecies transmission: the exemple of simian foamy viruses in Central Africa].

PubMed

Gessain, Antoine

2013-12-01

A large proportion of viral pathogens that have emerged during the last decades in humans are considered to have originated from various animal species. This is well exemplified by several recent epidemics such as those of Nipah, Severe Acute Respiratory Syndrome, Avian flu, Ebola, Monkeypox, and Hantaviruses. After the initial interspecies transmission per se, the viruses can disseminate into the human population through various and distinct mechanisms. Some of them are well characterized and understood, thus allowing a certain level of risk control and prevention. Surprisingly and in contrast, the initial steps that lead to the emergence of several viruses, and of their associated diseases, remain still poorly understood. Epidemiological field studies conducted in certain specific high-risk populations are thus necessary to obtain new insights into the early events of this emergence process. Human infections by simian viruses represent increasing public health concerns. Indeed, by virtue of their genetic andphysiological similarities, non-human primates (NHPs) are considered to be likely the sources of viruses that can infect humans and thus may pose a significant threat to human population. This is well illustrated by retroviruses, which have the ability to cross species, adapt to a new host and sometimes spread within these new species. Sequence comparison and phylogenetic studies have thus clearly showed that the emergence of human immunodeficiency virus type 1 (HIV-1) and HIV-2 in humans have resulted from several independent interspecies transmissions of different SIV types from Chimpanzees and African monkeys (including sooty mangabeys), respectively, probably during the first part of the last century. The situation for Human T cell Lymphotropic virus type 1 (HTLV-1) is, for certain aspects, quite comparable. Indeed, the origin of most HTLV-1 subtypes appears to be linked to interspecies transmission between STLV-1-infected monkeys and humans, followed by variable periods of evolution in the human host. In this review, after an introduction on emerging viruses, we will briefly present the results of a large epidemiological study performed in groups of Bantus and Pygmies living in villages and settlements located in the rain forest of the South region of Cameroon. These populations are living nearby the habitats of several monkeys and apes, often naturally infected by different retroviruses including SIV, STLV and simianfoamy virus. Most of the persons included in this study were hunters of such NHPs, thus at high risk of contact with infected body fluids (blood, saliva,...) during hunting activities. After reviewing the current available data on the discovery, cross-species transmission from monkeys and apes to humans of the simian foamy retroviruses, we will report the results of our study. Such infection is a unique natural model to study the different mechanisms of restriction of retroviral emergence in Humans.

Bacteria and game theory: the rise and fall of cooperation in spatially heterogeneous environments.

PubMed

Lambert, Guillaume; Vyawahare, Saurabh; Austin, Robert H

2014-08-06

One of the predictions of game theory is that cooperative behaviours are vulnerable to exploitation by selfish individuals, but this result seemingly contradicts the survival of cooperation observed in nature. In this review, we will introduce game theoretical concepts that lead to this conclusion and show how the spatial competition dynamics between microorganisms can be used to model the survival and maintenance of cooperation. In particular, we focus on how Escherichia coli bacteria with a growth advantage in stationary phase (GASP) phenotype maintain a proliferative phenotype when faced with overcrowding to gain a fitness advantage over wild-type populations. We review recent experimental approaches studying the growth dynamics of competing GASP and wild-type strains of E. coli inside interconnected microfabricated habitats and use a game theoretical approach to analyse the observed inter-species interactions. We describe how the use of evolutionary game theory and the ideal free distribution accurately models the spatial distribution of cooperative and selfish individuals in spatially heterogeneous environments. Using bacteria as a model system of cooperative and selfish behaviours may lead to a better understanding of the competition dynamics of other organisms-including tumour-host interactions during cancer development and metastasis.

Mitis group streptococci express variable pilus islet 2 pili.

PubMed

Zähner, Dorothea; Gandhi, Ashish R; Yi, Hong; Stephens, David S

2011-01-01

Streptococcus oralis, Streptococcus mitis, and Streptococcus sanguinis are members of the Mitis group of streptococci and agents of oral biofilm, dental plaque and infective endocarditis, disease processes that involve bacteria-bacteria and bacteria-host interactions. Their close relative, the human pathogen S. pneumoniae uses pilus-islet 2 (PI-2)-encoded pili to facilitate adhesion to eukaryotic cells. PI-2 pilus-encoding genetic islets were identified in S. oralis, S. mitis, and S. sanguinis, but were absent from other isolates of these species. The PI-2 islets resembled the genetic organization of the PI-2 islet of S. pneumoniae, but differed in the genes encoding the structural pilus proteins PitA and PitB. Two and three variants of pitA (a pseudogene in S. pneumoniae) and pitB, respectively, were identified that showed ≈20% difference in nucleotide as well as corresponding protein sequence. Species-independent combinations of pitA and pitB variants indicated prior intra- and interspecies horizontal gene transfer events. Polyclonal antisera developed against PitA and PitB of S. oralis type strain ATCC35037 revealed that PI-2 pili in oral streptococci were composed of PitA and PitB. Electronmicrographs showed pilus structures radiating >700 nm from the bacterial surface in the wild type strain, but not in an isogenic PI-2 deletion mutant. Anti-PitB-antiserum only reacted with pili containing the same PitB variant, whereas anti-PitA antiserum was cross-reactive with the other PitA variant. Electronic multilocus sequence analysis revealed that all PI-2-encoding oral streptococci were closely-related and cluster with non-PI-2-encoding S. oralis strains. This is the first identification of PI-2 pili in Mitis group oral streptococci. The findings provide a striking example of intra- and interspecies horizontal gene transfer. The PI-2 pilus diversity provides a possible key to link strain-specific bacterial interactions and/or tissue tropisms with pathogenic traits in the Mitis group streptococci.

Experimental and Molecular Modeling Evaluation of the Physicochemical Properties of Proline-Based Deep Eutectic Solvents.

PubMed

van den Bruinhorst, Adriaan; Spyriouni, Theodora; Hill, Jörg-Rüdiger; Kroon, Maaike C

2018-01-11

The liquid range and applicability of deep eutectic solvents (DESs) are determined by their physicochemical properties. In this work, the physicochemical properties of glycolic acid:proline and malic acid:proline were evaluated experimentally and with MD simulations at five different ratios. Both DESs exhibited esterification upon preparation, which affected the viscosity in particular. In order to minimize oligomer formation and water release, three different experimental preparation methods were explored, but none could prevent esterification. The experimental and calculated densities of the DESs were found to be in good agreement. The measured and modeled glass transition temperature showed similar trends with composition, as did the experimental viscosity and the calculated diffusivities. The MD simulations provided additional insight at the atomistic level, showing that at acid-rich compositions, the acid-acid hydrogen bonding (HB) interactions prevail. Malic acid-based DESs show stronger acid-acid HB interactions than glycolic acid-based ones, possibly explaining its extreme viscosity. Upon the addition of proline, the interspecies interactions become predominant, confirming the formation of the widely assumed HB network between the DESs constituents in the liquid phase.

A Bacterial Quorum-Sensing Precursor Induces Mortality in the Marine Coccolithophore, Emiliania huxleyi.

PubMed

Harvey, Elizabeth L; Deering, Robert W; Rowley, David C; El Gamal, Abrahim; Schorn, Michelle; Moore, Bradley S; Johnson, Matthew D; Mincer, Tracy J; Whalen, Kristen E

2016-01-01

Interactions between phytoplankton and bacteria play a central role in mediating biogeochemical cycling and food web structure in the ocean. However, deciphering the chemical drivers of these interspecies interactions remains challenging. Here, we report the isolation of 2-heptyl-4-quinolone (HHQ), released by Pseudoalteromonas piscicida, a marine gamma-proteobacteria previously reported to induce phytoplankton mortality through a hitherto unknown algicidal mechanism. HHQ functions as both an antibiotic and a bacterial signaling molecule in cell-cell communication in clinical infection models. Co-culture of the bloom-forming coccolithophore, Emiliania huxleyi with both live P. piscicida and cell-free filtrates caused a significant decrease in algal growth. Investigations of the P. piscicida exometabolome revealed HHQ, at nanomolar concentrations, induced mortality in three strains of E. huxleyi. Mortality of E. huxleyi in response to HHQ occurred slowly, implying static growth rather than a singular loss event (e.g., rapid cell lysis). In contrast, the marine chlorophyte, Dunaliella tertiolecta and diatom, Phaeodactylum tricornutum were unaffected by HHQ exposures. These results suggest that HHQ mediates the type of inter-domain interactions that cause shifts in phytoplankton population dynamics. These chemically mediated interactions, and other like it, ultimately influence large-scale oceanographic processes.

The gut eukaryotic microbiota influences the growth performance among cohabitating shrimp.

PubMed

Dai, Wenfang; Yu, Weina; Zhang, Jinjie; Zhu, Jinyong; Tao, Zhen; Xiong, Jinbo

2017-08-01

Increasing evidence has revealed a close interplay between the gut bacterial communities and host growth performance. However, until recently, studies generally ignored the contribution of eukaryotes, endobiotic organisms. To fill this gap, we used Illumina sequencing technology on eukaryotic 18S rRNA gene to compare the structures of gut eukaryotic communities among cohabitating retarded, overgrown, and normal shrimp obtained from identically managed ponds. Results showed that a significant difference between gut eukaryotic communities differed significantly between water and intestine and among three shrimp categories. Structural equation modeling revealed that changes in the gut eukaryotic community were positively related to digestive enzyme activities, which in turn influenced shrimp growth performance (λ = 0.97, P < 0.001). Overgrown shrimp exhibited a more complex and cooperative gut eukaryotic interspecies interaction than retarded and normal shrimp, which may facilitate their nutrient acquisition efficiency. Notably, the distribution of dominant eukaryotic genera and shifts in keystone species were closely concordant with shrimp growth performance. In summary, this study provides an integrated overview on direct roles of gut eukaryotic communities in shrimp growth performance instead of well-studied bacterial assembly.

Experimental Interspecies Transmission Studies of the Transmissible Spongiform Encephalopathies to Cattle: Comparison to Bovine Spongiform Encephalopathy in Cattle

USDA-ARS?s Scientific Manuscript database

Prion diseases or transmissible spongiform encephalopathies (TSEs) of animals include scrapie of sheep and goats; transmissible mink encephalopathy (TME); chronic wasting disease (CWD) of deer, elk and moose; and bovine spongiform encephalopathy (BSE) of cattle. Since the emergence of BSE and its pr...

Transmission of chronic wasting disease of white-tailed deer to Suffolk sheep following intracranial inoculation

USDA-ARS?s Scientific Manuscript database

Background: Interspecies transmission studies are an opportunity to better understand the potential host ranges of prion diseases. Chronic wasting disease (CWD) of cervids and scrapie of sheep and goats have a similar tissue distribution of abnormal prion protein (PrPSc) and prion disease exposure a...

EVALUATION OF INTERSPECIES DIFFERENCES IN PHARMACOKINETICS (PK) USING A PBPK MODEL FOR THE PESTICIDE DIMETHYLARSINIC ACID (DMAV)

EPA Science Inventory

DMAV is an organoarsenical pesticide registered for use on certain citrus crops and as a cotton defoliant. In lifetime oral route studies in rodents, DMAV causes statistically significant increases in bladder tumors in rats, but not in mice. We have developed a PBPK model for D...

Pulmonary Metabolism of Resveratrol: In Vitro and In Vivo Evidence

PubMed Central

Sharan, Satish

2013-01-01

The role of pulmonary metabolism in trans-resveratrol (RES) pharmacokinetics was studied in a mouse model. Plasma concentrations of RES and its major metabolites trans-resveratrol-3-sulfate (R3S) and trans-resveratrol-3-glucuronide (R3G) were compared after administration of RES by intravenous (IV) and intra-arterial (IA) routes. Total area under the curve (AUC) of RES decreased by approximately 50% when RES was administered by the IV route compared with the IA route. The AUC of R3G was also significantly higher in mice administered RES by the IV route compared with the IA route. In vitro studies performed with mouse and human lung fractions confirmed pulmonary metabolism of RES. Interestingly, mouse-lung fractions gave rise to both R3S and R3G, whereas human lung fractions yielded R3S. This indicates marked interspecies variation in RES conjugation, especially in the context of extrapolating rodent data to humans. Taken together, the results presented here underline, for the first time, the impact of pulmonary metabolism on resveratrol pharmacokinetics and interspecies differences in RES pulmonary metabolism. PMID:23474649

Resilient plant-bird interactions in a volcanic island ecosystem: pollination of Japanese Camellia mediated by the Japanese White-eye.

PubMed

Abe, Harue; Ueno, Saneyoshi; Takahashi, Toshimori; Tsumura, Yoshihiko; Hasegawa, Masami

2013-01-01

Observations of interspecies interactions during volcanic activity provide important opportunities to study how organisms respond to environmental devastation. Japanese camellia (Camellia japonica L.) and its main avian pollinator, the Japanese White-eye (Zosterops japonica), offer an excellent example of such an interaction as key members of the biotic community on Miyake-jima, which erupted in 2000 and continues to emit volcanic gases. Both species exhibit higher resistance to volcanic damage than other species. We examined the effects of volcanic activity on this plant-pollinator system by estimating pollen flow and the genetic diversity of the next generation. The results showed that despite a decrease in Camellia flowers, the partitioning of allelic richness among mother-tree pollen pools and seeds decreased while the migration rate of pollen from outside the study plot and the pollen donor diversity within a fruit increased as the index of volcanic damage increased. In areas with low food (flower) density due to volcanic damage, Z. japonica ranged over larger areas to satisfy its energy needs rather than moving to areas with higher food density. Consequently, the genetic diversity of the seeds (the next plant generation) increased with the index of volcanic damage. The results were consistent with previously published data on the movement of Z. japonica based on radio tracking and the genetic diversity of Camellia pollen adhering to pollinators. Overall, our results indicated that compensation mechanisms ensured better pollination after volcanic disturbance.

Potential for direct interspecies electron transfer in methanogenic wastewater digester aggregates.

PubMed

Morita, Masahiko; Malvankar, Nikhil S; Franks, Ashley E; Summers, Zarath M; Giloteaux, Ludovic; Rotaru, Amelia E; Rotaru, Camelia; Lovley, Derek R

2011-01-01

Mechanisms for electron transfer within microbial aggregates derived from an upflow anaerobic sludge blanket reactor converting brewery waste to methane were investigated in order to better understand the function of methanogenic consortia. The aggregates were electrically conductive, with conductivities 3-fold higher than the conductivities previously reported for dual-species aggregates of Geobacter species in which the two species appeared to exchange electrons via interspecies electron transfer. The temperature dependence response of the aggregate conductance was characteristic of the organic metallic-like conductance previously described for the conductive pili of Geobacter sulfurreducens and was inconsistent with electron conduction through minerals. Studies in which aggregates were incubated with high concentrations of potential electron donors demonstrated that the aggregates had no significant capacity for conversion of hydrogen to methane. The aggregates converted formate to methane but at rates too low to account for the rates at which that the aggregates syntrophically metabolized ethanol, an important component of the reactor influent. Geobacter species comprised 25% of 16S rRNA gene sequences recovered from the aggregates, suggesting that Geobacter species may have contributed to some but probably not all of the aggregate conductivity. Microorganisms most closely related to the acetate-utilizing Methanosaeta concilii accounted for more than 90% of the sequences that could be assigned to methane producers, consistent with the poor capacity for hydrogen and formate utilization. These results demonstrate for the first time that methanogenic wastewater aggregates can be electrically conductive and suggest that direct interspecies electron transfer could be an important mechanism for electron exchange in some methanogenic systems.

Widespread interspecies homologous recombination reveals reticulate evolution within the genus Streptomyces.

PubMed

Cheng, Kun; Rong, Xiaoying; Huang, Ying

2016-09-01

Homologous recombination is increasingly being recognized as a driving force in microbial evolution. However, recombination in streptomycetes, a rich source of diverse secondary metabolites, particularly among different species, remains minimally investigated. In this study, the largest sample of Streptomyces species to date, consisting of 142 type strains spanning the genus, with available sequences of 16S rRNA, atpD, gyrB, recA, rpoB and trpB genes, were collected and subjected to a comprehensive population genetic analysis to generate an overall estimate of the level of Streptomyces interspecies genetic exchange and its effect on the evolution of this genus. The results indicate frequent homologous recombination among Streptomyces species, which occurred three times more frequently and was nearly 14 times more important than point mutation in nucleotide sequence divergence (ρ/θw=3.10, r/m=13.74). As a result, a facilitating effect on the evolutionary process and confusion in phylogenetic relationships were observed, as well as a number of specific transfer events of the six gene fragments. A resultant phylogenetic network depicted extensive horizontal genetic exchange which decays clonality in streptomycetes. Moreover, seven evolutionary lineage groups were identified in the present sample in the Structure analysis, generally consistent with morphological and physiological data, and the contribution of recombination was detected to be varied among them. Our analyses demonstrated a reticulate evolution within Streptomyces due to the high level of interspecies gene exchange, which greatly challenges the traditional tree-shaped phylogeny in this genus and may advance our evolutionary understanding of a genuine Streptomyces species. Copyright © 2016 Elsevier Inc. All rights reserved.

Extracellular Electron Uptake: Among Autotrophs and Mediated by Surfaces.

PubMed

Tremblay, Pier-Luc; Angenent, Largus T; Zhang, Tian

2017-04-01

Autotrophic microbes can acquire electrons from solid donors such as steel, other microbial cells, or electrodes. Based on this feature, bioprocesses are being developed for the microbial electrosynthesis (MES) of useful products from the greenhouse gas CO 2 . Extracellular electron-transfer mechanisms involved in the acquisition of electrons from metals by electrical microbially influenced corrosion (EMIC), from other living cells by interspecies electron transfer (IET), or from an electrode during MES rely on: (i) mediators such as H 2 ; (ii) physical contact through electron-transfer proteins; or (iii) mediator-generating enzymes detached from cells. This review explores the interactions of autotrophs with solid electron donors and their importance in nature and for biosustainable technologies. Copyright © 2016 Elsevier Ltd. All rights reserved.

Automated aural classification used for inter-species discrimination of cetaceans.

PubMed

Binder, Carolyn M; Hines, Paul C

2014-04-01

Passive acoustic methods are in widespread use to detect and classify cetacean species; however, passive acoustic systems often suffer from large false detection rates resulting from numerous transient sources. To reduce the acoustic analyst workload, automatic recognition methods may be implemented in a two-stage process. First, a general automatic detector is implemented that produces many detections to ensure cetacean presence is noted. Then an automatic classifier is used to significantly reduce the number of false detections and classify the cetacean species. This process requires development of a robust classifier capable of performing inter-species classification. Because human analysts can aurally discriminate species, an automated aural classifier that uses perceptual signal features was tested on a cetacean data set. The classifier successfully discriminated between four species of cetaceans-bowhead, humpback, North Atlantic right, and sperm whales-with 85% accuracy. It also performed well (100% accuracy) for discriminating sperm whale clicks from right whale gunshots. An accuracy of 92% and area under the receiver operating characteristic curve of 0.97 were obtained for the relatively challenging bowhead and humpback recognition case. These results demonstrated that the perceptual features employed by the aural classifier provided powerful discrimination cues for inter-species classification of cetaceans.

Development of algal interspecies correlation estimation models for chemical hazard assessment.

PubMed

Brill, Jessica L; Belanger, Scott E; Chaney, Joel G; Dyer, Scott D; Raimondo, Sandy; Barron, Mace G; Pittinger, Charles A

2016-09-01

Web-based Interspecies Correlation Estimation (ICE) is an application developed to predict the acute toxicity of a chemical from 1 species to another taxon. Web-ICE models use the acute toxicity value for a surrogate species to predict effect values for other species, thus potentially filling in data gaps for a variety of environmental assessment purposes. Web-ICE has historically been dominated by aquatic and terrestrial animal prediction models. Web-ICE models for algal species were essentially absent and are addressed in the present study. A compilation of public and private sector-held algal toxicity data were compiled and reviewed for quality based on relevant aspects of individual studies. Interspecies correlations were constructed from the most commonly tested algal genera for a broad spectrum of chemicals. The ICE regressions were developed based on acute 72-h and 96-h endpoint values involving 1647 unique studies on 476 unique chemicals encompassing 40 genera and 70 species of green, blue-green, and diatom algae. Acceptance criteria for algal ICE models were established prior to evaluation of individual models and included a minimum sample size of 3, a statistically significant regression slope, and a slope estimation parameter ≥0.65. A total of 186 ICE models were possible at the genus level, with 21 meeting quality criteria; and 264 ICE models were developed at the species level, with 32 meeting quality criteria. Algal ICE models will have broad utility in screening environmental hazard assessments, data gap filling in certain regulatory scenarios, and as supplemental information to derive species sensitivity distributions. Environ Toxicol Chem 2016;35:2368-2378. Published 2016 Wiley Periodicals Inc. on behalf of SETAC. This article is a US government work and, as such, is in the public domain in the United States of America. Published 2016 Wiley Periodicals Inc. on behalf of SETAC. This article is a US government work and, as such, is in the public domain in the United States of America.

An interdomain network: the endobacterium of a mycorrhizal fungus promotes antioxidative responses in both fungal and plant hosts.

PubMed

Vannini, Candida; Carpentieri, Andrea; Salvioli, Alessandra; Novero, Mara; Marsoni, Milena; Testa, Lorenzo; de Pinto, Maria Concetta; Amoresano, Angela; Ortolani, Francesca; Bracale, Marcella; Bonfante, Paola

2016-07-01

Arbuscular mycorrhizal fungi (AMF) are obligate plant biotrophs that may contain endobacteria in their cytoplasm. Genome sequencing of Candidatus Glomeribacter gigasporarum revealed a reduced genome and dependence on the fungal host. RNA-seq analysis of the AMF Gigaspora margarita in the presence and absence of the endobacterium indicated that endobacteria have an important role in the fungal pre-symbiotic phase by enhancing fungal bioenergetic capacity. To improve the understanding of fungal-endobacterial interactions, iTRAQ (isobaric tags for relative and absolute quantification) quantitative proteomics was used to identify differentially expressed proteins in G. margarita germinating spores with endobacteria (B+), without endobacteria in the cured line (B-) and after application of the synthetic strigolactone GR24. Proteomic, transcriptomic and biochemical data identified several fungal and bacterial proteins involved in interspecies interactions. Endobacteria influenced fungal growth, calcium signalling and metabolism. The greatest effects were on fungal primary metabolism and respiration, which was 50% higher in B+ than in B-. A shift towards pentose phosphate metabolism was detected in B-. Quantification of carbonylated proteins indicated that the B- line had higher oxidative stress levels, which were also observed in two host plants. This study shows that endobacteria generate a complex interdomain network that affects AMF and fungal-plant interactions. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

PCP-B class pollen coat proteins are key regulators of the hydration checkpoint in Arabidopsis thaliana pollen-stigma interactions.

PubMed

Wang, Ludi; Clarke, Lisa A; Eason, Russell J; Parker, Christopher C; Qi, Baoxiu; Scott, Rod J; Doughty, James

2017-01-01

The establishment of pollen-pistil compatibility is strictly regulated by factors derived from both male and female reproductive structures. Highly diverse small cysteine-rich proteins (CRPs) have been found to play multiple roles in plant reproduction, including the earliest stages of the pollen-stigma interaction. Secreted CRPs found in the pollen coat of members of the Brassicaceae, the pollen coat proteins (PCPs), are emerging as important signalling molecules that regulate the pollen-stigma interaction. Using a combination of protein characterization, expression and phylogenetic analyses we identified a novel class of Arabidopsis thaliana pollen-borne CRPs, the PCP-Bs (for pollen coat protein B-class) that are related to embryo surrounding factor (ESF1) developmental regulators. Single and multiple PCP-B mutant lines were utilized in bioassays to assess effects on pollen hydration, adhesion and pollen tube growth. Our results revealed that pollen hydration is severely impaired when multiple PCP-Bs are lost from the pollen coat. The hydration defect also resulted in reduced pollen adhesion and delayed pollen tube growth in all mutants studied. These results demonstrate that AtPCP-Bs are key regulators of the hydration 'checkpoint' in establishment of pollen-stigma compatibility. In addition, we propose that interspecies diversity of PCP-Bs may contribute to reproductive barriers in the Brassicaceae. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Single-cell force spectroscopy of the medically important Staphylococcus epidermidis-Candida albicans interaction

NASA Astrophysics Data System (ADS)

Beaussart, Audrey; Herman, Philippe; El-Kirat-Chatel, Sofiane; Lipke, Peter N.; Kucharíková, Soňa; van Dijck, Patrick; Dufrêne, Yves F.

2013-10-01

Despite the clinical importance of bacterial-fungal interactions, their molecular details are poorly understood. A hallmark of such medically important interspecies associations is the interaction between the two nosocomial pathogens Staphylococcus aureus and Candida albicans, which can lead to mixed biofilm-associated infections with enhanced antibiotic resistance. Here, we use single-cell force spectroscopy (SCFS) to quantify the forces engaged in bacterial-fungal co-adhesion, focusing on the poorly investigated S. epidermidis-C. albicans interaction. Force curves recorded between single bacterial and fungal germ tubes showed large adhesion forces (~5 nN) with extended rupture lengths (up to 500 nm). By contrast, bacteria poorly adhered to yeast cells, emphasizing the important role of the yeast-to-hyphae transition in mediating adhesion to bacterial cells. Analysis of mutant strains altered in cell wall composition allowed us to distinguish the main fungal components involved in adhesion, i.e. Als proteins and O-mannosylations. We suggest that the measured co-adhesion forces are involved in the formation of mixed biofilms, thus possibly as well in promoting polymicrobial infections. In the future, we anticipate that this SCFS platform will be used in nanomedicine to decipher the molecular mechanisms of a wide variety of pathogen-pathogen interactions and may help in designing novel anti-adhesion agents.

"But-He'll Fall!": Children with Autism, Interspecies Intersubjectivity, and the Problem of 'Being Social'.

PubMed

Solomon, Olga

2015-06-01

'Being autistic' or 'having Autism Spectrum Disorder' implies a limited range of 'being social,' but the in situ organization of interaction, what Maynard and Marlaire (Qual Soc 15(2):177-202, 1992) call the 'interactional substrate,' within which this delimitation enfolds is usually hidden from sight. Analysis of processes constituting different 'interactional substrates' provides a view of how one comes to be known by and to self and others as a certain kind of being who is available (or not) for acting and feeling in certain ways. People diagnosed with Autism Spectrum Disorder (American Psychiatric Association, Diagnostic and statistical manual of mental disorders, 2013) are often described as 'being' impaired in intersubjective understanding of others. But the story of ASD as an impairment of sociality and intersubjectivity becomes more complicated when animals enter into the picture. I consider two interactional substrates: a psychological interview in a mental health clinic, and an animal-assisted activity in a child's neighborhood. I aim to elucidate the practical problems of 'being social' encountered by two children with ASD, both nine-year-old girls, within these two very differently organized interactional substrates. I consider ways in which 'being with' therapy animals provides a way of 'being social' through "sensory modalities of knowing" (Haraway, When species meet, 2008:371).

Bats: Body mass index, forearm mass index, blood glucose levels and SLC2A2 genes for diabetes

PubMed Central

Meng, Fanxing; Zhu, Lei; Huang, Wenjie; Irwin, David M.; Zhang, Shuyi

2016-01-01

Bats have an unusually large volume of endocrine tissue, with a large population of beta cells, and an elevated sensitivity to glucose and insulin. This makes them excellent animal models for studying diabetes mellitus. We evaluated bats as models for diabetes in terms of lifestyle and genetic factors. For lifestyle factors, we generated data sets of 149 body mass index (BMI) and 860 forearm mass index (FMI) measurements for different species of bats. Both showed negative inter-species correlations with blood glucose levels in sixteen bats examined. The negative inter-species correlations may reflect adaptation of a small insectivorous ancestor to a larger frugivore. We identified an 11 bp deletion in the proximal promoter of SLC2A2 that we predicted would disrupt binding sites for the transcription repressor ZNF354C. In frugivorous bats this could explain the relatively high expression of this gene, resulting in a better capacity to absorb glucose and decrease blood glucose levels. PMID:27439361

Tracking interspecies transmission and long-term evolution of an ancient retrovirus using the genomes of modern mammals

PubMed Central

Diehl, William E; Patel, Nirali; Halm, Kate; Johnson, Welkin E

2016-01-01

Mammalian genomes typically contain hundreds of thousands of endogenous retroviruses (ERVs), derived from ancient retroviral infections. Using this molecular 'fossil' record, we reconstructed the natural history of a specific retrovirus lineage (ERV-Fc) that disseminated widely between ~33 and ~15 million years ago, corresponding to the Oligocene and early Miocene epochs. Intercontinental viral spread, numerous instances of interspecies transmission and emergence in hosts representing at least 11 mammalian orders, and a significant role for recombination in diversification of this viral lineage were also revealed. By reconstructing the canonical retroviral genes, we identified patterns of adaptation consistent with selection to maintain essential viral protein functions. Our results demonstrate the unique potential of the ERV fossil record for studying the processes of viral spread and emergence as they play out across macro-evolutionary timescales, such that looking back in time may prove insightful for predicting the long-term consequences of newly emerging viral infections. DOI: http://dx.doi.org/10.7554/eLife.12704.001 PMID:26952212

Tracking interspecies transmission and long-term evolution of an ancient retrovirus using the genomes of modern mammals.

PubMed

Diehl, William E; Patel, Nirali; Halm, Kate; Johnson, Welkin E

2016-03-08

Mammalian genomes typically contain hundreds of thousands of endogenous retroviruses (ERVs), derived from ancient retroviral infections. Using this molecular 'fossil' record, we reconstructed the natural history of a specific retrovirus lineage (ERV-Fc) that disseminated widely between ~33 and ~15 million years ago, corresponding to the Oligocene and early Miocene epochs. Intercontinental viral spread, numerous instances of interspecies transmission and emergence in hosts representing at least 11 mammalian orders, and a significant role for recombination in diversification of this viral lineage were also revealed. By reconstructing the canonical retroviral genes, we identified patterns of adaptation consistent with selection to maintain essential viral protein functions. Our results demonstrate the unique potential of the ERV fossil record for studying the processes of viral spread and emergence as they play out across macro-evolutionary timescales, such that looking back in time may prove insightful for predicting the long-term consequences of newly emerging viral infections.

Inter-species variation in the oligomeric states of the higher plant Calvin cycle enzymes glyceraldehyde-3-phosphate dehydrogenase and phosphoribulokinase

PubMed Central

Lloyd, Julie C.; Raines, Christine A.

2011-01-01

In darkened leaves the Calvin cycle enzymes glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and phosphoribulokinase (PRK) form a regulatory multi-enzyme complex with the small chloroplast protein CP12. GAPDH also forms a high molecular weight regulatory mono-enzyme complex. Given that there are different reports as to the number and subunit composition of these complexes and that enzyme regulatory mechanisms are known to vary between species, it was reasoned that protein–protein interactions may also vary between species. Here, this variation is investigated. This study shows that two different tetramers of GAPDH (an A2B2 heterotetramer and an A4 homotetramer) have the capacity to form part of the PRK/GAPDH/CP12 complex. The role of the PRK/GAPDH/CP12 complex is not simply to regulate the ‘non-regulatory’ A4 GAPDH tetramer. This study also demonstrates that the abundance and nature of PRK/GAPDH/CP12 interactions are not equal in all species and that whilst NAD enhances complex formation in some species, this is not sufficient for complex formation in others. Furthermore, it is shown that the GAPDH mono-enzyme complex is more abundant as a 2(A2B2) complex, rather than the larger 4(A2B2) complex. This smaller complex is sensitive to cellular metabolites indicating that it is an important regulatory isoform of GAPDH. This comparative study has highlighted considerable heterogeneity in PRK and GAPDH protein interactions between closely related species and the possible underlying physiological basis for this is discussed. PMID:21498632

Inter-species variation in the oligomeric states of the higher plant Calvin cycle enzymes glyceraldehyde-3-phosphate dehydrogenase and phosphoribulokinase.

PubMed

Howard, Thomas P; Lloyd, Julie C; Raines, Christine A

2011-07-01

In darkened leaves the Calvin cycle enzymes glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and phosphoribulokinase (PRK) form a regulatory multi-enzyme complex with the small chloroplast protein CP12. GAPDH also forms a high molecular weight regulatory mono-enzyme complex. Given that there are different reports as to the number and subunit composition of these complexes and that enzyme regulatory mechanisms are known to vary between species, it was reasoned that protein-protein interactions may also vary between species. Here, this variation is investigated. This study shows that two different tetramers of GAPDH (an A2B2 heterotetramer and an A4 homotetramer) have the capacity to form part of the PRK/GAPDH/CP12 complex. The role of the PRK/GAPDH/CP12 complex is not simply to regulate the 'non-regulatory' A4 GAPDH tetramer. This study also demonstrates that the abundance and nature of PRK/GAPDH/CP12 interactions are not equal in all species and that whilst NAD enhances complex formation in some species, this is not sufficient for complex formation in others. Furthermore, it is shown that the GAPDH mono-enzyme complex is more abundant as a 2(A2B2) complex, rather than the larger 4(A2B2) complex. This smaller complex is sensitive to cellular metabolites indicating that it is an important regulatory isoform of GAPDH. This comparative study has highlighted considerable heterogeneity in PRK and GAPDH protein interactions between closely related species and the possible underlying physiological basis for this is discussed.

Novel mechanisms power bacterial gliding motility.

PubMed

Nan, Beiyan; Zusman, David R

2016-07-01

For many bacteria, motility is essential for survival, growth, virulence, biofilm formation and intra/interspecies interactions. Since natural environments differ, bacteria have evolved remarkable motility systems to adapt, including swimming in aqueous media, and swarming, twitching and gliding on solid and semi-solid surfaces. Although tremendous advances have been achieved in understanding swimming and swarming motilities powered by flagella, and twitching motility powered by Type IV pili, little is known about gliding motility. Bacterial gliders are a heterogeneous group containing diverse bacteria that utilize surface motilities that do not depend on traditional flagella or pili, but are powered by mechanisms that are less well understood. Recently, advances in our understanding of the molecular machineries for several gliding bacteria revealed the roles of modified ion channels, secretion systems and unique machinery for surface movements. These novel mechanisms provide rich source materials for studying the function and evolution of complex microbial nanomachines. In this review, we summarize recent findings made on the gliding mechanisms of the myxobacteria, flavobacteria and mycoplasmas. © 2016 John Wiley & Sons Ltd.

Global metabolic interaction network of the human gut microbiota for context-specific community-scale analysis

PubMed Central

Sung, Jaeyun; Kim, Seunghyeon; Cabatbat, Josephine Jill T.; Jang, Sungho; Jin, Yong-Su; Jung, Gyoo Yeol; Chia, Nicholas; Kim, Pan-Jun

2017-01-01

A system-level framework of complex microbe–microbe and host–microbe chemical cross-talk would help elucidate the role of our gut microbiota in health and disease. Here we report a literature-curated interspecies network of the human gut microbiota, called NJS16. This is an extensive data resource composed of ∼570 microbial species and 3 human cell types metabolically interacting through >4,400 small-molecule transport and macromolecule degradation events. Based on the contents of our network, we develop a mathematical approach to elucidate representative microbial and metabolic features of the gut microbial community in a given population, such as a disease cohort. Applying this strategy to microbiome data from type 2 diabetes patients reveals a context-specific infrastructure of the gut microbial ecosystem, core microbial entities with large metabolic influence, and frequently produced metabolic compounds that might indicate relevant community metabolic processes. Our network presents a foundation towards integrative investigations of community-scale microbial activities within the human gut. PMID:28585563

Network biology discovers pathogen contact points in host protein-protein interactomes.

PubMed

Ahmed, Hadia; Howton, T C; Sun, Yali; Weinberger, Natascha; Belkhadir, Youssef; Mukhtar, M Shahid

2018-06-13

In all organisms, major biological processes are controlled by complex protein-protein interactions networks (interactomes), yet their structural complexity presents major analytical challenges. Here, we integrate a compendium of over 4300 phenotypes with Arabidopsis interactome (AI-1 MAIN ). We show that nodes with high connectivity and betweenness are enriched and depleted in conditional and essential phenotypes, respectively. Such nodes are located in the innermost layers of AI-1 MAIN and are preferential targets of pathogen effectors. We extend these network-centric analyses to Cell Surface Interactome (CSI LRR ) and predict its 35 most influential nodes. To determine their biological relevance, we show that these proteins physically interact with pathogen effectors and modulate plant immunity. Overall, our findings contrast with centrality-lethality rule, discover fast information spreading nodes, and highlight the structural properties of pathogen targets in two different interactomes. Finally, this theoretical framework could possibly be applicable to other inter-species interactomes to reveal pathogen contact points.

Food of forage fishes in western Lake Erie, 1975-76

USGS Publications Warehouse

Muth, Kenneth M.; Busch, Wolf-Dieter N.

1989-01-01

In western Lake Erie in the summer and fall of 1975–1976, food eaten by seven forage fishes—emerald shiner (Notropis atherinoides), spottail shiner (Notropis hudsonius), trout-perch (Percopsis omiscomaycus), andyoung-of-the-year (YOY) of alewife (Alosa pseudoharengus), gizzard shad (Dorosoma cepedianum), white bass (Morone chrysops), and freshwater drum (Aplodi-notus grunniens)—was divided among six major taxa: Cladocera, Copepoda, Diptera, Ostracoda, Amphipoda, and Algae. In addition, fish were eaten by YOY white bass, and Rotifera were consumed by YOY gizzard shad. Interspecies diet overlap indices, calculated to compare the food of the different species and to evaluate diet similarities, were usually highest for YOY white bass and YOY freshwater drum when compared with the other species and usually lowest between emerald shiners and all other forage fishes. Understanding the feeding interactions among fishes that could influence production at the forage-food level of the food web could provide insight into how cascading trophic interactions influence the production of piscivorous predators.

Effect of cephalosporins on organic ion transport in renal membrane vesicles from rat and rabbit kidney cortex.

PubMed

Williams, P D; Hitchcock, M J; Hottendorf, G H

1985-03-01

The effects of cephaloridine and cephalothin on prototypical organic anion (p-aminohippurate, PAH) and cation (N-methylnicotinamide, NMN) transport were observed in brush border and basolateral membrane vesicles prepared from rat and rabbit renal cortex. The cephalosporins interacted with both the cationic and anionic transport systems. Cephalothin inhibited PAH transport in basolateral and brush border membrane in both rats and rabbits. Cephaloridine on the other hand inhibited PAH and NMN transport across rabbit basolateral membranes while it showed a lack of interaction with transport systems in rat basolateral membranes. Conversely, cephaloridine inhibited brush border transport of PAH and NMN in the rat but not in the rabbit. These results provide indirect evidence that cephalothin may be secreted across the renal tubule cell in rats and rabbits while cephaloridine may not accumulate in the rat kidney and becomes trapped in rabbit renal tubule cells. The differences in transport effects observed may explain intra- and interspecies differences in susceptibility to cephalosporin nephrotoxicity.

Metabolic resource allocation in individual microbes determines ecosystem interactions and spatial dynamics

PubMed Central

Harcombe, William R.; Riehl, William J.; Dukovski, Ilija; Granger, Brian R.; Betts, Alex; Lang, Alex H.; Bonilla, Gracia; Kar, Amrita; Leiby, Nicholas; Mehta, Pankaj; Marx, Christopher J.; Segrè, Daniel

2014-01-01

Summary The inter-species exchange of metabolites plays a key role in the spatio-temporal dynamics of microbial communities. This raises the question whether ecosystem-level behavior of structured communities can be predicted using genome-scale models of metabolism for multiple organisms. We developed a modeling framework that integrates dynamic flux balance analysis with diffusion on a lattice, and applied it to engineered consortia. First, we predicted, and experimentally confirmed, the species-ratio to which a 2-species mutualistic consortium converges, and the equilibrium composition of a newly engineered 3-member community. We next identified a specific spatial arrangement of colonies, which gives rise to what we term the “eclipse dilemma”: does a competitor placed between a colony and its cross-feeding partner benefit or hurt growth of the original colony? Our experimentally validated finding, that the net outcome is beneficial, highlights the complex nature of metabolic interactions in microbial communities, while at the same time demonstrating their predictability. PMID:24794435

Global metabolic interaction network of the human gut microbiota for context-specific community-scale analysis.

PubMed

Sung, Jaeyun; Kim, Seunghyeon; Cabatbat, Josephine Jill T; Jang, Sungho; Jin, Yong-Su; Jung, Gyoo Yeol; Chia, Nicholas; Kim, Pan-Jun

2017-06-06

A system-level framework of complex microbe-microbe and host-microbe chemical cross-talk would help elucidate the role of our gut microbiota in health and disease. Here we report a literature-curated interspecies network of the human gut microbiota, called NJS16. This is an extensive data resource composed of ∼570 microbial species and 3 human cell types metabolically interacting through >4,400 small-molecule transport and macromolecule degradation events. Based on the contents of our network, we develop a mathematical approach to elucidate representative microbial and metabolic features of the gut microbial community in a given population, such as a disease cohort. Applying this strategy to microbiome data from type 2 diabetes patients reveals a context-specific infrastructure of the gut microbial ecosystem, core microbial entities with large metabolic influence, and frequently produced metabolic compounds that might indicate relevant community metabolic processes. Our network presents a foundation towards integrative investigations of community-scale microbial activities within the human gut.

Electrode Cultivation and Interfacial Electron Transport in Subsurface Microorganisms

NASA Astrophysics Data System (ADS)

Karbelkar, A. A.; Jangir, Y.; Reese, B. K.; Wanger, G.; Anderson, C.; El-Naggar, M.; Amend, J.

2016-12-01

Continental subsurface environments can present significant energetic challenges to the resident microorganisms. While these environments are geologically diverse, potentially allowing energy harvesting by microorganisms that catalyze redox reactions, many of the abundant electron donors and acceptors are insoluble and therefore not directly bioavailable. Microbes can use extracellular electron transfer (EET) as a metabolic strategy to interact with redox active surfaces. This process can be mimicked on electrode surfaces and hence can lead to enrichment and quantification of subsurface microorganisms A primary bioelectrochemical enrichment with different oxidizing and reducing potentials set up in a single bioreactor was applied in situ to subsurface microorganisms residing in iron oxide rich deposits in the Sanford Underground Research Facility. Secondary enrichment revealed a plethora of classified and unclassified subsurface microbiota on both oxidizing and reducing potentials. From this enrichment, we have isolated a Gram-positive Bacillus along with Gram-negative Cupriavidus and Anaerospora strains (as electrode reducers) and Comamonas (as an electrode oxidizer). The Bacillus and Comamonas isolates were subjected to a detailed electrochemical characterization in half-reactors at anodic and cathodic potentials, respectively. An increase in cathodic current upon inoculation and cyclic voltammetry measurements confirm the hypothesis that Comamonas is capable of electron uptake from electrodes. In addition, measurements of Bacillus on anodes hint towards novel mechanisms that allow EET from Gram-positive bacteria. This study suggests that electrochemical approaches are well positioned to dissect such extracellular interactions that may be prevalent in the subsurface, while using physical electrodes to emulate the microhabitats, redox and geochemical gradients, and the spatially dependent interspecies interactions encountered in the subsurface. Electrochemical characterization of isolated strains can help us establish the possible mechanisms of EET, and hence provide an insight on survival strategies of subsurface microbiota in extreme environments. Continental subsurface environments can present significant energetic challenges to the resident microorganisms. While these environments are geologically diverse, potentially allowing energy harvesting by microorganisms that catalyze redox reactions, many of the abundant electron donors and acceptors are insoluble and therefore not directly bioavailable. Microbes can use extracellular electron transfer (EET) as a metabolic strategy to interact with redox active surfaces. This process can be mimicked on electrode surfaces and hence can lead to enrichment and quantification of subsurface microorganisms A primary bioelectrochemical enrichment with different oxidizing and reducing potentials set up in a single bioreactor was applied in situ to subsurface microorganisms residing in iron oxide rich deposits in the Sanford Underground Research Facility. Secondary enrichment revealed a plethora of classified and unclassified subsurface microbiota on both oxidizing and reducing potentials. From this enrichment, we have isolated a Gram-positive Bacillus along with Gram-negative Cupriavidus and Anaerospora strains (as electrode reducers) and Comamonas (as an electrode oxidizer). The Bacillus and Comamonas isolates were subjected to a detailed electrochemical characterization in half-reactors at anodic and cathodic potentials, respectively. An increase in cathodic current upon inoculation and cyclic voltammetry measurements confirm the hypothesis that Comamonas is capable of electron uptake from electrodes. In addition, measurements of Bacillus on anodes hint towards novel mechanisms that allow EET from Gram-positive bacteria. This study suggests that electrochemical approaches are well positioned to dissect such extracellular interactions that may be prevalent in the subsurface, while using physical electrodes to emulate the microhabitats, redox and geochemical gradients, and the spatially dependent interspecies interactions encountered in the subsurface. Electrochemical characterization of isolated strains can help us establish the possible mechanisms of EET, and hence provide an insight on survival strategies of subsurface microbiota in extreme environments.

Non-universal bound states of two identical heavy fermions and one light particle

NASA Astrophysics Data System (ADS)

Safavi, Arghavan; Rittenhouse, Seth; Blume, Dorte; Sadeghpour, Hossein

2013-05-01

We study a system of two identical heavy fermions of mass M and light particle of mass m. The interspecies interaction is modeled using a short-range two-body potential with positive s-wave scattering length. We impose a short-range boundary condition on the logarithmic derivative of the hyperradial wavefunction and show that, in the regime where Efimov states are absent, a non-universal three-body state ``cuts through'' the universal three-body states previously described by Kartavtsev and Malykh [O. I. Kartavtsev and A. V. Malykh, J. Phys. B 40, 1429 (2007)]. We study the effect of the non-universal state on the behavior of the universal states and use a simple quantum defect theory, utilizing hyperspherical coordinates, to explain the existence of the non-universal state. An empirical two-state model is employed to quantify the coupling of the non-universal state to the universal states. This work was supported by NSF through a grant for the Institute for Theoretical Atomic, Molecular and Optical Physics at Harvard University and Smithsonian Astrophysical Observatory and through grant PHY-1205443.

Interspecies Transmission of Feline Immunodeficiency Virus from the Domestic Cat to the Tsushima Cat (Felis bengalensis euptilura) in the Wild

PubMed Central

Nishimura, Yoshiaki; Goto, Yuko; Yoneda, Kumiko; Endo, Yasuyuki; Mizuno, Takuya; Hamachi, Masaharu; Maruyama, Hiroyuki; Kinoshita, Hirotoshi; Koga, Susumu; Komori, Mitsuru; Fushuku, Seigo; Ushinohama, Kanji; Akuzawa, Masao; Watari, Toshihiro; Hasegawa, Atsuhiko; Tsujimoto, Hajime

1999-01-01

Feline immunodeficiency virus (FIV) was isolated from a wild-caught Tsushima cat (Felis bengalensis euptilura), an endangered Japanese nondomestic subspecies of leopard cat (F. bengalensis). Phylogenetic analysis of the env gene sequences indicated that the FIV from the Tsushima cat belonged to a cluster of subtype D FIVs from domestic cats. FIVs from both the Tsushima cat and the domestic cat showed similar levels of replication and cytopathicity in lymphoid cell lines derived from these two species. The results indicated the occurrence of interspecies transmission of FIV from the domestic cat to the Tsushima cat in the wild. PMID:10438892

Integrating multiple vegetation indices via an artificial neural network model for estimating the leaf chlorophyll content of Spartina alterniflora under interspecies competition.

PubMed

Liu, Pudong; Shi, Runhe; Zhang, Chao; Zeng, Yuyan; Wang, Jiapeng; Tao, Zhu; Gao, Wei

2017-10-31

The invasive species Spartina alterniflora and native species Phragmites australis display a significant co-occurrence zonation pattern and this co-exist region exerts most competitive situations between these two species, competing for the limited space, directly influencing the co-exist distribution in the future. However, these two species have different growth ratios in this area, which increase the difficulty to detect the distribution situation directly by remote sensing. As chlorophyll content is a key indicator of plant growth and physiological status, the objective of this study was to reduce the effect of interspecies competition when estimating Cab content; we evaluated 79 published representative indices to determine the optimal indices for estimating the chlorophyll a and b (Cab) content. After performing a sensitivity analysis for all 79 spectral indices, five spectral indices were selected and integrated using an artificial neural network (ANN) to estimate the Cab content of different competition ratios: the Gitelson ratio green index, the transformed chlorophyll absorption ratio index/optimized soil-adjusted vegetation index, the modified normalized difference vegetation index, the chlorophyll fluorescence index, and the Vogelmann chlorophyll index. The ANN method yielded better results (R 2  = 0.7110 and RMSE = 8.3829 μg cm -2 ) on average than the best single spectral index (R 2  = 0.6319 and RMSE = 9.3535 μg cm -2 ), representing an increase of 10.78% in R 2 and a decrease of 10.38% in RMSE. Our results indicated that integrating multiple vegetation indices with an ANN can alleviate the impact of interspecies competition and achieve higher estimation accuracy than the traditional approach using a single index.

X. couchianus and X. hellerii genome models provide genomic variation insight among Xiphophorus species.

PubMed

Shen, Yingjia; Chalopin, Domitille; Garcia, Tzintzuni; Boswell, Mikki; Boswell, William; Shiryev, Sergey A; Agarwala, Richa; Volff, Jean-Nicolas; Postlethwait, John H; Schartl, Manfred; Minx, Patrick; Warren, Wesley C; Walter, Ronald B

2016-01-07

Xiphophorus fishes are represented by 26 live-bearing species of tropical fish that express many attributes (e.g., viviparity, genetic and phenotypic variation, ecological adaptation, varied sexual developmental mechanisms, ability to produce fertile interspecies hybrids) that have made attractive research models for over 85 years. Use of various interspecies hybrids to investigate the genetics underlying spontaneous and induced tumorigenesis has resulted in the development and maintenance of pedigreed Xiphophorus lines specifically bred for research. The recent availability of the X. maculatus reference genome assembly now provides unprecedented opportunities for novel and exciting comparative research studies among Xiphophorus species. We present sequencing, assembly and annotation of two new genomes representing Xiphophorus couchianus and Xiphophorus hellerii. The final X. couchianus and X. hellerii assemblies have total sizes of 708 Mb and 734 Mb and correspond to 98 % and 102 % of the X. maculatus Jp 163 A genome size, respectively. The rates of single nucleotide change range from 1 per 52 bp to 1 per 69 bp among the three genomes and the impact of putatively damaging variants are presented. In addition, a survey of transposable elements allowed us to deduce an ancestral TE landscape, uncovered potential active TEs and document a recent burst of TEs during evolution of this genus. Two new Xiphophorus genomes and their corresponding transcriptomes were efficiently assembled, the former using a novel guided assembly approach. Three assembled genome sequences within this single vertebrate order of new world live-bearing fishes will accelerate our understanding of relationship between environmental adaptation and genome evolution. In addition, these genome resources provide capability to determine allele specific gene regulation among interspecies hybrids produced by crossing any of the three species that are known to produce progeny predisposed to tumor development.

Secondary SCNT doubles the pre-implantation development rate of reconstructed interspecies embryos by using cytoplasts of Sannen dairy goat ova.

PubMed

Zhang, Ai Min; Chen, Jian Quan; Sha, Hong Ying; Chen, Juan; Xu, Xu Jun; Wu, You Bin; Ge, Lai Xiang; Da, Hu Wei; Cheng, Guo Xiang

2007-10-01

The aim of this study was to investigate whether ova of Sannen goat could support the pre-implantation development of interspecies embryos constructed through somatic cell nucleus transfer (SCNT) embryos and whether secondary SCNT (SSCNT) could improve the pre-implantation development of those embryos. The primary SCNT (PSCNT) embryos were produced by using Sannen goat ovum cytoplasts as recipients and fibroblast cells, derived from human, rabbit and Boer goat skins, as nucleus donors. The blastomeres of 8 to 16 cells stage of PSCNT embryos were subsequently used as nucleus donor cells and Sannen goat ovum cytoplasts as recipients to evaluate the effect of SSCNT on the pre-implantation development rate of these reconstructed interspecies embryos. Our results indicate that the pre-implantation development rates of SSCNT embryos reconstructed using these three different blastomeres are almost twice of that of corresponding PSCNT embryos (human, 15.8% vs. 7.8%; rabbit, 27.9% vs. 12.5%; Boer goat 55.3% vs. 24.5%; P < 0.05 in all three cases). The time durations that embryos need for the serial events of remodeling and reprogramming to take place vary, depending on the animal species of nucleus donors. These data suggest that remodeling and reprogramming of donor nucleus may be enhanced by prolonged exposure of donor nucleus to maternal cytoplast. We conclude that Sannen goat cytoplast can support the pre-implantation development of embryos constructed with nuclei from various donors, including fibroblasts of human, rabbit and Boer goat; and the somatic nucleus derived from different species requires more time to achieve its reprogramming necessary for pre-implantation development.

Using physiologically based pharmacokinetic modeling to address nonlinear kinetics and changes in rodent physiology and metabolism due to aging and adaptation in deriving reference values for propylene glycol methyl ether and propylene glycol methyl ether acetate.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kirman, C R.; Sweeney, Lisa M.; Corley, Rick A.

2005-04-01

Reference values, including an oral reference dose (RfD) and an inhalation reference concentration (RfC), were derived for propylene glycol methyl ether (PGME), and an oral RfD was derived for its acetate (PGMEA). These values were based upon transient sedation observed in F344 rats and B6C3F1 mice during a two-year inhalation study. The dose-response relationship for sedation was characterized using internal dose measures as predicted by a physiologically based pharmacokinetic (PBPK) model for PGME and its acetate. PBPK modeling was used to account for changes in rodent physiology and metabolism due to aging and adaptation, based on data collected during weeksmore » 1, 2, 26, 52, and 78 of a chronic inhalation study. The peak concentration of PGME in richly perfused tissues was selected as the most appropriate internal dose measure based upon a consideration of the mode of action for sedation and similarities in tissue partitioning between brain and other richly perfused tissues. Internal doses (peak tissue concentrations of PGME) were designated as either no-observed-adverse-effect levels (NOAELs) or lowest-observed-adverse-effect levels (LOAELs) based upon the presence or absence of sedation at each time-point, species, and sex in the two year study. Distributions of the NOAEL and LOAEL values expressed in terms of internal dose were characterized using an arithmetic mean and standard deviation, with the mean internal NOAEL serving as the basis for the reference values, which was then divided by appropriate uncertainty factors. Where data were permitting, chemical-specific adjustment factors were derived to replace default uncertainty factor values of ten. Nonlinear kinetics are were predicted by the model in all species at PGME concentrations exceeding 100 ppm, which complicates interspecies and low-dose extrapolations. To address this complication, reference values were derived using two approaches which differ with respect to the order in which these extrapolations were performed: (1) uncertainty factor application followed by interspecies extrapolation (PBPK modeling); and (2) interspecies extrapolation followed by uncertainty factor application. The resulting reference values for these two approaches are substantially different, with values from the former approach being 7-fold higher than those from the latter approach. Such a striking difference between the two approaches reveals an underlying issue that has received little attention in the literature regarding the application of uncertainty factors and interspecies extrapolations to compounds where saturable kinetics occur in the range of the NOAEL. Until such discussions have taken place, reference values based on the latter approach are recommended for risk assessments involving human exposures to PGME and PGMEA.« less

An in vitro approach for comparative interspecies metabolism of agrochemicals.

PubMed

Whalley, Paul M; Bartels, Michael; Bentley, Karin S; Corvaro, Marco; Funk, Dorothee; Himmelstein, Matthew W; Neumann, Birgit; Strupp, Christian; Zhang, Fagen; Mehta, Jyotigna

2017-08-01

The metabolism and elimination of a xenobiotic has a direct bearing on its potential to cause toxicity in an organism. The confidence with which data from safety studies can be extrapolated to humans depends, among other factors, upon knowing whether humans are systemically exposed to the same chemical entities (i.e. a parent compound and its metabolites) as the laboratory animals used to study toxicity. Ideally, to understand a metabolite in terms of safety, both the chemical structure and the systemic exposure would need to be determined. However, as systemic exposure data (i.e. blood concentration/time data of test material or metabolites) in humans will not be available for agrochemicals, an in vitro approach must be taken. This paper outlines an in vitro experimental approach for evaluating interspecies metabolic comparisons between humans and animal species used in safety studies. The aim is to ensure, where possible, that all potential human metabolites are also present in the species used in the safety studies. If a metabolite is only observed in human in vitro samples and is not present in a metabolic pathway defined in the toxicological species already, the toxicological relevance of this metabolite must be evaluated. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Microbial Surface Colonization and Biofilm Development in Marine Environments

PubMed Central

2015-01-01

SUMMARY Biotic and abiotic surfaces in marine waters are rapidly colonized by microorganisms. Surface colonization and subsequent biofilm formation and development provide numerous advantages to these organisms and support critical ecological and biogeochemical functions in the changing marine environment. Microbial surface association also contributes to deleterious effects such as biofouling, biocorrosion, and the persistence and transmission of harmful or pathogenic microorganisms and their genetic determinants. The processes and mechanisms of colonization as well as key players among the surface-associated microbiota have been studied for several decades. Accumulating evidence indicates that specific cell-surface, cell-cell, and interpopulation interactions shape the composition, structure, spatiotemporal dynamics, and functions of surface-associated microbial communities. Several key microbial processes and mechanisms, including (i) surface, population, and community sensing and signaling, (ii) intraspecies and interspecies communication and interaction, and (iii) the regulatory balance between cooperation and competition, have been identified as critical for the microbial surface association lifestyle. In this review, recent progress in the study of marine microbial surface colonization and biofilm development is synthesized and discussed. Major gaps in our knowledge remain. We pose questions for targeted investigation of surface-specific community-level microbial features, answers to which would advance our understanding of surface-associated microbial community ecology and the biogeochemical functions of these communities at levels from molecular mechanistic details through systems biological integration. PMID:26700108

Microbial Surface Colonization and Biofilm Development in Marine Environments.

PubMed

Dang, Hongyue; Lovell, Charles R

2016-03-01

Biotic and abiotic surfaces in marine waters are rapidly colonized by microorganisms. Surface colonization and subsequent biofilm formation and development provide numerous advantages to these organisms and support critical ecological and biogeochemical functions in the changing marine environment. Microbial surface association also contributes to deleterious effects such as biofouling, biocorrosion, and the persistence and transmission of harmful or pathogenic microorganisms and their genetic determinants. The processes and mechanisms of colonization as well as key players among the surface-associated microbiota have been studied for several decades. Accumulating evidence indicates that specific cell-surface, cell-cell, and interpopulation interactions shape the composition, structure, spatiotemporal dynamics, and functions of surface-associated microbial communities. Several key microbial processes and mechanisms, including (i) surface, population, and community sensing and signaling, (ii) intraspecies and interspecies communication and interaction, and (iii) the regulatory balance between cooperation and competition, have been identified as critical for the microbial surface association lifestyle. In this review, recent progress in the study of marine microbial surface colonization and biofilm development is synthesized and discussed. Major gaps in our knowledge remain. We pose questions for targeted investigation of surface-specific community-level microbial features, answers to which would advance our understanding of surface-associated microbial community ecology and the biogeochemical functions of these communities at levels from molecular mechanistic details through systems biological integration. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Allelic variants of hexose transporter Hxt3p and hexokinases Hxk1p/Hxk2p in strains of Saccharomyces cerevisiae and interspecies hybrids.

PubMed

Zuchowska, Magdalena; Jaenicke, Elmar; König, Helmut; Claus, Harald

2015-11-01

The transport of sugars across the plasma membrane is a critical step in the utilization of glucose and fructose by Saccharomyces cerevisiae during must fermentations. Variations in the molecular structure of hexose transporters and kinases may affect the ability of wine yeast strains to finish sugar fermentation, even under stressful wine conditions. In this context, we sequenced and compared genes encoding the hexose transporter Hxt3p and the kinases Hxk1p/Hxk2p of Saccharomyces strains and interspecies hybrids with different industrial usages and regional backgrounds. The Hxt3p primary structure varied in a small set of amino acids, which characterized robust yeast strains used for the production of sparkling wine or to restart stuck fermentations. In addition, interspecies hybrid strains, previously isolated at the end of spontaneous fermentations, revealed a common amino acid signature. The location and potential influence of the amino acids exchanges is discussed by means of a first modelled Hxt3p structure. In comparison, hexokinase genes were more conserved in different Saccharomyces strains and hybrids. Thus, molecular variants of the hexose carrier Hxt3p, but not of kinases, correlate with different fermentation performances of yeast. Copyright © 2015 John Wiley & Sons, Ltd.

Involvement of formate as an interspecies electron carrier in a syntrophic acetate-oxidizing anaerobic microorganism in coculture with methanogens.

PubMed

Hattori, S; Luo, H; Shoun, H; Kamagata, Y

2001-01-01

To determine whether formate is involved in interspecies electron transfer between substrate-oxidizing bacteria and hydrogenotrophic microorganisms under anaerobic conditions, a syntrophic acetate-oxidizing bacterium Thermacetogenium phaeum strain PB was cocultured either with a formate /H2-utilizing methanogen strain TM (designated as PB/TM coculture), or an H2-utilizing methanogen strain deltaH (designated as PB/deltaH coculture). Acetate oxidation and subsequent methanogenesis in PB/TM coculture were found to be significantly faster than in PB/deltaH coculture. Formate dehydrogenase and hydrogenase were both detected in strains PB and TM. H2 partial pressures in the PB/TM coculture were kept lower (20 to 40 Pa) than those of the PB/deltaH coculture (40 to 60 Pa) during the exponential growth phase. Formate was also detected in both PB/TM and PB/deltaH cocultures, and the concentration of formate was maintained at a lower level in the PB/TM coculture (5 to 9 microM) than in the PB/deltaH coculture. Thermodynamic calculations revealed that the concentrations of both H2 and formate severely affect the syntrophic oxidation of acetate. These results strongly indicate that not only H2 but also formate may be involved in interspecies electron transfer.

Interspecies scaling of a camptothecin analogue: human predictions for intravenous topotecan using animal data.

PubMed

Ahlawat, P; Srinivas, N R

2008-11-01

As a class, camptothecin analogues via market entry of topotecan and irinotecan, have shown promise for the treatment of various solid tumours. Topotecan, in particular, was chosen as the substrate for allometric scaling and prediction of human parameter values for both total clearance (CL) and volume of distribution (V(ss)). The availability of published data in mouse, rat, dog, and monkey paved the way for interspecies scaling via allometry. Although it appeared that at a minimum mouse, rat, and dog would reasonably fit in a three-species allometry scale-up, the inclusion of monkey data enabled a better prediction of the human parameter values for total topotecan-e.g., CL: allometric equation: 1.5234W(0.7865); predicted value = 43.04 l h(-1): observed CL = 24-53 l h(-1); V(ss): allometric equation: 1.1939W(1.0208); predicted value = 91.29 litres: observed V(ss) = 66-146 litres. The proximity of the allometric exponent values of CL (0.7885) and V(ss) (1.0208) to the suggested values of 0.75 and 1.00 was not only encouraging, but also confirmed the applicability of interspecies scaling approach for topotecan. The data suggest that allometric scaling approaches with suitable correction factors could potentially be used to predict the human pharmacokinetics of novel CPT analogues prospectively.

Molecular interactions of plant oil components with stratum corneum lipids correlate with clinical measures of skin barrier function

PubMed Central

Mack Correa, Mary Catherine; Mao, Guangru; Saad, Peter; Flach, Carol R; Mendelsohn, Richard; Walters, Russel M

2014-01-01

Plant-derived oils consisting of triglycerides and small amounts of free fatty acids (FFAs) are commonly used in skincare regimens. FFAs are known to disrupt skin barrier function. The objective of this study was to mechanistically study the effects of FFAs, triglycerides and their mixtures on skin barrier function. The effects of oleic acid (OA), glyceryl trioleate (GT) and OA/GT mixtures on skin barrier were assessed in vivo through measurement of transepidermal water loss (TEWL) and fluorescein dye penetration before and after a single application. OA's effects on stratum corneum (SC) lipid order in vivo were measured with infrared spectroscopy through application of perdeuterated OA (OA-d34). Studies of the interaction of OA and GT with skin lipids included imaging the distribution of OA-d34 and GT ex vivo with IR microspectroscopy and thermodynamic analysis of mixtures in aqueous monolayers. The oil mixtures increased both TEWL and fluorescein penetration 24 h after a single application in an OA dose-dependent manner, with the highest increase from treatment with pure OA. OA-d34 penetrated into skin and disordered SC lipids. Furthermore, the ex vivo IR imaging studies showed that OA-d34 permeated to the dermal/epidermal junction while GT remained in the SC. The monolayer experiments showed preferential interspecies interactions between OA and SC lipids, while the mixing between GT and SC lipids was not thermodynamically preferred. The FFA component of plant oils may disrupt skin barrier function. The affinity between plant oil components and SC lipids likely determines the extent of their penetration and clinically measurable effects on skin barrier functions. PMID:24372651

Inter-species and Seasonal Variability in Mg / Ca in Larger Benthic Foraminifera: Implications for Paleo-proxy

NASA Astrophysics Data System (ADS)

Singh, A.; Saraswati, P. K.; Pande, K.; Sanyal, P.

2015-12-01

The reports of inter-species variability to intra-test heterogeneity in Mg/Ca in several species of foraminifera have raised question about its use in estimation of seawater temperatures and necessitate field and culture studies to verify it for species from different habitats. In this study, we attempt to investigate if Mg/Ca in larger benthic foraminifera (LBF) could be a potential proxy of seawater temperatures for shallow marine carbonates. The samples were collected in different seasons from coral reef at Akajima (Okinawa, Japan). The Ca and Mg of 13 species of LBF and small benthic foraminifera from the same season were determined to examine variation in Mg/Ca among the species calcified under presumably the same temperature and salinity conditions. We also analyzed Amphistegina lessoni from different seasons for Ca, Mg and δ18O to determine variation in Mg/Ca with temperature and see how the two proxies of temperatures, Mg/Ca and δ18O, correlate in the same species. The species cluster about two distinctly separated Mg/Ca values. The first group comprising species of Amphistegina, Gypsina, Ammonia and Elphidium have relatively lower Mg/Ca, varying from 30 to 45 mmol/mol. The second group, having average Mg/Ca ranging from ~110 to 170 mmol/mol, includes species of Schlumbergerella, Baculogypsinoides, Baculogypsina, Heterostegina, Operculina, Calcarina, Amphisorus, Alveolinella and Poroeponides. The result suggests large interspecies variability implying vital effect in foraminiferal Mg/Ca. There is no distinct difference in Mg/Ca values between porcelaneous and hyaline types or symbiont-bearing and symbiont-free types. In Amphistegina lessoni the variation in Mg/Ca between individuals of the same season is as large as variation across the seasons. There is no correlation between Mg/Ca and seawater temperature. Lack of correlation between Mg/Ca and δ18O further suggests that Mg/Ca in the species is not primarily controlled by temperature.

Dissipative hydrodynamics for multi-component systems

NASA Astrophysics Data System (ADS)

El, Andrej; Bouras, Ioannis; Wesp, Christian; Xu, Zhe; Greiner, Carsten

2012-11-01

Second-order dissipative hydrodynamic equations for each component of a multi-component system are derived using the entropy principle. Comparison of the solutions with kinetic transport results demonstrates validity of the obtained equations. We demonstrate how the shear viscosity of the total system can be calculated in terms of the involved cross-sections and partial densities. The presence of the inter-species interactions leads to a characteristic time dependence of the shear viscosity of the mixture, which also means that the shear viscosity of a mixture cannot be calculated using the Green-Kubo formalism the way it has been done recently. This finding is of interest for understanding of the shear viscosity of a quark-gluon plasma extracted from comparisons of hydrodynamic simulations with experimental results from RHIC and LHC.

A simple spatiotemporal rabies model for skunk and bat interaction in northeast Texas.

PubMed

Borchering, Rebecca K; Liu, Hao; Steinhaus, Mara C; Gardner, Carl L; Kuang, Yang

2012-12-07

We formulate a simple partial differential equation model in an effort to qualitatively reproduce the spread dynamics and spatial pattern of rabies in northeast Texas with overlapping reservoir species (skunks and bats). Most existing models ignore reservoir species or model them with patchy models by ordinary differential equations. In our model, we incorporate interspecies rabies infection in addition to rabid population random movement. We apply this model to the confirmed case data from northeast Texas with most parameter values obtained or computed from the literature. Results of simulations using both our skunk-only model and our skunk and bat model demonstrate that the model with overlapping reservoir species more accurately reproduces the progression of rabies spread in northeast Texas. Copyright © 2012 Elsevier Ltd. All rights reserved.

Dual species entanglement of Rb and Cs qubits with Rydberg blockade for crosstalk free qubit measurements

NASA Astrophysics Data System (ADS)

Baker, Kevin; Yu, Zhaoning; Ebert, Matthew; Sun, Yuan; Saffman, Mark

2016-05-01

One of the outstanding challenges facing neutral atom qubit approaches to quantum computation is suppression of crosstalk between proximal qubits due to scattered light that is generated during optical pumping and measurement operations. We have recently proposed a dual species approach to solving this challenge whereby computational qubits encoded in Cs atoms are entangled with Rb atoms via an interspecies Rydberg interaction. The quantum state of a Cs atom can then be readout by measuring the state of a Rb atom. The difference in resonant wavelengths of the two species effectively suppresses crosstalk. We will present progress towards experimental demonstration of dual species entanglement using Rb and Cs atoms cotrapped in a single beam optical trap. Work supported by the ARL CDQI.

Eco-evolutionary feedbacks drive species interactions

PubMed Central

Andrade-Domínguez, Andrés; Salazar, Emmanuel; del Carmen Vargas-Lagunas, María; Kolter, Roberto; Encarnación, Sergio

2014-01-01

In the biosphere, many species live in close proximity and can thus interact in many different ways. Such interactions are dynamic and fall along a continuum between antagonism and cooperation. Because interspecies interactions are the key to understanding biological communities, it is important to know how species interactions arise and evolve. Here, we show that the feedback between ecological and evolutionary processes has a fundamental role in the emergence and dynamics of species interaction. Using a two-species artificial community, we demonstrate that ecological processes and rapid evolution interact to influence the dynamics of the symbiosis between a eukaryote (Saccharomyces cerevisiae) and a bacterium (Rhizobium etli). The simplicity of our experimental design enables an explicit statement of causality. The niche-constructing activities of the fungus were the key ecological process: it allowed the establishment of a commensal relationship that switched to ammensalism and provided the selective conditions necessary for the adaptive evolution of the bacteria. In this latter state, the bacterial population radiates into more than five genotypes that vary with respect to nutrient transport, metabolic strategies and global regulation. Evolutionary diversification of the bacterial populations has strong effects on the community; the nature of interaction subsequently switches from ammensalism to antagonism where bacteria promote yeast extinction. Our results demonstrate the importance of the evolution-to-ecology pathway in the persistence of interactions and the stability of communities. Thus, eco-evolutionary dynamics have the potential to transform the structure and functioning of ecosystems. Our results suggest that these dynamics should be considered to improve our understanding of beneficial and detrimental host–microbe interactions. PMID:24304674

INTERSPECIES COMPARISONS OF BENZO(A)PYRENE METABOLISM AND DNA-ADDUCT FORMATION IN CULTURED HUMAN AND ANIMAL BLADDER AND TRACHEOBRONCHIAL TISSUES

EPA Science Inventory

Cultured bladder and tracheobronchial explants from human, monkey, dog, hamster, and rat were used to study the metabolism, covalent binding to DNA, and DNA:adduct formation of (3H0benzo(a)pyrene (BP). Both organs from all species formed large amounts (40 to 70% of total 3H in th...

Animal models and conserved processes

PubMed Central

2012-01-01

Background The concept of conserved processes presents unique opportunities for using nonhuman animal models in biomedical research. However, the concept must be examined in the context that humans and nonhuman animals are evolved, complex, adaptive systems. Given that nonhuman animals are examples of living systems that are differently complex from humans, what does the existence of a conserved gene or process imply for inter-species extrapolation? Methods We surveyed the literature including philosophy of science, biological complexity, conserved processes, evolutionary biology, comparative medicine, anti-neoplastic agents, inhalational anesthetics, and drug development journals in order to determine the value of nonhuman animal models when studying conserved processes. Results Evolution through natural selection has employed components and processes both to produce the same outcomes among species but also to generate different functions and traits. Many genes and processes are conserved, but new combinations of these processes or different regulation of the genes involved in these processes have resulted in unique organisms. Further, there is a hierarchy of organization in complex living systems. At some levels, the components are simple systems that can be analyzed by mathematics or the physical sciences, while at other levels the system cannot be fully analyzed by reducing it to a physical system. The study of complex living systems must alternate between focusing on the parts and examining the intact whole organism while taking into account the connections between the two. Systems biology aims for this holism. We examined the actions of inhalational anesthetic agents and anti-neoplastic agents in order to address what the characteristics of complex living systems imply for inter-species extrapolation of traits and responses related to conserved processes. Conclusion We conclude that even the presence of conserved processes is insufficient for inter-species extrapolation when the trait or response being studied is located at higher levels of organization, is in a different module, or is influenced by other modules. However, when the examination of the conserved process occurs at the same level of organization or in the same module, and hence is subject to study solely by reductionism, then extrapolation is possible. PMID:22963674

Acute Toxicity Prediction to Threatened and Endangered Species Using Interspecies Correlation Estimation (ICE) Models.

PubMed

Willming, Morgan M; Lilavois, Crystal R; Barron, Mace G; Raimondo, Sandy

2016-10-04

Evaluating contaminant sensitivity of threatened and endangered (listed) species and protectiveness of chemical regulations often depends on toxicity data for commonly tested surrogate species. The U.S. EPA's Internet application Web-ICE is a suite of Interspecies Correlation Estimation (ICE) models that can extrapolate species sensitivity to listed taxa using least-squares regressions of the sensitivity of a surrogate species and a predicted taxon (species, genus, or family). Web-ICE was expanded with new models that can predict toxicity to over 250 listed species. A case study was used to assess protectiveness of genus and family model estimates derived from either geometric mean or minimum taxa toxicity values for listed species. Models developed from the most sensitive value for each chemical were generally protective of the most sensitive species within predicted taxa, including listed species, and were more protective than geometric means models. ICE model estimates were compared to HC5 values derived from Species Sensitivity Distributions for the case study chemicals to assess protectiveness of the two approaches. ICE models provide robust toxicity predictions and can generate protective toxicity estimates for assessing contaminant risk to listed species.

Comparisons of Auricular Cartilage Tissues from Different Species.

PubMed

Chiu, Loraine L Y; Giardini-Rosa, Renata; Weber, Joanna F; Cushing, Sharon L; Waldman, Stephen D

2017-12-01

Tissue engineering of auricular cartilage has great potential in providing readily available materials for reconstructive surgeries. As the field of tissue engineering moves forward to developing human tissues, there needs to be an interspecies comparison of the native auricular cartilage in order to determine a suitable animal model to assess the performance of engineered auricular cartilage in vivo. Here, we performed interspecies comparisons of auricular cartilage by comparing tissue microstructure, protein localization, biochemical composition, and mechanical properties of auricular cartilage tissues from rat, rabbit, pig, cow, and human. Human, pig, and cow auricular cartilage have smaller lacunae compared to rat and rabbit cartilage ( P < .05). Despite differences in tissue microstructure, human auricular cartilage has similar biochemical composition to both rat and rabbit. Auricular cartilage from pig and cow, alternatively, display significantly higher glycosaminoglycan and collagen contents compared to human, rat, and rabbit ( P < .05). The mechanical properties of human auricular cartilage were comparable to that of all 4 animal species. This is the first study that compares the microstructural, biochemical, and mechanical properties of auricular cartilage from different species. This study showed that different experimental animal models of human auricular cartilage may be suitable in different cases.

Long-time behavior and Turing instability induced by cross-diffusion in a three species food chain model with a Holling type-II functional response.

PubMed

Haile, Dawit; Xie, Zhifu

2015-09-01

In this paper, we study a strongly coupled reaction-diffusion system describing three interacting species in a food chain model, where the third species preys on the second one and simultaneously the second species preys on the first one. An intra-species competition b2 among the second predator is introduced to the food chain model. This parameter produces some very interesting result in linear stability and Turing instability. We first show that the unique positive equilibrium solution is locally asymptotically stable for the corresponding ODE system when the intra-species competition exists among the second predator. The positive equilibrium solution remains linearly stable for the reaction diffusion system without cross diffusion, hence it does not belong to the classical Turing instability scheme. But it becomes linearly unstable only when cross-diffusion also plays a role in the reaction-diffusion system, hence the instability is driven solely from the effect of cross diffusion. Our results also exhibit some interesting combining effects of cross-diffusion, intra-species competitions and inter-species interactions. Numerically, we conduct a one parameter analysis which illustrate how the interactions change the existence of stable equilibrium, limit cycle, and chaos. Some interesting dynamical phenomena occur when we perform analysis of interactions in terms of self-production of prey and intra-species competition of the middle predator. By numerical simulations, it illustrates the existence of nonuniform steady solutions and new patterns such as spot patterns, strip patterns and fluctuations due to the diffusion and cross diffusion in two-dimension. Published by Elsevier Inc.

Aligning Biomolecular Networks Using Modular Graph Kernels

NASA Astrophysics Data System (ADS)

Towfic, Fadi; Greenlee, M. Heather West; Honavar, Vasant

Comparative analysis of biomolecular networks constructed using measurements from different conditions, tissues, and organisms offer a powerful approach to understanding the structure, function, dynamics, and evolution of complex biological systems. We explore a class of algorithms for aligning large biomolecular networks by breaking down such networks into subgraphs and computing the alignment of the networks based on the alignment of their subgraphs. The resulting subnetworks are compared using graph kernels as scoring functions. We provide implementations of the resulting algorithms as part of BiNA, an open source biomolecular network alignment toolkit. Our experiments using Drosophila melanogaster, Saccharomyces cerevisiae, Mus musculus and Homo sapiens protein-protein interaction networks extracted from the DIP repository of protein-protein interaction data demonstrate that the performance of the proposed algorithms (as measured by % GO term enrichment of subnetworks identified by the alignment) is competitive with some of the state-of-the-art algorithms for pair-wise alignment of large protein-protein interaction networks. Our results also show that the inter-species similarity scores computed based on graph kernels can be used to cluster the species into a species tree that is consistent with the known phylogenetic relationships among the species.

The role of receptor binding specificity in interspecies transmission of influenza viruses

PubMed Central

Imai, Masaki; Kawaoka, Yoshihiro

2017-01-01

Influenza A virus infection begins with the binding of the hemagglutinin (HA) glycoprotein to sialic acid-containing receptors on the surface of the target cell. Avian influenza viruses, including avian H5N1, H7, and H9N2 viruses, can occasionally cross the species barrier and infect humans; however, these viruses do not spread efficiently from person to person, perhaps, in part, due to differences in the receptor-binding specificities of human and avian influenza viruses. The HAs of avian influenza viruses must adapt to receptors in humans to acquire efficient human-to-human transmissibility. In this review, we discuss the receptor binding specificity of influenza A viruses and its role in interspecies transmission. PMID:22445963

Reprogramming of Somatic Cells Towards Pluripotency by Cell Fusion.

PubMed

Malinowski, Andrzej R; Fisher, Amanda G

2016-01-01

Pluripotent reprogramming can be dominantly induced in a somatic nucleus upon fusion with a pluripotent cell such as embryonic stem (ES) cell. Cell fusion between ES cells and somatic cells results in the formation of heterokaryons, in which the somatic nuclei begin to acquire features of the pluripotent partner. The generation of interspecies heterokaryons between mouse ES- and human somatic cells allows an experimenter to distinguish the nuclear events occurring specifically within the reprogrammed nucleus. Therefore, cell fusion provides a simple and rapid approach to look at the early nuclear events underlying pluripotent reprogramming. Here, we describe a polyethylene glycol (PEG)-mediated cell fusion protocol to generate interspecies heterokaryons and intraspecies hybrids between ES cells and B lymphocytes or fibroblasts.

Revisiting AI-2 quorum sensing inhibitors: direct comparison of alkyl-DPD analogues and a natural product fimbrolide.

PubMed

Lowery, Colin A; Abe, Takumi; Park, Junguk; Eubanks, Lisa M; Sawada, Daisuke; Kaufmann, Gunnar F; Janda, Kim D

2009-11-04

Quorum sensing (QS) systems have been discovered in a wide variety of bacteria, and mediate both intra- and interspecies communication. The AI-2-based QS system represents the most studied of these proposed interspecies systems and has been shown to regulate diverse functions such as bioluminescence, expression of virulence factors, and biofilm formation. As such, the development of modulatory compounds, both agonists and antagonists, is of great interest for the study of unknown AI-2-based QS systems and the potential treatment of bacterial infections. The fimbrolide class of natural products has exhibited excellent inhibitory activity against AI-2-based QS and as such may be considered the "gold standard" of AI-2 inhibitors. Thus, we sought to include a fimbrolide as a control compound for our recently developed alkyl-DPD panel of AI-2 modulators. Herein, we present a revised synthesis of a commonly studied fimbrolide as well as a direct comparison between the fimbrolide and alkyl-DPD analogues. We demonstrate that our alkyl-DPD analogues are more potent inhibitors of QS in both Vibrio harveyi and Salmonella typhimurium, the two organisms with defined AI-2 QS systems, and in doing so call into question the widely accepted use of fimbrolide-derived compounds as the "gold standard" of AI-2 inhibition.

A deer (subfamily Cervinae) genetic linkage map and the evolution of ruminant genomes.

PubMed Central

Slate, Jon; Van Stijn, Tracey C; Anderson, Rayna M; McEwan, K Mary; Maqbool, Nauman J; Mathias, Helen C; Bixley, Matthew J; Stevens, Deirdre R; Molenaar, Adrian J; Beever, Jonathan E; Galloway, Susan M; Tate, Michael L

2002-01-01

Comparative maps between ruminant species and humans are increasingly important tools for the discovery of genes underlying economically important traits. In this article we present a primary linkage map of the deer genome derived from an interspecies hybrid between red deer (Cervus elaphus) and Père David's deer (Elaphurus davidianus). The map is approximately 2500 cM long and contains >600 markers including both evolutionary conserved type I markers and highly polymorphic type II markers (microsatellites). Comparative mapping by annotation and sequence similarity (COMPASS) was demonstrated to be a useful tool for mapping bovine and ovine ESTs in deer. Using marker order as a phylogenetic character and comparative map information from human, mouse, deer, cattle, and sheep, we reconstructed the karyotype of the ancestral Pecoran mammal and identified the chromosome rearrangements that have occurred in the sheep, cattle, and deer lineages. The deer map and interspecies hybrid pedigrees described here are a valuable resource for (1) predicting the location of orthologs to human genes in ruminants, (2) mapping QTL in farmed and wild deer populations, and (3) ruminant phylogenetic studies. PMID:11973312

A DNA Barcode Library for Korean Chironomidae (Insecta: Diptera) and Indexes for Defining Barcode Gap

PubMed Central

Kim, Sungmin; Song, Kyo-Hong; Ree, Han-Il; Kim, Won

2012-01-01

Non-biting midges (Diptera: Chironomidae) are a diverse population that commonly causes respiratory allergies in humans. Chironomid larvae can be used to indicate freshwater pollution, but accurate identification on the basis of morphological characteristics is difficult. In this study, we constructed a mitochondrial cytochrome c oxidase subunit I (COI)-based DNA barcode library for Korean chironomids. This library consists of 211 specimens from 49 species, including adults and unidentified larvae. The interspecies and intraspecies COI sequence variations were analyzed. Sophisticated indexes were developed in order to properly evaluate indistinct barcode gaps that are created by insufficient sampling on both the interspecies and intraspecies levels and by variable mutation rates across taxa. In a variety of insect datasets, these indexes were useful for re-evaluating large barcode datasets and for defining COI barcode gaps. The COI-based DNA barcode library will provide a rapid and reliable tool for the molecular identification of Korean chironomid species. Furthermore, this reverse-taxonomic approach will be improved by the continuous addition of other speceis’ sequences to the library. PMID:22138764

[Effect of TSA and VPA treatment on long-tailed macaque (Macaca fascicularis)-pig interspecies somatic cell nuclear transfer].

PubMed

Qin, Zu-Xing; Huang, Gao-Bo; Luo, Jun; Ning, Shu-Fang; Lu, Sheng-Sheng; Lu, Ke-Huan

2012-03-01

Long-tailed macaque-pig interspecies somatic cell nuclear transfer (iSCNT) is beneficial to yield embryonic stem cells from iSCNT embryos with similar genetic background as human, which can be used as materials for medical and basic research. The primary objective of this study was to investigate the effects of concentrations and treatment duration of two histone deacetylase inhibitors-Trichostatin A (TSA) and Valproic acid (VPA) and two different embryo culture media (PZM-3 and HECM-10) on the in vitro development of iSCNT embryos. The results suggested that when PZM-3 was used as the embryo culture medium, the blastocyst rate of 10 nmol/L TSA treatment for 48 h was significantly higher than the control group (22.78% vs 9.86%, P< 0.05). However, neither in PZM-3 nor in HECM-10, 2-10 mmol/L VPA treatment did not increase the in vitro developmental potential of iSCNT embryos. It was concluded that TSA treatment could enhance the in vitro developmental potential of long-tailed macaque-pig iSCNT embryos.

Lotka-Volterra systems in environments with randomly disordered temporal periodicity

NASA Astrophysics Data System (ADS)

Naess, Arvid; Dimentberg, Michael F.; Gaidai, Oleg

2008-08-01

A generalized Lotka-Volterra model for a pair of interacting populations of predators and prey is studied. The model accounts for the prey’s interspecies competition and therefore is asymptotically stable, whereas its oscillatory behavior is induced by temporal variations in environmental conditions simulated by those in the prey’s reproduction rate. Two models of the variations are considered, each of them combining randomness with “hidden” periodicity. The stationary joint probability density function (PDF) of the number of predators and prey is calculated numerically by the path integration (PI) method based on the use of characteristic functions and the fast Fourier transform. The numerical results match those for the asymptotic case of white-noise variations for which an analytical solution is available. Several examples are studied, with calculations of important characteristics of oscillations, for example the expected rate of up-crossings given the level of the predator number. The calculated PDFs may be of predominantly random (unimodal) or predominantly periodic nature (bimodal). Thus, the PI method has been demonstrated to be a powerful tool for studies of the dynamics of predator-prey pairs. The method captures the random oscillations as observed in nature, taking into account potential periodicity in the environmental conditions.

Lotka-Volterra systems in environments with randomly disordered temporal periodicity.

PubMed

Naess, Arvid; Dimentberg, Michael F; Gaidai, Oleg

2008-08-01

A generalized Lotka-Volterra model for a pair of interacting populations of predators and prey is studied. The model accounts for the prey's interspecies competition and therefore is asymptotically stable, whereas its oscillatory behavior is induced by temporal variations in environmental conditions simulated by those in the prey's reproduction rate. Two models of the variations are considered, each of them combining randomness with "hidden" periodicity. The stationary joint probability density function (PDF) of the number of predators and prey is calculated numerically by the path integration (PI) method based on the use of characteristic functions and the fast Fourier transform. The numerical results match those for the asymptotic case of white-noise variations for which an analytical solution is available. Several examples are studied, with calculations of important characteristics of oscillations, for example the expected rate of up-crossings given the level of the predator number. The calculated PDFs may be of predominantly random (unimodal) or predominantly periodic nature (bimodal). Thus, the PI method has been demonstrated to be a powerful tool for studies of the dynamics of predator-prey pairs. The method captures the random oscillations as observed in nature, taking into account potential periodicity in the environmental conditions.

Interspecies protein substitution to investigate the role of the lyssavirus glycoprotein.

PubMed

Marston, Denise A; McElhinney, Lorraine M; Banyard, Ashley C; Horton, Daniel L; Núñez, Alejandro; Koser, Martin L; Schnell, Matthias J; Fooks, Anthony R

2013-02-01

European bat lyssaviruses type 1 (EBLV-1) and type 2 (EBLV-2) circulate within bat populations throughout Europe and are capable of causing disease indistinguishable from that caused by classical rabies virus (RABV). However, the determinants of viral fitness and pathogenicity are poorly understood. Full-length genome clones based on the highly attenuated, non-neuroinvasive, RABV vaccine strain (SAD-B19) were constructed with the glycoprotein (G) of either SAD-B19 (SN), of EBLV-1 (SN-1) or EBLV-2 (SN-2). In vitro characterization of SN-1 and SN-2 in comparison to wild-type EBLVs demonstrated that the substitution of G affected the final virus titre and antigenicity. In vivo, following peripheral infection with a high viral dose (10(4) f.f.u.), animals infected with SN-1 had reduced survivorship relative to infection with SN, resulting in survivorship similar to animals infected with EBLV-1. The histopathological changes and antigen distribution observed for SN-1 were more representative of those observed with SN than with EBLV-1. EBLV-2 was unable to achieve a titre equivalent to that of the other viruses. Therefore, a reduced-dose experiment (10(3) f.f.u.) was undertaken in vivo to compare EBLV-2 and SN-2, which resulted in 100 % survivorship for all recombinant viruses (SN, SN-1 and SN-2) while clinical disease developed in mice infected with the EBLVs. These data indicate that interspecies replacement of G has an effect on virus titre in vitro, probably as a result of suboptimal G-matrix protein interactions, and influences the survival outcome following a peripheral challenge with a high virus titre in mice.

Arginine-Ornithine Antiporter ArcD Controls Arginine Metabolism and Interspecies Biofilm Development of Streptococcus gordonii*♦

PubMed Central

Sakanaka, Akito; Kuboniwa, Masae; Takeuchi, Hiroki; Hashino, Ei; Amano, Atsuo

2015-01-01

Arginine is utilized by the oral inhabitant Streptococcus gordonii as a substrate of the arginine deiminase system (ADS), eventually producing ATP and NH3, the latter of which is responsible for microbial resistance to pH stress. S. gordonii expresses a putative arginine-ornithine antiporter (ArcD) whose function has not been investigated despite relevance to the ADS and potential influence on inter-bacterial communication with periodontal pathogens that utilize amino acids as a main energy source. Here, we generated an S. gordonii ΔarcD mutant to explore the role of ArcD in physiological homeostasis and bacterial cross-feeding. First, we confirmed that S. gordonii ArcD plays crucial roles for mediating arginine uptake and promoting bacterial growth, particularly under arginine-limited conditions. Next, metabolomic profiling and transcriptional analysis of the ΔarcD mutant revealed that deletion of this gene caused intracellular accumulation of ornithine leading to malfunction of the ADS and suppression of de novo arginine biosynthesis. The mutant strain also showed increased susceptibility to low pH stress due to reduced production of ammonia. Finally, accumulation of Fusobacterium nucleatum was found to be significantly decreased in biofilm formed by the ΔarcD mutant as compared with the wild-type strain, although ornithine supplementation restored fusobacterium biovolume in dual-species biofilms with the ΔarcD mutant and also enhanced single species biofilm development by F. nucleatum. Our results are the first direct evidence showing that S. gordonii ArcD modulates not only alkali and energy production but also interspecies interaction with F. nucleatum, thus initiating a middle stage of periodontopathic biofilm formation, by metabolic cross-feeding. PMID:26085091

Rapid evolution of binding specificities and expression patterns of inhibitory CD33-related Siglecs in primates

PubMed Central

Padler-Karavani, Vered; Hurtado-Ziola, Nancy; Chang, Yung-Chi; Sonnenburg, Justin L.; Ronaghy, Arash; Yu, Hai; Verhagen, Andrea; Nizet, Victor; Chen, Xi; Varki, Nissi; Varki, Ajit; Angata, Takashi

2014-01-01

Siglecs are sialic acid-binding Ig-like lectins that recognize sialoglycans via amino-terminal V-set domains. CD33-related Siglecs (CD33rSiglecs) on innate immune cells recognize endogenous sialoglycans as “self-associated molecular patterns” (SAMPs), dampening immune responses via cytosolic immunoreceptor tyrosine-based inhibition motifs that recruit tyrosine phosphatases. However, sialic acid-expressing pathogens subvert this mechanism through molecular mimicry. Meanwhile, endogenous host SAMPs must continually evolve to evade other pathogens that exploit sialic acids as invasion targets. We hypothesized that these opposing selection forces have accelerated CD33rSiglec evolution. We address this by comparative analysis of major CD33rSiglec (Siglec-3, Siglec-5, and Siglec-9) orthologs in humans, chimpanzees, and baboons. Recombinant soluble molecules displaying ligand-binding domains show marked quantitative and qualitative interspecies differences in interactions with strains of the sialylated pathogen, group B Streptococcus, and with sialoglycans presented as gangliosides or in the form of sialoglycan microarrays, including variations such as N-glycolyl and O-acetyl groups. Primate Siglecs also show quantitative and qualitative intra- and interspecies variations in expression patterns on leukocytes, both in circulation and in tissues. Taken together our data explain why the CD33rSiglec-encoding gene cluster is undergoing rapid evolution via multiple mechanisms, driven by the need to maintain self-recognition by innate immune cells, while escaping 2 distinct mechanisms of pathogen subversion.—Padler-Karavani, V., Hurtado-Ziola, N., Chang, Y.-C., Sonnenburg, J. L., Ronaghy, A., Yu, H., Verhagen, A., Nizet, V., Chen, X., Varki, N., Varki, A., Angata, T. Rapid evolution of binding specificities and expression patterns of inhibitory CD33-related Siglecs in primates. PMID:24308974

Balance of Interactions Determines Optimal Survival in Multi-Species Communities.

PubMed

Choudhary, Anshul; Sinha, Sudeshna

2015-01-01

We consider a multi-species community modelled as a complex network of populations, where the links are given by a random asymmetric connectivity matrix J, with fraction 1 - C of zero entries, where C reflects the over-all connectivity of the system. The non-zero elements of J are drawn from a Gaussian distribution with mean μ and standard deviation σ. The signs of the elements Jij reflect the nature of density-dependent interactions, such as predatory-prey, mutualism or competition, and their magnitudes reflect the strength of the interaction. In this study we try to uncover the broad features of the inter-species interactions that determine the global robustness of this network, as indicated by the average number of active nodes (i.e. non-extinct species) in the network, and the total population, reflecting the biomass yield. We find that the network transitions from a completely extinct system to one where all nodes are active, as the mean interaction strength goes from negative to positive, with the transition getting sharper for increasing C and decreasing σ. We also find that the total population, displays distinct non-monotonic scaling behaviour with respect to the product μC, implying that survival is dependent not merely on the number of links, but rather on the combination of the sparseness of the connectivity matrix and the net interaction strength. Interestingly, in an intermediate window of positive μC, the total population is maximal, indicating that too little or too much positive interactions is detrimental to survival. Rather, the total population levels are optimal when the network has intermediate net positive connection strengths. At the local level we observe marked qualitative changes in dynamical patterns, ranging from anti-phase clusters of period 2 cycles and chaotic bands, to fixed points, under the variation of mean μ of the interaction strengths. We also study the correlation between synchronization and survival, and find that synchronization does not necessarily lead to extinction. Lastly, we propose an effective low dimensional map to capture the behavior of the entire network, and this provides a broad understanding of the interplay of the local dynamical patterns and the global robustness trends in the network.

Sensitivity of species to chemicals: dose-response characteristics for various test types (coldbloodedLC50, cold-blooded LR50 and warm-blooded LD50) and modes of action

EPA Science Inventory

While sensitivity of model species to common toxicants has been addressed, a systematic analysis of inter-species variability for different test types, modes of action and species is as yet lacking. Hence, the aim of the present study was to identify similarities and differences ...

Inter-species protein trafficking endows dodder (Cuscuta pentagona) with a host-specific herbicide-tolerant trait.

PubMed

Jiang, Linjian; Qu, Feng; Li, Zhaohu; Doohan, Douglas

2013-06-01

· Besides photosynthates, dodder (Cuscuta spp.) acquires phloem-mobile proteins from host; however, whether this could mediate inter-species phenotype transfer was not demonstrated. Specifically, we test whether phosphinothricin acetyl transferase (PAT) that confers host plant glufosinate herbicide tolerance traffics and functions inter-specifically. · Dodder tendrils excised from hosts can grow in vitro for weeks or resume in vivo by parasitizing new hosts. The level of PAT in in vivo and in vitro dodder tendrils was quantified by enzyme-linked immunosorbent assay. The glufosinate sensitivity was examined by dipping the distal end of in vivo and in vitro tendrils, growing on or excised from LibertyLink (LL; PAT-transgenic and glufosinate tolerant) and conventional (CN; glufosinate sensitive) soybean hosts, into glufosinate solutions for 5 s. After in vitro tendrils excised from LL hosts reparasitized new CN and LL hosts, the PAT level and the glufosinate sensitivity were also examined. · When growing on LL host, dodder tolerated glufosinate and contained PAT at a level of 0.3% of that encountered in LL soybean leaf. After PAT was largely degraded in dodders, they became glufosinate sensitive. PAT mRNA was not detected by reverse transcription PCR in dodders. · In conclusion, the results indicated that PAT inter-species trafficking confers dodder glufosinate tolerance. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

Molecular evidence for interspecies transmission of H3N2pM/H3N2v influenza A viruses at an Ohio agricultural fair, July 2012

PubMed Central

Bowman, Andrew S; Sreevatsan, Srinand; Killian, Mary L; Page, Shannon L; Nelson, Sarah W; Nolting, Jacqueline M; Cardona, Carol; Slemons, Richard D

2012-01-01

Evidence accumulating in 2011–2012 indicates that there is significant intra- and inter-species transmission of influenza A viruses at agricultural fairs, which has renewed interest in this unique human/swine interface. Six human cases of influenza A (H3N2) variant (H3N2v) virus infections were epidemiologically linked to swine exposure at fairs in the United States in 2011. In 2012, the number of H3N2v cases in the Midwest had exceeded 300 from early July to September, 2012. Prospective influenza A virus surveillance among pigs at Ohio fairs resulted in the detection of H3N2pM (H3N2 influenza A viruses containing the matrix (M) gene from the influenza A (H1N1) pdm09 virus). These H3N2pM viruses were temporally and spatially linked to several human H3N2v cases. Complete genomic analyses of these H3N2pM isolates demonstrated >99% nucleotide similarity to the H3N2v isolates recovered from human cases. Actions to mitigate the bidirectional interspecies transmission of influenza A virus between people and animals at agricultural fairs may be warranted. PMID:26038404

Cloning of an endangered species (Bos gaurus) using interspecies nuclear transfer.

PubMed

Lanza, R P; Cibelli, J B; Diaz, F; Moraes, C T; Farin, P W; Farin, C E; Hammer, C J; West, M D; Damiani, P

2000-01-01

Approximately 100 species become extinct a day. Despite increasing interest in using cloning to rescue endangered species, successful interspecies nuclear transfer has not been previously described, and only a few reports of in vitro embryo formation exist. Here we show that interspecies nuclear transfer can be used to clone an endangered species with normal karyotypic and phenotypic development through implantation and the late stages of fetal growth. Somatic cells from a gaur bull (Bos gaurus), a large wild ox on the verge of extinction, (Species Survival Plan < 100 animals) were electrofused with enucleated oocytes from domestic cows. Twelve percent of the reconstructed oocytes developed to the blastocyst stage, and 18% of these embryos developed to the fetal stage when transferred to surrogate mothers. Three of the fetuses were electively removed at days 46 to 54 of gestation, and two continued gestation longer than 180 (ongoing) and 200 days, respectively. Microsatellite marker and cytogenetic analyses confirmed that the nuclear genome of the cloned animals was gaurus in origin. The gaur nuclei were shown to direct normal fetal development, with differentiation into complex tissue and organs, even though the mitochondrial DNA (mtDNA) within all the tissue types evaluated was derived exclusively from the recipient bovine oocytes. These results suggest that somatic cell cloning methods could be used to restore endangered, or even extinct, species and populations.

Universal Fermi Gases in Mixed Dimensions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nishida, Yusuke; Tan, Shina

2008-10-24

We investigate a two-species Fermi gas in which one species is confined in a two-dimensional plane (2D) or one-dimensional line (1D) while the other is free in the three-dimensional space (3D). We discuss the realization of such a system with the interspecies interaction tuned to resonance. When the mass ratio is in the range 0.0351

Diverse Contexts of Zoonotic Transmission of Simian Foamy Viruses in Asia

PubMed Central

May, Cynthia C.; Engel, Gregory A.; Steinkraus, Katherine A.; Schillaci, Michael A.; Fuentes, Agustin; Rompis, Aida; Chalise, Mukesh K.; Aggimarangsee, Nantiya; Feeroz, Mohammed M.; Grant, Richard; Allan, Jonathan S.; Putra, Arta; Wandia, I. Nengah; Watanabe, Robin; Kuller, LaRene; Thongsawat, Satawat; Chaiwarith, Romanee; Kyes, Randall C.; Linial, Maxine L.

2008-01-01

In Asia, contact between persons and nonhuman primates is widespread in multiple occupational and nonoccupational contexts. Simian foamy viruses (SFVs) are retroviruses that are prevalent in all species of nonhuman primates. To determine SFV prevalence in humans, we tested 305 persons who lived or worked around nonhuman primates in several South and Southeast Asian countries; 8 (2.6%) were confirmed SFV positive by Western blot and, for some, by PCR. The interspecies interactions that likely resulted in virus transmission were diverse; 5 macaque taxa were implicated as a potential source of infection. Phylogenetic analysis showed that SFV from 3 infected persons was similar to that from the nonhuman primate populations with which the infected persons reported contact. Thus, SFV infections are likely to be prevalent among persons who live or work near nonhuman primates in Asia. PMID:18680642

Surface-Enhanced Raman Scattering Spectroscopy for Label-Free Analysis of P. aeruginosa Quorum Sensing

PubMed Central

Bodelón, Gustavo; Montes-García, Verónica; Pérez-Juste, Jorge; Pastoriza-Santos, Isabel

2018-01-01

Bacterial quorum sensing systems regulate the production of an ample variety of bioactive extracellular compounds that are involved in interspecies microbial interactions and in the interplay between the microbes and their hosts. The development of new approaches for enabling chemical detection of such cellular activities is important in order to gain new insight into their function and biological significance. In recent years, surface-enhanced Raman scattering (SERS) spectroscopy has emerged as an ultrasensitive analytical tool employing rationally designed plasmonic nanostructured substrates. This review highlights recent advances of SERS spectroscopy for label-free detection and imaging of quorum sensing-regulated processes in the human opportunistic pathogen Pseudomonas aeruginosa. We also briefly describe the challenges and limitations of the technique and conclude with a summary of future prospects for the field. PMID:29868499

Ecological distribution and population physiology defined by proteomics in a natural microbial community

DOE Office of Scientific and Technical Information (OSTI.GOV)

Muller, R; Denef, Vincent; Kalnejals, Linda

An important challenge in microbial ecology is developing methods that simultaneously examine the physiology of organisms at the molecular level and their ecosystem level interactions in complex natural systems.We integrated extensive proteomic, geochemical, and biological information from 28 microbial communities collected from an acid mine drainage environment and representing a range of biofilm development stages and geochemical conditions to evaluate how the physiologies of the dominant and less abundant organisms change along environmental gradients. The initial colonist dominates across all environments, but its proteome changes between two stable states as communities diversify, implying that interspecies interactions affect this organism smore » metabolism. Its overall physiology is robust to abiotic environmental factors, but strong correlations exist between these factors and certain subsets of proteins, possibly accounting for its wide environmental distribution. Lower abundance populations are patchier in their distribution, and proteomic data indicate that their environmental niches may be constrained by specific sets of abiotic environmental factors. This research establishes an effective strategy to investigate ecological relationships between microbial physiology and the environment for whole communities in situ« less

Dark-bright soliton pairs: Bifurcations and collisions

NASA Astrophysics Data System (ADS)

Katsimiga, G. C.; Kevrekidis, P. G.; Prinari, B.; Biondini, G.; Schmelcher, P.

2018-04-01

The statics, stability, and dynamical properties of dark-bright soliton pairs are investigated here, motivated by applications in a homogeneous two-component repulsively interacting Bose-Einstein condensate. One of the intraspecies interaction coefficients is used as the relevant parameter controlling the deviation from the integrable Manakov limit. Two different families of stationary states are identified consisting of dark-bright solitons that are either antisymmetric (out-of-phase) or asymmetric (mass imbalanced) with respect to their bright soliton. Both of the above dark-bright configurations coexist at the integrable limit of equal intra and interspecies repulsions and are degenerate in that limit. However, they are found to bifurcate from it in a transcritical bifurcation. This bifurcation interchanges the stability properties of the bound dark-bright pairs rendering the antisymmetric states unstable and the asymmetric ones stable past the associated critical point (and vice versa before it). Finally, on the dynamical side, it is found that large kinetic energies and thus rapid soliton collisions are essentially unaffected by the intraspecies variation, while cases involving near equilibrium states or breathing dynamics are significantly modified under such a variation.

Ecological distribution and population physiology defined by proteomics in a natural microbial community

USGS Publications Warehouse

Mueller, Ryan S.; Denef, Vincent J.; Kalnejais, Linda H.; Suttle, K. Blake; Thomas, Brian C.; Wilmes, Paul; Smith, Richard L.; Nordstrom, D. Kirk; McCleskey, R. Blaine; Shah, Menesh B.; VerBekmoes, Nathan C.; Hettich, Robert L.; Banfield, Jillian F.

2010-01-01

An important challenge in microbial ecology is developing methods that simultaneously examine the physiology of organisms at the molecular level and their ecosystem level interactions in complex natural systems. We integrated extensive proteomic, geochemical, and biological information from 28 microbial communities collected from an acid mine drainage environment and representing a range of biofilm development stages and geochemical conditions to evaluate how the physiologies of the dominant and less abundant organisms change along environmental gradients. The initial colonist dominates across all environments, but its proteome changes between two stable states as communities diversify, implying that interspecies interactions affect this organism's metabolism. Its overall physiology is robust to abiotic environmental factors, but strong correlations exist between these factors and certain subsets of proteins, possibly accounting for its wide environmental distribution. Lower abundance populations are patchier in their distribution, and proteomic data indicate that their environmental niches may be constrained by specific sets of abiotic environmental factors. This research establishes an effective strategy to investigate ecological relationships between microbial physiology and the environment for whole communities in situ.

Analysis of nuclear export using photoactivatable GFP fusion proteins and interspecies heterokaryons.

PubMed

Nakrieko, Kerry-Ann; Ivanova, Iordanka A; Dagnino, Lina

2010-01-01

In this chapter, we review protocols for the analysis of nucleocytoplasmic shuttling of transcription factors and nuclear proteins, using two different approaches. The first involves the use of photoactivatable forms of the protein of interest by fusion to photoactivatable green fluorescent protein to follow its movement out of the nucleus by live-cell confocal microscopy. This methodology allows for the kinetic characterization of protein movements as well as measurement of steady-state levels. In a second procedure to assess the ability of a nuclear protein to move into and out of the nucleus, we describe the use of interspecies heterokaryon assays, which provide a measurement of steady-state distribution. These technologies are directly applicable to the analysis of nucleocytoplasmic movements not only of transcription factors, but also other nuclear proteins.

[An overview on swine influenza viruses].

PubMed

Yang, Shuai; Zhu, Wen-Fei; Shu, Yue-Long

2013-05-01

Swine influenza viruses (SIVs) are respiratory pathogens of pigs. They cause both economic bur den in livestock-dependent industries and serious global public health concerns in humans. Because of their dual susceptibility to human and avian influenza viruses, pigs are recognized as intermediate hosts for genetic reassortment and interspecies transmission. Subtypes H1N1, H1N2, and H3N2 circulate in swine populations around the world, with varied origin and genetic characteristics among different continents and regions. In this review, the role of pigs in evolution of influenza A viruses, the genetic evolution of SIVs and interspecies transmission of SIVs are described. Considering the possibility that pigs might produce novel influenza viruses causing more outbreaks and pandemics, routine epidemiological surveillance of influenza viruses in pig populations is highly recommended.

Chimeric mice with humanized liver: Application in drug metabolism and pharmacokinetics studies for drug discovery.

PubMed

Naritomi, Yoichi; Sanoh, Seigo; Ohta, Shigeru

2018-02-01

Predicting human drug metabolism and pharmacokinetics (PK) is key to drug discovery. In particular, it is important to predict human PK, metabolite profiles and drug-drug interactions (DDIs). Various methods have been used for such predictions, including in vitro metabolic studies using human biological samples, such as hepatic microsomes and hepatocytes, and in vivo studies using experimental animals. However, prediction studies using these methods are often inconclusive due to discrepancies between in vitro and in vivo results, and interspecies differences in drug metabolism. Further, the prediction methods have changed from qualitative to quantitative to solve these issues. Chimeric mice with humanized liver have been developed, in which mouse liver cells are mostly replaced with human hepatocytes. Since human drug metabolizing enzymes are expressed in the liver of these mice, they are regarded as suitable models for mimicking the drug metabolism and PK observed in humans; therefore, these mice are useful for predicting human drug metabolism and PK. In this review, we discuss the current state, issues, and future directions of predicting human drug metabolism and PK using chimeric mice with humanized liver in drug discovery. Copyright © 2017 The Japanese Society for the Study of Xenobiotics. Published by Elsevier Ltd. All rights reserved.

Data integration aids understanding of butterfly-host plant networks

NASA Astrophysics Data System (ADS)

Muto-Fujita, Ai; Takemoto, Kazuhiro; Kanaya, Shigehiko; Nakazato, Takeru; Tokimatsu, Toshiaki; Matsumoto, Natsushi; Kono, Mayo; Chubachi, Yuko; Ozaki, Katsuhisa; Kotera, Masaaki

2017-03-01

Although host-plant selection is a central topic in ecology, its general underpinnings are poorly understood. Here, we performed a case study focusing on the publicly available data on Japanese butterflies. A combined statistical analysis of plant-herbivore relationships and taxonomy revealed that some butterfly subfamilies in different families feed on the same plant families, and the occurrence of this phenomenon more than just by chance, thus indicating the independent acquisition of adaptive phenotypes to the same hosts. We consequently integrated plant-herbivore and plant-compound relationship data and conducted a statistical analysis to identify compounds unique to host plants of specific butterfly families. Some of the identified plant compounds are known to attract certain butterfly groups while repelling others. The additional incorporation of insect-compound relationship data revealed potential metabolic processes that are related to host plant selection. Our results demonstrate that data integration enables the computational detection of compounds putatively involved in particular interspecies interactions and that further data enrichment and integration of genomic and transcriptomic data facilitates the unveiling of the molecular mechanisms involved in host plant selection.

Data integration aids understanding of butterfly–host plant networks

PubMed Central

Muto-Fujita, Ai; Takemoto, Kazuhiro; Kanaya, Shigehiko; Nakazato, Takeru; Tokimatsu, Toshiaki; Matsumoto, Natsushi; Kono, Mayo; Chubachi, Yuko; Ozaki, Katsuhisa; Kotera, Masaaki

2017-01-01

Although host-plant selection is a central topic in ecology, its general underpinnings are poorly understood. Here, we performed a case study focusing on the publicly available data on Japanese butterflies. A combined statistical analysis of plant–herbivore relationships and taxonomy revealed that some butterfly subfamilies in different families feed on the same plant families, and the occurrence of this phenomenon more than just by chance, thus indicating the independent acquisition of adaptive phenotypes to the same hosts. We consequently integrated plant–herbivore and plant–compound relationship data and conducted a statistical analysis to identify compounds unique to host plants of specific butterfly families. Some of the identified plant compounds are known to attract certain butterfly groups while repelling others. The additional incorporation of insect–compound relationship data revealed potential metabolic processes that are related to host plant selection. Our results demonstrate that data integration enables the computational detection of compounds putatively involved in particular interspecies interactions and that further data enrichment and integration of genomic and transcriptomic data facilitates the unveiling of the molecular mechanisms involved in host plant selection. PMID:28262809

Genetic architecture of hybrid male sterility in Drosophila: analysis of intraspecies variation for interspecies isolation.

PubMed

Reed, Laura K; LaFlamme, Brooke A; Markow, Therese A

2008-08-27

The genetic basis of postzygotic isolation is a central puzzle in evolutionary biology. Evolutionary forces causing hybrid sterility or inviability act on the responsible genes while they still are polymorphic, thus we have to study these traits as they arise, before isolation is complete. Isofemale strains of D. mojavensis vary significantly in their production of sterile F(1) sons when females are crossed to D. arizonae males. We took advantage of the intraspecific polymorphism, in a novel design, to perform quantitative trait locus (QTL) mapping analyses directly on F(1) hybrid male sterility itself. We found that the genetic architecture of the polymorphism for hybrid male sterility (HMS) in the F(1) is complex, involving multiple QTL, epistasis, and cytoplasmic effects. The role of extensive intraspecific polymorphism, multiple QTL, and epistatic interactions in HMS in this young species pair shows that HMS is arising as a complex trait in this system. Directional selection alone would be unlikely to maintain polymorphism at multiple loci, thus we hypothesize that directional selection is unlikely to be the only evolutionary force influencing postzygotic isolation.

Restriction endonuclease analysis of chloroplast DNA in interspecies somatic Hybrids of Petunia.

PubMed

Kumar, A; Cocking, E C; Bovenberg, W A; Kool, A J

1982-12-01

Restriction endonuclease cleavage pattern analysis of chloroplast DNA (cpDNA) of three different interspecific somatic hybrid plants revealed that the cytoplasms of the hybrids contained only cpDNA of P. parodii. The somatic hybrid plants analysed were those between P. parodii (wild type) + P. hybrida (wild type); P. parodii (wild type)+P. inflata (cytoplasmic albino mutant); P. parodii (wild type) + P. parviflora (nuclear albino mutant). The presence of only P. parodii chloroplasts in the somatic hybrid of P. parodii + P. inflata is possibly due to the stringent selection used for somatic hybrid production. However, in the case of the two other somatic hybrids P. parodii + P. hybrida and P. parodii + P. parviflora it was not possible to determine whether the presence of only P. parodii chloroplasts in these somatic hybrid plants was due to the nature of the selection schemes used or simply occurred by chance. The relevance of such somatic hybrid material for the study of genomic-cytoplasmic interaction is discussed, as well as the use of restriction endonuclease fragment patterns for the analysis of taxonomic and evolutionary inter-relationships in the genus Petunia.

Kinetic theory of dark solitons with tunable friction.

PubMed

Hurst, Hilary M; Efimkin, Dmitry K; Spielman, I B; Galitski, Victor

2017-05-01

We study controllable friction in a system consisting of a dark soliton in a one-dimensional Bose-Einstein condensate coupled to a noninteracting Fermi gas. The fermions act as impurity atoms, not part of the original condensate, that scatter off of the soliton. We study semiclassical dynamics of the dark soliton, a particlelike object with negative mass, and calculate its friction coefficient. Surprisingly, it depends periodically on the ratio of interspecies (impurity-condensate) to intraspecies (condensate-condensate) interaction strengths. By tuning this ratio, one can access a regime where the friction coefficient vanishes. We develop a general theory of stochastic dynamics for negative-mass objects and find that their dynamics are drastically different from their positive-mass counterparts: they do not undergo Brownian motion. From the exact phase-space probability distribution function (i.e., in position and velocity), we find that both the trajectory and lifetime of the soliton are altered by friction, and the soliton can undergo Brownian motion only in the presence of friction and a confining potential. These results agree qualitatively with experimental observations by Aycock et al. [Proc. Natl. Acad. Sci. USA 114 , 2503 (2017)] in a similar system with bosonic impurity scatterers.

Kinetic theory of dark solitons with tunable friction

PubMed Central

Hurst, Hilary M.; Efimkin, Dmitry K.; Spielman, I. B.; Galitski, Victor

2018-01-01

We study controllable friction in a system consisting of a dark soliton in a one-dimensional Bose-Einstein condensate coupled to a noninteracting Fermi gas. The fermions act as impurity atoms, not part of the original condensate, that scatter off of the soliton. We study semiclassical dynamics of the dark soliton, a particlelike object with negative mass, and calculate its friction coefficient. Surprisingly, it depends periodically on the ratio of interspecies (impurity-condensate) to intraspecies (condensate-condensate) interaction strengths. By tuning this ratio, one can access a regime where the friction coefficient vanishes. We develop a general theory of stochastic dynamics for negative-mass objects and find that their dynamics are drastically different from their positive-mass counterparts: they do not undergo Brownian motion. From the exact phase-space probability distribution function (i.e., in position and velocity), we find that both the trajectory and lifetime of the soliton are altered by friction, and the soliton can undergo Brownian motion only in the presence of friction and a confining potential. These results agree qualitatively with experimental observations by Aycock et al. [Proc. Natl. Acad. Sci. USA 114, 2503 (2017)] in a similar system with bosonic impurity scatterers. PMID:29744482

Unraveling the Molecular Mechanisms Underlying the Nasopharyngeal Bacterial Community Structure.

PubMed

de Steenhuijsen Piters, Wouter A A; Bogaert, Debby

2016-02-02

The upper respiratory tract is colonized by a diverse array of commensal bacteria that harbor potential pathogens, such as Streptococcus pneumoniae. As long as the local microbial ecosystem-also called "microbiome"-is in balance, these potentially pathogenic bacterial residents cause no harm to the host. However, similar to macrobiological ecosystems, when the bacterial community structure gets perturbed, potential pathogens can overtake the niche and cause mild to severe infections. Recent studies using next-generation sequencing show that S. pneumoniae, as well as other potential pathogens, might be kept at bay by certain commensal bacteria, including Corynebacterium and Dolosigranulum spp. Bomar and colleagues are the first to explore a specific biological mechanism contributing to the antagonistic interaction between Corynebacterium accolens and S. pneumoniae in vitro [L. Bomar, S. D. Brugger, B. H. Yost, S. S. Davies, K. P. Lemon, mBio 7(1):e01725-15, 2016, doi:10.1128/mBio.01725-15]. The authors comprehensively show that C. accolens is capable of hydrolyzing host triacylglycerols into free fatty acids, which display antipneumococcal properties, suggesting that these bacteria might contribute to the containment of pneumococcus. This work exemplifies how molecular epidemiological findings can lay the foundation for mechanistic studies to elucidate the host-microbe and microbial interspecies interactions underlying the bacterial community structure. Next, translation of these results to an in vivo setting seems necessary to unveil the magnitude and importance of the observed effect in its natural, polymicrobial setting. Copyright © 2016 de Steenhuijsen Piters and Bogaert.

Unraveling the Molecular Mechanisms Underlying the Nasopharyngeal Bacterial Community Structure

PubMed Central

de Steenhuijsen Piters, Wouter A. A.

2016-01-01

ABSTRACT The upper respiratory tract is colonized by a diverse array of commensal bacteria that harbor potential pathogens, such as Streptococcus pneumoniae. As long as the local microbial ecosystem—also called “microbiome”—is in balance, these potentially pathogenic bacterial residents cause no harm to the host. However, similar to macrobiological ecosystems, when the bacterial community structure gets perturbed, potential pathogens can overtake the niche and cause mild to severe infections. Recent studies using next-generation sequencing show that S. pneumoniae, as well as other potential pathogens, might be kept at bay by certain commensal bacteria, including Corynebacterium and Dolosigranulum spp. Bomar and colleagues are the first to explore a specific biological mechanism contributing to the antagonistic interaction between Corynebacterium accolens and S. pneumoniae in vitro [L. Bomar, S. D. Brugger, B. H. Yost, S. S. Davies, K. P. Lemon, mBio 7(1):e01725-15, 2016, doi:10.1128/mBio.01725-15]. The authors comprehensively show that C. accolens is capable of hydrolyzing host triacylglycerols into free fatty acids, which display antipneumococcal properties, suggesting that these bacteria might contribute to the containment of pneumococcus. This work exemplifies how molecular epidemiological findings can lay the foundation for mechanistic studies to elucidate the host-microbe and microbial interspecies interactions underlying the bacterial community structure. Next, translation of these results to an in vivo setting seems necessary to unveil the magnitude and importance of the observed effect in its natural, polymicrobial setting. PMID:26838716

Dissection of the complex genetic basis of craniofacial anomalies using haploid genetics and interspecies hybrids in Nasonia wasps

PubMed Central

Werren, John H.; Cohen, Lorna B.; Gadau, Juergen; Ponce, Rita; Baudry, Emmanuelle; Lynch, Jeremy A.

2016-01-01

The animal head is a complex structure where numerous sensory, structural and alimentary structures are concentrated and integrated, and its ontogeny requires precise and delicate interactions among genes, cells, and tissues. Thus, it is perhaps unsurprising that craniofacial abnormalities are among the most common birth defects in people, or that these defects have a complex genetic basis involving interactions among multiple loci. Developmental processes that depend on such epistatic interactions become exponentially more difficult to study in diploid organisms as the number of genes involved increases. Here, we present hybrid haploid males of the wasp species pair Nasonia vitripennis and Nasonia giraulti, which have distinct male head morphologies, as a genetic model of craniofacial development that possesses the genetic advantages of haploidy, along with many powerful genomic tools. Viable, fertile hybrids can be made between the species, and quantitative trail loci related to shape differences have been identified. In addition, a subset of hybrid males show head abnormalities, including clefting at the midline and asymmetries. Crucially, epistatic interactions among multiple loci underlie several developmental differences and defects observed in the F2 hybrid males. Furthermore, we demonstrate an introgression of a chromosomal region from N. giraulti into N. vitripennis that shows an abnormality in relative eye size, which maps to a region containing a major QTL for this trait. Therefore, the genetic sources of head morphology can, in principle, be identified by positional cloning. Thus, Nasonia is well positioned to be a uniquely powerful model invertebrate system with which to probe both development and complex genetics of craniofacial patterning and defects. PMID:26721604

Interspecific relationships between American coots and waterfowl during fall migration

USGS Publications Warehouse

Eddleman, William R.; Patterson, Craig T.; Knopf, Fritz L.

1985-01-01

Interactions between American Coots (Fulica americana) and water-fowl during the breeding season are well-documented (Ryder 1959, Nudds 1981). Ducks and coots use similar nesting, feeding, brooding, and loafing sites during the breeding season (Munro 1939, Sooter 1945, Ryder 1959). Coots create potential nest sites, repulse predators, provide predation buffers for ducks (Sooter 1945; Ryder 1958, 1959), and may also destroy eggs and young of other marsh-nesting birds (Munro 1937, Burger 1973, McNicholl 1975). Coots, ducks, and swans often feed cooperatively (Ryder 1959, Anderson 1974, Ryan 1981); and American Wigeon (Anas americana) and Gadwell () may rob feeding coots (Knapton and Knudsen 1978, Ryan 1981). Interspecies aggression between coots and waterfowl usually occurs when ducks approach coot nests or broods (Ryan and Dinsmore 1979). Despite these interactions, the numbers of duck broods produced in areas in Utah with nesting coots and in areas where coots have been removed were similar (Ryder 1958, 1961). Densities of coots and ducks, and brood counts of coots and ducks for a 26-year period in Saskatchewan also indicated no significant relationship between numbers of coots and waterfowl (Nudds 1981). Coots and waterfowl from large areas of breeding habitat concentrate on smaller areas during the nonbreeding season (Weller 1975:102). These species may also change diets and habitats during migration and while wintering (Weller 1975). This study documents associations between waterfowl and coots during fall migration and examines feeding and behavioral interactions between coots and waterfowl in mixed flocks. Specifically, we (1) describe temporal and spatial overlap among migrations of coots and waterfowl, (2) present behavioral interactions among species, and (3) document food habits of birds feeding sympatrically during fall migration in Oklahoma.

Predicting carcinogenicity of diverse chemicals using probabilistic neural network modeling approaches

DOE Office of Scientific and Technical Information (OSTI.GOV)

Singh, Kunwar P., E-mail: kpsingh_52@yahoo.com; Environmental Chemistry Division, CSIR-Indian Institute of Toxicology Research, Post Box 80, Mahatma Gandhi Marg, Lucknow 226 001; Gupta, Shikha

Robust global models capable of discriminating positive and non-positive carcinogens; and predicting carcinogenic potency of chemicals in rodents were developed. The dataset of 834 structurally diverse chemicals extracted from Carcinogenic Potency Database (CPDB) was used which contained 466 positive and 368 non-positive carcinogens. Twelve non-quantum mechanical molecular descriptors were derived. Structural diversity of the chemicals and nonlinearity in the data were evaluated using Tanimoto similarity index and Brock–Dechert–Scheinkman statistics. Probabilistic neural network (PNN) and generalized regression neural network (GRNN) models were constructed for classification and function optimization problems using the carcinogenicity end point in rat. Validation of the models wasmore » performed using the internal and external procedures employing a wide series of statistical checks. PNN constructed using five descriptors rendered classification accuracy of 92.09% in complete rat data. The PNN model rendered classification accuracies of 91.77%, 80.70% and 92.08% in mouse, hamster and pesticide data, respectively. The GRNN constructed with nine descriptors yielded correlation coefficient of 0.896 between the measured and predicted carcinogenic potency with mean squared error (MSE) of 0.44 in complete rat data. The rat carcinogenicity model (GRNN) applied to the mouse and hamster data yielded correlation coefficient and MSE of 0.758, 0.71 and 0.760, 0.46, respectively. The results suggest for wide applicability of the inter-species models in predicting carcinogenic potency of chemicals. Both the PNN and GRNN (inter-species) models constructed here can be useful tools in predicting the carcinogenicity of new chemicals for regulatory purposes. - Graphical abstract: Figure (a) shows classification accuracies (positive and non-positive carcinogens) in rat, mouse, hamster, and pesticide data yielded by optimal PNN model. Figure (b) shows generalization and predictive abilities of the interspecies GRNN model to predict the carcinogenic potency of diverse chemicals. - Highlights: • Global robust models constructed for carcinogenicity prediction of diverse chemicals. • Tanimoto/BDS test revealed structural diversity of chemicals and nonlinearity in data. • PNN/GRNN successfully predicted carcinogenicity/carcinogenic potency of chemicals. • Developed interspecies PNN/GRNN models for carcinogenicity prediction. • Proposed models can be used as tool to predict carcinogenicity of new chemicals.« less

Bacterial discrimination by Dictyostelid amoebae reveals the complexity of ancient interspecies interactions

PubMed Central

Nasser, Waleed; Santhanam, Balaji; Miranda, Edward Roshan; Parikh, Anup; Juneja, Kavina; Rot, Gregor; Dinh, Chris; Chen, Rui; Zupan, Blaz; Shaulsky, Gad; Kuspa, Adam

2014-01-01

Background Amoebae and bacteria interact within predator/prey and host/pathogen relationships, but the general response of amoeba to bacteria is not well understood. The amoeba Dictyostelium discoideum feeds on, and is colonized by diverse bacterial species including Gram-positive [Gram(+)] and Gram-negative [Gram(−)] bacteria, two major groups of bacteria that differ in structure and macromolecular composition. Results Transcriptional profiling of D. discoideum revealed sets of genes whose expression is enriched in amoebae interacting with different species of bacteria, including sets that appear specific to amoebae interacting with Gram(+), or with Gram(−) bacteria. In a genetic screen utilizing the growth of mutant amoebae on a variety of bacteria as a phenotypic readout, we identified amoebal genes that are only required for growth on Gram(+) bacteria, including one that encodes the cell surface protein gp130, as well as several genes that are only required for growth on Gram(−) bacteria including one that encodes a putative lysozyme, AlyL. These genes are required for parts of the transcriptional response of wild-type amoebae, and this allowed their classification into potential response pathways. Conclusions We have defined genes that are critical for amoebal survival during feeding on Gram(+), or Gram(−), bacteria which we propose form part of a regulatory network that allows D. discoideum to elicit specific cellular responses to different species of bacteria in order to optimize survival. PMID:23664307

Let there be bioluminescence – Development of a biophotonic imaging platform for in situ analyses of oral biofilms in animal models

PubMed Central

Merritt, Justin; Senpuku, Hidenobu; Kreth, Jens

2016-01-01

Summary In the current study, we describe a novel biophotonic imaging-based reporter system that is particularly useful for the study of virulence in polymicrobial infections and interspecies interactions within animal models. A suite of luciferase enzymes was compared using three early colonizing species of the human oral flora (Streptococcus mutans, Streptococcus gordonii, and Streptococcus sanguinis) to determine the utility of the different reporters for multiplexed imaging studies in vivo. Using the multiplex approach, we were able to track individual species within a dual species oral infection model in mice with both temporal and spatial resolution. We also demonstrate how biophotonic imaging of multiplexed luciferase reporters could be adapted for real-time quantification of bacterial gene expression in situ. By creating an inducible dual-luciferase expressing reporter strain of S. mutans, we were able to exogenously control and measure expression of nlmAB (encoding the bacteriocin mutacin IV) within mice to assess its importance for the persistence ability of S. mutans in the oral cavity. The imaging system described in the current study circumvents many of the inherent limitations of current animal model systems, which should now make it feasible to test hypotheses that were previously impractical to model. PMID:26119252

Identification of Recombinant Human Rhinovirus A and C in Circulating Strains from Upper and Lower Respiratory Infections

PubMed Central

Kim, Hak; Kim, Kisoon; Kim, Dae-Won; Jung, Hee-Dong; Min Cheong, Hyang; Kim, Ki Hwan; Soo Kim, Dong; Kim, You-Jin

2013-01-01

Human rhinoviruses (HRVs), in the Enterovirus genus within the family Picornaviridae, are a highly prevalent cause of acute respiratory infection (ARI). Enteroviruses are genetically highly variable, and recombination between serotypes is known to be a major contribution to their diversity. Recently it was reported that recombination events in HRVs cause the diversity of HRV-C. This study analyzed parts of the viral genes spanning the 5′ non- coding region (NCR) through to the viral protein (VP) encoding sequences of 105 HRV field isolates from 51 outpatient cases of Acute Respiratory Infectious Network (ARINET) and 54 inpatient cases of severe lower respiratory infection (SLRI) surveillance, in order to identify recombination in field samples. When analyzing parts of the 5′NCR and VP4/VP2 encoding sequences, we found intra- and interspecies recombinants in field strains of HRV-A and -C. Nineteen cases of recombination events (18.1%) were found among 105 field strains. For HRV-A, there were five cases (4.8%) of intraspecies recombination events and three cases (2.8%) of interspecies recombination events. For HRV-C, there were four cases (3.8%) of intraspecies recombination events and seven cases (6.7%) of interspecies recombination events. Recombination events were significantly more frequently observed in the ARINET samples (18 cases) than in the SLRI samples (1 case; P< 0.0001). The recombination breakpoints were located in nucleotides (nt) 472–554, which comprise stem-loop 5 in the internal ribosomal entry site (IRES), based on the HRV-B 35 sequence (accession no. FJ445187). Our findings regarding genomic recombination in circulating HRV-A and -C strains suggest that recombination might play a role in HRV fitness and could be a possible determinant of disease severity caused by various HRV infections in patients with ARI. PMID:23826363

Multi-phenology WorldView-2 imagery improves remote sensing of savannah tree species

NASA Astrophysics Data System (ADS)

Madonsela, Sabelo; Cho, Moses Azong; Mathieu, Renaud; Mutanga, Onisimo; Ramoelo, Abel; Kaszta, Żaneta; Kerchove, Ruben Van De; Wolff, Eléonore

2017-06-01

Biodiversity mapping in African savannah is important for monitoring changes and ensuring sustainable use of ecosystem resources. Biodiversity mapping can benefit from multi-spectral instruments such as WorldView-2 with very high spatial resolution and a spectral configuration encompassing important spectral regions not previously available for vegetation mapping. This study investigated i) the benefits of the eight-band WorldView-2 (WV-2) spectral configuration for discriminating tree species in Southern African savannah and ii) if multiple-images acquired at key points of the typical phenological development of savannahs (peak productivity, transition to senescence) improve on tree species classifications. We first assessed the discriminatory power of WV-2 bands using interspecies-Spectral Angle Mapper (SAM) via Band Add-On procedure and tested the spectral capability of WorldView-2 against simulated IKONOS for tree species classification. The results from interspecies-SAM procedure identified the yellow and red bands as the most statistically significant bands (p = 0.000251 and p = 0.000039 respectively) in the discriminatory power of WV-2 during the transition from wet to dry season (April). Using Random Forest classifier, the classification scenarios investigated showed that i) the 8-bands of the WV-2 sensor achieved higher classification accuracy for the April date (transition from wet to dry season, senescence) compared to the March date (peak productivity season) ii) the WV-2 spectral configuration systematically outperformed the IKONOS sensor spectral configuration and iii) the multi-temporal approach (March and April combined) improved the discrimination of tress species and produced the highest overall accuracy results at 80.4%. Consistent with the interspecies-SAM procedure, the yellow (605 nm) band also showed a statistically significant contribution in the improved classification accuracy from WV-2. These results highlight the mapping opportunities presented by WV-2 data for monitoring the distribution status of e.g. species often harvested by local communities (e.g. Sclerocharya birrea), encroaching species, or species-specific tree losses induced by elephants.

Inter-Species Grafting Caused Extensive and Heritable Alterations of DNA Methylation in Solanaceae Plants

PubMed Central

Lin, Yan; Ma, Yiqiao; Liu, Gang; Yu, Xiaoming; Zhong, Silin; Liu, Bao

2013-01-01

Background Grafting has been extensively used to enhance the performance of horticultural crops. Since Charles Darwin coined the term “graft hybrid” meaning that asexual combination of different plant species may generate products that are genetically distinct, highly discrepant opinions exist supporting or against the concept. Recent studies have documented that grafting enables exchanges of both RNA and DNA molecules between the grafting partners, thus providing a molecular basis for grafting-induced genetic variation. DNA methylation is known as prone to alterations as a result of perturbation of internal and external conditions. Given characteristics of grafting, it is interesting to test whether the process may cause an alteration of this epigenetic marker in the grafted organismal products. Methodology/Principal Findings We analyzed relative global DNA methylation levels and locus-specific methylation patterns by the MSAP marker and locus-specific bisulfite-sequencing in the seed plants (wild-type controls), self- and hetero-grafted scions/rootstocks, selfed progenies of scions and their seed-plant controls, involving three Solanaceae species. We quantified expression of putative genes involved in establishing and/or maintaining DNA methylation by q-(RT)-PCR. We found that (1) hetero-grafting caused extensive alteration of DNA methylation patterns in a locus-specific manner, especially in scions, although relative methylation levels remain largely unaltered; (2) the altered methylation patterns in the hetero-grafting-derived scions could be inherited to sexual progenies with some sites showing further alterations or revisions; (3) hetero-grafting caused dynamic changes in steady-state transcript abundance of genes encoding for a set of enzymes functionally relevant to DNA methylation. Conclusions/Significance Our results demonstrate that inter-species grafting in plants could produce extensive and heritable alterations in DNA methylation. We suggest that these readily altered, yet heritable, epigenetic modifications due to interspecies hetero-grafting may shed one facet of insight into the molecular underpinnings for the still contentious concept of graft hybrid. PMID:23614002

Does interspecies hybridization affect the host specificity of parasites in cyprinid fish?

PubMed

Simková, Andrea; Dávidová, Martina; Papoušek, Ivo; Vetešník, Lukáš

2013-04-12

Host specificity varies among parasite species. Some parasites are strictly host-specific, others show a specificity for congeneric or non-congeneric phylogenetically related host species, whilst some others are non-specific (generalists). Two cyprinids, Cyprinus carpio and Carassius gibelio, plus their respective hybrids were investigated for metazoan parasites. The aim of this study was to analyze whether interspecies hybridization affects host specificity. The different degrees of host specificity within a phylogenetic framework were taken into consideration (i.e. strict specialist, intermediate specialist, and intermediate generalist). Fish were collected during harvesting the pond and identified using meristic traits and molecular markers. Metazoan parasite species were collected. Host specificity of parasites was determined using the following classification: strict specialist, intermediate specialist, intermediate generalist and generalist. Parasite species richness was compared between parental species and their hybrids. The effect of host species on abundance of parasites differing in host specificity was tested. Hybrids harbored more different parasite species but their total parasite abundance was lower in comparison with parental species. Interspecies hybridization affected the host specificity of ecto- and endoparasites. Parasite species exhibiting different degrees of host specificity for C. carpio and C. gibelio were also present in hybrids. The abundance of strict specialists of C. carpio was significantly higher in parental species than in hybrids. Intermediate generalists parasitizing C. carpio and C. gibelio as two phylogenetically closely related host species preferentially infected C. gibelio when compared to C. carpio, based on prevalence and maximum intensity of infection. Hybrids were less infected by intermediate generalists when compared to C. gibelio. This finding does not support strict co-adaptation between host and parasite genotypes resulting in narrow host specificity, and showed that hybrid genotypes are susceptible to parasites exhibiting host specificity. The immune mechanisms specific to parental species might represent potential mechanisms explaining the low abundance of parasites in C. gibelio x C. carpio hybrids.

Interspecies modulation of bacterial development through iron competition and siderophore piracy

PubMed Central

Traxler, Matthew F.; Seyedsayamdost, Mohammad R.; Clardy, Jon; Kolter, Roberto

2012-01-01

Summary While soil-dwelling actinomycetes are renowned for secreting natural products, little is known about the roles of these molecules in mediating actinomycete interactions. In a previous co-culture screen, we found that one actinomycete, Amycolatopsis sp. AA4, inhibited aerial hyphae formation in adjacent colonies of Streptomyces coelicolor. A siderophore, amychelin, mediated this developmental arrest. Here we present genetic evidence that confirms the role of the amc locus in the production of amychelin and in the inhibition of S. coelicolor development. We further characterize the Amycolatopsis sp. AA4 - S. coelicolor interaction by examining expression of developmental and iron acquisition genes over time in co-culture. Manipulation of iron availability and/or growth near Amycolatopsis sp. AA4 led to alterations in expression of the critical developmental gene bldN, and other key down-stream genes in the S. coelicolor transcriptional cascade. In Amycolatopsis sp. AA4, siderophore genes were down-regulated when grown near S. coelicolor, leading us to find that deferrioxamine E, produced by S. coelicolor, could be readily utilized by Amycolatopsis sp. AA4. Collectively these results suggest that competition for iron via siderophore piracy and species-specific siderophores can alter patterns of gene expression and morphological differentiation during actinomycete interactions. PMID:22931126

Interspecies modulation of bacterial development through iron competition and siderophore piracy.

PubMed

Traxler, Matthew F; Seyedsayamdost, Mohammad R; Clardy, Jon; Kolter, Roberto

2012-11-01

While soil-dwelling actinomycetes are renowned for secreting natural products, little is known about the roles of these molecules in mediating actinomycete interactions. In a previous co-culture screen, we found that one actinomycete, Amycolatopsis sp. AA4, inhibited aerial hyphae formation in adjacent colonies of Streptomyces coelicolor. A siderophore, amychelin, mediated this developmental arrest. Here we present genetic evidence that confirms the role of the amc locus in the production of amychelin and in the inhibition of S. coelicolor development. We further characterize the Amycolatopsis sp. AA4 - S. coelicolor interaction by examining expression of developmental and iron acquisition genes over time in co-culture. Manipulation of iron availability and/or growth near Amycolatopsis sp. AA4 led to alterations in expression of the critical developmental gene bldN, and other key downstream genes in the S. coelicolor transcriptional cascade. In Amycolatopsis sp. AA4, siderophore genes were downregulated when grown near S. coelicolor, leading us to find that deferrioxamine E, produced by S. coelicolor, could be readily utilized by Amycolatopsis sp. AA4. Collectively these results suggest that competition for iron via siderophore piracy and species-specific siderophores can alter patterns of gene expression and morphological differentiation during actinomycete interactions. © 2012 Blackwell Publishing Ltd.

Evidence for quorum sensing and differential metabolite production by a marine bacterium in response to DMSP.

PubMed

Johnson, Winifred M; Kido Soule, Melissa C; Kujawinski, Elizabeth B

2016-09-01

Microbes, the foundation of the marine foodweb, do not function in isolation, but rather rely on molecular level interactions among species to thrive. Although certain types of interactions between autotrophic and heterotrophic microorganisms have been well documented, the role of specific organic molecules in regulating inter-species relationships and supporting growth are only beginning to be understood. Here, we examine one such interaction by characterizing the metabolic response of a heterotrophic marine bacterium, Ruegeria pomeroyi DSS-3, to growth on dimethylsulfoniopropionate (DMSP), an abundant organosulfur metabolite produced by phytoplankton. When cultivated on DMSP, R. pomeroyi synthesized a quorum-sensing molecule, N-(3-oxotetradecanoyl)-l-homoserine lactone, at significantly higher levels than during growth on propionate. Concomitant with the production of a quorum-sensing molecule, we observed differential production of intra- and extracellular metabolites including glutamine, vitamin B2 and biosynthetic intermediates of cyclic amino acids. Our metabolomics data indicate that R. pomeroyi changes regulation of its biochemical pathways in a manner that is adaptive for a cooperative lifestyle in the presence of DMSP, in anticipation of phytoplankton-derived nutrients and higher microbial density. This behavior is likely to occur on sinking marine particles, indicating that this response may impact the fate of organic matter.

Production of rhesus monkey cloned embryos expressing monomeric red fluorescent protein by interspecies somatic cell nuclear transfer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhu, Hai-Ying; Kang, Jin-Dan; Li, Suo

2014-02-21

Highlights: • Rhesus monkey cells were electroporated with a plasmid containing mRFP1, and an mRFP1-expressing cell line was generated. • For the first time, mRFP1-expressing rhesus monkey cells were used as donor cells for iSCNT. • The effect of VPA on the development of embryos cloned using iSCNT was determined. - Abstract: Interspecies somatic cell nuclear transfer (iSCNT) is a promising method to clone endangered animals from which oocytes are difficult to obtain. Monomeric red fluorescent protein 1 (mRFP1) is an excellent selection marker for transgenically modified cloned embryos during somatic cell nuclear transfer (SCNT). In this study, mRFP-expressing rhesusmore » monkey cells or porcine cells were transferred into enucleated porcine oocytes to generate iSCNT and SCNT embryos, respectively. The development of these embryos was studied in vitro. The percentage of embryos that underwent cleavage did not significantly differ between iSCNT and SCNT embryos (P > 0.05; 71.53% vs. 80.30%). However, significantly fewer iSCNT embryos than SCNT embryos reached the blastocyst stage (2.04% vs. 10.19%, P < 0.05). Valproic acid was used in an attempt to increase the percentage of iSCNT embryos that developed to the blastocyst stage. However, the percentages of embryos that underwent cleavage and reached the blastocyst stage were similar between untreated iSCNT embryos and iSCNT embryos treated with 2 mM valproic acid for 24 h (72.12% vs. 70.83% and 2.67% vs. 2.35%, respectively). These data suggest that porcine-rhesus monkey interspecies embryos can be generated that efficiently express mRFP1. However, a significantly lower proportion of iSCNT embryos than SCNT embryos reach the blastocyst stage. Valproic acid does not increase the percentage of porcine-rhesus monkey iSCNT embryos that reach the blastocyst stage. The mechanisms underling nuclear reprogramming and epigenetic modifications in iSCNT need to be investigated further.« less

On the distribution of interspecies correlation for Markov models of character evolution on Yule trees.

PubMed

Mulder, Willem H; Crawford, Forrest W

2015-01-07

Efforts to reconstruct phylogenetic trees and understand evolutionary processes depend fundamentally on stochastic models of speciation and mutation. The simplest continuous-time model for speciation in phylogenetic trees is the Yule process, in which new species are "born" from existing lineages at a constant rate. Recent work has illuminated some of the structural properties of Yule trees, but it remains mostly unknown how these properties affect sequence and trait patterns observed at the tips of the phylogenetic tree. Understanding the interplay between speciation and mutation under simple models of evolution is essential for deriving valid phylogenetic inference methods and gives insight into the optimal design of phylogenetic studies. In this work, we derive the probability distribution of interspecies covariance under Brownian motion and Ornstein-Uhlenbeck models of phenotypic change on a Yule tree. We compute the probability distribution of the number of mutations shared between two randomly chosen taxa in a Yule tree under discrete Markov mutation models. Our results suggest summary measures of phylogenetic information content, illuminate the correlation between site patterns in sequences or traits of related organisms, and provide heuristics for experimental design and reconstruction of phylogenetic trees. Copyright © 2014 Elsevier Ltd. All rights reserved.

Interspecies quantitative structure-activity relationships (QSARs) for eco-toxicity screening of chemicals: the role of physicochemical properties.

PubMed

Furuhama, A; Hasunuma, K; Aoki, Y

2015-01-01

In addition to molecular structure profiles, descriptors based on physicochemical properties are useful for explaining the eco-toxicities of chemicals. In a previous study we reported that a criterion based on the difference between the partition coefficient (log POW) and distribution coefficient (log D) values of chemicals enabled us to identify aromatic amines and phenols for which interspecies relationships with strong correlations could be developed for fish-daphnid and algal-daphnid toxicities. The chemicals that met the log D-based criterion were expected to have similar toxicity mechanisms (related to membrane penetration). Here, we investigated the applicability of log D-based criteria to the eco-toxicity of other kinds of chemicals, including aliphatic compounds. At pH 10, use of a log POW - log D > 0 criterion and omission of outliers resulted in the selection of more than 100 chemicals whose acute fish toxicities or algal growth inhibition toxicities were almost equal to their acute daphnid toxicities. The advantage of log D-based criteria is that they allow for simple, rapid screening and prioritizing of chemicals. However, inorganic molecules and chemicals containing certain structural elements cannot be evaluated, because calculated log D values are unavailable.

Control of membrane biofouling in MBR for wastewater treatment by quorum quenching bacteria encapsulated in microporous membrane.

PubMed

Oh, Hyun-Suk; Yeon, Kyung-Min; Yang, Cheon-Seok; Kim, Sang-Ryoung; Lee, Chung-Hak; Park, Son Young; Han, Jong Yun; Lee, Jung-Kee

2012-05-01

Recently, enzymatic quorum quenching has proven its potential as an innovative approach for biofouling control in the membrane bioreactor (MBR) for advanced wastewater treatment. However, practical issues on the cost and stability of enzymes are yet to be solved, which requires more effective quorum quenching methods. In this study, a novel quorum quenching strategy, interspecies quorum quenching by bacterial cell, was elaborated and proved to be efficient and economically feasible biofouling control in MBR. A recombinant Escherichia coli which producing N-acyl homoserine lactonase or quorum quenching Rhodococcus sp. isolated from a real MBR plant was encapsulated inside the lumen of microporous hollow fiber membrane, respectively. The porous membrane containing these functional bacteria (i.e., "microbial-vessel") was put into the submerged MBR to alleviate biofouling on the surface of filtration membrane. The effect of biofouling inhibition by the microbial-vessel was evaluated over 80 days of MBR operation. Successful control of biofouling in a laboratory scale MBR suggests that the biofouling control through the interspecies quorum quenching could be expanded to the plant scale of MBR and various environmental engineering systems with economic feasibility. © 2012 American Chemical Society

Emergence of Human G2P[4] Rotaviruses in the Post-vaccination Era in South Korea: Footprints of Multiple Interspecies Re-assortment Events.

PubMed

Thanh, Hien Dang; Tran, Van Trung; Lim, Inseok; Kim, Wonyong

2018-04-16

After the introduction of two global rotavirus vaccines, RotaTeq in 2007 and Rotarix in 2008 in South Korea, G1[P8] rotavirus was the major rotavirus genotype in the country until 2012. However, in this study, an emergence of G2P[4] as the dominant genotype during the 2013 to 2015 season has been reported. Genetic analysis revealed that these viruses had typical DS-1-like genotype constellation and showed evidence of re-assortment in one or more genome segments, including the incorporation of NSP4 genes from strains B-47/2008 from a cow and R4/Haryana/2007 from a buffalo in India, and the VP1 and VP3 genes from strain GO34/1999 from a goat in Bangladesh. Compared to the G2 RotaTeq vaccine strain, 17-24 amino acid changes, specifically A87T, D96N, S213D, and S242N substitutions in G2 epitopes, were observed. These results suggest that multiple interspecies re-assortment events might have contributed to the emergence of G2P[4] rotaviruses in the post-vaccination era in South Korea.

Interspecies variation of Kitasatospora recifensis endophytic from yam bean producing thermostable amylases in alternative media.

PubMed

Stamford, Tania Lucia Montenegro; Stamford, Thayza Christina Montenegro; Stamford, Newton Pereira; Santos, Carolina Etienne Rosália Silva; de Lyra, Maria do Carmo Catanho Pereira; Ha-Park, Yong; Bae, Jin-Won; Araújo, Janete Magali

2007-12-01

An endophytic actinomycete isolated from tubers of yam beam (Pachyrhizus erosus L. Urban) was classified as a novel species nominated Kitasatospora recifensis based in phenotypic and genotypic analysis (16S rDNA gene sequence). Monosporic culture using specific ISP2 media revealed three interspecies, which were identified by DNA southern hybridization (Wild strain 13817 W, Aerial Mycelium strain 13817 AM and Vegetative Mycelium strain 13817 VM). The strains were tested for the production of amylolitic enzymes in alternative media. Maximum yields for both enzymes were observed in starch-casein. Higher α-amylase was obtained with strain 13817 W in starch-urea, and amyloglucosidase with strain 13817 AM in starch-ammonium that are economic sources and may be important for industrial purposes. Type strain (DAUFPE 13817(T) = KCTC 9972(T )= DSM 44943(T)).

Hybridization and adaptive evolution of diverse Saccharomyces species for cellulosic biofuel production

DOE PAGES

Peris, David; Moriarty, Ryan V.; Alexander, William G.; ...

2017-03-27

Here, lignocellulosic biomass is a common resource across the globe, and its fermentation offers a promising option for generating renewable liquid transportation fuels. The deconstruction of lignocellulosic biomass releases sugars that can be fermented by microbes, but these processes also produce fermentation inhibitors, such as aromatic acids and aldehydes. Several research projects have investigated lignocellulosic biomass fermentation by the baker’s yeast Saccharomyces cerevisiae. Most projects have taken synthetic biological approaches or have explored naturally occurring diversity in S. cerevisiae to enhance stress tolerance, xylose consumption, or ethanol production. Despite these efforts, improved strains with new properties are needed. In othermore » industrial processes, such as wine and beer fermentation, interspecies hybrids have combined important traits from multiple species, suggesting that interspecies hybridization may also offer potential for biofuel research.« less

Promoting Interspecies Electron Transfer with Biochar

PubMed Central

Chen, Shanshan; Rotaru, Amelia-Elena; Shrestha, Pravin Malla; Malvankar, Nikhil S.; Liu, Fanghua; Fan, Wei; Nevin, Kelly P.; Lovley, Derek R.

2014-01-01

Biochar, a charcoal-like product of the incomplete combustion of organic materials, is an increasingly popular soil amendment designed to improve soil fertility. We investigated the possibility that biochar could promote direct interspecies electron transfer (DIET) in a manner similar to that previously reported for granular activated carbon (GAC). Although the biochars investigated were 1000 times less conductive than GAC, they stimulated DIET in co-cultures of Geobacter metallireducens with Geobacter sulfurreducens or Methanosarcina barkeri in which ethanol was the electron donor. Cells were attached to the biochar, yet not in close contact, suggesting that electrons were likely conducted through the biochar, rather than biological electrical connections. The finding that biochar can stimulate DIET may be an important consideration when amending soils with biochar and can help explain why biochar may enhance methane production from organic wastes under anaerobic conditions. PMID:24846283

Hydrodynamic flow of ions and atoms in partially ionized plasmas.

PubMed

Nemirovsky, R A; Fredkin, D R; Ron, A

2002-12-01

We have derived the hydrodynamic equations of motion for a partially ionized plasma, when the ionized component and the neutral components have different flow velocities and kinetic temperatures. Starting from the kinetic equations for a gas of ions and a gas of atoms we have considered various processes of encounters between the two species: self-collisions, interspecies collisions, ionization, recombination, and charge exchange. Our results were obtained by developing a general approach for the hydrodynamics of a gas in a binary mixture, in particular when the components drift with respect to each other. This was applied to a partially ionized plasma, when the neutral-species gas and the charged-species gas have separate velocities. We have further suggested a generalized version of the relaxation time approximation and obtained the contributions of the interspecies encounters to the transport equations.

Hybridization and adaptive evolution of diverse Saccharomyces species for cellulosic biofuel production

DOE Office of Scientific and Technical Information (OSTI.GOV)

Peris, David; Moriarty, Ryan V.; Alexander, William G.

Here, lignocellulosic biomass is a common resource across the globe, and its fermentation offers a promising option for generating renewable liquid transportation fuels. The deconstruction of lignocellulosic biomass releases sugars that can be fermented by microbes, but these processes also produce fermentation inhibitors, such as aromatic acids and aldehydes. Several research projects have investigated lignocellulosic biomass fermentation by the baker’s yeast Saccharomyces cerevisiae. Most projects have taken synthetic biological approaches or have explored naturally occurring diversity in S. cerevisiae to enhance stress tolerance, xylose consumption, or ethanol production. Despite these efforts, improved strains with new properties are needed. In othermore » industrial processes, such as wine and beer fermentation, interspecies hybrids have combined important traits from multiple species, suggesting that interspecies hybridization may also offer potential for biofuel research.« less

A review on computational systems biology of pathogen–host interactions

PubMed Central

Durmuş, Saliha; Çakır, Tunahan; Özgür, Arzucan; Guthke, Reinhard

2015-01-01

Pathogens manipulate the cellular mechanisms of host organisms via pathogen–host interactions (PHIs) in order to take advantage of the capabilities of host cells, leading to infections. The crucial role of these interspecies molecular interactions in initiating and sustaining infections necessitates a thorough understanding of the corresponding mechanisms. Unlike the traditional approach of considering the host or pathogen separately, a systems-level approach, considering the PHI system as a whole is indispensable to elucidate the mechanisms of infection. Following the technological advances in the post-genomic era, PHI data have been produced in large-scale within the last decade. Systems biology-based methods for the inference and analysis of PHI regulatory, metabolic, and protein–protein networks to shed light on infection mechanisms are gaining increasing demand thanks to the availability of omics data. The knowledge derived from the PHIs may largely contribute to the identification of new and more efficient therapeutics to prevent or cure infections. There are recent efforts for the detailed documentation of these experimentally verified PHI data through Web-based databases. Despite these advances in data archiving, there are still large amounts of PHI data in the biomedical literature yet to be discovered, and novel text mining methods are in development to unearth such hidden data. Here, we review a collection of recent studies on computational systems biology of PHIs with a special focus on the methods for the inference and analysis of PHI networks, covering also the Web-based databases and text-mining efforts to unravel the data hidden in the literature. PMID:25914674

Visualization of Microbiota in Tick Guts by Whole-mount In Situ Hybridization.

PubMed

Moss, Caitlin E; Robson, Andrew; Fikrig, Erol; Narasimhan, Sukanya

2018-06-01

Infectious diseases transmitted by arthropod vectors continue to pose a significant threat to human health worldwide. The pathogens causing these diseases, do not exist in isolation when they colonize the vector; rather, they likely engage in interactions with resident microorganisms in the gut lumen. The vector microbiota has been demonstrated to play an important role in pathogen transmission for several vector-borne diseases. Whether resident bacteria in the gut of the Ixodes scapularis tick, the vector of several human pathogens including Borrelia burgdorferi, influence tick transmission of pathogens is not determined. We require methods for characterizing the composition of the bacteria associated with the tick gut to facilitate a better understanding of potential interspecies interactions in the tick gut. Using whole-mount in situ hybridization to visualize RNA transcripts associated with particular bacterial species allows for the collection of qualitative data regarding the abundance and distribution of the microbiota in intact tissue. This technique can be used to examine changes in the gut microbiota milieu over the course of tick feeding and can also be applied to analyze expression of tick genes. Staining of whole tick guts yield information about the gross spatial distribution of target RNA in the tissue without the need for three-dimensional reconstruction and is less affected by environmental contamination, which often confounds the sequencing-based methods frequently used to study complex microbial communities. Overall, this technique is a valuable tool that can be used to better understand vector-pathogen-microbiota interactions and their role in disease transmission.

Quantitative systems pharmacology analysis of drug combination and scaling to humans: the interaction between noradrenaline and vasopressin on vasoconstriction.

PubMed

Yin, Anyue; Yamada, Akihiro; Stam, Wiro B; van Hasselt, Johan G C; van der Graaf, Piet H

2018-06-02

Development of combination therapies has received significant interest in recent years. Previously a two-receptor one-transducer (2R-1T) model was proposed to characterize drug interactions with two receptors that lead to the same phenotypic response through a common transducer pathway. We applied, for the first time, the 2R-1T model to characterize the interaction of noradrenaline and arginine-vasopressin on vasoconstriction, and performed inter-species scaling to humans using this mechanism-based model. Contractile data was obtained from in vitro rat small mesenteric arteries after exposure to single or combined challenges of noradrenaline and arginine-vasopressin with or without pre-treatment with the irreversible α-adrenoceptor antagonist, phenoxybenzamine. Data was analysed using the 2R-1T model to characterize the observed exposure-response relationships and drug-drug interaction. The model was then scaled to humans by accounting for differences in receptor density. With receptor affinities set to literature values, the 2R-1T model satisfactorily characterized the interaction between noradrenaline and arginine-vasopressin in rat small mesenteric arteries (relative standard error ≤ 20%), as well as the effect of phenoxybenzamine. Furthermore, after scaling the model to human vascular tissue, the model also adequately predicted the interaction between both agents on human renal arteries. The 2R-1T model can be of relevance to quantitatively characterize the interaction between two drugs that interact via different receptors and a common transducer pathway. Its mechanistic properties are valuable for scaling the model across species. This approach is therefore of significant value to rationally optimize novel combination treatments. This article is protected by copyright. All rights reserved.

Tripartite assembly of RND multidrug efflux pumps

NASA Astrophysics Data System (ADS)

Daury, Laetitia; Orange, François; Taveau, Jean-Christophe; Verchère, Alice; Monlezun, Laura; Gounou, Céline; Marreddy, Ravi K. R.; Picard, Martin; Broutin, Isabelle; Pos, Klaas M.; Lambert, Olivier

2016-02-01

Tripartite multidrug efflux systems of Gram-negative bacteria are composed of an inner membrane transporter, an outer membrane channel and a periplasmic adaptor protein. They are assumed to form ducts inside the periplasm facilitating drug exit across the outer membrane. Here we present the reconstitution of native Pseudomonas aeruginosa MexAB-OprM and Escherichia coli AcrAB-TolC tripartite Resistance Nodulation and cell Division (RND) efflux systems in a lipid nanodisc system. Single-particle analysis by electron microscopy reveals the inner and outer membrane protein components linked together via the periplasmic adaptor protein. This intrinsic ability of the native components to self-assemble also leads to the formation of a stable interspecies AcrA-MexB-TolC complex suggesting a common mechanism of tripartite assembly. Projection structures of all three complexes emphasize the role of the periplasmic adaptor protein as part of the exit duct with no physical interaction between the inner and outer membrane components.

Spin-exchange-induced spin-orbit coupling in a superfluid mixture

NASA Astrophysics Data System (ADS)

Chen, Li; Zhu, Chuanzhou; Zhang, Yunbo; Pu, Han

2018-03-01

We investigate the ground-state properties of a dual-species spin-1/2 Bose-Einstein condensate. One of the species is subjected to a pair of Raman laser beams that induces spin-orbit (SO) coupling, whereas the other species is not coupled to the Raman laser. In certain limits, analytical results can be obtained. It is clearly shown that, through the interspecies spin-exchange interaction, the second species also exhibits SO coupling. This mixture system displays a very rich phase diagram, with many of the phases not present in an SO-coupled single-species condensate. Our work provides a way of creating SO coupling in atomic quantum gases, and opens up an avenue of research in SO-coupled superfluid mixtures. From a practical point of view, the spin-exchange-induced SO coupling may overcome the heating issue for certain atomic species when subjected to Raman beams.

Metabolomic profiling of the nectars of Aquilegia pubescens and A. Canadensis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Noutsos, Christos; Perera, Ann M.; Nikolau, Basil J.

To date, variation in nectar chemistry of flowering plants has not been studied in detail. Such variation exerts considerable influence on pollinator–plant interactions, as well as on flower traits that play important roles in the selection of a plant for visitation by specific pollinators. Over the past 60 years the Aquilegia genus has been used as a key model for speciation studies. In this study, we defined the metabolomic profiles of flower samples of two Aquilegia species, A. Canadensis and A. pubescens. We identified a total of 75 metabolites that were classified into six main categories: organic acids, fattymore » acids, amino acids, esters, sugars, and unknowns. The mean abundances of 25 of these metabolites were significantly different between the two species, providing insights into interspecies variation in floral chemistry. Using the PlantSEED biochemistry database, we found that the majority of these metabolites are involved in biosynthetic pathways. Finally, we explored the annotated genome of A. coerulea, using the PlantSEED pipeline and reconstructed the metabolic network of Aquilegia. As a result, this network, which contains the metabolic pathways involved in generating the observed chemical variation, is now publicly available from the DOE Systems Biology Knowledge Base (KBase; http://kbase.us).« less

Metabolomic profiling of the nectars of Aquilegia pubescens and A. Canadensis

DOE PAGES

Noutsos, Christos; Perera, Ann M.; Nikolau, Basil J.; ...

2015-05-01

To date, variation in nectar chemistry of flowering plants has not been studied in detail. Such variation exerts considerable influence on pollinator–plant interactions, as well as on flower traits that play important roles in the selection of a plant for visitation by specific pollinators. Over the past 60 years the Aquilegia genus has been used as a key model for speciation studies. In this study, we defined the metabolomic profiles of flower samples of two Aquilegia species, A. Canadensis and A. pubescens. We identified a total of 75 metabolites that were classified into six main categories: organic acids, fattymore » acids, amino acids, esters, sugars, and unknowns. The mean abundances of 25 of these metabolites were significantly different between the two species, providing insights into interspecies variation in floral chemistry. Using the PlantSEED biochemistry database, we found that the majority of these metabolites are involved in biosynthetic pathways. Finally, we explored the annotated genome of A. coerulea, using the PlantSEED pipeline and reconstructed the metabolic network of Aquilegia. As a result, this network, which contains the metabolic pathways involved in generating the observed chemical variation, is now publicly available from the DOE Systems Biology Knowledge Base (KBase; http://kbase.us).« less

Staphylococcus aureus undergoes major transcriptional reorganization during growth with Enterococcus faecalis in milk.

PubMed

Viçosa, Gabriela Nogueira; Botta, Cristian; Ferrocino, Ilario; Bertolino, Marta; Ventura, Marco; Nero, Luís Augusto; Cocolin, Luca

2018-08-01

Previous studies have demonstrated the antagonistic potential of lactic acid bacteria (LAB) present in raw milk microbiota over Staphylococcus aureus, albeit the molecular mechanisms underlying this inhibitory effect are not fully understood. In this study, we compared the behavior of S. aureus ATCC 29213 alone and in the presence of a cheese-isolated LAB strain, Enterococcus faecalis 41FL1 in skimmed milk at 30 °C for 24 h using phenotypical and molecular approaches. Phenotypic analysis showed the absence of classical staphylococcal enterotoxins in co-culture with a 1.2-log decrease in S. aureus final population compared to single culture. Transcriptional activity of several exotoxins and global regulators, including agr, was negatively impacted in co-culture, contrasting with the accumulation of transcripts coding for surface proteins. After 24 h, the number of transcripts coding for several metabolite responsive elements, as well as enzymes involved in glycolysis and acetoin metabolism was increased in co-culture. The present study discusses the complexity of the transcriptomic mechanisms possibly leading to S. aureus attenuated virulence in the presence of E. faecalis and provides insights into this interspecies interaction in a simulated food context. Copyright © 2018 Elsevier Ltd. All rights reserved.

Transcriptional Response to Lactic Acid Stress in the Hybrid Yeast Zygosaccharomyces parabailii

PubMed Central

2017-01-01

ABSTRACT Lactic acid has a wide range of applications starting from its undissociated form, and its production using cell factories requires stress-tolerant microbial hosts. The interspecies hybrid yeast Zygosaccharomyces parabailii has great potential to be exploited as a novel host for lactic acid production, due to high organic acid tolerance at low pH and a fermentative metabolism with a high growth rate. Here we used mRNA sequencing (RNA-seq) to analyze Z. parabailii's transcriptional response to lactic acid added exogenously, and we explore the biological mechanisms involved in tolerance. Z. parabailii contains two homeologous copies of most genes. Under lactic acid stress, the two genes in each homeolog pair tend to diverge in expression to a significantly greater extent than under control conditions, indicating that stress tolerance is facilitated by interactions between the two gene sets in the hybrid. Lactic acid induces downregulation of genes related to cell wall and plasma membrane functions, possibly altering the rate of diffusion of lactic acid into cells. Genes related to iron transport and redox processes were upregulated, suggesting an important role for respiratory functions and oxidative stress defense. We found differences in the expression profiles of genes putatively regulated by Haa1 and Aft1/Aft2, previously described as lactic acid responsive in Saccharomyces cerevisiae. Furthermore, formate dehydrogenase (FDH) genes form a lactic acid-responsive gene family that has been specifically amplified in Z. parabailii in comparison to other closely related species. Our study provides a useful starting point for the engineering of Z. parabailii as a host for lactic acid production. IMPORTANCE Hybrid yeasts are important in biotechnology because of their tolerance to harsh industrial conditions. The molecular mechanisms of tolerance can be studied by analyzing differential gene expression under conditions of interest and relating gene expression patterns to protein functions. However, hybrid organisms present a challenge to the standard use of mRNA sequencing (RNA-seq) to study transcriptional responses to stress, because their genomes contain two similar copies of almost every gene. Here we used stringent mapping methods and a high-quality genome sequence to study the transcriptional response to lactic acid stress in Zygosaccharomyces parabailii ATCC 60483, a natural interspecies hybrid yeast that contains two complete subgenomes that are approximately 7% divergent in sequence. Beyond the insights we gained into lactic acid tolerance in this study, the methods we developed will be broadly applicable to other yeast hybrid strains. PMID:29269498

Transcriptional Response to Lactic Acid Stress in the Hybrid Yeast Zygosaccharomyces parabailii.

PubMed

Ortiz-Merino, Raúl A; Kuanyshev, Nurzhan; Byrne, Kevin P; Varela, Javier A; Morrissey, John P; Porro, Danilo; Wolfe, Kenneth H; Branduardi, Paola

2018-03-01

Lactic acid has a wide range of applications starting from its undissociated form, and its production using cell factories requires stress-tolerant microbial hosts. The interspecies hybrid yeast Zygosaccharomyces parabailii has great potential to be exploited as a novel host for lactic acid production, due to high organic acid tolerance at low pH and a fermentative metabolism with a high growth rate. Here we used mRNA sequencing (RNA-seq) to analyze Z. parabailii 's transcriptional response to lactic acid added exogenously, and we explore the biological mechanisms involved in tolerance. Z. parabailii contains two homeologous copies of most genes. Under lactic acid stress, the two genes in each homeolog pair tend to diverge in expression to a significantly greater extent than under control conditions, indicating that stress tolerance is facilitated by interactions between the two gene sets in the hybrid. Lactic acid induces downregulation of genes related to cell wall and plasma membrane functions, possibly altering the rate of diffusion of lactic acid into cells. Genes related to iron transport and redox processes were upregulated, suggesting an important role for respiratory functions and oxidative stress defense. We found differences in the expression profiles of genes putatively regulated by Haa1 and Aft1/Aft2, previously described as lactic acid responsive in Saccharomyces cerevisiae Furthermore, formate dehydrogenase ( FDH ) genes form a lactic acid-responsive gene family that has been specifically amplified in Z. parabailii in comparison to other closely related species. Our study provides a useful starting point for the engineering of Z. parabailii as a host for lactic acid production. IMPORTANCE Hybrid yeasts are important in biotechnology because of their tolerance to harsh industrial conditions. The molecular mechanisms of tolerance can be studied by analyzing differential gene expression under conditions of interest and relating gene expression patterns to protein functions. However, hybrid organisms present a challenge to the standard use of mRNA sequencing (RNA-seq) to study transcriptional responses to stress, because their genomes contain two similar copies of almost every gene. Here we used stringent mapping methods and a high-quality genome sequence to study the transcriptional response to lactic acid stress in Zygosaccharomyces parabailii ATCC 60483, a natural interspecies hybrid yeast that contains two complete subgenomes that are approximately 7% divergent in sequence. Beyond the insights we gained into lactic acid tolerance in this study, the methods we developed will be broadly applicable to other yeast hybrid strains. Copyright © 2018 Ortiz-Merino et al.

Endangered species toxicity extrapolation using ICE models

EPA Science Inventory

The National Research Council’s (NRC) report on assessing pesticide risks to threatened and endangered species (T&E) included the recommendation of using interspecies correlation models (ICE) as an alternative to general safety factors for extrapolating across species. ...

Bat-to-human: spike features determining 'host jump' of coronaviruses SARS-CoV, MERS-CoV, and beyond.

PubMed

Lu, Guangwen; Wang, Qihui; Gao, George F

2015-08-01

Both severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) are zoonotic pathogens that crossed the species barriers to infect humans. The mechanism of viral interspecies transmission is an important scientific question to be addressed. These coronaviruses contain a surface-located spike (S) protein that initiates infection by mediating receptor-recognition and membrane fusion and is therefore a key factor in host specificity. In addition, the S protein needs to be cleaved by host proteases before executing fusion, making these proteases a second determinant of coronavirus interspecies infection. Here, we summarize the progress made in the past decade in understanding the cross-species transmission of SARS-CoV and MERS-CoV by focusing on the features of the S protein, its receptor-binding characteristics, and the cleavage process involved in priming. Copyright © 2015 Elsevier Ltd. All rights reserved.

Intense Sperm-Mediated Sexual Conflict Promotes Reproductive Isolation in Caenorhabditis Nematodes

PubMed Central

Leung, Gemma; Shin, Na-Ra; Cutter, Asher D.; Haag, Eric S.

2014-01-01

Conflict between the sexes over reproductive interests can drive rapid evolution of reproductive traits and promote speciation. Here we show that inter-species mating between Caenorhabditis nematodes sterilizes maternal individuals. The principal effectors of male-induced harm are sperm cells, which induce sterility and shorten lifespan by displacing conspecific sperm, invading the ovary, and sometimes breaching the gonad to infiltrate other tissues. This sperm-mediated harm is pervasive across species, but idiosyncrasies in its magnitude implicate both independent histories of sexually antagonistic coevolution within species and differences in reproductive mode (self-fertilizing hermaphrodites versus females) in determining its severity. Consistent with this conclusion, in androdioecious species the hermaphrodites are more vulnerable, the males more benign, or both. Patterns of assortative mating and a low incidence of invasive sperm occurring with conspecific mating are indicative of ongoing intra-specific sexual conflict that results in inter-species reproductive incompatibility. PMID:25072732

Streptococcus agalactiae Serotype IV in Humans and Cattle, Northern Europe1

PubMed Central

Lyhs, Ulrike; Kulkas, Laura; Katholm, Jørgen; Waller, Karin Persson; Saha, Kerttu; Tomusk, Richard J.

2016-01-01

Streptococcus agalactiae is an emerging pathogen of nonpregnant human adults worldwide and a reemerging pathogen of dairy cattle in parts of Europe. To learn more about interspecies transmission of this bacterium, we compared contemporaneously collected isolates from humans and cattle in Finland and Sweden. Multilocus sequence typing identified 5 sequence types (STs) (ST1, 8, 12, 23, and 196) shared across the 2 host species, suggesting possible interspecies transmission. More than 54% of the isolates belonged to those STs. Molecular serotyping and pilus island typing of those isolates did not differentiate between populations isolated from different host species. Isolates from humans and cattle differed in lactose fermentation, which is encoded on the accessory genome and represents an adaptation to the bovine mammary gland. Serotype IV-ST196 isolates were obtained from multiple dairy herds in both countries. Cattle may constitute a previously unknown reservoir of this strain. PMID:27869599

Enhancement of methanogenesis via direct interspecies electron transfer between Geobacteraceae and Methanosaetaceae conducted by granular activated carbon.

PubMed

Zhang, Shuo; Chang, Jiali; Lin, Chao; Pan, Yiran; Cui, Kangping; Zhang, Xiaoyuan; Liang, Peng; Huang, Xia

2017-12-01

To understand how granular activated carbon (GAC) promotes methanogenesis, batch tests of CH 4 production potential in anaerobic serum bottles with addition of GAC or not were conducted. Tests showed that GAC promoted methanogenesis remarkably, but the non-conductive zeolite did not. The qPCR demonstrated that the biomass on GAC contributed little to the promotion. High-throughput sequencing data implied that promotion was related with direct interspecies electron transfer between Geobacteraceae and Methanosaetaceae. According to the c-type cytochromes (c-Cyts) response to the supplement of GAC, it was speculated that GAC may play the role of c-Cyts' substitution. In the undefined cultures, the phenomenon that c-Cyts were repressed by GAC was first observed. This research provided new evidence to microbial mechanism of promoting methanogenesis via GAC. Copyright © 2017 Elsevier Ltd. All rights reserved.

Direct Interspecies Electron Transfer in Anaerobic Digestion: A Review.

PubMed

Dubé, Charles-David; Guiot, Serge R

2015-01-01

Direct interspecies electrons transfer (DIET) is a syntrophic metabolism in which free electrons flow from one cell to another without being shuttled by reduced molecules such as molecular hydrogen or formate. As more and more microorganisms show a capacity for electron exchange, either to export or import them, it becomes obvious that DIET is a syntrophic metabolism that is much more present in nature than previously thought. This article reviews literature related to DIET, specifically in reference to anaerobic digestion. Anaerobic granular sludge, a biofilm, is a specialized microenvironment where syntrophic bacterial and archaeal organisms grow together in close proximity. Exoelectrogenic bacteria degrading organic substrates or intermediates need an electron sink and electrotrophic methanogens represent perfect partners to assimilate those electrons and produce methane. The granule extracellular polymeric substances by making the biofilm matrix more conductive, play a role as electrons carrier in DIET.

Interspecies H2 transfer in cellulose degradation between fibrolytic bacteria and H2-utilizing microorganisms from the human colon.

PubMed

Robert, C; Del'Homme, C; Bernalier-Donadille, A

2001-12-18

Interspecies H2 transfer between two newly isolated fibrolytic strains (18P13 and 18P16) and H2-utilizing methanogen or acetogen from the human colon was investigated during in vitro cellulose degradation. Both H2-consuming microorganisms utilized efficiently H2 produced from cellulose fermentation by the fibrolytic species. H2 utilization by Methanobrevibacter smithii did not change the metabolism and the cellulolytic activity of strain 18P16 whereas it induced a metabolic shift in strain 18P13. However, this metabolic shift was not associated with enhancement of cellulose degradation. In contrast, an increase in cellulose breakdown was observed when strain 18P13 was cultivated with Ruminococcus hydrogenotrophicus. This stimulating effect could be attributed to both the autotrophic and the heterotrophic metabolism of the acetogen in the coculture.

Efficient engineering of marker-free synthetic allotetraploids of Saccharomyces.

PubMed

Alexander, William G; Peris, David; Pfannenstiel, Brandon T; Opulente, Dana A; Kuang, Meihua; Hittinger, Chris Todd

2016-04-01

Saccharomyces interspecies hybrids are critical biocatalysts in the fermented beverage industry, including in the production of lager beers, Belgian ales, ciders, and cold-fermented wines. Current methods for making synthetic interspecies hybrids are cumbersome and/or require genome modifications. We have developed a simple, robust, and efficient method for generating allotetraploid strains of prototrophic Saccharomyces without sporulation or nuclear genome manipulation. S. cerevisiae×S. eubayanus, S. cerevisiae×S. kudriavzevii, and S. cerevisiae×S. uvarum designer hybrid strains were created as synthetic lager, Belgian, and cider strains, respectively. The ploidy and hybrid nature of the strains were confirmed using flow cytometry and PCR-RFLP analysis, respectively. This method provides an efficient means for producing novel synthetic hybrids for beverage and biofuel production, as well as for constructing tetraploids to be used for basic research in evolutionary genetics and genome stability. Copyright © 2015 Elsevier Inc. All rights reserved.

An alternative pluripotent state confers interspecies chimaeric competency

PubMed Central

Wu, Jun; Okamura, Daiji; Li, Mo; Suzuki, Keiichiro; Luo, Chongyuan; Ma, Li; He, Yupeng; Li, Zhongwei; Benner, Chris; Tamura, Isao; Krause, Marie N.; Nery, Joseph R.; Du, Tingting; Zhang, Zhuzhu; Hishida, Tomoaki; Takahashi, Yuta; Aizawa, Emi; Kim, Na Young; Lajara, Jeronimo; Guillen, Pedro; Campistol, Josep M.; Esteban, Concepcion Rodriguez; Ross, Pablo J.; Saghatelian, Alan; Ren, Bing; Ecker, Joseph R.; Belmonte, Juan Carlos Izpisua

2017-01-01

Pluripotency, the ability to generate any cell type of the body, is an evanescent attribute of embryonic cells. Transitory pluripotent cells can be captured at different time points during embryogenesis and maintained as embryonic stem cells or epiblast stem cells in culture. Since ontogenesis is a dynamic process in both space and time, it seems counterintuitive that these two temporal states represent the full spectrum of organismal pluripotency. Here we show that by modulating culture parameters, a stem-cell type with unique spatial characteristics and distinct molecular and functional features, designated as region-selective pluripotent stem cells (rsPSCs), can be efficiently obtained from mouse embryos and primate pluripotent stem cells, including humans. The ease of culturing and editing the genome of human rsPSCs offers advantages for regenerative medicine applications. The unique ability of human rsPSCs to generate post-implantation interspecies chimaeric embryos may facilitate our understanding of early human development and evolution. PMID:25945737

A Trichosporonales genome tree based on 27 haploid and three evolutionarily conserved 'natural' hybrid genomes.

PubMed

Takashima, Masako; Sriswasdi, Sira; Manabe, Ri-Ichiroh; Ohkuma, Moriya; Sugita, Takashi; Iwasaki, Wataru

2018-01-01

To construct a backbone tree consisting of basidiomycetous yeasts, draft genome sequences from 25 species of Trichosporonales (Tremellomycetes, Basidiomycota) were generated. In addition to the hybrid genomes of Trichosporon coremiiforme and Trichosporon ovoides that we described previously, we identified an interspecies hybrid genome in Cutaneotrichosporon mucoides (formerly Trichosporon mucoides). This hybrid genome had a gene retention rate of ~55%, and its closest haploid relative was Cutaneotrichosporon dermatis. After constructing the C. mucoides subgenomes, we generated a phylogenetic tree using genome data from the 27 haploid species and the subgenome data from the three hybrid genome species. It was a high-quality tree with 100% bootstrap support for all of the branches. The genome-based tree provided superior resolution compared with previous multi-gene analyses. Although our backbone tree does not include all Trichosporonales genera (e.g. Cryptotrichosporon), it will be valuable for future analyses of genome data. Interest in interspecies hybrid fungal genomes has recently increased because they may provide a basis for new technologies. The three Trichosporonales hybrid genomes described in this study are different from well-characterized hybrid genomes (e.g. those of Saccharomyces pastorianus and Saccharomyces bayanus) because these hybridization events probably occurred in the distant evolutionary past. Hence, they will be useful for studying genome stability following hybridization and speciation events. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Sodium butyrate improves the cloned yak embryo viability and corrects gene expression patterns.

PubMed

Xiong, Xian-rong; Lan, Dao-liang; Li, Jian; Wang, Yong; Zhong, Jin-cheng

2015-02-01

Interspecies somatic cell nuclear transfer (iSCNT), a powerful tool in basic scientific research, has been used widely to increase and preserve the population of endangered species. Yak (Bos grunniens) is one of these species. Development to term of interspecies cloned yak embryos has not been achieved, possibly due to abnormal epigenetic reprogramming. Previous studies have demonstrated that treatment of intraspecies cloned embryos with (NaBu) significantly improves nuclear-cytoplasmic reprogramming and viability in vitro. Therefore, in this study, we evaluated the effect of optimal NaBu concentration and exposure time on preimplantation development of yak iSCNT embryos and on the expression patterns of developmentally important genes. The results showed that 8-cell rate, blastocyst formation rate and total cell number increased significantly compared with their untreated counterparts when yak iSCNT embryos were treated with 5 nM NaBu for 12 h after activation, but that the 2-cell stage embryo rate was not significantly different. The treatment of NaBu also increased significantly the expression levels of Oct-4 and decreased the expression levels of HDAC-2, Dnmt-1 and IGF-1; the expression patterns of these genes were more similar to that of their bovine-yak in vitro fertilization (BY-IVF) counterparts. The results described above indicated that NaBu treatment improved developmental competence in vitro and 'corrected' the gene expression patterns of yak iSCNT embryos.

Characterizing interspecies uncertainty using data from studies of anti-neoplastic agents in animals and humans

DOE Office of Scientific and Technical Information (OSTI.GOV)

Price, Paul S.; Keenan, Russell E.; Swartout, Jeffrey C.

For most chemicals, the Reference Dose (RfD) is based on data from animal testing. The uncertainty introduced by the use of animal models has been termed interspecies uncertainty. The magnitude of the differences between the toxicity of a chemical in humans and test animals and its uncertainty can be investigated by evaluating the inter-chemical variation in the ratios of the doses associated with similar toxicological endpoints in test animals and humans. This study performs such an evaluation on a data set of 64 anti-neoplastic drugs. The data set provides matched responses in humans and four species of test animals: mice,more » rats, monkeys, and dogs. While the data have a number of limitations, the data show that when the drugs are evaluated on a body weight basis: 1) toxicity generally increases with a species' body weight; however, humans are not always more sensitive than test animals; 2) the animal to human dose ratios were less than 10 for most, but not all, drugs; 3) the current practice of using data from multiple species when setting RfDs lowers the probability of having a large value for the ratio. These findings provide insight into inter-chemical variation in animal to human extrapolations and suggest the need for additional collection and analysis of matched toxicity data in humans and test animals.« less

Intra- and interspecies gene expression models for predicting drug response in canine osteosarcoma.

PubMed

Fowles, Jared S; Brown, Kristen C; Hess, Ann M; Duval, Dawn L; Gustafson, Daniel L

2016-02-19

Genomics-based predictors of drug response have the potential to improve outcomes associated with cancer therapy. Osteosarcoma (OS), the most common primary bone cancer in dogs, is commonly treated with adjuvant doxorubicin or carboplatin following amputation of the affected limb. We evaluated the use of gene-expression based models built in an intra- or interspecies manner to predict chemosensitivity and treatment outcome in canine OS. Models were built and evaluated using microarray gene expression and drug sensitivity data from human and canine cancer cell lines, and canine OS tumor datasets. The "COXEN" method was utilized to filter gene signatures between human and dog datasets based on strong co-expression patterns. Models were built using linear discriminant analysis via the misclassification penalized posterior algorithm. The best doxorubicin model involved genes identified in human lines that were co-expressed and trained on canine OS tumor data, which accurately predicted clinical outcome in 73 % of dogs (p = 0.0262, binomial). The best carboplatin model utilized canine lines for gene identification and model training, with canine OS tumor data for co-expression. Dogs whose treatment matched our predictions had significantly better clinical outcomes than those that didn't (p = 0.0006, Log Rank), and this predictor significantly associated with longer disease free intervals in a Cox multivariate analysis (hazard ratio = 0.3102, p = 0.0124). Our data show that intra- and interspecies gene expression models can successfully predict response in canine OS, which may improve outcome in dogs and serve as pre-clinical validation for similar methods in human cancer research.

Microbial communication leading to the activation of silent fungal secondary metabolite gene clusters

PubMed Central

Netzker, Tina; Fischer, Juliane; Weber, Jakob; Mattern, Derek J.; König, Claudia C.; Valiante, Vito; Schroeckh, Volker; Brakhage, Axel A.

2015-01-01

Microorganisms form diverse multispecies communities in various ecosystems. The high abundance of fungal and bacterial species in these consortia results in specific communication between the microorganisms. A key role in this communication is played by secondary metabolites (SMs), which are also called natural products. Recently, it was shown that interspecies “talk” between microorganisms represents a physiological trigger to activate silent gene clusters leading to the formation of novel SMs by the involved species. This review focuses on mixed microbial cultivation, mainly between bacteria and fungi, with a special emphasis on the induced formation of fungal SMs in co-cultures. In addition, the role of chromatin remodeling in the induction is examined, and methodical perspectives for the analysis of natural products are presented. As an example for an intermicrobial interaction elucidated at the molecular level, we discuss the specific interaction between the filamentous fungi Aspergillus nidulans and Aspergillus fumigatus with the soil bacterium Streptomyces rapamycinicus, which provides an excellent model system to enlighten molecular concepts behind regulatory mechanisms and will pave the way to a novel avenue of drug discovery through targeted activation of silent SM gene clusters through co-cultivations of microorganisms. PMID:25941517

Microbial communication leading to the activation of silent fungal secondary metabolite gene clusters.

PubMed

Netzker, Tina; Fischer, Juliane; Weber, Jakob; Mattern, Derek J; König, Claudia C; Valiante, Vito; Schroeckh, Volker; Brakhage, Axel A

2015-01-01

Microorganisms form diverse multispecies communities in various ecosystems. The high abundance of fungal and bacterial species in these consortia results in specific communication between the microorganisms. A key role in this communication is played by secondary metabolites (SMs), which are also called natural products. Recently, it was shown that interspecies "talk" between microorganisms represents a physiological trigger to activate silent gene clusters leading to the formation of novel SMs by the involved species. This review focuses on mixed microbial cultivation, mainly between bacteria and fungi, with a special emphasis on the induced formation of fungal SMs in co-cultures. In addition, the role of chromatin remodeling in the induction is examined, and methodical perspectives for the analysis of natural products are presented. As an example for an intermicrobial interaction elucidated at the molecular level, we discuss the specific interaction between the filamentous fungi Aspergillus nidulans and Aspergillus fumigatus with the soil bacterium Streptomyces rapamycinicus, which provides an excellent model system to enlighten molecular concepts behind regulatory mechanisms and will pave the way to a novel avenue of drug discovery through targeted activation of silent SM gene clusters through co-cultivations of microorganisms.

Dual-species transcriptional profiling during systemic candidiasis reveals organ-specific host-pathogen interactions.

PubMed

Hebecker, Betty; Vlaic, Sebastian; Conrad, Theresia; Bauer, Michael; Brunke, Sascha; Kapitan, Mario; Linde, Jörg; Hube, Bernhard; Jacobsen, Ilse D

2016-11-03

Candida albicans is a common cause of life-threatening fungal bloodstream infections. In the murine model of systemic candidiasis, the kidney is the primary target organ while the fungal load declines over time in liver and spleen. To better understand these organ-specific differences in host-pathogen interaction, we performed gene expression profiling of murine kidney, liver and spleen and determined the fungal transcriptome in liver and kidney. We observed a delayed transcriptional immune response accompanied by late induction of fungal stress response genes in the kidneys. In contrast, early upregulation of the proinflammatory response in the liver was associated with a fungal transcriptome resembling response to phagocytosis, suggesting that phagocytes contribute significantly to fungal control in the liver. Notably, C. albicans hypha-associated genes were upregulated in the absence of visible filamentation in the liver, indicating an uncoupling of gene expression and morphology and a morphology-independent effect by hypha-associated genes in this organ. Consistently, integration of host and pathogen transcriptional data in an inter-species gene regulatory network indicated connections of C. albicans cell wall remodelling and metabolism to the organ-specific immune responses.

CoryneRegNet 3.0--an interactive systems biology platform for the analysis of gene regulatory networks in corynebacteria and Escherichia coli.

PubMed

Baumbach, Jan; Wittkop, Tobias; Rademacher, Katrin; Rahmann, Sven; Brinkrolf, Karina; Tauch, Andreas

2007-04-30

CoryneRegNet is an ontology-based data warehouse for the reconstruction and visualization of transcriptional regulatory interactions in prokaryotes. To extend the biological content of CoryneRegNet, we added comprehensive data on transcriptional regulations in the model organism Escherichia coli K-12, originally deposited in the international reference database RegulonDB. The enhanced web interface of CoryneRegNet offers several types of search options. The results of a search are displayed in a table-based style and include a visualization of the genetic organization of the respective gene region. Information on DNA binding sites of transcriptional regulators is depicted by sequence logos. The results can also be displayed by several layouters implemented in the graphical user interface GraphVis, allowing, for instance, the visualization of genome-wide network reconstructions and the homology-based inter-species comparison of reconstructed gene regulatory networks. In an application example, we compare the composition of the gene regulatory networks involved in the SOS response of E. coli and Corynebacterium glutamicum. CoryneRegNet is available at the following URL: http://www.cebitec.uni-bielefeld.de/groups/gi/software/coryneregnet/.

Dual-species transcriptional profiling during systemic candidiasis reveals organ-specific host-pathogen interactions

PubMed Central

Hebecker, Betty; Vlaic, Sebastian; Conrad, Theresia; Bauer, Michael; Brunke, Sascha; Kapitan, Mario; Linde, Jörg; Hube, Bernhard; Jacobsen, Ilse D.

2016-01-01

Candida albicans is a common cause of life-threatening fungal bloodstream infections. In the murine model of systemic candidiasis, the kidney is the primary target organ while the fungal load declines over time in liver and spleen. To better understand these organ-specific differences in host-pathogen interaction, we performed gene expression profiling of murine kidney, liver and spleen and determined the fungal transcriptome in liver and kidney. We observed a delayed transcriptional immune response accompanied by late induction of fungal stress response genes in the kidneys. In contrast, early upregulation of the proinflammatory response in the liver was associated with a fungal transcriptome resembling response to phagocytosis, suggesting that phagocytes contribute significantly to fungal control in the liver. Notably, C. albicans hypha-associated genes were upregulated in the absence of visible filamentation in the liver, indicating an uncoupling of gene expression and morphology and a morphology-independent effect by hypha-associated genes in this organ. Consistently, integration of host and pathogen transcriptional data in an inter-species gene regulatory network indicated connections of C. albicans cell wall remodelling and metabolism to the organ-specific immune responses. PMID:27808111

SU(3) Orbital Kondo Effect with Ultracold Atoms

NASA Astrophysics Data System (ADS)

Nishida, Yusuke

2013-09-01

We propose a simple but novel scheme to realize the Kondo effect with ultracold atoms. Our system consists of a Fermi sea of spinless fermions interacting with an impurity atom of different species which is confined by an isotropic potential. The interspecies attraction can be tuned with an s-wave Feshbach resonance so that the impurity atom and a spinless fermion form a bound dimer that occupies a threefold-degenerate p orbital of the confinement potential. Many-body scatterings of this dimer and surrounding spinless fermions occur with exchanging their angular momenta and thus exhibit the SU(3) orbital Kondo effect. The associated Kondo temperature has a universal leading exponent given by TK∝exp⁡[-π/(3apkF3)] that depends only on an effective p-wave scattering volume ap and a Fermi wave vector kF. We also elucidate a Kondo singlet formation at zero temperature and an anisotropic interdimer interaction mediated by surrounding spinless fermions. The Kondo effect thus realized in ultracold atom experiments may be observed as an increasing atom loss by lowering the temperature or with radio-frequency spectroscopy. Our scheme and its extension to a dense Kondo lattice will be useful to develop new insights into yet unresolved aspects of Kondo physics.

Temporal changes in fungal communities from buckwheat seeds and their effects on seed germination and seedling secondary metabolism.

PubMed

Kovačec, Eva; Likar, Matevž; Regvar, Marjana

2016-05-01

Seed-associated fungal communities affect multiple parameters of seed quality at all stages of production, from seed development to post-harvest storage and germination. We therefore investigated the diversity and dynamics of fungal communities in the seeds of common buckwheat (Fagopyrum esculentum) and Tartary buckwheat (F. tataricum) from harvest to 1 y of storage. Fungal populations in seeds were relatively stable, comprised mainly of field fungi. Incidence of fungi was most likely determined by fungal interspecies direct interactions, as well as by their synthesis of volatile organic compounds. Most prominent antagonistic interactions were seen for two plant pathogens, Alternaria alternata on Botrytis cinerea. Detrimental effects of the fungi on seed germination and seedling development were related to fungal extracellular enzyme activity, and in particular to amylase, cellulase and, polyphenol oxidase. Polyphenol and tannin concentrations in buckwheat seedlings were related to fungal growth rate and intensity of fungal cellulase activity, respectively, which suggests that physical penetration of the fungi through the host tissues is probably the stimulus for the activation of plant defence reactions in these seedlings. Copyright © 2016 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Species- and dose-specific pancreatic responses and progression in single- and repeat-dose studies with GI181771X: a novel cholecystokinin 1 receptor agonist in mice, rats, and monkeys.

PubMed

Myer, James R; Romach, Elizabeth H; Elangbam, Chandikumar S

2014-01-01

Compound-induced pancreatic injury is a serious liability in preclinical toxicity studies. However, its relevance to humans should be cautiously evaluated because of interspecies variations. To highlight such variations, we evaluated the species- and dose-specific pancreatic responses and progression caused by GI181771X, a novel cholecystokinin 1 receptor agonist investigated by GlaxoSmithKline for the treatment of obesity. Acute (up to 2,000 mg/kg GI181771X, as single dose) and repeat-dose studies in mice and/or rats (0.25-250 mg/kg/day for 7 days to 26 weeks) showed wide-ranging morphological changes in the pancreas that were dose and duration dependent, including necrotizing pancreatitis, acinar cell hypertrophy/atrophy, zymogen degranulation, focal acinar cell hyperplasia, and interstitial inflammation. In contrast to rodents, pancreatic changes were not observed in cynomolgus monkeys given GI181771X (1-500 mg/kg/day with higher systemic exposure than rats) for up to 52 weeks. Similarly, no GI181771X treatment-associated abnormalities in pancreatic structure were noted in a 24-week clinical trial with obese patients (body mass index >30 or >27 kg/m(2)) as assessed by abdominal ultrasound or by magnetic resonance imaging. Mechanisms for interspecies variations in the pancreatic response to CCK among rodents, monkeys, and humans and their relevance to human risk are discussed.

ESTIMATION OF AQUATIC SPECIES SENSITIVITY AND POPULATION-LEVEL RESPONSES

EPA Science Inventory

Determining species sensitivity and population-level responses of aquatic organisms to contaminants are critical components of criteria development and ecological risk assessment. To address data gaps in species sensitivity, the U.S. EPA developed the Interspecies Correlation Est...

NASAL TRACT UPTAKE IN HUMANS

EPA Science Inventory

Current Agency default procedures proscribed in the inhalation RfC Methodology (U.S. EPA, 1994)for interspecies adjustment of inhaled gases are nonempirical deterministic projections based on surface area of various regions of the respiratory tract (such as the extrathoracic or E...

Augmenting aquatic species sensitivity distributions with interspecies toxicity estimation models

EPA Science Inventory

Species sensitivity distributions (SSD) are cumulative distribution functions of species toxicity values. The SSD approach is increasingly being used in ecological risk assessment, but is often limited by available toxicity data necessary for diverse species representation. In ...

Themes from variation: probing the commonalities of symbiotic associations.

PubMed

Saffo, Mary Beth

2002-04-01

Research on symbiosis (including antagonistic and mutualistic associations) wrestles, directly or indirectly, with the paradox: why are symbiotic associations so prevalent in the biosphere in the face of ubiquitous immune or antibiotic defenses among organisms? The symposium "Living Together: the Dynamics of Symbiotic Interactions" considered several questions: 1. How do symbiotic species partners come together? Do symbioses share similar patterns of signal recognition and response? 2. What roles do nutrients and metabolites play in symbiotic interactions, and how are metabolic exchanges affected by environmental changes? 3. In what ways do the dynamics of multispecies symbioses differ from two-species associations? 4. How do antagonistic (parasitic, pathogenic) symbioses differ from mutualistic ones? In what ways do changes in the biotic and physical environment affect the evolutionary balance of symbiotic associations? 5. What are the coevolutionary patterns of symbiotic associations? 6. Which research techniques, and strategies of experimental design, might be useful across a broad range of symbiotic associations?Two themes emerged from the symposium. First, all the participants have incorporated multiple techniques and perspectives into their work, approaches which facilitate the understanding of symbiotic dynamics at several levels of biological organization. Secondly, many of the papers addressed genetic and environmental variation in symbiotic interactions. Such approaches are useful tools for analysis of the mechanics of interspecies interactions and for characterization of the most important factors which influence them. They provide us with the tools to evaluate symbioses in a world of complexity, variation and change.

The effects of metabolite molecules produced by drinking water-isolated bacteria on their single and multispecies biofilms.

PubMed

Simões, Lúcia Chaves; Simões, Manuel; Vieira, Maria João

2011-08-01

The elucidation of the mechanisms by which diverse species survive and interact in drinking water (DW) biofilm communities may allow the identification of new biofilm control strategies. The purpose of the present study was to investigate the effects of metabolite molecules produced by bacteria isolated from DW on biofilm formation. Six opportunistic bacteria, viz. Acinetobacter calcoaceticus, Burkholderia cepacia, Methylobacterium sp., Mycobacterium mucogenicum, Sphingomonas capsulata and Staphylococcus sp. isolated from a drinking water distribution systems (DWDS) were used to form single and multispecies biofilms in the presence and absence of crude cell-free supernatants produced by the partner bacteria. Biofilms were characterized in terms of mass and metabolic activity. Additionally, several physiological aspects regulating interspecies interactions (sessile growth rates, antimicrobial activity of cell-free supernatants, and production of iron chelators) were studied to identify bacterial species with biocontrol potential in DWDS. Biofilms of Methylobacterium sp. had the highest growth rate and M. mucogenicum biofilms the lowest. Only B. cepacia was able to produce extracellular iron-chelating molecules. A. calcoaceticus, B. cepacia, Methylobacterium sp. and M. mucogenicum biofilms were strongly inhibited by crude cell-free supernatants from the other bacteria. The crude cell-free supernatants of M. mucogenicum and S. capsulata demonstrated a high potential for inhibiting the growth of counterpart biofilms. Multispecies biofilm formation was strongly inhibited in the absence of A. calcoaceticus. Only crude cell-free supernatants produced by B. cepacia and A. calcoaceticus had no inhibitory effects on multispecies biofilm formation, while metabolite molecules of M. mucogenicum showed the most significant biocontrol potential.

Impact of Gestational Bisphenol A on Oxidative Stress and Free Fatty Acids: Human Association and Interspecies Animal Testing Studies

PubMed Central

Veiga-Lopez, Almudena; Pennathur, Subramaniam; Kannan, Kurunthachalam; Patisaul, Heather B.; Dolinoy, Dana C.; Zeng, Lixia

2015-01-01

Bisphenol A (BPA) is a high production volume chemical and an endocrine disruptor. Developmental exposures to BPA have been linked to adult metabolic pathologies, but the pathways through which these disruptions occur remain unknown. This is a comprehensive interspecies association vs causal study to evaluate risks posed by prenatal BPA exposure and to facilitate discovery of biomarkers of relevance to BPA toxicity. Samples from human pregnancies during the first trimester and at term, as well as fetal and/or adult samples from prenatally BPA-treated sheep, rats, and mice, were collected to assess the impact of BPA on free fatty acid and oxidative stress dynamics. Mothers exposed to higher BPA during early to midpregnancy and their matching term cord samples displayed increased 3-nitrotyrosine (NY), a marker of nitrosative stress. Maternal samples had increased palmitic acid, which was positively correlated with NY. Sheep fetuses and adult sheep and rats prenatally exposed to a human-relevant exposure dose of BPA showed increased systemic nitrosative stress. The strongest effect of BPA on circulating free fatty acids was observed in adult mice in the absence of increased oxidative stress. This is the first multispecies study that combines human association and animal causal studies assessing the risk posed by prenatal BPA exposure to metabolic health. This study provides evidence of the induction of nitrosative stress by prenatal BPA in both the mother and fetus at time of birth and is thus supportive of the use of maternal NY as a biomarker for offspring health. PMID:25603046

Translating dosages from animal models to human clinical trials--revisiting body surface area scaling.

PubMed

Blanchard, Otis L; Smoliga, James M

2015-05-01

Body surface area (BSA) scaling has been used for prescribing individualized dosages of various drugs and has also been recommended by the U.S. Food and Drug Administration as one method for using data from animal model species to establish safe starting dosages for first-in-human clinical trials. Although BSA conversion equations have been used in certain clinical applications for decades, recent recommendations to use BSA to derive interspecies equivalents for therapeutic dosages of drug and natural products are inappropriate. A thorough review of the literature reveals that BSA conversions are based on antiquated science and have little justification in current translational medicine compared to more advanced allometric and physiologically based pharmacokinetic modeling. Misunderstood and misinterpreted use of BSA conversions may have disastrous consequences, including underdosing leading to abandonment of potentially efficacious investigational drugs, and unexpected deadly adverse events. We aim to demonstrate that recent recommendations for BSA are not appropriate for animal-to-human dosage conversions and use pharmacokinetic data from resveratrol studies to demonstrate how confusion between the "human equivalent dose" and "pharmacologically active dose" can lead to inappropriate dose recommendations. To optimize drug development, future recommendations for interspecies scaling must be scientifically justified using physiologic, pharmacokinetic, and toxicology data rather than simple BSA conversion. © FASEB.

Full genome analysis of bovine astrovirus from fecal samples of cattle in Japan: identification of possible interspecies transmission of bovine astrovirus.

PubMed

Nagai, Makoto; Omatsu, Tsutomu; Aoki, Hiroshi; Otomaru, Konosuke; Uto, Takehiko; Koizumi, Motoya; Minami-Fukuda, Fujiko; Takai, Hikaru; Murakami, Toshiaki; Masuda, Tsuneyuki; Yamasato, Hiroshi; Shiokawa, Mai; Tsuchiaka, Shinobu; Naoi, Yuki; Sano, Kaori; Okazaki, Sachiko; Katayama, Yukie; Oba, Mami; Furuya, Tetsuya; Shirai, Junsuke; Mizutani, Tetsuya

2015-10-01

A viral metagenomics approach was used to investigate fecal samples of Japanese calves with and without diarrhea. Of the different viral pathogens detected, read counts gave nearly complete astrovirus-related RNA sequences in 15 of the 146 fecal samples collected in three distinct areas (Hokkaido, Ishikawa, and Kagoshima Prefectures) between 2009 and 2015. Due to the lack of genetic information about bovine astroviruses (BoAstVs) in Japan, these sequences were analyzed in this study. Nine of the 15 Japanese BoAstVs were closely related to Chinese BoAstVs and clustered into a lineage (tentatively named lineage 1) in all phylogenetic trees. Three of 15 strains were phylogenetically separate from lineage 1, showing low sequence identities, and clustered instead with an American strain isolated from cattle with respiratory disease (tentatively named lineage 2). Interestingly, two of 15 strains clustered with lineage 1 in the open reading frame (ORF)1a and ORF1b regions, while they clustered with lineage 2 in the ORF2 region. Remarkably, one of 15 strains exhibited low amino acid sequence similarity to other BoAstVs and was clustered separately with porcine astrovirus type 5 in all trees, and ovine astrovirus in the ORF2 region, suggesting past interspecies transmission.

Interspecies sexual behaviour between a male Japanese macaque and female sika deer.

PubMed

Pelé, Marie; Bonnefoy, Alexandre; Shimada, Masaki; Sueur, Cédric

2017-04-01

Interspecies sexual behaviour or 'reproductive interference' has been reported across a wide range of animal taxa. However, most of these occurrences were observed in phylogenetically close species and were mainly discussed in terms of their effect on fitness, hybridization and species survival. The few cases of heterospecific mating in distant species occurred between animals that were bred and maintained in captivity. Only one scientific study has reported this phenomenon, describing sexual harassment of king penguins by an Antarctic fur seal. This is the first article to report mating behaviour between a male Japanese macaque (Macaca fuscata yakui) and female sika deer (Cervus nippon yakushimae) on Yakushima Island, Japan. Although Japanese macaques are known to ride deer, this individual showed clearly sexual behaviour towards several female deer, some of which tried to escape whilst others accepted the mount. This male seems to belong to a group of peripheral males. Although this phenomenon may be explained as copulation learning, this is highly unlikely. The most realistic hypothesis would be that of mate deprivation, which states that males with limited access to females are more likely to display this behaviour. Whatever the cause for this event may be, the observation of highly unusual animal behaviour may be a key to understanding the evolution of heterospecific mating behaviour in the animal kingdom.

Evidence for presumable feline origin of sporadic G6P[9] rotaviruses in humans.

PubMed

Pietsch, Corinna; Liebert, Uwe G

2018-05-31

Species A rotaviruses are highly diverse and impose a substantial burden to human and animal health. Interspecies transmission between livestock, domestic animals and humans is commonly observed, but spread of animal-like rotaviruses within the human population is limited. During the continued monitoring of rotavirus strains in Germany, an unusual G6P[9] rotavirus strain was detected in feces of a child. The complete rotavirus coding sequences revealed a unique G6-P[9]-I2-R2-C2-M2-A3-N2-T3-E2-H3 genotype constellation. The virus was phylogenetically related to feline G3P[9] strains and other human G6P[9] rotaviruses of presumable zoonotic origin. Analysis of primer binding sites of G6 specific genotyping revealed further evidence of a G6P[9] feline reservoir. Moreover, substantial deficits of conventional semi-nested PCR genotyping approaches in detecting contemporary G6P[9] were revealed. Rotavirus strain GER29-14 most likely resulted from a direct or recent interspecies transmission from a cat to human. Further studies could assess nucleic acid sequences and genotype constellations of feline rotavirus to confirm the likely feline origin of sporadic human G6P[9] strains. Copyright © 2018 Elsevier B.V. All rights reserved.

Viral Diversity, Prey Preference, and Bartonella Prevalence in Desmodus rotundus in Guatemala

PubMed Central

Wray, Amy K.; Olival, Kevin J.; Morán, David; Lopez, Maria Renee; Alvarez, Danilo; Navarrete-Macias, Isamara; Liang, Eliza; Simmons, Nancy B.; Lipkin, W. Ian; Daszak, Peter; Anthony, Simon J.

2016-01-01

Certain bat species serve as natural reservoirs for pathogens in several key viral families including henipa-, lyssa-, corona-, and filoviruses, which may pose serious threats to human health. The Common Vampire Bat (Desmodus rotundus), due to its abundance, sanguivorous feeding habit involving humans and domestic animals, and highly social behavioral ecology, may have an unusually high potential for interspecies disease transmission. Previous studies have investigated rabies dynamics in D. rotundus, yet the diversity of other viruses, bacteria, and other microbes that these bats may carry remains largely unknown. We screened 396 blood, urine, saliva, and fecal samples from D. rotundus captured in Guatemala for 13 viral families and genera. Positive results were found for rhabdovirus, adenovirus, and herpesvirus assays. We also screened these samples for Bartonella spp. and found that 38% of individuals tested positive. To characterize potential for interspecies transmission associated with feeding behavior, we also analyzed cytochrome B sequences from fecal samples to identify prey species and found that domestic cattle (Bos taurus) made up the majority of blood meals. Our findings suggest that the risk of pathogen spillover from Desmodus rotundus, including between domestic animal species, is possible and warrants further investigation to characterize this microbial diversity and expand our understanding of foraging ecology in their populations. PMID:27660213

Influenza A virus infection of healthy piglets in an abattoir in Brazil: animal-human interface and risk for interspecies transmission

PubMed Central

Amorim, Ariane Ribeiro; Fornells, Luz Alba Maria Garcete; Reis, Felicidade da Costa; Rezende, Daiana Jacinto; Mendes, Gabriella da Silva; Couceiro, José Nelson dos Santos Silva; Santos, Norma Suely de Oliveira

2013-01-01

Asymptomatic influenza virus infections in pigs are frequent and the lack of measures for controlling viral spread facilitates the circulation of different virus strains between pigs. The goal of this study was to demonstrate the circulation of influenza A virus strains among asymptomatic piglets in an abattoir in Brazil and discuss the potential public health impacts. Tracheal samples (n = 330) were collected from asymptomatic animals by a veterinarian that also performed visual lung tissue examinations. No slaughtered animals presented with any noticeable macroscopic signs of influenza infection following examination of lung tissues. Samples were then analysed by reverse transcription-polymerase chain reaction that resulted in the identification of 30 (9%) influenza A positive samples. The presence of asymptomatic pig infections suggested that these animals could facilitate virus dissemination and act as a source of infection for the herd, thereby enabling the emergence of influenza outbreaks associated with significant economic losses. Furthermore, the continuous exposure of the farm and abattoir workers to the virus increases the risk for interspecies transmission. Monitoring measures of swine influenza virus infections and vaccination and monitoring of employees for influenza infection should also be considered. In addition regulatory agencies should consider the public health ramifications regarding the potential zoonotic viral transmission between humans and pigs. PMID:23903968

mEBT: multiple-matching Evidence-based Translator of Murine Genomic Responses for Human Immunity Studies.

PubMed

Tae, Donghyun; Seok, Junhee

2018-05-29

In this paper, we introduce multiple-matching Evidence-based Translator (mEBT) to discover genomic responses from murine expression data for human immune studies, which are significant in the given condition of mice and likely have similar responses in the corresponding condition of human. mEBT is evaluated over multiple data sets and shows improved inter-species agreement. mEBT is expected to be useful for research groups who use murine models to study human immunity. http://cdal.korea.ac.kr/mebt/. jseok14@korea.ac.kr. Supplementary data are available at Bioinformatics online.

Advancing One Health Policy and Implementation Through the Concept of One Medicine One Science.

PubMed

Cardona, Carol; Travis, Dominic A; Berger, Kavita; Coat, Gwenaële; Kennedy, Shaun; Steer, Clifford J; Murtaugh, Michael P; Sriramarao, P

2015-09-01

Numerous interspecies disease transmission events, Ebola virus being a recent and cogent example, highlight the complex interactions between human, animal, and environmental health and the importance of addressing medicine and health in a comprehensive scientific manner. The diversity of information gained from the natural, social, behavioral, and systems sciences is critical to developing and sustainably promoting integrated health approaches that can be implemented at the local, national, and international levels to meet grand challenges. The Concept of One Medicine One Science (COMOS) as outlined herein describes the interplay between scientific knowledge that underpins health and medicine and efforts toward stabilizing local systems using 2 linked case studies: the food system and emerging infectious disease. Forums such as the International Conference of One Medicine One Science (iCOMOS), where science and policy can be debated together, missing pieces identified, and science-based collaborations formed among industry, governmental, and nongovernmental policy makers and funders, is an essential step in addressing global health. The expertise of multiple disciplines and research foci to support policy development is critical to the implementation of one health and the successful achievement of global health security goals.

Genetic Architecture of Hybrid Male Sterility in Drosophila: Analysis of Intraspecies Variation for Interspecies Isolation

PubMed Central

Reed, Laura K.; LaFlamme, Brooke A.; Markow, Therese A.

2008-01-01

Background The genetic basis of postzygotic isolation is a central puzzle in evolutionary biology. Evolutionary forces causing hybrid sterility or inviability act on the responsible genes while they still are polymorphic, thus we have to study these traits as they arise, before isolation is complete. Methodology/Principal Findings Isofemale strains of D. mojavensis vary significantly in their production of sterile F1 sons when females are crossed to D. arizonae males. We took advantage of the intraspecific polymorphism, in a novel design, to perform quantitative trait locus (QTL) mapping analyses directly on F1 hybrid male sterility itself. We found that the genetic architecture of the polymorphism for hybrid male sterility (HMS) in the F1 is complex, involving multiple QTL, epistasis, and cytoplasmic effects. Conclusions/Significance The role of extensive intraspecific polymorphism, multiple QTL, and epistatic interactions in HMS in this young species pair shows that HMS is arising as a complex trait in this system. Directional selection alone would be unlikely to maintain polymorphism at multiple loci, thus we hypothesize that directional selection is unlikely to be the only evolutionary force influencing postzygotic isolation. PMID:18728782

A comparative analysis of acute-phase proteins as inflammatory biomarkers in preclinical toxicology studies: implications for preclinical to clinical translation.

PubMed

Watterson, Claire; Lanevschi, Anne; Horner, Judith; Louden, Calvert

2009-01-01

Recently, in early clinical development, a few biologics and small molecules intended as antitumor or anti-inflammatory agents have caused a severe adverse pro-inflammatory systemic reaction also known as systemic inflammatory response syndrome (SIRS). This toxicity could result from expected pharmacological effects of a therapeutic antibody and/or from interaction with antigens expressed on cells/tissues other than the intended target. Clinical monitoring of SIRS is challenging because of the narrow diagnostic window to institute a successful intervening therapeutic strategy prior to acute circulatory collapse. Furthermore, for these classes of therapeutic agents, studies in animals have low predictive ability to identify potential human hazards. In vitro screens with human cells, though promising, need further development. Therefore, identification of improved preclinical diagnostic markers of SIRS will enable clinicians to select applicable markers for clinical testing and avoid potentially catastrophic events. There is limited preclinical toxicology data describing the interspecies performance of acute-phase proteins because the response time, type, and duration of major acute-phase proteins vary significantly between species. This review will attempt to address this intellectual gap, as well as the use and applicability of acute-phase proteins as preclinical to clinical translational biomarkers of SIRS.

Pseudomonas aeruginosa Las quorum sensing autoinducer suppresses growth and biofilm production in Legionella species.

PubMed

Kimura, Soichiro; Tateda, Kazuhiro; Ishii, Yoshikazu; Horikawa, Manabu; Miyairi, Shinichi; Gotoh, Naomasa; Ishiguro, Masaji; Yamaguchi, Keizo

2009-06-01

Bacteria commonly communicate with each other by a cell-to-cell signalling mechanism known as quorum sensing (QS). Recent studies have shown that the Las QS autoinducer N-(3-oxododecanoyl)-l-homoserine lactone (3-oxo-C(12)-HSL) of Pseudomonas aeruginosa performs a variety of functions not only in intraspecies communication, but also in interspecies and interkingdom interactions. In this study, we report the effects of Pseudomonas 3-oxo-C(12)-HSL on the growth and suppression of virulence factors in other bacterial species that frequently co-exist with Ps. aeruginosa in nature. It was found that 3-oxo-C(12)-HSL, but not its analogues, suppressed the growth of Legionella pneumophila in a dose-dependent manner. However, 3-oxo-C(12)-HSL did not exhibit a growth-suppressive effect on Serratia marcescens, Proteus mirabilis, Escherichia coli, Alcaligenes faecalis and Stenotrophomonas maltophilia. A concentration of 50 microM 3-oxo-C(12)-HSL completely inhibited the growth of L. pneumophila. Additionally, a significant suppression of biofilm formation was demonstrated in L. pneumophila exposed to 3-oxo-C(12)-HSL. Our results suggest that the Pseudomonas QS autoinducer 3-oxo-C(12)-HSL exerts both bacteriostatic and virulence factor-suppressive activities on L. pneumophila alone.

Interactions and accumulation differences of metal(loid)s in three sea cucumber species collected from the Northern Mediterranean Sea.

PubMed

Tunca, Evren; Aydın, Mehmet; Şahin, ÜlküAlver

2016-10-01

This study was conducted on Holothuria polii, Holothuria tubulosa, and Holothuria mammata collected from five stations with different depths in the Northern Mediterranean Sea. The body walls and guts of these holothurians were examined in terms of interactions of 10 metals (iron (Fe), copper (Cu), manganese (Mn), zinc (Zn), chromium (Cr), cobalt (Co), vanadium (V), nickel (Ni), cadmium (Cd), and lead (Pb)) and one metalloid (arsenic (As)) using a multivariate analysis, and interspecies differences were determined. The multivariate analysis of variance (MANOVA) revealed significant differences between the species in terms of metal(loid) accumulations. The principal component analysis (PCA) showed a more association between H. tubulosa and H. polii with regard to the accumulation. The cluster analysis (CA) located Pb concentrations of the guts to the farthest place from all elements regardless of the species. A correlation analysis displayed that the element concentrations of the guts were more closely related to each other compared with those of the walls. The most inconsistent element in terms of correlations was the gut Fe contents. Accordingly, while Fe concentrations of H. mammata and H. tubulosa were correlated with all elements (except Pb) in divalent metal transporter 1 (DMT1) (divalent cation transporter 1 (DCT1) or natural resistance-associated macrophage protein 2 (NRAMP2)) belonging to the NRAM protein family, this was not the case in H. polii. Consequently, significant relationships between accumulated metal(loid)s that changed by tissues and sea cucumber species were observed.

Quantitative prediction of shrimp disease incidence via the profiles of gut eukaryotic microbiota.

PubMed

Xiong, Jinbo; Yu, Weina; Dai, Wenfang; Zhang, Jinjie; Qiu, Qiongfen; Ou, Changrong

2018-04-01

One common notion is emerging that gut eukaryotes are commensal or beneficial, rather than detrimental. To date, however, surprisingly few studies have been taken to discern the factors that govern the assembly of gut eukaryotes, despite growing interest in the dysbiosis of gut microbiota-disease relationship. Herein, we firstly explored how the gut eukaryotic microbiotas were assembled over shrimp postlarval to adult stages and a disease progression. The gut eukaryotic communities changed markedly as healthy shrimp aged, and converged toward an adult-microbiota configuration. However, the adult-like stability was distorted by disease exacerbation. A null model untangled that the deterministic processes that governed the gut eukaryotic assembly tended to be more important over healthy shrimp development, whereas this trend was inverted as the disease progressed. After ruling out the baseline of gut eukaryotes over shrimp ages, we identified disease-discriminatory taxa (species level afforded the highest accuracy of prediction) that characteristic of shrimp health status. The profiles of these taxa contributed an overall 92.4% accuracy in predicting shrimp health status. Notably, this model can accurately diagnose the onset of shrimp disease. Interspecies interaction analysis depicted how the disease-discriminatory taxa interacted with one another in sustaining shrimp health. Taken together, our findings offer novel insights into the underlying ecological processes that govern the assembly of gut eukaryotes over shrimp postlarval to adult stages and a disease progression. Intriguingly, the established model can quantitatively and accurately predict the incidences of shrimp disease.

Streptococcus mutans competence-stimulating peptide inhibits Candida albicans hypha formation.

PubMed

Jarosz, Lucja M; Deng, Dong Mei; van der Mei, Henny C; Crielaard, Wim; Krom, Bastiaan P

2009-11-01

The oral cavity is colonized by microorganisms growing in biofilms in which interspecies interactions take place. Streptococcus mutans grows in biofilms on enamel surfaces and is considered one of the main etiological agents of human dental caries. Candida albicans is also commonly found in the human oral cavity, where it interacts with S. mutans. C. albicans is a polymorphic fungus, and the yeast-to-hypha transition is involved in virulence and biofilm formation. The aim of this study was to investigate interkingdom communication between C. albicans and S. mutans based on the production of secreted molecules. S. mutans UA159 inhibited C. albicans germ tube (GT) formation in cocultures even when physically separated from C. albicans. Only S. mutans spent medium collected in the early exponential phase (4-h-old cultures) inhibited the GT formation of C. albicans. During this phase, S. mutans UA159 produces a quorum-sensing molecule, competence-stimulating peptide (CSP). The role of CSP in inhibiting GT formation was confirmed by using synthetic CSP and a comC deletion strain of S. mutans UA159, which lacks the ability to produce CSP. Other S. mutans strains and other Streptococcus spp. also inhibited GT formation but to different extents, possibly reflecting differences in CSP amino acid sequences among Streptococcus spp. or differences in CSP accumulation in the media. In conclusion, CSP, an S. mutans quorum-sensing molecule secreted during the early stages of growth, inhibits the C. albicans morphological switch.

Time-of-flight expansion of binary Bose–Einstein condensates at finite temperature

NASA Astrophysics Data System (ADS)

Lee, K. L.; Jørgensen, N. B.; Wacker, L. J.; Skou, M. G.; Skalmstang, K. T.; Arlt, J. J.; Proukakis, N. P.

2018-05-01

Ultracold quantum gases provide a unique setting for studying and understanding the properties of interacting quantum systems. Here, we investigate a multi-component system of 87Rb–39K Bose–Einstein condensates (BECs) with tunable interactions both theoretically and experimentally. Such multi-component systems can be characterized by their miscibility, where miscible components lead to a mixed ground state and immiscible components form a phase-separated state. Here we perform the first full simulation of the dynamical expansion of this system including both BECs and thermal clouds, which allows for a detailed comparison with experimental results. In particular we show that striking features emerge in time-of-flight (TOF) for BECs with strong interspecies repulsion, even for systems which were separated in situ by a large gravitational sag. An analysis of the centre of mass positions of the BECs after expansion yields qualitative agreement with the homogeneous criterion for phase-separation, but reveals no clear transition point between the mixed and the separated phases. Instead one can identify a transition region, for which the presence of a gravitational sag is found to be advantageous. Moreover, we analyse the situation where only one component is condensed and show that the density distribution of the thermal component also shows some distinct features. Our work sheds new light on the analysis of multi-component systems after TOF and will guide future experiments on the detection of miscibility in these systems.

Daytime behavior of Pteropus vampyrus in a natural habitat: the driver of viral transmission.

PubMed

Hengjan, Yupadee; Pramono, Didik; Takemae, Hitoshi; Kobayashi, Ryosuke; Iida, Keisuke; Ando, Takeshi; Kasmono, Supratikno; Basri, Chaerul; Fitriana, Yuli Sulistya; Arifin, Eko M Z; Ohmori, Yasushige; Maeda, Ken; Agungpriyono, Srihadi; Hondo, Eiichi

2017-06-29

Flying foxes, the genus Pteropus, are considered viral reservoirs. Their colonial nature and long flight capability enhance their ability to spread viruses quickly. To understand how the viral transmission occurs between flying foxes and other animals, we investigated daytime behavior of the large flying fox (Pteropus vampyrus) in the Leuweung Sancang conservation area, Indonesia, by using instantaneous scan sampling and all-occurrence focal sampling. The data were obtained from 0700 to 1700 hr, during May 11-25, 2016. Almost half of the flying foxes (46.9 ± 10.6% of all recorded bats) were awake and showed various levels of activity during daytime. The potential behaviors driving disease transmission, such as self-grooming, mating/courtship and aggression, peaked in the early morning. Males were more active and spent more time on sexual activities than females. There was no significant difference in time spent for negative social behaviors between sexes. Positive social behaviors, especially maternal cares, were performed only by females. Sexual activities and negative/positive social behaviors enable fluid exchange between bats and thus facilitate intraspecies transmission. Conflicts for living space between the flying foxes and the ebony leaf monkey (Trachypithecus auratus) were observed, and this caused daily roosting shifts of flying foxes. The ecological interactions between bats and other wildlife increase the risk of interspecies infection. This study provides the details of the flying fox's behavior and its interaction with other wildlife in South-East Asia that may help explain how pathogen spillover occurs in the wild.

Trends of the Major Porin Gene (ompF) Evolution: Insight from the Genus Yersinia

PubMed Central

Stenkova, Anna M.; Isaeva, Marina P.; Shubin, Felix N.; Rasskazov, Valeri A.; Rakin, Alexander V.

2011-01-01

OmpF is one of the major general porins of Enterobacteriaceae that belongs to the first line of bacterial defense and interactions with the biotic as well as abiotic environments. Porins are surface exposed and their structures strongly reflect the history of multiple interactions with the environmental challenges. Unfortunately, little is known on diversity of porin genes of Enterobacteriaceae and the genus Yersinia especially. We analyzed the sequences of the ompF gene from 73 Yersinia strains covering 14 known species. The phylogenetic analysis placed most of the Yersinia strains in the same line assigned by 16S rDNA-gyrB tree. Very high congruence in the tree topologies was observed for Y. enterocolitica, Y. kristensenii, Y. ruckeri, indicating that intragenic recombination in these species had no effect on the ompF gene. A significant level of intra- and interspecies recombination was found for Y. aleksiciae, Y. intermedia and Y. mollaretii. Our analysis shows that the ompF gene of Yersinia has evolved with nonrandom mutational rate under purifying selection. However, several surface loops in the OmpF porin contain positively selected sites, which very likely reflect adaptive diversification Yersinia to their ecological niches. To our knowledge, this is a first investigation of diversity of the porin gene covering the whole genus of the family Enterobacteriaceae. This study demonstrates that recombination and positive selection both contribute to evolution of ompF, but the relative contribution of these evolutionary forces are different among Yersinia species. PMID:21655186

Adaptation of Pseudomonas aeruginosa in Cystic Fibrosis Airways Influences Virulence of Staphylococcus aureus In Vitro and Murine Models of Co-Infection

PubMed Central

Baldan, Rossella; Cigana, Cristina; Testa, Francesca; Bianconi, Irene; De Simone, Maura; Pellin, Danilo; Di Serio, Clelia

2014-01-01

Cystic fibrosis (CF) airways disease represents an example of polymicrobial infection whereby different bacterial species can interact and influence each other. In CF patients Staphylococcus aureus is often the initial pathogen colonizing the lungs during childhood, while Pseudomonas aeruginosa is the predominant pathogen isolated in adolescents and adults. During chronic infection, P. aeruginosa undergoes adaptation to cope with antimicrobial therapy, host response and co-infecting pathogens. However, S. aureus and P. aeruginosa often co-exist in the same niche influencing the CF pathogenesis. The goal of this study was to investigate the reciprocal interaction of P. aeruginosa and S. aureus and understand the influence of P. aeruginosa adaptation to the CF lung in order to gain important insight on the interplay occurring between the two main pathogens of CF airways, which is still largely unknown. P. aeruginosa reference strains and eight lineages of clinical strains, including early and late clonal isolates from different patients with CF, were tested for growth inhibition of S. aureus. Next, P. aeruginosa/S. aureus competition was investigated in planktonic co-culture, biofilm, and mouse pneumonia model. P. aeruginosa reference and early strains, isolated at the onset of chronic infection, outcompeted S. aureus in vitro and in vivo models of co-infection. On the contrary, our results indicated a reduced capacity to outcompete S. aureus of P. aeruginosa patho-adaptive strains, isolated after several years of chronic infection and carrying several phenotypic changes temporally associated with CF lung adaptation. Our findings provide relevant information with respect to interspecies interaction and disease progression in CF. PMID:24603807

Methanogenic archaea and sulfate reducing bacteria co-cultured on acetate: teamwork or coexistence?

PubMed

Ozuolmez, Derya; Na, Hyunsoo; Lever, Mark A; Kjeldsen, Kasper U; Jørgensen, Bo B; Plugge, Caroline M

2015-01-01

Acetate is a major product of fermentation processes and an important substrate for sulfate reducing bacteria and methanogenic archaea. Most studies on acetate catabolism by sulfate reducers and methanogens have used pure cultures. Less is known about acetate conversion by mixed pure cultures and the interactions between both groups. We tested interspecies hydrogen transfer and coexistence between marine methanogens and sulfate reducers using mixed pure cultures of two types of microorganisms. First, Desulfovibrio vulgaris subsp. vulgaris (DSM 1744), a hydrogenotrophic sulfate reducer, was cocultured together with the obligate aceticlastic methanogen Methanosaeta concilii using acetate as carbon and energy source. Next, Methanococcus maripaludis S2, an obligate H2- and formate-utilizing methanogen, was used as a partner organism to M. concilii in the presence of acetate. Finally, we performed a coexistence experiment between M. concilii and an acetotrophic sulfate reducer Desulfobacter latus AcSR2. Our results showed that D. vulgaris was able to reduce sulfate and grow from hydrogen leaked by M. concilii. In the other coculture, M. maripaludis was sustained by hydrogen leaked by M. concilii as revealed by qPCR. The growth of the two aceticlastic microbes indicated co-existence rather than competition. Altogether, our results indicate that H2 leaking from M. concilii could be used by efficient H2-scavengers. This metabolic trait, revealed from coculture studies, brings new insight to the metabolic flexibility of methanogens and sulfate reducers residing in marine environments in response to changing environmental conditions and community compositions. Using dedicated physiological studies we were able to unravel the occurrence of less obvious interactions between marine methanogens and sulfate-reducing bacteria.

Methanogenic archaea and sulfate reducing bacteria co-cultured on acetate: teamwork or coexistence?

PubMed Central

Ozuolmez, Derya; Na, Hyunsoo; Lever, Mark A.; Kjeldsen, Kasper U.; Jørgensen, Bo B.; Plugge, Caroline M.

2015-01-01

Acetate is a major product of fermentation processes and an important substrate for sulfate reducing bacteria and methanogenic archaea. Most studies on acetate catabolism by sulfate reducers and methanogens have used pure cultures. Less is known about acetate conversion by mixed pure cultures and the interactions between both groups. We tested interspecies hydrogen transfer and coexistence between marine methanogens and sulfate reducers using mixed pure cultures of two types of microorganisms. First, Desulfovibrio vulgaris subsp. vulgaris (DSM 1744), a hydrogenotrophic sulfate reducer, was cocultured together with the obligate aceticlastic methanogen Methanosaeta concilii using acetate as carbon and energy source. Next, Methanococcus maripaludis S2, an obligate H2- and formate-utilizing methanogen, was used as a partner organism to M. concilii in the presence of acetate. Finally, we performed a coexistence experiment between M. concilii and an acetotrophic sulfate reducer Desulfobacter latus AcSR2. Our results showed that D. vulgaris was able to reduce sulfate and grow from hydrogen leaked by M. concilii. In the other coculture, M. maripaludis was sustained by hydrogen leaked by M. concilii as revealed by qPCR. The growth of the two aceticlastic microbes indicated co-existence rather than competition. Altogether, our results indicate that H2 leaking from M. concilii could be used by efficient H2-scavengers. This metabolic trait, revealed from coculture studies, brings new insight to the metabolic flexibility of methanogens and sulfate reducers residing in marine environments in response to changing environmental conditions and community compositions. Using dedicated physiological studies we were able to unravel the occurrence of less obvious interactions between marine methanogens and sulfate-reducing bacteria. PMID:26074892

Stringent DDI-based prediction of H. sapiens-M. tuberculosis H37Rv protein-protein interactions.

PubMed

Zhou, Hufeng; Rezaei, Javad; Hugo, Willy; Gao, Shangzhi; Jin, Jingjing; Fan, Mengyuan; Yong, Chern-Han; Wozniak, Michal; Wong, Limsoon

2013-01-01

H. sapiens-M. tuberculosis H37Rv protein-protein interaction (PPI) data are very important information to illuminate the infection mechanism of M. tuberculosis H37Rv. But current H. sapiens-M. tuberculosis H37Rv PPI data are very scarce. This seriously limits the study of the interaction between this important pathogen and its host H. sapiens. Computational prediction of H. sapiens-M. tuberculosis H37Rv PPIs is an important strategy to fill in the gap. Domain-domain interaction (DDI) based prediction is one of the frequently used computational approaches in predicting both intra-species and inter-species PPIs. However, the performance of DDI-based host-pathogen PPI prediction has been rather limited. We develop a stringent DDI-based prediction approach with emphasis on (i) differences between the specific domain sequences on annotated regions of proteins under the same domain ID and (ii) calculation of the interaction strength of predicted PPIs based on the interacting residues in their interaction interfaces. We compare our stringent DDI-based approach to a conventional DDI-based approach for predicting PPIs based on gold standard intra-species PPIs and coherent informative Gene Ontology terms assessment. The assessment results show that our stringent DDI-based approach achieves much better performance in predicting PPIs than the conventional approach. Using our stringent DDI-based approach, we have predicted a small set of reliable H. sapiens-M. tuberculosis H37Rv PPIs which could be very useful for a variety of related studies. We also analyze the H. sapiens-M. tuberculosis H37Rv PPIs predicted by our stringent DDI-based approach using cellular compartment distribution analysis, functional category enrichment analysis and pathway enrichment analysis. The analyses support the validity of our prediction result. Also, based on an analysis of the H. sapiens-M. tuberculosis H37Rv PPI network predicted by our stringent DDI-based approach, we have discovered some important properties of domains involved in host-pathogen PPIs. We find that both host and pathogen proteins involved in host-pathogen PPIs tend to have more domains than proteins involved in intra-species PPIs, and these domains have more interaction partners than domains on proteins involved in intra-species PPI. The stringent DDI-based prediction approach reported in this work provides a stringent strategy for predicting host-pathogen PPIs. It also performs better than a conventional DDI-based approach in predicting PPIs. We have predicted a small set of accurate H. sapiens-M. tuberculosis H37Rv PPIs which could be very useful for a variety of related studies.

Species-specific viability analysis of Pseudomonas aeruginosa, Burkholderia cepacia and Staphylococcus aureus in mixed culture by flow cytometry

PubMed Central

2014-01-01

Background Bacterial species coexist commonly in mixed communities, for instance those occurring in microbial infections of humans. Interspecies effects contribute to alterations in composition of communities with respect to species and thus, to the course and severity of infection. Therefore, knowledge concerning growth and viability of single species in medically-relevant mixed communities is of high interest to resolve complexity of interspecies dynamics and to support development of treatment strategies. In this study, a flow cytometric method was established to assess the species-specific viability in defined three-species mixed cultures. The method enables the characterization of viability of Pseudomonas aeruginosa, Burkholderia cepacia and Staphylococcus aureus, which are relevant to lung infections of Cystic Fibrosis (CF) patients. The method combines fluorescence detection by antibody and lectin labeling with viability fluorescence staining using SYBR®Green I and propidium iodide. In addition, species-specific cell enumeration analysis using quantitative terminal restriction fragment length polymorphisms (qT-RFLP) was used to monitor the growth dynamics. Finally, to investigate the impact of substrate availability on growth and viability, concentrations of main substrates and metabolites released were determined. Results For each species, the time course of growth and viability during mixed culture cultivations was obtained by using qT-RFLP analysis in combination with flow cytometry. Comparison between mixed and pure cultures revealed for every species differences in growth properties, e.g. enhanced growth of P. aeruginosa in mixed culture. Differences were also observed for B. cepacia and S. aureus in the time course of viability, e.g. an early and drastic reduction of viability of S. aureus in mixed culture. Overall, P. aeruginosa clearly dominated the mixed culture with regard to obtained cell concentrations. Conclusions In combination with qT-RFLP analysis, the methods enabled monitoring of species-specific cell concentrations and viability during co-cultivation of theses strains. Experimental findings suggest that the predominance of P. aeruginosa over B. cepacia and S. aureus in mixed culture under the chosen cultivation conditions is promoted by more efficient substrate consumption of P. aeruginosa, and antagonistic interspecies effects induced by P. aeruginosa. PMID:24606608

Interspecies differences in metabolism of arsenic by cultured primary hepatocytes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Drobna, Zuzana; Walton, Felecia S.; Harmon, Anne W.

2010-05-15

Biomethylation is the major pathway for the metabolism of inorganic arsenic (iAs) in many mammalian species, including the human. However, significant interspecies differences have been reported in the rate of in vivo metabolism of iAs and in yields of iAs metabolites found in urine. Liver is considered the primary site for the methylation of iAs and arsenic (+3 oxidation state) methyltransferase (As3mt) is the key enzyme in this pathway. Thus, the As3mt-catalyzed methylation of iAs in the liver determines in part the rate and the pattern of iAs metabolism in various species. We examined kinetics and concentration-response patterns for iAsmore » methylation by cultured primary hepatocytes derived from human, rat, mice, dog, rabbit, and rhesus monkey. Hepatocytes were exposed to [{sup 73}As]arsenite (iAs{sup III}; 0.3, 0.9, 3.0, 9.0 or 30 nmol As/mg protein) for 24 h and radiolabeled metabolites were analyzed in cells and culture media. Hepatocytes from all six species methylated iAs{sup III} to methylarsenic (MAs) and dimethylarsenic (DMAs). Notably, dog, rat and monkey hepatocytes were considerably more efficient methylators of iAs{sup III} than mouse, rabbit or human hepatocytes. The low efficiency of mouse, rabbit and human hepatocytes to methylate iAs{sup III} was associated with inhibition of DMAs production by moderate concentrations of iAs{sup III} and with retention of iAs and MAs in cells. No significant correlations were found between the rate of iAs methylation and the thioredoxin reductase activity or glutathione concentration, two factors that modulate the activity of recombinant As3mt. No associations between the rates of iAs methylation and As3mt protein structures were found for the six species examined. Immunoblot analyses indicate that the superior arsenic methylation capacities of dog, rat and monkey hepatocytes examined in this study may be associated with a higher As3mt expression. However, factors other than As3mt expression may also contribute to the interspecies differences in the hepatocyte capacity to methylate iAs.« less

The nuclear question: rethinking species importance in multi-species animal groups.

PubMed

Srinivasan, Umesh; Raza, Rashid Hasnain; Quader, Suhel

2010-09-01

1. Animals group for various benefits, and may form either simple single-species groups, or more complex multi-species associations. Multi-species groups are thought to provide anti-predator and foraging benefits to participant individuals. 2. Despite detailed studies on multi-species animal groups, the importance of species in group initiation and maintenance is still rated qualitatively as 'nuclear' (maintaining groups) or 'attendant' (species following nuclear species) based on species-specific traits. This overly simplifies and limits understanding of inherently complex associations, and is biologically unrealistic, because species roles in multi-species groups are: (i) likely to be context-specific and not simply a fixed species property, and (ii) much more variable than this dichotomy indicates. 3. We propose a new view of species importance (measured as number of inter-species associations), along a continuum from 'most nuclear' to 'least nuclear'. Using mixed-species bird flocks from a tropical rainforest in India as an example, we derive inter-species association measures from randomizations on bird species abundance data (which takes into account species 'availability') and data on 86 mixed-species flocks from two different flock types. Our results show that the number and average strength of inter-species associations covary positively, and we argue that species with many, strong associations are the most nuclear. 4. From our data, group size and foraging method are ecological and behavioural traits of species that best explain nuclearity in mixed-species bird flocks. Parallels have been observed in multi-species fish shoals, in which group size and foraging method, as well as diet, have been shown to correlate with nuclearity. Further, the context in which multi-species groups occur, in conjunction with species-specific traits, influences the role played by a species in a multi-species group, and this highlights the importance of extrinsic factors in shaping species importance. 5. Our view of nuclearity provides predictive power in examining species roles in a variety of situations (e.g. predicting leadership in differently composed communities), and can be applied to examine a broad range of ecological and evolutionary questions pertinent to multi-species groups in general.

On the surprising lack of differences between two congeneric calanoid copepod species, Calanus finmarchicus and C. helgolandicus

NASA Astrophysics Data System (ADS)

Wilson, Robert J.; Speirs, Douglas C.; Heath, Michael R.

2015-05-01

The important calanoid copepod species Calanus finmarchicus and C. helgolandicus have distinct geographic ranges which are changing under the influence of climate change. Understanding the mechanisms underlying their distributions is becoming increasingly important as a result of the possible ecological impacts of these range shifts. Here we review inter-species differences in key life cycle traits that influence each species' geographic distribution, in particular development and growth, fecundity, feeding behaviour, vertical migration and overwintering behaviour. The distinct temperature niche of each species leads to an a priori assumption that the response of life cycle traits to temperature is a key determinant of their contrasting geographic distributions. A new development model was created to reconcile published experimental development times for each species. Model output indicates that at temperatures below approximately 12-13 °C, C. finmarchicus is the faster developing species, but above these temperatures C. helgolandicus develops more quickly. Conventionally Calanus development time is assumed to decrease monotonically with temperature; however our model indicates that the response of development time to temperature is instead U-shaped. Differences in life cycle aspects such as seasonality and vertical structuring are interpreted in light of this development model. Body size and lipid accumulation abilities could be significant influences on each species' geographic distribution; however evidence is consistent with inter-species differences not existing for these traits. Published evidence shows that inter-species differences in egg production may exist, but do not follow a clear pattern. Diapause is an important and well studied life cycle adaptation of C. finmarchicus, but has received little attention in C. helgolandicus. We reviewed knowledge of diapause and suggest the hypothesis that C. helgolandicus is restricted to continental shelf regions as a result of an inability to diapause for significant periods. This synthesised view of each species' respective life cycle traits is that response of growth and development to temperature is the only known difference between each species, which indicates a promising direction for the extension of population models of C. finmarchicus to C. helgolandicus.

INTERSPECIES CORRELATION ESTIMATES PREDICT PROTECTIVE ENVIRONMENTAL CONCENTRATIONS

EPA Science Inventory

Environmental risk assessments often use multiple single species toxicity test results and species sensitivity distributions (SSDs) to derive a predicted no-effect concentration in the environment, typically the 5th percentile of the SSD, termed the HC5. The shape and location of...

IDENTIFICATION OF INTERSPECIES CONCORDANCE OF MECHANISMS OF ARSENIC-INDUCED BLADDER CANCER

EPA Science Inventory

Exposure to arsenic causes cancer by inducing a variety of responses that affect the expression of genes associated with numerous biological pathways leading to altered cell growth and proliferation, signaling, apoptosis and oxidative stress response. Affymetrix GeneChip® arrays ...

Interspecies Correlation Estimation - Applications in Water Quality Criteria and Ecological Risk Assessment

EPA Science Inventory

Water quality criteria (WQC) designate the maximum concentrations of water-borne toxicants that do not adversely affect specific protection goals under certain natural conditions. As the foundation of water quality standards, WQC provide a critical scientific basis for environmen...

Live Animal Markets in Minnesota: A Potential Source for Emergence of Novel Influenza A Viruses and Interspecies Transmission

PubMed Central

Choi, Mary J.; Torremorell, Montserrat; Bender, Jeff B.; Smith, Kirk; Boxrud, David; Ertl, Jon R.; Yang, My; Suwannakarn, Kamol; Her, Duachi; Nguyen, Jennifer; Uyeki, Timothy M.; Levine, Min; Lindstrom, Stephen; Katz, Jacqueline M.; Jhung, Michael; Vetter, Sara; Wong, Karen K.; Sreevatsan, Srinand; Lynfield, Ruth

2015-01-01

Background. Live animal markets have been implicated in transmission of influenza A viruses (IAVs) from animals to people. We sought to characterize IAVs at 2 live animal markets in Minnesota to assess potential routes of occupational exposure and risk for interspecies transmission. Methods. We implemented surveillance for IAVs among employees, swine, and environment (air and surfaces) during a 12-week period (October 2012–January 2013) at 2 markets epidemiologically associated with persons with swine-origin IAV (variant) infections. Real-time reverse transcription polymerase chain reaction (rRT-PCR), viral culture, and whole-genome sequencing were performed on respiratory and environmental specimens, and serology on sera from employees at beginning and end of surveillance. Results. Nasal swabs from 11 of 17 (65%) employees tested positive for IAVs by rRT-PCR; 7 employees tested positive on multiple occasions and 1 employee reported influenza-like illness. Eleven of 15 (73%) employees had baseline hemagglutination inhibition antibody titers ≥40 to swine-origin IAVs, but only 1 demonstrated a 4-fold titer increase to both swine-origin and pandemic A/Mexico/4108/2009 IAVs. IAVs were isolated from swine (72/84), air (30/45), and pen railings (5/21). Whole-genome sequencing of 122 IAVs isolated from swine and environmental specimens revealed multiple strains and subtype codetections. Multiple gene segment exchanges among and within subtypes were observed, resulting in new genetic constellations and reassortant viruses. Genetic sequence similarities of 99%–100% among IAVs of 1 market customer and swine indicated interspecies transmission. Conclusions. At markets where swine and persons are in close contact, swine-origin IAVs are prevalent and potentially provide conditions for novel IAV emergence. PMID:26223994

Prion replication without host adaptation during interspecies transmissions.

PubMed

Bian, Jifeng; Khaychuk, Vadim; Angers, Rachel C; Fernández-Borges, Natalia; Vidal, Enric; Meyerett-Reid, Crystal; Kim, Sehun; Calvi, Carla L; Bartz, Jason C; Hoover, Edward A; Agrimi, Umberto; Richt, Jürgen A; Castilla, Joaquín; Telling, Glenn C

2017-01-31

Adaptation of prions to new species is thought to reflect the capacity of the host-encoded cellular form of the prion protein (PrP C ) to selectively propagate optimized prion conformations from larger ensembles generated in the species of origin. Here we describe an alternate replicative process, termed nonadaptive prion amplification (NAPA), in which dominant conformers bypass this requirement during particular interspecies transmissions. To model susceptibility of horses to prions, we produced transgenic (Tg) mice expressing cognate PrP C Although disease transmission to only a subset of infected TgEq indicated a significant barrier to EqPrP C conversion, the resulting horse prions unexpectedly failed to cause disease upon further passage to TgEq. TgD expressing deer PrP C was similarly refractory to deer prions from diseased TgD infected with mink prions. In both cases, the resulting prions transmitted to mice expressing PrP C from the species of prion origin, demonstrating that transmission barrier eradication of the originating prions was ephemeral and adaptation superficial in TgEq and TgD. Horse prions produced in vitro by protein misfolding cyclic amplification of mouse prions using horse PrP C also failed to infect TgEq but retained tropism for wild-type mice. Concordant patterns of neuropathology and prion deposition in susceptible mice infected with NAPA prions and the corresponding prion of origin confirmed preservation of strain properties. The comparable responses of both prion types to guanidine hydrochloride denaturation indicated this occurs because NAPA precludes selection of novel prion conformations. Our findings provide insights into mechanisms regulating interspecies prion transmission and a framework to reconcile puzzling epidemiological features of certain prion disorders.

Prion replication without host adaptation during interspecies transmissions

PubMed Central

Bian, Jifeng; Khaychuk, Vadim; Angers, Rachel C.; Fernández-Borges, Natalia; Meyerett-Reid, Crystal; Kim, Sehun; Calvi, Carla L.; Bartz, Jason C.; Hoover, Edward A.; Agrimi, Umberto; Richt, Jürgen A.; Castilla, Joaquín; Telling, Glenn C.

2017-01-01

Adaptation of prions to new species is thought to reflect the capacity of the host-encoded cellular form of the prion protein (PrPC) to selectively propagate optimized prion conformations from larger ensembles generated in the species of origin. Here we describe an alternate replicative process, termed nonadaptive prion amplification (NAPA), in which dominant conformers bypass this requirement during particular interspecies transmissions. To model susceptibility of horses to prions, we produced transgenic (Tg) mice expressing cognate PrPC. Although disease transmission to only a subset of infected TgEq indicated a significant barrier to EqPrPC conversion, the resulting horse prions unexpectedly failed to cause disease upon further passage to TgEq. TgD expressing deer PrPC was similarly refractory to deer prions from diseased TgD infected with mink prions. In both cases, the resulting prions transmitted to mice expressing PrPC from the species of prion origin, demonstrating that transmission barrier eradication of the originating prions was ephemeral and adaptation superficial in TgEq and TgD. Horse prions produced in vitro by protein misfolding cyclic amplification of mouse prions using horse PrPC also failed to infect TgEq but retained tropism for wild-type mice. Concordant patterns of neuropathology and prion deposition in susceptible mice infected with NAPA prions and the corresponding prion of origin confirmed preservation of strain properties. The comparable responses of both prion types to guanidine hydrochloride denaturation indicated this occurs because NAPA precludes selection of novel prion conformations. Our findings provide insights into mechanisms regulating interspecies prion transmission and a framework to reconcile puzzling epidemiological features of certain prion disorders. PMID:28096357

Interspecies difference in placement of developing teeth and its relationship with cross-sectional geometry of the mandibular symphysis in four primate species including modern humans.

PubMed

Fukase, Hitoshi

2012-02-01

The form of the anthropoid mandibular symphysis has recently been addressed in association with spatial requirements for the forming anterior teeth. To evaluate potential relationships between the symphyseal shape and teeth further, the growth patterns of the symphyseal region and the positioning of the tooth crypts were examined using CT data, comparing four primate species (modern humans, chimpanzees, Japanese monkeys, and hamadryas baboons) with varied symphyseal curvature and tooth size. First, results showed that interspecies differences in overall mandibular shape including symphyseal inclination and bicanine width are consistently expressed throughout postnatal ontogeny, although local symphyseal configurations related to the superior transverse torus (STT) tended to change considerably during growth in chimpanzees. Second, the four species were found to exhibit differentiated formation positions of the incisor and canine crypts. In particular, I2 developed between I1 and C in humans with a broad bicanine space and small teeth, whereas it was positioned posterior to I1 and above C in the cercopithecines with an extremely narrow bicanine space. In chimpanzees, despite the large bicanine width, I1 and I2 grew with a large antero-posterior overlap owing to their large size. These results indicate that the dental positioning is determined in concert with the size balance of the available mandibular space and forming teeth. Finally, the positions/contours of I2 crypt were shown to correspond strongly with the STT across the taxa. This suggests that interspecies differences in symphyseal shape should be interpreted partially by the species-specific positional relationships of the developing anterior teeth. Copyright © 2011 Wiley Periodicals, Inc.

Effects of Inversions on Within- and Between-Species Recombination and Divergence

PubMed Central

Stevison, Laurie S.; Hoehn, Kenneth B.; Noor, Mohamed A. F.

2011-01-01

Chromosomal inversions disrupt recombination in heterozygotes by both reducing crossing-over within inverted regions and increasing it elsewhere in the genome. The reduction of recombination in inverted regions facilitates the maintenance of hybridizing species, as outlined by various models of chromosomal speciation. We present a comprehensive comparison of the effects of inversions on recombination rates and on nucleotide divergence. Within an inversion differentiating Drosophila pseudoobscura and Drosophila persimilis, we detected one double recombinant among 9,739 progeny from F1 hybrids screened, consistent with published double-crossover frequencies observed within species. Despite similar rates of exchange within and between species, we found no sequence-based evidence of ongoing gene exchange between species within this inversion, but significant exchange was inferred within species. We also observed greater differentiation at regions near inversion breakpoints between species versus within species. Moreover, we observed strong “interchromosomal effect” (higher recombination in inversion heterozygotes between species) with up to 9-fold higher recombination rates along collinear segments of chromosome two in hybrids. Further, we observed that regions most susceptible to changes in recombination rates corresponded to regions with lower recombination rates in homokaryotypes. Finally, we showed that interspecies nucleotide divergence is lower in regions with greater increases in recombination rate, potentially resulting from greater interspecies exchange. Overall, we have identified several similarities and differences between inversions segregating within versus between species in their effects on recombination and divergence. We conclude that these differences are most likely due to lower frequency of heterokaryotypes and to fitness consequences from the accumulation of various incompatibilities between species. Additionally, we have identified possible effects of inversions on interspecies gene exchange that had not been considered previously. PMID:21828374

Interspecies and interregional comparisons of the chemistry of PAHs and trace elements in mosses Hylocomium splendens (Hedw.) B.S.G. and Pleurozium schreberi (Brid.) Mitt. from Poland and Alaska

USGS Publications Warehouse

Migaszewski, Z.M.; Galuszka, A.; Crock, J.G.; Lamothe, P.J.; Dolegowska, S.

2009-01-01

Comparative biogeochemical studies performed on the same plant species in remote areas enable pinpointing interspecies and interregional differences of chemical composition. This report presents baseline concentrations of PAHs and trace elements in moss species Hylocomium splendens and Pleurozium schreberi from the Holy Cross Mountains (south-central Poland) (HCM) and Wrangell-Saint Elias National Park and Preserve (Alaska) and Denali National Park and Preserve (Alaska). Total PAH concentrations in the mosses of HCM were in the range of 473-2970 ??g kg-1 (dry weight basis; DW), whereas those in the same species of Alaska were 80-3390 ??g kg-1 DW. Nearly all the moss samples displayed the similar ring sequence: 3 > 4 > 5 > 6 for the PAHs. The 3 + 4 ring/total PAH ratios show statistically significant differences between HCM (0.73) and Alaska (0.91). The elevated concentrations of PAHs observed in some sampling locations of the Alaskan parks were linked to local combustion of wood, with a component of vehicle particle- and vapor-phase emissions. In HCM, the principal source of PAH emissions has been linked to residential and industrial combustion of coal and vehicle traffic. In contrast to HCM, the Alaskan mosses were distinctly elevated in most of the trace elements, bearing a signature of??the underlying geology. H.??splendens and P. schreberi showed diverse bioaccumulative capabilities of PAHs in all three study areas. ?? 2008 Elsevier Ltd.

Reducing uncertainty in species sensitivity distributions with interspecies toxicity estimation models

EPA Science Inventory

Determining harmful levels of contaminants for a wide range of species is limited by available toxicological data. Ecological risk assessments typically depend on empirical data from only a few species that represent a narrow range of the life history spectrum. Extrapolation mo...

Bringing the Biosphere Home.

ERIC Educational Resources Information Center

Thomashow, Mitchell

2002-01-01

Discusses an orientation to the local environment as the lens through which to detect global change. Discusses how students can relate to a structure that includes the intertemporal, interspatial, intergenerational, and interspecies realities of place leading to a comprehensive view of biology. Discusses the existential tensions intrinsic to…

Development and Practical Application of Petroleum and Dispersant Interspecies Correlation Models for Aquatic Species

EPA Science Inventory

Assessing the acute toxicity of physically and chemically dispersed oil following an oil spill has generally relied on existing toxicological data for a relatively limited number of aquatic species. Recognition of differences in species sensitivities to contaminants has facilitat...

Syntrophic anaerobic photosynthesis via direct interspecies electron transfer

DOE PAGES

Ha, Phuc T.; Lindemann, Stephen R.; Shi, Liang; ...

2017-01-09

Microbial phototrophs, key primary producers on Earth, use H 2O, H 2, H 2S and other reduced inorganic compounds as electron donors. Here we describe a form of metabolism linking anoxygenic photosynthesis to anaerobic respiration that we call ‘syntrophic anaerobic photosynthesis’. We show that photoautotrophy in the green sulfur bacterium Prosthecochloris aestaurii can be driven by either electrons from a solid electrode or acetate oxidation via direct interspecies electron transfer from a heterotrophic partner bacterium, Geobacter sulfurreducens. Photosynthetic growth of P. aestuarii using reductant provided by either an electrode or syntrophy is robust and light-dependent. In contrast, P. aestuarii doesmore » not grow in co-culture with a G. sulfurreducens mutant lacking a trans-outer membrane porin-cytochrome protein complex required for direct intercellular electron transfer. Syntrophic anaerobic photosynthesis is therefore a carbon cycling process that could take place in anoxic environments. Lastly, this process could be exploited for biotechnological applications, such as waste treatment and bioenergy production, using engineered phototrophic microbial communities.« less

Octopus lipid and vitamin E composition: interspecies, interorigin, and nutritional variability.

PubMed

Torrinha, Alvaro; Cruz, Rebeca; Gomes, Filipa; Mendes, Eulália; Casal, Susana; Morais, Simone

2014-08-20

Octopus vulgaris, Octopus maya, and Eledone cirrhosa from distinct marine environments [Northeast Atlantic (NEA), Northwest Atlantic (NWA), Eastern Central Atlantic, Western Central Atlantic (WCA), Pacific Ocean, and Mediterranean Sea] were characterized regarding their lipid and vitamin E composition. These species are those commercially more relevant worldwide. Significant interspecies and interorigin differences were observed. Unsaturated fatty acids account for more than 65% of total fatty acids, mostly ω-3 PUFA due to docosahexaenoic (18.4-29.3%) and eicosapentanoic acid (11.4-23.9%) contributions. The highest ω-3 PUFA amounts and ω-3/ω-6 ratios were quantified in the heaviest specimens, O. vulgaris from NWA, with high market price, and simultaneously in the lowest graded samples, E. cirrhosa from NEA, of reduced dimensions. Although having the highest cholesterol contents, E. cirrhosa from NEA and O. maya from WCA have also higher protective fatty acid indexes. Chemometric discrimination allowed clustering the selected species and several origins based on lipid and vitamin E profiles.

Serological detection systems for identification of cows shedding bovine foamy virus via milk.

PubMed

Romen, Fabian; Backes, Perdita; Materniak, Magda; Sting, Reinhard; Vahlenkamp, Thomas W; Riebe, Roland; Pawlita, Michael; Kuzmak, Jacek; Löchelt, Martin

2007-07-20

The biology of foamy viruses, their mode of transmission and disease potential in their natural host and after interspecies transmission are largely unknown. To gain insights into the prevalence of bovine foamy virus (BFV) and its zoonotic potential, enzyme-linked immunosorbent assays (ELISAs) were established to determine antibody responses against Gag, Env, and the non-structural protein Bet in bovine serum and milk. In Polish cattle, strong Gag reactivity was most frequent (41.5%) and strongly associated with Bet antibodies, Env antibodies were less frequent. German cattle showed a low overall BFV antibody prevalence of 6.8%. Besides clearly BFV-positive animals, a substantial number of weakly reacting cattle were identified. BFV-specific antibodies were also detectable in milk. BFV was isolated from PBLs and milk cells of BFV-positive cattle but not from antibody-negative or weakly reacting animals. The implications of these findings for the potential interspecies transmission of BFV to humans will be discussed.

Polarized electrode enhances biological direct interspecies electron transfer for methane production in upflow anaerobic bioelectrochemical reactor.

PubMed

Feng, Qing; Song, Young-Chae; Yoo, Kyuseon; Kuppanan, Nanthakumar; Subudhi, Sanjukta; Lal, Banwari

2018-08-01

The influence of polarized electrodes on the methane production, which depends on the sludge concentration, was investigated in upflow anaerobic bioelectrochemical (UABE) reactor. When the polarized electrode was placed in the bottom zone with a high sludge concentration, the methane production was 5.34 L/L.d, which was 53% higher than upflow anaerobic sludge blanket (UASB) reactor. However, the methane production was reduced to 4.34 L/L.d by placing the electrode in the upper zone of the UABE reactor with lower sludge concentration. In the UABE reactor, the methane production was mainly improved by the enhanced biological direct interspecies electron transfer (bDIET) pathway, and the methane production via the electrode was a minor fraction of less than 4% of total methane production. The polarized electrodes that placed in the bottom zone with a high sludge concentration enhance the bDIET for methane production in the UABE reactor and greatly improve the methane production. Copyright © 2018. Published by Elsevier Ltd.

Interspecies radioimmunoassay for the major structural proteins of primate type-D retroviruses

DOE Office of Scientific and Technical Information (OSTI.GOV)

Colcher, D.; Teramoto, Y.A.; Schlom, J.

1977-12-01

A competition radioimmunoassay has been developed in which type-D retroviruses from three primate species compete. The assay utilizes the major structural protein (36,000 daltons) of the endogenous squirrel monkey retrovirus and antisera directed against the major structural protein (27,000 daltons) of the Mason-Pfizer monkey virus isolated from rhesus monkeys. Purified preparations of both viruses grown in heterologous cells, as well as extracts of heterologous cells infected with squirrel monkey retrovirus or Mason-Pfizer monkey virus, compete completely in the assay. Addition of an endogenous virus of the langur monkey also results in complete blocking. No blocking in the assay is observedmore » with type-C baboon viruses, woolly monkey virus, and gibbon virus. Various other type-C and type-B viruses also showed no reactivity. An interspecies assay has thus been developed that recognizes the type-D retroviruses from both Old World monkey (rhesus and langur) and New World monkey (squirrel) species.« less

Syntrophic anaerobic photosynthesis via direct interspecies electron transfer

PubMed Central

Ha, Phuc T.; Lindemann, Stephen R.; Shi, Liang; Dohnalkova, Alice C.; Fredrickson, James K.; Madigan, Michael T.; Beyenal, Haluk

2017-01-01

Microbial phototrophs, key primary producers on Earth, use H2O, H2, H2S and other reduced inorganic compounds as electron donors. Here we describe a form of metabolism linking anoxygenic photosynthesis to anaerobic respiration that we call ‘syntrophic anaerobic photosynthesis'. We show that photoautotrophy in the green sulfur bacterium Prosthecochloris aestaurii can be driven by either electrons from a solid electrode or acetate oxidation via direct interspecies electron transfer from a heterotrophic partner bacterium, Geobacter sulfurreducens. Photosynthetic growth of P. aestuarii using reductant provided by either an electrode or syntrophy is robust and light-dependent. In contrast, P. aestuarii does not grow in co-culture with a G. sulfurreducens mutant lacking a trans-outer membrane porin-cytochrome protein complex required for direct intercellular electron transfer. Syntrophic anaerobic photosynthesis is therefore a carbon cycling process that could take place in anoxic environments. This process could be exploited for biotechnological applications, such as waste treatment and bioenergy production, using engineered phototrophic microbial communities. PMID:28067226

Interactions between visitors and Formosan macaques (Macaca cyclopis) at Shou-Shan Nature Park, Taiwan.

PubMed

Hsu, Minna J; Kao, Chien-Ching; Agoramoorthy, Govindasamy

2009-03-01

Ecotourism involving feeding wildlife has raised public attention and is a controversial issue, especially concerning nonhuman primates. Between July 2002 and April 2005, the behavior of monkeys and tourists was collected through scan samplings, focal samplings and behavior samplings at the Shou-Shan Nature Park located in Taiwan's second largest city--Kaohsiung. In addition, the number of tourists and monkeys was counted in different hours and places within the park. Four hundred visitors were interviewed using a questionnaire to gather data on sex, age, purpose and frequency of visit to the park. The number of tourists was significantly higher during weekends than in weekdays in all locations. Humans dominated in the initiation of interspecies interactions--the overall ratio of human-initiated and monkey-initiated interactions was 2.44:1. Human-monkey conflicts accounted for only 16.4% of the total interactions (n=2,166), and adult human males and adult male macaques participated in higher rates than other age/sex groups in these conflicts. Visitors showed more affiliative behavior (15.9%) than agonistic behavior (8%) toward the macaques. In response to visitors' threat or attack, the Formosan macaques mostly showed submissive behavior with bared teeth, squealed or ran away to avoid confrontation (69.1%)--only few responded with counteraggression (18.7%). This study for the first time provided evidence that food provisioning increased both the frequency and duration of aggression among Formosan macaques (P<0.001). During food provisioning, the average frequency and the duration of agonistic events of macaques were more than 4 times higher compared with those without food provisioning. The average frequency of food provision by tourists was 0.73 times/hr--more than twice the incident that monkeys grabbed the food from tourists (0.34 times/hr). If people refrain from feeding monkeys and destroying the city park's natural vegetation, monkeys can be used to educate public about nature conservation in an urban setting. (c) 2008 Wiley-Liss, Inc.

Quantification of dynamic soil - vegetation feedbacks following an isotopically labelled precipitation pulse

NASA Astrophysics Data System (ADS)

Piayda, Arndt; Dubbert, Maren; Siegwolf, Rolf; Cuntz, Matthias; Werner, Christiane

2017-04-01

The presence of vegetation alters hydrological cycles of ecosystems. Complex plant-soil interactions govern the fate of precipitation input and water transitions through ecosystem compartments. Disentangling these interactions is a major challenge in the field of ecohydrology and pivotal foundation for understanding the carbon cycle of semi-arid ecosystems. Stable water isotopes can be used in this context as tracer to quantify water movement through soil-vegetation-atmosphere interfaces. The aim of this study is to disentangle vegetation effects on soil water infiltration and distribution as well as dynamics of soil evaporation and grassland water-use in a Mediterranean cork-oak woodland during dry conditions. An irrigation experiment using δ18O-labeled water was carried out in order to quantify distinct effects of tree and herbaceous vegetation on infiltration and distribution of event water in the soil profile. Dynamic responses of soil and herbaceous vegetation fluxes to precipitation regarding event water-use, water uptake depth plasticity and contribution to ecosystem evapotranspiration were quantified. Total water loss to the atmosphere from bare soil was as high as from vegetated soil, utilizing large amounts of unproductive water loss for biomass production, carbon sequestration and nitrogen fixation. During the experiment no adjustments of main root water uptake depth to changes of water availability could be observed, rendering light to medium precipitation events under dry conditions useless. This forces understory plants to compete with adjacent trees for soil water in deeper soil layers. Thus understory plants are faster subject to chronic drought, leading to premature senescence at the onset of drought. Despite this water competition, the presence of Cork oak trees fosters infiltration to large degrees. That reduces drought stress, caused by evapotranspiration, due to favourable micro climatic conditions under tree crown shading. This study highlights complex soil-plant-atmosphere and inter-species interactions in both space and time controlling the fate of rain pulse transitions through a typical Mediterranean savannah ecosystem, disentangled by the use of stable water isotopes.

Quantification of dynamic soil-vegetation feedbacks following an isotopically labelled precipitation pulse

NASA Astrophysics Data System (ADS)

Piayda, Arndt; Dubbert, Maren; Siegwolf, Rolf; Cuntz, Matthias; Werner, Christiane

2017-05-01

The presence of vegetation alters hydrological cycles of ecosystems. Complex plant-soil interactions govern the fate of precipitation input and water transitions through ecosystem compartments. Disentangling these interactions is a major challenge in the field of ecohydrology and a pivotal foundation for understanding the carbon cycle of semi-arid ecosystems. Stable water isotopes can be used in this context as tracer to quantify water movement through soil-vegetation-atmosphere interfaces. The aim of this study is to disentangle vegetation effects on soil water infiltration and distribution as well as dynamics of soil evaporation and grassland water use in a Mediterranean cork oak woodland during dry conditions. An irrigation experiment using δ18O labelled water was carried out in order to quantify distinct effects of tree and herbaceous vegetation on the infiltration and distribution of event water in the soil profile. Dynamic responses of soil and herbaceous vegetation fluxes to precipitation regarding event water use, water uptake depth plasticity, and contribution to ecosystem soil evaporation and transpiration were quantified. Total water loss to the atmosphere from bare soil was as high as from vegetated soil, utilizing large amounts of unproductive evaporation for transpiration, but infiltration rates decreased. No adjustments of main root water uptake depth to changes in water availability could be observed during the experiment. This forces understorey plants to compete with adjacent trees for water in deeper soil layers at the onset of summer. Thus, understorey plants are subjected to chronic water deficits faster, leading to premature senescence at the onset of drought. Despite this water competition, the presence of cork oak trees fosters infiltration and reduces evapotranspirative water losses from the understorey and the soil, both due to altered microclimatic conditions under crown shading. This study highlights complex soil-plant-atmosphere and inter-species interactions controlling rain pulse transitions through a typical Mediterranean savannah ecosystem, disentangled by the use of stable water isotopes.

Two-species boson mixture on a ring: A group-theoretic approach to the quantum dynamics of low-energy excitations

NASA Astrophysics Data System (ADS)

Penna, Vittorio; Richaud, Andrea

2017-11-01

We investigate the weak excitations of a system made up of two condensates trapped in a Bose-Hubbard ring and coupled by an interspecies repulsive interaction. Our approach, based on the Bogoliubov approximation scheme, shows that one can reduce the problem Hamiltonian to the sum of sub-Hamiltonians Ĥk, each one associated to momentum modes ±k . Each Ĥk is then recognized to be an element of a dynamical algebra. This uncommon and remarkable property allows us to present a straightforward diagonalization scheme, to find constants of motion, to highlight the significant microscopic processes, and to compute their time evolution. The proposed solution scheme is applied to a simple but nontrivial closed circuit, the trimer. The dynamics of low-energy excitations, corresponding to weakly populated vortices, is investigated considering different choices of the initial conditions and the angular-momentum transfer between the two condensates is evidenced. Finally, the condition for which the spectral collapse and dynamical instability are observed is derived analytically.

Emerging zoonoses in the southern United States: toxocariasis, bovine tuberculosis and southern tick-associated rash illness.

PubMed

Clinton, Rachel M; Carabin, Hélène; Little, Susan E

2010-09-01

The majority of emerging diseases in humans have been linked to zoonotic pathogens originating in domestic animals or wildlife. This is a public health concern because zoonotic infections affect several aspects of the society. The complex interactions among pathogen, host and environment also pose challenges in estimating the true burden of those infections. However, the recent development of new molecular diagnostic tools has allowed for better diagnosis of zoonotic infections. This review focuses on 3 emerging zoonoses, namely toxocariasis, bovine tuberculosis and southern tick-associated rash illness, and demonstrates that these infections may be more prevalent in the southern United States than previously recognized. This review places special emphasis on the recent epidemiologic trends, intra/interspecies transmission and clinical features of each of these zoonoses. In addition, treatment and prevention for each zoonotic pathogen are discussed. Clinicians working in the southern United States should be aware of the presence of those zoonotic infections.

Cytology of pollutant metals in marine invertebrates: A review of microanalytical applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nott, J.A.

1991-03-01

x-ray microanalysis (XRMA) is customized for investigations of the metabolic and detoxification strategies of heavy metals taken by marine organisms from polluted environments. Sites of uptake, intracellular accumulation, transport and excretion are visualized, analysed and quantified. Cryopreparation techniques are required to prevent the translocation or loss from specimens of soluble metal species. In marine invertebrates, metals are detoxified by systems of chemical binding and intracellular compartmentalization. XRMA investigations have concentrated on marine molluscs and crustaceans and even within these restricted groups there are marked inter-species differences in the biochemical and cytological processes which reduce metal bioavailability. Some detoxification systems alsomore » protect the carnivores which ingest the metal-laden tissues of the prey. This results in the bioreduction of metals along a food chain. These processes are investigated by XRMA which can be tuned to observe the complex interactions which operate at all levels within and between the biota and polluted environments. 90 refs.« less

Corynebacterium accolens Releases Antipneumococcal Free Fatty Acids from Human Nostril and Skin Surface Triacylglycerols

PubMed Central

Bomar, Lindsey; Brugger, Silvio D.; Yost, Brian H.; Davies, Sean S.

2016-01-01

ABSTRACT Bacterial interspecies interactions play clinically important roles in shaping microbial community composition. We observed that Corynebacterium spp. are overrepresented in children free of Streptococcus pneumoniae (pneumococcus), a common pediatric nasal colonizer and an important infectious agent. Corynebacterium accolens, a benign lipid-requiring species, inhibits pneumococcal growth during in vitro cocultivation on medium supplemented with human skin surface triacylglycerols (TAGs) that are likely present in the nostrils. This inhibition depends on LipS1, a TAG lipase necessary for C. accolens growth on TAGs such as triolein. We determined that C. accolens hydrolysis of triolein releases oleic acid, which inhibits pneumococcus, as do other free fatty acids (FFAs) that might be released by LipS1 from human skin surface TAGs. Our results support a model in which C. accolens hydrolyzes skin surface TAGS in vivo releasing antipneumococcal FFAs. These data indicate that C. accolens may play a beneficial role in sculpting the human microbiome. PMID:26733066

Optical Feshbach resonances and ground-state-molecule production in the RbHg system

NASA Astrophysics Data System (ADS)

Borkowski, Mateusz; Muñoz Rodriguez, Rodolfo; Kosicki, Maciej B.; Ciuryło, Roman; Żuchowski, Piotr S.

2017-12-01

We present the prospects for photoassociation, optical control of interspecies scattering lengths, and, finally, the production of ultracold absolute ground-state molecules in the Rb+Hg system. We use the state-of-the-art ab initio methods for the calculations of ground- [CCSD(T)] and excited-state (EOM-CCSD) potential curves. The RbHg system, thanks to the wide range of stable Hg bosonic isotopes, offers possibilities for mass tuning of ground-state interactions. The optical lengths describing the strengths of optical Feshbach resonances near the Rb transitions are favorable even at large laser detunings. Ground-state RbHg molecules can be produced with efficiencies ranging from about 20% for deeply bound to at least 50% for weakly bound states close to the dissociation limit. Finally, electronic transitions with favorable Franck-Condon factors can be found for the purposes of a STIRAP transfer of the weakly bound RbHg molecules to the absolute ground state using commercially available lasers.

Effects of acute gamma-irradiation on the aquatic microbial microcosm in comparison with chemicals.

PubMed

Fuma, Shoichi; Ishii, Nobuyoshi; Takeda, Hiroshi; Miyamoto, Kiriko; Yanagisawa, Kei; Doi, Kazutaka; Kawaguchi, Isao; Tanaka, Nobuyuki; Inamori, Yuhei; Polikarpov, Gennady G

2009-12-01

Effects of acute gamma-irradiation were investigated in the aquatic microcosm consisting of green algae (Chlorella sp. and Scenedesmus sp.) and a blue-green alga (Tolypothrix sp.) as producers; an oligochaete (Aeolosoma hemprichi), rotifers (Lecane sp. and Philodina sp.) and a ciliate protozoan (Cyclidium glaucoma) as consumers; and more than four species of bacteria as decomposers. At 100 Gy, populations were not affected in any taxa. At 500-5000 Gy, one or three taxa died out and populations of two or three taxa decreased over time, while that of Tolypothrix sp. increased. This Tolypothrix sp. increase was likely an indirect effect due to interspecies interactions. The principal response curve analysis revealed that the main trend of the effects was a dose-dependent population decrease. For a better understanding of radiation risks in aquatic microbial communities, effect doses of gamma-rays compared with copper, herbicides and detergents were evaluated using the radiochemoecological conceptual model and the effect index for microcosm.

Surviving in sympatry: paragenital divergence and sexual mimicry between a pair of traumatically inseminating plant bugs.

PubMed

Tatarnic, Nikolai J; Cassis, Gerasimos

2013-10-01

Reproductive interactions between species can carry significant costs (e.g., wasted time, energy, and gametes). In traumatically inseminating insects, heterospecific mating costs may be intensified, with indiscriminate mating and damaging genitalia leading to damage or death. When closely related traumatically inseminating species are sympatric, we predict selection should favor the rapid evolution of reproductive isolation. Here we report on a cryptic species of traumatically inseminating plant bug, Coridromius taravao, living sympatrically with its sister species, Coridromius tahitiensis, in French Polynesia. Despite their sister-species relationship, they exhibit striking differences in reproductive morphology, with females of each species stabbed and inseminated through different parts of their abdomens. Furthermore, C. tahitiensis is sexually dimorphic in coloration and vestiture, while both sexes of C. taravao share the C. tahitiensis male expression of these traits. These findings support a role for (1) reproductive character divergence and (2) interspecies sexual mimicry in limiting interspecific mating brought about by indiscriminate male mating behavior.

Identification of the WBSCR9 gene, encoding a novel transcriptional regulator, in the Williams-Beuren syndrome deletion at 7q11.23.

PubMed

Peoples, R J; Cisco, M J; Kaplan, P; Francke, U

1998-01-01

We have identified a novel gene (WBSCR9) within the common Williams-Beuren syndrome (WBS) deletion by interspecies sequence conservation. The WBSCR9 gene encodes a roughly 7-kb transcript with an open reading frame of 1483 amino acids and a predicted protein product size of 170.8 kDa. WBSCR9 is comprised of at least 20 exons extending over 60 kb. The transcript is expressed ubiquitously throughout development and is subject to alternative splicing. Functional motifs identified by sequence homology searches include a bromodomain; a PHD, or C4HC3, finger; several putative nuclear localization signals; four nuclear receptor binding motifs; a polyglutamate stretch and two PEST sequences. Bromodomains, PHD motifs and nuclear receptor binding motifs are cardinal features of proteins that are involved in chromatin remodeling and modulation of transcription. Haploinsufficiency for WBSCR9 gene products may contribute to the complex phenotype of WBS by interacting with tissue-specific regulatory factors during development.

Web-based Interspecies Correlation Estimation (Web-ICE) for Acute Toxicity: User Manual 3.2

EPA Science Inventory

The Web-ICE Endangered Species module simultaneously estimates toxicity to taxa representing threatened or endangered species using up to 25 surrogates. This module batch processes toxicity values for endangered species from all species, genus, and family level models available f...

Web-based Interspecies Correlation Estimation

EPA Science Inventory

Web-ICE estimates acute toxicity (LC50/LD50) of a chemical to a species, genus, or family from the known toxicity of the chemical to a surrogate species. Web-ICE has modules to predict acute toxicity to aquatic (fish and invertebrates) and wildlife (birds and mammals) taxa for us...

Interspecies Correlation Estimation (ICE) models predict supplemental toxicity data for SSDs

EPA Science Inventory

Species sensitivity distributions (SSD) require a large number of toxicity values for a diversity of taxa to define a hazard level protective of multiple species. For most chemicals, measured toxicity data are limited to a few standard test species that are unlikely to adequately...

Advances in Inhalation Gas Dosimetry for Derivation of a Reference Concentration (RfC) and Use in Risk Assessment

EPA Science Inventory

This status report provides a review of advances in the state of the science for interspecies inhalation gas dosimetry related to extrathoracic (ET) or upper respiratory tract (URT), tracheobronchial (TB), pulmonary (PU), and extrarespiratory (systemic, SYS) effects.

Incorporating Aquatic Interspecies Toxicity Estimates into Large Databases: Model Evaluations and Data Gains

EPA Science Inventory

The Chemical Aquatic Fate and Effects (CAFE) database, developed by NOAA’s Emergency Response Division (ERD), is a centralized data repository that allows for unrestricted access to fate and effects data. While this database was originally designed to help support decisions...

Changes in the Structure of the Microbial Community Associated with Nannochloropsis salina following Treatments with Antibiotics and Bioactive Compounds

PubMed Central

Geng, Haifeng; Tran-Gyamfi, Mary B.; Lane, Todd W.; Sale, Kenneth L.; Yu, Eizadora T.

2016-01-01

Open microalgae cultures host a myriad of bacteria, creating a complex system of interacting species that influence algal growth and health. Many algal microbiota studies have been conducted to determine the relative importance of bacterial taxa to algal culture health and physiological states, but these studies have not characterized the interspecies relationships in the microbial communities. We subjected Nanochroloropsis salina cultures to multiple chemical treatments (antibiotics and quorum sensing compounds) and obtained dense time-series data on changes to the microbial community using 16S gene amplicon metagenomic sequencing (21,029,577 reads for 23 samples) to measure microbial taxa-taxa abundance correlations. Short-term treatment with antibiotics resulted in substantially larger shifts in the microbiota structure compared to changes observed following treatment with signaling compounds and glucose. We also calculated operational taxonomic unit (OTU) associations and generated OTU correlation networks to provide an overview of possible bacterial OTU interactions. This analysis identified five major cohesive modules of microbiota with similar co-abundance profiles across different chemical treatments. The Eigengenes of OTU modules were examined for correlation with different external treatment factors. This correlation-based analysis revealed that culture age (time) and treatment types have primary effects on forming network modules and shaping the community structure. Additional network analysis detected Alteromonadeles and Alphaproteobacteria as having the highest centrality, suggesting these species are “keystone” OTUs in the microbial community. Furthermore, we illustrated that the chemical tropodithietic acid, which is secreted by several species in the Alphaproteobacteria taxon, is able to drastically change the structure of the microbiota within 3 h. Taken together, these results provide valuable insights into the structure of the microbiota associated with N. salina cultures and how these structures change in response to chemical perturbations. PMID:27507966

Towards a New Paradigm of Non-Captive Research on Cetacean Cognition

PubMed Central

Marino, Lori; Frohoff, Toni

2011-01-01

Contemporary knowledge of impressive neurophysiology and behavior in cetaceans, combined with increasing opportunities for studying free-ranging cetaceans who initiate sociable interaction with humans, are converging to highlight serious ethical considerations and emerging opportunities for a new era of progressive and less-invasive cetacean research. Most research on cetacean cognition has taken place in controlled captive settings, e.g., research labs, marine parks. While these environments afford a certain amount of experimental rigor and logistical control they are fraught with limitations in external validity, impose tremendous stress on the part of the captive animals, and place burdens on populations from which they are often captured. Alternatively, over the past three decades, some researchers have sought to focus their attention on the presence of free-ranging cetacean individuals and groups who have initiated, or chosen to participate in, sociable interactions with humans in the wild. This new approach, defined as Interspecies Collaborative Research between cetacean and human, involves developing novel ways to address research questions under natural conditions and respecting the individual cetacean's autonomy. It also offers a range of potential direct benefits to the cetaceans studied, as well as allowing for unprecedented cognitive and psychological research on sociable mysticetes. Yet stringent precautions are warranted so as to not increase their vulnerability to human activities or pathogens. When conducted in its best and most responsible form, collaborative research with free-ranging cetaceans can deliver methodological innovation and invaluable new insights while not necessitating the ethical and scientific compromises that characterize research in captivity. Further, it is representative of a new epoch in science in which research is designed so that the participating cetaceans are the direct recipients of the benefits. PMID:21915286

Dispersal and Transmission of Avian Paramyxovirus Serotype 4 among Wild Birds and Domestic Poultry.

PubMed

Yin, Renfu; Zhang, Pingze; Liu, Xinxin; Chen, Yanyu; Tao, Zhi; Ai, Lili; Li, Junjiao; Yang, Yingying; Li, Mingxin; Xue, Cong; Qian, Jing; Wang, Xueli; Chen, Jing; Li, Yong; Xiong, Yanping; Zhang, Jun; Stoeger, Tobias; Bi, Yuhai; Chen, Jianjun; Ding, Zhuang

2017-01-01

Avian paramyxovirus serotype 4 (APMV-4) is found sporadically in wild birds worldwide, and it is an economically important poultry pathogen. Despite the existence of several published strains, very little is known about the distribution, host species, and transmission of APMV-4 strains. To better understand the relationships among these factors, we conducted an APMV-4 surveillance of wild birds and domestic poultry in six provinces of China suspected of being intercontinental flyways and sites of interspecies transmission. APMV-4 surveillance was conducted in 9,160 wild birds representing seven species, and 1,461 domestic poultry in live bird markets (LMBs) from December 2013 to June 2016. The rate of APMV-4 isolation was 0.10% (11/10,621), and viruses were isolated from swan geese, bean geese, cormorants, mallards, and chickens. Sequencing and phylogenetic analyses of the 11 isolated viruses indicated that all the isolates belonging to genotype I were epidemiologically connected with wild bird-origin viruses from the Ukraine and Italy. Moreover, chicken-origin APMV-4 strains isolated from the LBMs were highly similar to wild bird-origin viruses from nearby lakes with free-living wild birds. In additional, a hemagglutination-negative APMV-4 virus was identified. These findings, together with recent APMV-4 studies, suggest potential virus interspecies transmission between wild birds and domestic poultry, and reveal possible epidemiological intercontinental connections between APMV-4 transmission by wild birds.

A genomic landscape of mitochondrial DNA insertions in the pig nuclear genome provides evolutionary signatures of interspecies admixture.

PubMed

Schiavo, Giuseppina; Hoffmann, Orsolya Ivett; Ribani, Anisa; Utzeri, Valerio Joe; Ghionda, Marco Ciro; Bertolini, Francesca; Geraci, Claudia; Bovo, Samuele; Fontanesi, Luca

2017-10-01

Nuclear DNA sequences of mitochondrial origin (numts) are derived by insertion of mitochondrial DNA (mtDNA), into the nuclear genome. In this study, we provide, for the first time, a genome picture of numts inserted in the pig nuclear genome. The Sus scrofa reference nuclear genome (Sscrofa10.2) was aligned with circularized and consensus mtDNA sequences using LAST software. A total of 430 numt sequences that may represent 246 different numt integration events (57 numt regions determined by at least two numt sequences and 189 singletons) were identified, covering about 0.0078% of the nuclear genome. Numt integration events were correlated (0.99) to the chromosome length. The longest numt sequence (about 11 kbp) was located on SSC2. Six numts were sequenced and PCR amplified in pigs of European commercial and local pig breeds, of the Chinese Meishan breed and in European wild boars. Three of them were polymorphic for the presence or absence of the insertion. Surprisingly, the estimated age of insertion of two of the three polymorphic numts was more ancient than that of the speciation time of the Sus scrofa, supporting that these polymorphic sites were originated from interspecies admixture that contributed to shape the pig genome. © The Author 2017. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

Dispersal and Transmission of Avian Paramyxovirus Serotype 4 among Wild Birds and Domestic Poultry

PubMed Central

Yin, Renfu; Zhang, Pingze; Liu, Xinxin; Chen, Yanyu; Tao, Zhi; Ai, Lili; Li, Junjiao; Yang, Yingying; Li, Mingxin; Xue, Cong; Qian, Jing; Wang, Xueli; Chen, Jing; Li, Yong; Xiong, Yanping; Zhang, Jun; Stoeger, Tobias; Bi, Yuhai; Chen, Jianjun; Ding, Zhuang

2017-01-01

Avian paramyxovirus serotype 4 (APMV-4) is found sporadically in wild birds worldwide, and it is an economically important poultry pathogen. Despite the existence of several published strains, very little is known about the distribution, host species, and transmission of APMV-4 strains. To better understand the relationships among these factors, we conducted an APMV-4 surveillance of wild birds and domestic poultry in six provinces of China suspected of being intercontinental flyways and sites of interspecies transmission. APMV-4 surveillance was conducted in 9,160 wild birds representing seven species, and 1,461 domestic poultry in live bird markets (LMBs) from December 2013 to June 2016. The rate of APMV-4 isolation was 0.10% (11/10,621), and viruses were isolated from swan geese, bean geese, cormorants, mallards, and chickens. Sequencing and phylogenetic analyses of the 11 isolated viruses indicated that all the isolates belonging to genotype I were epidemiologically connected with wild bird-origin viruses from the Ukraine and Italy. Moreover, chicken-origin APMV-4 strains isolated from the LBMs were highly similar to wild bird-origin viruses from nearby lakes with free-living wild birds. In additional, a hemagglutination-negative APMV-4 virus was identified. These findings, together with recent APMV-4 studies, suggest potential virus interspecies transmission between wild birds and domestic poultry, and reveal possible epidemiological intercontinental connections between APMV-4 transmission by wild birds. PMID:28603697

Malate dehydrogenase isozymes in the longnose dace, Rhinichthys cataractae.

PubMed

Starzyk, R M; Merritt, R B

1980-08-01

The interspecies homology of dace supernatant (A2,AB,B2) and mitochondrial (C2) malate dehydrogenase isozymes has been established through cell fractionation and tissue distribution studies. Isolated supernatant malate dehydrogenase (s-MDH) isozymes show significant differences in Michaelis constants for oxaloacetate and in pH optima. Shifts in s-MDH isozyme pH optima with temperature may result in immediate compensation for increase in ectotherm body pH with decrease in temperature, but duplicate s-MDH isozymes are probably maintained through selection for tissue specific regulation of metabolism.

Potential of Burkholderia seminalis TC3.4.2R3 as Biocontrol Agent Against Fusarium oxysporum Evaluated by Mass Spectrometry Imaging

NASA Astrophysics Data System (ADS)

Araújo, Francisca Diana da Silva; Araújo, Welington Luiz; Eberlin, Marcos Nogueira

2017-05-01

Species of genus Burkholderia display different interaction profiles in the environment, causing either several diseases in plants and animals or being beneficial to some plants, promoting their growth, and suppressing phytopathogens. Burkholderia spp. also produce many types of biomolecules with antimicrobial activity, which may be commercially used to protect crops of economic interest, mainly against fungal diseases. Herein we have applied matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) to investigate secondary metabolites produced by B. seminalis TC3.4.2R3 in monoculture and coculture with plant pathogen Fusarium oxysporum. The siderophore pyochelin and the rhamnolipid Rha-Rha-C15-C14 were detected in wild-type B. seminalis strain, and their productions were found to vary in mutant strains carrying disruptions in gene clusters associated with antimicrobial compounds. Two mycotoxins were detected in F. oxysporum. During coculture with B. seminalis, metabolites probably related to defense mechanisms of these microorganisms were observed in the interspecies interaction zone. Our findings demonstrate the effective application of MALDI-MSI in the detection of bioactive molecules involved in the defense mechanism of B. seminalis, and these findings suggest the potential use of this bacterium in the biocontrol of plant diseases caused by F. oxysporum.

Sniffing on microbes: diverse roles of microbial volatile organic compounds in plant health.

PubMed

Bitas, Vasileios; Kim, Hye-Seon; Bennett, Joan W; Kang, Seogchan

2013-08-01

Secreted proteins and metabolites play diverse and critical roles in organismal and organism-environment interactions. Volatile organic compounds (VOC) can travel far from the point of production through the atmosphere, porous soils, and liquid, making them ideal info-chemicals for mediating both short- and long-distance intercellular and organismal interactions. Critical ecological roles for animal- and plant-derived VOC in directing animal behaviors and for VOC as a language for plant-to-plant communication and regulators of various physiological processes have been well documented. Similarly, microbial VOC appear to be involved in antagonism, mutualism, intra- and interspecies regulation of cellular and developmental processes, and modification of their surrounding environments. However, the available knowledge of how microbial VOC affect other organisms is very limited. Evidence supporting diverse roles of microbial VOC with the focus on their impact on plant health is reviewed here. Given the vast diversity of microbes in nature and the critical importance of microbial communities associated with plants for their ecology and fitness, systematic exploration of microbial VOC and characterization of their biological functions and ecological roles will likely uncover novel mechanisms for controlling diverse biological processes critical to plant health and will also offer tangible practical benefits in addressing agricultural and environmental problems.

DOSIMETRY MODELING OF INHALED FORMALDEHYDE: BINNING NASAL FLUX PREDICTIONS FOR QUANTITATIVE RISK ASSESSMENT

EPA Science Inventory

Dosimetry Modeling of Inhaled Formaldehyde: Binning Nasal Flux Predictions for Quantitative Risk Assessment. Kimbell, J.S., Overton, J.H., Subramaniam, R.P., Schlosser, P.M., Morgan, K.T., Conolly, R.B., and Miller, F.J. (2001). Toxicol. Sci. 000, 000:000.

Interspecies e...

MODULAR APPLICATION OF COMPUTATIONAL MODELS OF INHALED REACTIVE GAS DOSIMETRY FOR RISK ASSESSMENT OF RESPIRATORY TRACT TOXICITY: CHLORINE

EPA Science Inventory

Inhaled reactive gases typically cause respiratory tract toxicity with a prominent proximal to distal lesion pattern. This pattern is largely driven by airflow and interspecies differences between rodents and humans result from factors such as airway architecture, ventilation ra...

GENOMIC AND PROTEOMIC BASIS FOR INTERSPECIES EXTRAPOLATIONS BASED UPON ESTROGEN AND ANDROGEN RECEPTORSTRUCTURE AND FUNCTION AMONG ANIMALS

EPA Science Inventory

Most in vitro hazard assessments for the screening and identification of endocrine disrupting compounds (EDCs), including those outlined in the EDSP Tier 1 Screening (T1S) protocols, use mammalian steroid hormone receptors. There is uncertainty, however, concerning differences th...

Novel technologies in rumen microbiology: What have we learned?

USDA-ARS?s Scientific Manuscript database

Beginning in the 1950s, rumen microbiology enjoyed a golden age in which the secrets of the rumen began to be teased out through the isolation of numerous new microbial species and the discovery of such important concepts as interspecies hydrogen transfer and the quantitative aspects of bacterial gr...

INTER-SPECIES COMPARISONS AND SAR MODELLING OF ESTROGENICITY USING RAINBOW TROUT ER BINDING DATA

EPA Science Inventory

The U.S. EPA has been mandated to screen industrial chemicals and pesticides for potential endocrine activity. Structure-activity relationships (SARs) to predict receptor binding are being developed as a first step to rank and prioritize chemicals for testing in bioassays. First ...

77 FR 23135 - 2,4-D; Order Denying NRDC's Petition To Revoke Tolerances

Federal Register 2010, 2011, 2012, 2013, 2014

2012-04-18

... cannot be determined (``non-threshold effects''). Because EPA identified only threshold effect risks for... uncertainty or safety factors \\1\\ in conjunction with experimental toxicity data in assessing risk to humans... difference in sensitivity between humans and experimental animals (i.e., inter-species sensitivity) and...

Web-based Interspecies Correlation Estimation (Web-ICE) for Acute Toxicity: User Manual Version 3.3

EPA Science Inventory

Information on the acute toxicity to multiple species is needed for the assessment of the risks to, and the protection of, individuals, populations, and ecological communities. However, toxicity data are limited for the majority of species, while standard test species are general...

Estimation of Wildlife Hazard Levels Using Interspecies Correlation Models and Standard Laboratory Rodent Toxicity Data

EPA Science Inventory

Toxicity data from laboratory rodents are widely available and frequently used in human health assessments as an animal model. We explore the possibility of using single rodent acute toxicity values to predict chemical toxicity to a diversity of wildlife species and to estimate ...

Differences in Uptake, Metabolism and Clearance of Atrazine and Tamoxifen in a Fish and a Rat Species

EPA Science Inventory

Atrazine and tamoxifen are known endocrine-disrupting chemicals (EDCs) that have metabolites exhibiting biological activities that are equally or more potent than the parent compound. To evaluate if uptake, metabolism and clearance of such EDCs is a concern in interspecies extrap...

Differences in Uptake, Metabolism and Clearance ofAtrazine and Tamoxifen in a Fish and a Rat Species

EPA Science Inventory

Atrazine and tamoxifen are known endocrine-disrupting chemicals (EDCs) that have metabolites exhibiting biological activities that are equally or more potent than the parent compound. To evaluate if uptake, metabolism and clearance of such EDCs is a concern in interspecies extrap...

INFLUENCE OF SOOT CARBON ON THE BIOACCULUMATION OF SEDIMENT-BOUND POLYCYCLIC AROMATIC HYDROCARBONS BY MARINE BENTHIC INVERTEBRATES: AN INTERSPECIES COMPARISON

EPA Science Inventory

The sorption of polycyclic aromatic hydrocarbons (PAHs) to soot carbon in marine sediments has been hypothesized to reduce PAH bioavailability. This hypothesis was tested for eight species of marine benthic invertebrates (four polychaete worms, Clymenella torquata, Nereis virens,...

IDENTIFICATION OF INTERSPECIES CONCORDANCE OF MECHANISMS OF ARSENIC INDUCED BLADDER CANCER BY GENE EXPRESSION.

EPA Science Inventory

Arsenic is a human carcinogen that induces urinary bladder cancer. Several mechanisms have been proposed for arsenic-induced cancer. Although inorganic arsenic (iAs) does not induce tumors in adult rodents, dimethylarsinic acid (DMA), a major metabolite of iAs, is a rat bladder c...

Daytime behavior of Pteropus vampyrus in a natural habitat: the driver of viral transmission

PubMed Central

HENGJAN, Yupadee; PRAMONO, Didik; TAKEMAE, Hitoshi; KOBAYASHI, Ryosuke; IIDA, Keisuke; ANDO, Takeshi; KASMONO, Supratikno; BASRI, Chaerul; FITRIANA, Yuli Sulistya; ARIFIN, Eko M. Z.; OHMORI, Yasushige; MAEDA, Ken; AGUNGPRIYONO, Srihadi; HONDO, Eiichi

2017-01-01

Flying foxes, the genus Pteropus, are considered viral reservoirs. Their colonial nature and long flight capability enhance their ability to spread viruses quickly. To understand how the viral transmission occurs between flying foxes and other animals, we investigated daytime behavior of the large flying fox (Pteropus vampyrus) in the Leuweung Sancang conservation area, Indonesia, by using instantaneous scan sampling and all-occurrence focal sampling. The data were obtained from 0700 to 1700 hr, during May 11–25, 2016. Almost half of the flying foxes (46.9 ± 10.6% of all recorded bats) were awake and showed various levels of activity during daytime. The potential behaviors driving disease transmission, such as self-grooming, mating/courtship and aggression, peaked in the early morning. Males were more active and spent more time on sexual activities than females. There was no significant difference in time spent for negative social behaviors between sexes. Positive social behaviors, especially maternal cares, were performed only by females. Sexual activities and negative/positive social behaviors enable fluid exchange between bats and thus facilitate intraspecies transmission. Conflicts for living space between the flying foxes and the ebony leaf monkey (Trachypithecus auratus) were observed, and this caused daily roosting shifts of flying foxes. The ecological interactions between bats and other wildlife increase the risk of interspecies infection. This study provides the details of the flying fox’s behavior and its interaction with other wildlife in South-East Asia that may help explain how pathogen spillover occurs in the wild. PMID:28496012

Rice-Map: a new-generation rice genome browser.

PubMed

Wang, Jun; Kong, Lei; Zhao, Shuqi; Zhang, He; Tang, Liang; Li, Zhe; Gu, Xiaocheng; Luo, Jingchu; Gao, Ge

2011-03-30

The concurrent release of rice genome sequences for two subspecies (Oryza sativa L. ssp. japonica and Oryza sativa L. ssp. indica) facilitates rice studies at the whole genome level. Since the advent of high-throughput analysis, huge amounts of functional genomics data have been delivered rapidly, making an integrated online genome browser indispensable for scientists to visualize and analyze these data. Based on next-generation web technologies and high-throughput experimental data, we have developed Rice-Map, a novel genome browser for researchers to navigate, analyze and annotate rice genome interactively. More than one hundred annotation tracks (81 for japonica and 82 for indica) have been compiled and loaded into Rice-Map. These pre-computed annotations cover gene models, transcript evidences, expression profiling, epigenetic modifications, inter-species and intra-species homologies, genetic markers and other genomic features. In addition to these pre-computed tracks, registered users can interactively add comments and research notes to Rice-Map as User-Defined Annotation entries. By smoothly scrolling, dragging and zooming, users can browse various genomic features simultaneously at multiple scales. On-the-fly analysis for selected entries could be performed through dedicated bioinformatic analysis platforms such as WebLab and Galaxy. Furthermore, a BioMart-powered data warehouse "Rice Mart" is offered for advanced users to fetch bulk datasets based on complex criteria. Rice-Map delivers abundant up-to-date japonica and indica annotations, providing a valuable resource for both computational and bench biologists. Rice-Map is publicly accessible at http://www.ricemap.org/, with all data available for free downloading.

Interactions of xylazine and detomidine with alpha2-adrenoceptors in brain tissue from cattle, swine and rats.

PubMed

Törneke, K; Bergström, U; Neil, A

2003-06-01

Xylazine is an alpha2-adrenoceptor agonist sedative with a much higher interspecies variability in effect than detomidine, another alpha2-agonist used in veterinary practice. In the present study, we have used radioligand binding in brain tissue to investigate if the high species variation in sensitivity to xylazine could be explained in terms of receptor interactions. Species known to be more (cattle) or less (swine and rats) sensitive to xylazine were used. There was no variation in the density or the subtype pattern of the alpha2-adrenoceptors that could explain the species variation recorded in vivo, as a homogenous population of the alpha2A/D-subtype (200-300 fmol/mg protein) was found in all species. The species differences in the affinities of xylazine and detomidine were minor and similar for the two drugs. The only parameter investigated where a significant species difference was found for xylazine but not for detomidine was the slope of the inhibition binding curve when the G-protein coupling was diminished. For xylazine this slope was considerably lower than unity (i.e. 0.77 +/- 0.075) using cattle preparations compared with 0.92 +/- 0.037 (mean +/- SE) and 0.90 +/- 0.028, respectively for swine and rats, while for detomidine this parameter was close to unity in all species (cattle, swine, rat). This finding indicates that the species variation in effect for xylazine could be due to differences at the G-protein level or further down-stream in the effect cascade.

Interspecies Variation in the Functional Consequences of Mutation of Cytochrome c

PubMed Central

Josephs, Tracy M.; Hibbs, Moira E.; Ong, Lily; Morison, Ian M.; Ledgerwood, Elizabeth C.

2015-01-01

The naturally occurring human cytochrome c variant (G41S) is associated with a mild autosomal dominant thrombocytopenia (Thrombocytopenia Cargeeg) caused by dysregulation of platelet production. The molecular basis of the platelet production defect is unknown. Despite high conservation of cytochrome c between human and mouse (91.4% identity), introducing the G41S mutation into mouse cytochrome c in a knockin mouse (Cycs G41S/G41S) did not recapitulate the low platelet phenotype of Thrombocytopenia Cargeeg. While investigating the cause of this disparity we found a lack of conservation of the functional impact of cytochrome c mutations on caspase activation across species. Mutation of cytochrome c at residue 41 has distinct effects on the ability of cytochrome c to activate caspases depending on the species of both the cytochrome c and its binding partner Apaf-1. In contrast to our previous results showing the G41S mutation increases the ability of human cytochrome c to activate caspases, here we find this activity is decreased in mouse G41S cytochrome c. Additionally unlike wildtype human cytochrome c, G41S cytochrome c is unable to activate caspases in Xenopus embryo extracts. Taken together these results demonstrate a previously unreported species-specific component to the interaction of cytochrome c with Apaf-1. This suggests that the electrostatic interaction between cytochrome c and Apaf-1 is not the sole determinant of binding, with additional factors controlling binding specificity and affinity. These results have important implications for studies of the effects of cytochrome c mutations on the intrinsic apoptosis pathway. PMID:26086723

Current knowledge and future challenges in camelid reproduction.

PubMed

Tibary, A; Anouassi, A; Sghiri, A; Khatir, H

2007-01-01

Reproductive biology research on camelids offers some interesting peculiarities and challenges to scientists and animal production specialists. The objective of this paper is to review camelid reproduction, advances in reproductive physiology and reproductive biotechnologies in camelids and discuss some areas for further research. In the female, the focus has been on understanding follicular dynamics. This has allowed development of synchronization and superovulation strategies to support embryo transfer technologies which are now commonly used in camels. Some advances have been achieved in preservation of embryos by vitrification. Fertilization, early embryo development and embryo signaling for maternal recognition of pregnancy are still not fully understood. New information on the interaction of the developing embryo and the endometrium may shed some light on this signaling as well as the mechanism of prevention of luteolysis. The presence of a seminal ovulation-inducing factor (OIF) was confirmed in llamas and alpacas. Chronology of oocytes maturation has been described. In vitro production of embryos has been achieved resulting in successful pregnancies and births in the dromedary. These techniques offer a new tool for the production and study of interspecies/cross-species embryos and their effect on pregnancy. Male reproductive function remains poorly studied. Semen preservation and artificial insemination still present many challenges and are not used in production at the moment. The involvement of climatic and nutritional conditions as well as the role of leptin in the regulation of reproductive function need to be evaluated.

Efficiency for preforming molecules from mixtures of light Fermi and heavy Bose atoms in optical lattices: The strong-coupling-expansion method

NASA Astrophysics Data System (ADS)

Hu, Anzi; Freericks, J. K.; Maśka, M. M.; Williams, C. J.

2011-04-01

We discuss the application of a strong-coupling expansion (perturbation theory in the hopping) for studying light-Fermi-heavy-Bose (like K40-Rb87) mixtures in optical lattices. We use the strong-coupling method to evaluate the efficiency for preforming molecules, the entropy per particle, and the thermal fluctuations. We show that within the strong interaction regime (and at high temperature), the strong-coupling expansion is an economical way to study this problem. In some cases, it remains valid even down to low temperatures. Because the computational effort is minimal, the strong-coupling approach allows us to work with much larger system sizes, where boundary effects can be eliminated, which is particularly important at higher temperatures. Since the strong-coupling approach is so efficient and accurate, it allows one to rapidly scan through parameter space in order to optimize the preforming of molecules on a lattice (by choosing the lattice depth and interspecies attraction). Based on the strong-coupling calculations, we test the thermometry scheme based on the fluctuation-dissipation theorem and find the scheme gives accurate temperature estimation even at very low temperature. We believe this approach and the calculation results will be useful in the design of the next generation of experiments and will hopefully lead to the ability to form dipolar matter in the quantum degenerate regime.

Analysis of the Pseudoalteromonas tunicata genome reveals properties of a surface-associated life style in the marine environment.

PubMed

Thomas, Torsten; Evans, Flavia F; Schleheck, David; Mai-Prochnow, Anne; Burke, Catherine; Penesyan, Anahit; Dalisay, Doralyn S; Stelzer-Braid, Sacha; Saunders, Neil; Johnson, Justin; Ferriera, Steve; Kjelleberg, Staffan; Egan, Suhelen

2008-09-24

Colonisation of sessile eukaryotic host surfaces (e.g. invertebrates and seaweeds) by bacteria is common in the marine environment and is expected to create significant inter-species competition and other interactions. The bacterium Pseudoalteromonas tunicata is a successful competitor on marine surfaces owing primarily to its ability to produce a number of inhibitory molecules. As such P. tunicata has become a model organism for the studies into processes of surface colonisation and eukaryotic host-bacteria interactions. To gain a broader understanding into the adaptation to a surface-associated life-style, we have sequenced and analysed the genome of P. tunicata and compared it to the genomes of closely related strains. We found that the P. tunicata genome contains several genes and gene clusters that are involved in the production of inhibitory compounds against surface competitors and secondary colonisers. Features of P. tunicata's oxidative stress response, iron scavenging and nutrient acquisition show that the organism is well adapted to high-density communities on surfaces. Variation of the P. tunicata genome is suggested by several landmarks of genetic rearrangements and mobile genetic elements (e.g. transposons, CRISPRs, phage). Surface attachment is likely to be mediated by curli, novel pili, a number of extracellular polymers and potentially other unexpected cell surface proteins. The P. tunicata genome also shows a utilisation pattern of extracellular polymers that would avoid a degradation of its recognised hosts, while potentially causing detrimental effects on other host types. In addition, the prevalence of recognised virulence genes suggests that P. tunicata has the potential for pathogenic interactions. The genome analysis has revealed several physiological features that would provide P. tunciata with competitive advantage against other members of the surface-associated community. We have also identified properties that could mediate interactions with surfaces other than its currently recognised hosts. This together with the detection of known virulence genes leads to the hypothesis that P. tunicata maintains a carefully regulated balance between beneficial and detrimental interactions with a range of host surfaces.

Plant interspecies competition for sunlight: a mathematical model of canopy partitioning.

PubMed

Nevai, Andrew L; Vance, Richard R

2007-07-01

We examine the influence of canopy partitioning on the outcome of competition between two plant species that interact only by mutually shading each other. This analysis is based on a Kolmogorov-type canopy partitioning model for plant species with clonal growth form and fixed vertical leaf profiles (Vance and Nevai in J. Theor. Biol., 2007, to appear). We show that canopy partitioning is necessary for the stable coexistence of the two competing plant species. We also use implicit methods to show that, under certain conditions, the species' nullclines can intersect at most once. We use nullcline endpoint analysis to show that when the nullclines do intersect, and in such a way that they cross, then the resulting equilibrium point is always stable. We also construct surfaces that divide parameter space into regions within which the various outcomes of competition occur, and then study parameter dependence in the locations of these surfaces. The analysis presented here and in a companion paper (Nevai and Vance, The role of leaf height in plant competition for sunlight: analysis of a canopy partitioning model, in review) together shows that canopy partitioning is both necessary and, under appropriate parameter values, sufficient for the stable coexistence of two hypothetical plant species whose structure and growth are described by our model.

Concepts and tools for predictive modeling of microbial dynamics.

PubMed

Bernaerts, Kristel; Dens, Els; Vereecken, Karen; Geeraerd, Annemie H; Standaert, Arnout R; Devlieghere, Frank; Debevere, Johan; Van Impe, Jan F

2004-09-01

Description of microbial cell (population) behavior as influenced by dynamically changing environmental conditions intrinsically needs dynamic mathematical models. In the past, major effort has been put into the modeling of microbial growth and inactivation within a constant environment (static models). In the early 1990s, differential equation models (dynamic models) were introduced in the field of predictive microbiology. Here, we present a general dynamic model-building concept describing microbial evolution under dynamic conditions. Starting from an elementary model building block, the model structure can be gradually complexified to incorporate increasing numbers of influencing factors. Based on two case studies, the fundamentals of both macroscopic (population) and microscopic (individual) modeling approaches are revisited. These illustrations deal with the modeling of (i) microbial lag under variable temperature conditions and (ii) interspecies microbial interactions mediated by lactic acid production (product inhibition). Current and future research trends should address the need for (i) more specific measurements at the cell and/or population level, (ii) measurements under dynamic conditions, and (iii) more comprehensive (mechanistically inspired) model structures. In the context of quantitative microbial risk assessment, complexity of the mathematical model must be kept under control. An important challenge for the future is determination of a satisfactory trade-off between predictive power and manageability of predictive microbiology models.

Genomics of Escherichia and Shigella

NASA Astrophysics Data System (ADS)

Perna, Nicole T.

The laboratory workhorse Escherichia coli K-12 is among the most intensively studied living organisms on earth, and this single strain serves as the model system behind much of our understanding of prokaryotic molecular biology. Dense genome sequencing and recent insightful comparative analyses are making the species E. coli, as a whole, an emerging system for studying prokaryotic population genetics and the relationship between system-scale, or genome-scale, molecular evolution and complex traits like host range and pathogenic potential. Genomic perspective has revealed a coherent but dynamic species united by intraspecific gene flow via homologous lateral or horizontal transfer and differentiated by content flux mediated by acquisition of DNA segments from interspecies transfers.

Formation of nucleoli in interspecies nuclear transfer embryos derived from bovine, porcine, and rabbit oocytes and nuclear donor cells of various species.

PubMed

Lagutina, Irina; Zakhartchenko, Valeri; Fulka, Helena; Colleoni, Silvia; Wolf, Eckhard; Fulka, Josef; Lazzari, Giovanna; Galli, Cesare

2011-04-01

The most successful development of interspecies somatic cell nuclear transfer (iSCNT) embryos has been achieved in closely related species. The analyses of embryonic gene activity in iSCNT embryos of different species combinations have revealed the existence of significant aberrations in expression of housekeeping genes and genes dependent on the major embryonic genome activation (EGA). However, there are many studies with successful blastocyst (BL) development of iSCNT embryos derived from donor cells and oocytes of animal species with distant taxonomical relations (inter-family/inter-class) that should indicate proper EGA at least in terms of RNA polymerase I activation, nucleoli formation, and activation of genes engaged in morula and BL formation. We investigated the ability of bovine, porcine, and rabbit oocytes to activate embryonic nucleoli formation in the nuclei of somatic cells of different mammalian species. In iSCNT embryos, nucleoli precursor bodies originate from the oocyte, while most proteins engaged in the formation of mature nucleoli should be transcribed from genes de novo in the donor nucleus at the time of EGA. Thus, the success of nucleoli formation depends on species compatibility of many components of this complex process. We demonstrate that the time and cell stage of nucleoli formation are under the control of recipient ooplasm. Oocytes of the studied species possess different abilities to support nucleoli formation. Formation of nucleoli, which is a complex but small part of the whole process of EGA, is essential but not absolutely sufficient for the development of iSCNT embryos to the morula and BL stages.

Interspecies differences in the accumulation of tributyltin and its metabolites under dietary exposure in sea perch, Lateolabrax japonicus, and red sea bream, Pagrus major.

PubMed

Uno, Seiichi; Murakami, Masayo; Kokushi, Emiko; Koyama, Jiro

2011-02-01

Interspecies differences in the accumulation of dietary tributyltin (TBT) between sea perch, Lateolabrax japonicus, and red sea bream, Pagrus major, were studied. Although TBTs in both species reached steady-state condition in low-concentration group (L-group, 200 ng/g nominal concentration) by 1 week, it increased up to the end of exposure in high-concentration group (H-group, 3000 ng/g nominal concentration). In H-group, the accumulation rate of TBT in sea perch from 1 to 2 weeks was much higher than in red sea bream, which were 2.4-fold for sea perch and 1.7-fold for red sea bream, although TBT concentrations were similar between sea perch and red sea bream in L-group. Furthermore, in the H-group, the concentrations of TBT at 1 and 2 weeks were about 1.3- and 1.9-fold, respectively, higher in the sea perch than in the red sea bream. On the other hand, DBT residue in red sea bream was about 1.4-fold higher in sea perch for the L-group but concentrations were similar in both fishes for the H-group. These results suggest that red sea bream could metabolize faster the TBT to DBT than sea perch. This study also reveals that fish probably could absorb TBT through the food chain. The uptake of TBT by fish should be regarded in the real environment, because TBT concentration in seawater has been decreasing and now already at significantly low level. Copyright © 2009 Wiley Periodicals, Inc.

Stringent DDI-based Prediction of H. sapiens-M. tuberculosis H37Rv Protein-Protein Interactions

PubMed Central

2013-01-01

Background H. sapiens-M. tuberculosis H37Rv protein-protein interaction (PPI) data are very important information to illuminate the infection mechanism of M. tuberculosis H37Rv. But current H. sapiens-M. tuberculosis H37Rv PPI data are very scarce. This seriously limits the study of the interaction between this important pathogen and its host H. sapiens. Computational prediction of H. sapiens-M. tuberculosis H37Rv PPIs is an important strategy to fill in the gap. Domain-domain interaction (DDI) based prediction is one of the frequently used computational approaches in predicting both intra-species and inter-species PPIs. However, the performance of DDI-based host-pathogen PPI prediction has been rather limited. Results We develop a stringent DDI-based prediction approach with emphasis on (i) differences between the specific domain sequences on annotated regions of proteins under the same domain ID and (ii) calculation of the interaction strength of predicted PPIs based on the interacting residues in their interaction interfaces. We compare our stringent DDI-based approach to a conventional DDI-based approach for predicting PPIs based on gold standard intra-species PPIs and coherent informative Gene Ontology terms assessment. The assessment results show that our stringent DDI-based approach achieves much better performance in predicting PPIs than the conventional approach. Using our stringent DDI-based approach, we have predicted a small set of reliable H. sapiens-M. tuberculosis H37Rv PPIs which could be very useful for a variety of related studies. We also analyze the H. sapiens-M. tuberculosis H37Rv PPIs predicted by our stringent DDI-based approach using cellular compartment distribution analysis, functional category enrichment analysis and pathway enrichment analysis. The analyses support the validity of our prediction result. Also, based on an analysis of the H. sapiens-M. tuberculosis H37Rv PPI network predicted by our stringent DDI-based approach, we have discovered some important properties of domains involved in host-pathogen PPIs. We find that both host and pathogen proteins involved in host-pathogen PPIs tend to have more domains than proteins involved in intra-species PPIs, and these domains have more interaction partners than domains on proteins involved in intra-species PPI. Conclusions The stringent DDI-based prediction approach reported in this work provides a stringent strategy for predicting host-pathogen PPIs. It also performs better than a conventional DDI-based approach in predicting PPIs. We have predicted a small set of accurate H. sapiens-M. tuberculosis H37Rv PPIs which could be very useful for a variety of related studies. PMID:24564941

Interspecies synteny mapping identifies a quantitative trait locus for bone mineral density on human chromosome Xp22.

PubMed

Parsons, Claire A; Mroczkowski, H Joel; McGuigan, Fiona E A; Albagha, Omar M E; Manolagas, Stavros; Reid, David M; Ralston, Stuart H; Shmookler Reis, Robert J

2005-11-01

Bone mineral density (BMD) is a complex trait with a strong genetic component and an important predictor of osteoporotic fracture risk. Here we report the use of a cross-species strategy to identify genes that regulate BMD, proceeding from quantitative trait mapping in mice to association mapping of the syntenic region in the human genome. We identified a quantitative trait locus (QTL) on the mouse X-chromosome for post-maturity change in spine BMD in a cross of SAMP6 and AKR/J mice and conducted association mapping of the syntenic region on human chromosome Xp22. We studied 76 single nucleotide polymorphisms (SNP) from the human region in two sets of DNA pools prepared from individuals with lumbar spine-BMD (LS-BMD) values falling into the top and bottom 13th percentiles of a population-based study of 3100 post-menopausal women. This procedure identified a region of significant association for two adjacent SNP (rs234494 and rs234495) within the Xp22 locus (P<0.001). Individual genotyping for rs234494 in the BMD pools confirmed the presence of an association for alleles (P=0.018) and genotypes (P=0.008). Analysis of rs234494 and rs234495 in 1053 women derived from the same population who were not selected for BMD values showed an association with LS-BMD for rs234495 (P=0.01) and for haplotypes defined by both SNP (P=0.002). Our study illustrates that interspecies synteny can be used to identify and refine QTL for complex traits and represents the first example where a human QTL for BMD regulation has been mapped using this approach.

An interspecies comparison of mercury inhibition on muscarinic acetylcholine receptor binding in the cerebral cortex and cerebellum

DOE Office of Scientific and Technical Information (OSTI.GOV)

Basu, Niladri; Department of Natural Resource Sciences, McGill University, Ste.-Anne-de-Bellevue, Quebec, H9X 3V9; Stamler, Christopher J.

2005-05-15

Mercury (Hg) is a ubiquitous pollutant that can disrupt neurochemical signaling pathways in mammals. It is well documented that inorganic Hg (HgCl{sub 2}) and methyl Hg (MeHg) can inhibit the binding of radioligands to the muscarinic acetylcholine (mACh) receptor in rat brains. However, little is known concerning this relationship in specific anatomical regions of the brain or in other species, including humans. The purpose of this study was to explore the inhibitory effects of HgCl{sub 2} and MeHg on [{sup 3}H]-quinuclidinyl benzilate ([{sup 3}H]-QNB) binding to the mACh receptor in the cerebellum and cerebral cortex regions from human, rat, mouse,more » mink, and river otter brain tissues. Saturation binding curves were obtained from each sample to calculate receptor density (B {sub max}) and ligand affinity (K {sub d}). Subsequently, samples were exposed to HgCl{sub 2} or MeHg to derive IC50 values and inhibition constants (K {sub i}). Results demonstrate that HgCl{sub 2} is a more potent inhibitor of mACh receptor binding than MeHg, and the receptors in the cerebellum are more sensitive to Hg-mediated mACh receptor inhibition than those in the cerebral cortex. Species sensitivities, irrespective of Hg type and brain region, can be ranked from most to least sensitive: river otter > rat > mink > mouse > humans. In summary, our data demonstrate that Hg can inhibit the binding [{sup 3}H]-QNB to the mACh receptor in a range of mammalian species. This comparative study provides data on interspecies differences and a framework for interpreting results from human, murine, and wildlife studies.« less

Framework for Optimizing Selection of Interspecies Correlation Estimation Models to Address Species Diversity and Toxicity Gaps in an Aquatic Database

EPA Science Inventory

The Chemical Aquatic Fate and Effects (CAFE) database is a tool that facilitates assessments of accidental chemical releases into aquatic environments. CAFE contains aquatic toxicity data used in the development of species sensitivity distributions (SSDs) and the estimation of ha...

SETAC Short Course: Introduction to interspecies toxicity extrapolation using EPA’s Web-ICE tool

EPA Science Inventory

The Web-ICE tool is a user friendly interface that contains modules to predict acute toxicity to over 500 species of aquatic (algae, invertebrates, fish) and terrestrial (birds and mammals) taxa. The tool contains a suite of over 3000 ICE models developed from a database of over ...

Genome Diversity and Intra- and Inter-Species Recombination Events in Grapevine fanleaf virus

USDA-ARS?s Scientific Manuscript database

Grapevine fanleaf virus (GFLV) was documented in four wine grape (Vitis vinifera) cultivars grown as own-rooted vines. GFLV was found as a mixed virus infection in cvs. Pinot Noir and Chardonnay, but not in cvs. Merlot and Cabernet Franc. Fanleaf disease symptoms were observed only in the first two...

76 FR 43999 - Notice of Availability of the External Review Draft of the Guidance for Applying Quantitative...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-22

... ENVIRONMENTAL PROTECTION AGENCY [EPA-HQ-ORD-2009-0694; FRL-9442-8] Notice of Availability of the External Review Draft of the Guidance for Applying Quantitative Data to Develop Data-Derived Extrapolation... Quantitative Data to Develop Data-Derived Extrapolation Factors for Interspecies and Intraspecies Extrapolation...

SPECIES DIFFERENCES IN ANDROGEN AND ESTROGEN RECEPTOR STRUCTURE AND FUNCTION AMONG VERTEBRATES AND INVERTEBRATES FOR INTERSPECIES EXTRAPOLATION OF ENDOCRINE DISRUPTING CHEMICALS

EPA Science Inventory

In vitro screening assays designed to identify hormone minics or antagonists, including the EDSTAC Tier 1 Screening (TIS) Battery, typically use only mammalian estrogen (ER) and androgen receptors (AR). However, there is uncertainty concerning species differences in binding affin...

Recultivating Intergenerational Resilience: Possibilities for "Scaling DEEP" through Disruptive Pedagogies of Decolonization and Reconciliation

ERIC Educational Resources Information Center

Williams, Lewis; Claxton, Nick

2017-01-01

In the face of declining human-ecological systems, as well as intercultural and interspecies trauma, we are currently witnessing a renaissance of activist-orientated environmental education. In Canada, this work is increasingly viewed as part of a broader healing response of "DEEP" reconciliation work between Indigenous and…

Working together for the common good: cell-cell communication in bacteria.

PubMed

Stevens, Ann M; Schuster, Martin; Rumbaugh, Kendra P

2012-05-01

The 4th ASM Conference on Cell-Cell Communication in Bacteria was held in Miami, FL, from 6 to 9 November 2011. This review highlights three key themes that emerged from the many exciting talks and poster presentations in the area of quorum sensing: sociomicrobiology, signal transduction mechanisms, and interspecies communication.

On being a (modern) scientist: risks of public engagement in the UK interspecies embryo debate.

PubMed

Porter, James; Williams, Clare; Wainwright, Steven; Cribb, Alan

2012-12-01

In 2006, a small group of UK academic scientists made headlines when they proposed the creation of interspecies embryos - mixing human and animal genetic material. A public campaign was fought to mobilize support for the research. Drawing on interviews with the key scientists involved, this paper argues that engaging the public through communicating their ideas via the media can result in tensions between the necessity of, and inherent dangers in, scientists campaigning on controversial issues. Some scientists believed that communicating science had damaged their professional standing in the eyes of their peers, who, in turn, policed the boundaries around what they believed constituted a "good" scientist. Tensions between promoting "science" versus promotion of the "scientist;" engaging the public versus publishing peer-reviewed articles and winning grants; and building expectations versus overhyping the science reveal the difficult choices scientists in the modern world have to make over the potential gains and risks of communicating science. We conclude that although scientists' participation in public debates is often encouraged, the rewards of such engagement remain. Moreover, this participation can detrimentally affect scientists' careers.

Anaerobic granule-based biofilms formation reduces propionate accumulation under high H2 partial pressure using conductive carbon felt particles.

PubMed

Xu, Heng; Wang, Cuiping; Yan, Kun; Wu, Jing; Zuo, Jiane; Wang, Kaijun

2016-09-01

Syngas based co-digestion is not only more economically attractive than separate syngas methanation but also able to upgrade biogas and increase overall CH4 amount simultaneously. However, high H2 concentration in the syngas could inhibit syntrophic degradation of propionate, resulting in propionate accumulation and even failure of the co-digestion system. In an attempt to reduce propionate accumulation via enhancing both H2 interspecies transfer (HIT) and direct interspecies electron transfer (DIET) pathways, layered granule-based biofilms induced by conductive carbon felt particles (CCFP) was employed. The results showed that propionate accumulation was effectively reduced with influent COD load up to 7gL(-1)d(-1). Two types of granule-based biofilms, namely biofilm adhered to CCFP (B-CCFP) and granules formed by self-immobilization (B-SI) were formed in the reactor. Clostridium, Syntrophobacter, Methanospirillum were possibly involved in HIT and Clostridium, Geobacter, Anaerolineaceae, Methanosaeta in DIET, both of which might be responsible for the high-rate propionate degradation. Copyright © 2016 Elsevier Ltd. All rights reserved.

[Achene morphology cluster analysis of Taraxacum F. H. Wigg. from northeast China and molecule systematics evidence determined by SRAP].

PubMed

Li, Hai-juan; Zhao, Xin; Jia, Qing-fei; Li, Tian-lai; Ning, Wei

2012-08-01

The achenes morphological and micro-morphological characteristics of six species of genus Taraxacum from northeastern China as well as SRAP cluster analysis were observed for their classification evidences. The achenes were observed by microscope and EPMA. Cluster analysis was given on the basis of the size, shape, cone proportion, color and surface sculpture of achenes. The Taraxacum inter-species achene shape characteristic difference is obvious, particularly spinulose distribution and size, achene color and achene size; with the Taraxacum plant achene shape the cluster method T. antungense Kitag. and the T. urbanum Kitag. should combine for the identical kind; the achene morphology cluster analysis and the SRAP tagged molecule systematics's cluster result retrieves in the table with "the Chinese flora". The class group to divide the result is consistent. Taraxacum plant achene shape characteristic stable conservative, may carry on the inter-species division and the sibship analysis according to the achene shape characteristic combination difference; the achene morphology cluster analysis as well as the SRAP tagged molecule systematics confirmation support dandelion classification result of "the Chinese flora".

Radial Distribution Functions of Strongly Coupled Two-Temperature Plasmas

NASA Astrophysics Data System (ADS)

Shaffer, Nathaniel R.; Tiwari, Sanat Kumar; Baalrud, Scott D.

2017-10-01

We present tests of three theoretical models for the radial distribution functions (RDFs) in two-temperature strongly coupled plasmas. RDFs are useful in extending plasma thermodynamics and kinetic theory to strong coupling, but they are usually known only for thermal equilibrium or for approximate one-component model plasmas. Accurate two-component modeling is necessary to understand the impact of strong coupling on inter-species transport, e.g., ambipolar diffusion and electron-ion temperature relaxation. We demonstrate that the Seuferling-Vogel-Toeppfer (SVT) extension of the hypernetted chain equations not only gives accurate RDFs (as compared with classical molecular dynamics simulations), but also has a simple connection with the Yukawa OCP model. This connection gives a practical means to recover the structure of the electron background from knowledge of the ion-ion RDF alone. Using the model RDFs in Effective Potential Theory, we report the first predictions of inter-species transport coefficients of strongly coupled plasmas far from equilibrium. This work is supported by NSF Grant No. PHY-1453736, AFSOR Award No. FA9550-16-1-0221, and used XSEDE computational resources.

Systems Level Dissection of Anaerobic Methane Cycling: Quantitative Measurements of Single Cell Ecophysiology, Genetic Mechanisms, and Microbial Interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Orphan, Victoria; Tyson, Gene; Meile, Christof

The global biological CH4 cycle is largely controlled through coordinated and often intimate microbial interactions between archaea and bacteria, the majority of which are still unknown or have been only cursorily identified. Members of the methanotrophic archaea, aka ‘ANME’, are believed to play a major role in the cycling of methane in anoxic environments coupled to sulfate, nitrate, and possibly iron and manganese oxides, frequently forming diverse physical and metabolic partnerships with a range of bacteria. The thermodynamic challenges overcome by the ANME and their bacterial partners and corresponding slow rates of growth are common characteristics in anaerobic ecosystems, and,more » in stark contrast to most cultured microorganisms, this type of energy and resource limited microbial lifestyle is likely the norm in the environment. While we have gained an in-depth systems level understanding of fast-growing, energy-replete microorganisms, comparatively little is known about the dynamics of cell respiration, growth, protein turnover, gene expression, and energy storage in the slow-growing microbial majority. These fundamental properties, combined with the observed metabolic and symbiotic versatility of methanotrophic ANME, make these cooperative microbial systems a relevant (albeit challenging) system to study and for which to develop and optimize culture-independent methodologies, which enable a systems-level understanding of microbial interactions and metabolic networks. We used an integrative systems biology approach to study anaerobic sediment microcosms and methane-oxidizing bioreactors and expanded our understanding of the methanotrophic ANME archaea, their interactions with physically-associated bacteria, ecophysiological characteristics, and underlying genetic basis for cooperative microbial methane-oxidation linked with different terminal electron acceptors. Our approach is inherently multi-disciplinary and multi-scaled, combining transcriptional and proteomic analyses with high resolution microscopy techniques, and stable isotopic and chemical analyses that span community level ‘omics investigations (cm scale) to interspecies consortia (µm scale), to the individual cell and its subcellular components (nm scale). We have organized our methodological approach into three broad categories, RNA-based, Protein-targeted and Geochemical, each encompassing a range of scales, with many techniques and resulting datasets that are highly complementary with one another, and together, offer a unique systems-level perspective of methane-based microbial interactions.« less

Live Animal Markets in Minnesota: A Potential Source for Emergence of Novel Influenza A Viruses and Interspecies Transmission.

PubMed

Choi, Mary J; Torremorell, Montserrat; Bender, Jeff B; Smith, Kirk; Boxrud, David; Ertl, Jon R; Yang, My; Suwannakarn, Kamol; Her, Duachi; Nguyen, Jennifer; Uyeki, Timothy M; Levine, Min; Lindstrom, Stephen; Katz, Jacqueline M; Jhung, Michael; Vetter, Sara; Wong, Karen K; Sreevatsan, Srinand; Lynfield, Ruth

2015-11-01

Live animal markets have been implicated in transmission of influenza A viruses (IAVs) from animals to people. We sought to characterize IAVs at 2 live animal markets in Minnesota to assess potential routes of occupational exposure and risk for interspecies transmission. We implemented surveillance for IAVs among employees, swine, and environment (air and surfaces) during a 12-week period (October 2012-January 2013) at 2 markets epidemiologically associated with persons with swine-origin IAV (variant) infections. Real-time reverse transcription polymerase chain reaction (rRT-PCR), viral culture, and whole-genome sequencing were performed on respiratory and environmental specimens, and serology on sera from employees at beginning and end of surveillance. Nasal swabs from 11 of 17 (65%) employees tested positive for IAVs by rRT-PCR; 7 employees tested positive on multiple occasions and 1 employee reported influenza-like illness. Eleven of 15 (73%) employees had baseline hemagglutination inhibition antibody titers ≥40 to swine-origin IAVs, but only 1 demonstrated a 4-fold titer increase to both swine-origin and pandemic A/Mexico/4108/2009 IAVs. IAVs were isolated from swine (72/84), air (30/45), and pen railings (5/21). Whole-genome sequencing of 122 IAVs isolated from swine and environmental specimens revealed multiple strains and subtype codetections. Multiple gene segment exchanges among and within subtypes were observed, resulting in new genetic constellations and reassortant viruses. Genetic sequence similarities of 99%-100% among IAVs of 1 market customer and swine indicated interspecies transmission. At markets where swine and persons are in close contact, swine-origin IAVs are prevalent and potentially provide conditions for novel IAV emergence. © The Author 2015. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Interspecific in vitro assay for the chimera-forming ability of human pluripotent stem cells.

PubMed

Masaki, Hideki; Kato-Itoh, Megumi; Umino, Ayumi; Sato, Hideyuki; Hamanaka, Sanae; Kobayashi, Toshihiro; Yamaguchi, Tomoyuki; Nishimura, Ken; Ohtaka, Manami; Nakanishi, Mahito; Nakauchi, Hiromitsu

2015-09-15

Functional assay limitations are an emerging issue in characterizing human pluripotent stem cells (PSCs). With rodent PSCs, chimera formation using pre-implantation embryos is the gold-standard assay of pluripotency (competence of progeny to differentiate into all three germ layers). In human PSCs (hPSCs), however, this can only be monitored via teratoma formation or in vitro differentiation, as ethical concerns preclude generation of human-human or human-animal chimeras. To circumvent this issue, we developed a functional assay utilizing interspecific blastocyst injection and in vitro culture (interspecies in vitro chimera assay) that enables the development and observation of embryos up to headfold stage. The assay uses mouse pre-implantation embryos and rat, monkey and human PSCs to create interspecies chimeras cultured in vitro to the early egg-cylinder stage. Intra- and interspecific chimera assays with rodent PSC lines were performed to confirm the consistency of results in vitro and in vivo. The behavior of chimeras developed in vitro appeared to recapitulate that of chimeras developed in vivo; that is, PSC-derived cells survived and were integrated into the epiblast of egg-cylinder-stage embryos. This indicates that the interspecific in vitro chimera assay is useful in evaluating the chimera-forming ability of rodent PSCs. However, when human induced PSCs (both conventional and naïve-like types) were injected into mouse embryos and cultured, some human cells survived but were segregated; unlike epiblast-stage rodent PSCs, they never integrated into the epiblast of egg-cylinder-stage embryos. These data suggest that the mouse-human interspecies in vitro chimera assay does not accurately reflect the early developmental potential/process of hPSCs. The use of evolutionarily more closely related species as host embryos might be necessary to evaluate the developmental potency of hPSCs. © 2015. Published by The Company of Biologists Ltd.

Long-term infection and vertical transmission of a gammaretrovirus in a foreign host species.

PubMed

Sakuma, Toshie; Tonne, Jason M; Malcolm, Jessica A; Thatava, Tayaramma; Ohmine, Seiga; Peng, Kah-Whye; Ikeda, Yasuhiro

2012-01-01

Increasing evidence has indicated natural transspecies transmission of gammaretroviruses; however, viral-host interactions after initial xeno-exposure remain poorly understood. Potential association of xenotropic murine leukemia virus-related virus (XMRV) in patients with prostate cancer and chronic fatigue syndrome has attracted broad interests in this topic. Although recent studies have indicated that XMRV is unlikely a human pathogen, further understanding of XMRV xenoinfection would allow in vivo modeling of the initial steps of gammaretroviral interspecies transmission, evolution and dissemination in a new host population. In this study, we monitored the long-term consequences of XMRV infection and its possible vertical transmission in a permissive foreign host, wild-derived Mus pahari mice. One year post-infection, XMRV-infected mice showed no notable pathological changes, while proviral DNA was detected in three out of eight mice. XMRV-infected mice remained seropositive throughout the study although the levels of gp70 Env- and p30 capsid-specific antibodies gradually decreased. When vertical XMRV transmission was assessed, no viremia, humoral immune responses nor endogenization were observed in nine offspring from infected mothers, yet one offspring was found PCR-positive for XMRV-specific sequences. Amplified viral sequences from the offspring showed several mutations, including one amino acid deletion in the receptor binding domain of Env SU. Our results therefore demonstrate long-term asymptomatic infection, low incidence of vertical transmission and limited evolution of XMRV upon transspecies infection of a permissive new host, Mus pahari.

The genome sequence of four isolates from the family Lichtheimiaceae.

PubMed

Chibucos, Marcus C; Etienne, Kizee A; Orvis, Joshua; Lee, Hongkyu; Daugherty, Sean; Lockhart, Shawn R; Ibrahim, Ashraf S; Bruno, Vincent M

2015-07-01

This study reports the release of draft genome sequences of two isolates of Lichtheimia corymbifera and two isolates of L. ramosa. Phylogenetic analyses indicate that the two L. corymbifera strains (CDC-B2541 and 008-049) are closely related to the previously sequenced L. corymbifera isolate (FSU 9682) while our two L. ramosa strains CDC-B5399 and CDC-B5792 cluster apart from them. These genome sequences will further the understanding of intraspecies and interspecies genetic variation within the Mucoraceae family of pathogenic fungi. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Coulomb collisions in the solar wind

NASA Technical Reports Server (NTRS)

Klein, L. W.; Ogilvie, K. W.; Burlaga, L. F.

1985-01-01

A major improvement of the present investigation over previous studies of the subject is related to the use of helium temperatures obtained from helium ion measurements uncontaminated by the high-velocity tail of the proton distribution. More observations, covering a large parameter range, were employed, and the effects of interspecies drift were taken into account. It is shown in a more definite way than has been done previously, that Coulomb collisions provide the most important mechanism bringing about equilibrium between helium and protons in the solar wind. Other mechanisms may play some part in restricted regions, but Coulomb collisions are dominant on the macroscale.

Interplay of a non-conjugative integrative element and a conjugative plasmid in the spread of antibiotic resistance via suicidal plasmid transfer from an aquaculture Vibrio isolate.

PubMed

Nonaka, Lisa; Yamamoto, Tatsuya; Maruyama, Fumito; Hirose, Yuu; Onishi, Yuki; Kobayashi, Takeshi; Suzuki, Satoru; Nomura, Nobuhiko; Masuda, Michiaki; Yano, Hirokazu

2018-01-01

The capture of antimicrobial resistance genes (ARGs) by mobile genetic elements (MGEs) plays a critical role in resistance acquisition for human-associated bacteria. Although aquaculture environments are recognized as important reservoirs of ARGs, intra- and intercellular mobility of MGEs discovered in marine organisms is poorly characterized. Here, we show a new pattern of interspecies ARGs transfer involving a 'non-conjugative' integrative element. To identify active MGEs in a Vibrio ponticus isolate, we conducted whole-genome sequencing of a transconjugant obtained by mating between Escherichia coli and Vibrio ponticus. This revealed integration of a plasmid (designated pSEA1) into the chromosome, consisting of a self-transmissible plasmid backbone of the MOBH group, ARGs, and a 13.8-kb integrative element Tn6283. Molecular genetics analysis suggested a two-step gene transfer model. First, Tn6283 integrates into the recipient chromosome during suicidal plasmid transfer, followed by homologous recombination between the Tn6283 copy in the chromosome and that in the newly transferred pSEA1. Tn6283 is unusual among integrative elements in that it apparently does not encode transfer function and its excision barely generates unoccupied donor sites. Thus, its movement is analogous to the transposition of insertion sequences rather than to that of canonical integrative and conjugative elements. Overall, this study reveals the presence of a previously unrecognized type of MGE in a marine organism, highlighting diversity in the mode of interspecies gene transfer.

Inter-species and intra-annual variations of moss nitrogen utilization: Implications for nitrogen deposition assessment.

PubMed

Dong, Yu-Ping; Liu, Xue-Yan; Sun, Xin-Chao; Song, Wei; Zheng, Xu-Dong; Li, Rui; Liu, Cong-Qiang

2017-11-01

Moss nitrogen (N) concentrations and natural 15 N abundance (δ 15 N values) have been widely employed to evaluate annual levels and major sources of atmospheric N deposition. However, different moss species and one-off sampling were often used among extant studies, it remains unclear whether moss N parameters differ with species and different samplings, which prevented more accurate assessment of N deposition via moss survey. Here concentrations, isotopic ratios of bulk carbon (C) and bulk N in natural epilithic mosses (Bryum argenteum, Eurohypnum leptothallum, Haplocladium microphyllum and Hypnum plumaeforme) were measured monthly from August 2006 to August 2007 at Guiyang, SW China. The H. plumaeforme had significantly (P < 0.05) lower bulk N concentrations and higher δ 13 C values than other species. Moss N concentrations were significantly (P < 0.05) lower in warmer months than in cooler months, while moss δ 13 C values exhibited an opposite pattern. The variance component analyses showed that different species contributed more variations of moss N concentrations and δ 13 C values than different samplings. Differently, δ 15 N values did not differ significantly between moss species, and its variance mainly reflected variations of assimilated N sources, with ammonium as the dominant contributor. These results unambiguously reveal the influence of inter-species and intra-annual variations of moss N utilization on N deposition assessment. Copyright © 2017 Elsevier Ltd. All rights reserved.

RAPD-SCAR marker and genetic relationship analysis of three Demodex species (Acari: Demodicidae).

PubMed

Zhao, Ya-E; Wu, Li-Ping

2012-06-01

For a long time, classification of Demodex mites has been mainly based on their hosts and phenotype characteristics. The study was the first to conduct molecular identification and genetic relationship analysis for six isolates of three Demodex species by random amplified polymorphic DNA (RAPD) and sequence-characterized amplified region (SCAR) marker. Totally, 239 DNA fragments were amplified from six Demodex isolates with 10 random primers in RAPD, of which 165 were polymorphic. Using a single primer, at least five fragments and at most 40 in the six isolates were amplified, whereas within a single isolate, a range of 35-49 fragments were amplified. DNA fingerprints of primers CZ 1-9 revealed intra- and interspecies difference in six Demodex isolates, whereas primer CZ 10 only revealed interspecies difference. The genetic distance and dendrogram showed the intraspecific genetic distances were closer than the interspecific genetic distances. The interspecific genetic distances of Demodex folliculorum and Demodex canis (0.7931-0.8140) were shorter than that of Demodex brevis and D. canis (0.8182-0.8987). The RAPD-SCAR marker displayed primer CZ 10 could be applied to identify the three Demodex species. The 479-bp fragment was specific for D. brevis, and the 261-bp fragment was specific for D. canis. The conclusion was that the RAPD-SCAR multi-marker was effective in molecular identification of three Demodex species. The genetic relationship between D. folliculorum and D. canis was nearer than that between D. folliculorum and D. brevis.

Comparative study of the organisation and phenotypes of bladder interstitial cells in human, mouse and rat.

PubMed

Gevaert, Thomas; Neuhaus, Jochen; Vanstreels, Els; Daelemans, Dirk; Everaerts, Wouter; Der Aa, Frank Van; Timmermans, Jean-Pierre; Roskams, Tania; Steiner, Clara; Pintelon, Isabel; De Ridder, Dirk

2017-12-01

With most research on interstitial cells (IC) in the bladder being conducted on animal models, it remains unclear whether all structural and functional data on IC from animal models can be translated to the human context. This prompted us to compare the structural and immunohistochemical properties of IC in bladders from mouse, rat and human. Tissue samples were obtained from the bladder dome and subsequently processed for immunohistochemistry and electron microscopy. The ultrastructural properties of IC were compared by means of electron microscopy and IC were additionally characterized with single/double immunohistochemistry/immunofluorescence. Our results reveal a similar organization of the IC network in the upper lamina propria (ULP), the deep lamina propria (DLP) and the detrusor muscle in human, rat and mouse bladders. Furthermore, despite several similarities in IC phenotypes, we also found several obvious inter-species differences in IC, especially in the ULP. Most remarkably in this respect, ULP IC in human bladder predominantly displayed a myoid phenotype with abundant presence of contractile micro-filaments, while those in rat and mouse bladders showed a fibroblast phenotype. In conclusion, the organization of ULP IC, DLP IC and detrusor IC is comparable in human, rat and mouse bladders, although several obvious inter-species differences in IC phenotypes were found. The present data show that translating research data on IC in laboratory animals to the human setting should be carried out with caution.

Preferential uptake of soil nitrogen forms by grassland plant species.

PubMed

Weigelt, Alexandra; Bol, Roland; Bardgett, Richard D

2005-02-01

In this study, we assessed whether a range of temperate grassland species showed preferential uptake for different chemical forms of N, including inorganic N and a range of amino acids that commonly occur in temperate grassland soil. Preferential uptake of dual-labelled (13C and 15N) glycine, serine, arginine and phenylalanine, as compared to inorganic N, was tested using plants growing in pots with natural field soil. We selected five grass species representing a gradient from fertilised, productive pastures to extensive, low productivity pastures (Lolium perenne, Holcus lanatus, Anthoxanthum odoratum, Deschampsia flexuosa, and Nardus stricta). Our data show that all grass species were able to take up directly a diversity of soil amino acids of varying complexity. Moreover, we present evidence of marked inter-species differences in preferential use of chemical forms of N of varying complexity. L. perenne was relatively more effective at using inorganic N and glycine compared to the most complex amino acid phenylalanine, whereas N. stricta showed a significant preference for serine over inorganic N. Total plant N acquisition, measured as root and shoot concentration of labelled compounds, also revealed pronounced inter-species differences which were related to plant growth rate: plants with higher biomass production were found to take up more inorganic N. Our findings indicate that species-specific differences in direct uptake of different N forms combined with total N acquisition could explain changes in competitive dominance of grass species in grasslands of differing fertility.

The effect of the breeding season, cryopreservation and physiological extender on selected sperm and semen parameters of four ferret species: implications for captive breeding in the endangered black-footed ferret.

PubMed

van der Horst, G; Kitchin, R M; van der Horst, M; Atherton, R W

2009-01-01

In the present investigation, comparative baseline information on selected sperm characteristics of ejaculate spermatozoa of the domestic (Mustela putorius furo), fitch (Mustela sp.) and black-footed ferrets (Mustela nigripes) and the Siberian polecat (Mustela eversmanni) are presented. The main emphasis was to establish differences and similarities among these species in relation to semen and sperm quality during the breeding season, in cryopreservation success and in supporting sperm motility in different extenders or physiological media. The results confirm that most sperm morphology abnormalities were evident during the beginning of the breeding cycle in all four species. No significant interspecies differences were apparent in the sperm attributes examined, for all sampling months during the breeding season. Moreover, all species exhibited comparable patterns of reproductive seasonality. Cryopreservation suppressed sperm characteristics equally in all species studied. Ejaculate spermatozoa of closely related ferret species shared many similar motion characteristics using computer-aided sperm motility analysis. These results suggest that the basic sperm physiology of the ferret species under examination is very similar. Disparate to the interspecies comparisons, there were significant differences for most sperm motion parameters when spermatozoa of any of the ferrets were compared in different extenders. Assisted reproductive technologies developed for use in domestic ferret, fitch ferret or Siberian polecat may be successfully applied to captive breeding of the black-footed ferret using semen during any of the functional breeding months.

Molecular Model of Prion Transmission to Humans

PubMed Central

Wight, Darren; Barron, Rona; Jeffrey, Martin; Manson, Jean; Prowse, Christopher; Ironside, James W.; Head, Mark W.

2009-01-01

To assess interspecies barriers to transmission of transmissible spongiform encephalopathies, we investigated the ability of disease-associated prion proteins (PrPd) to initiate conversion of the human normal cellular form of prion protein of the 3 major PRNP polymorphic variants in vitro. Protein misfolding cyclic amplification showed that conformation of PrPd partly determines host susceptibility. PMID:19961689

Overcoming obstacles to interspecies hybridization of ash

Treesearch

Jennifer L. Koch; David W. Carey; Mary E. Mason; M. Nurul Islam-Faridi

2010-01-01

Tree species that share a long co-evolutionary history with insects and pathogens are likely to have developed mechanisms of resistance that allow them to coexist. When insects and pathogens are introduced to different parts of the world, high levels of susceptibility can be observed, presumably in part due to the lack of co-evolutionary history between the insect (or...

Thermodynamic evaluation of mass diffusion in ionic mixtures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kagan, Grigory; Tang, Xian-Zhu

2014-02-15

The thermodynamic technique of Landau and Lifshitz originally developed for inter-species diffusion in a binary neutral gas mixture is extended to a quasi-neutral plasma with two ion species. It is shown that, while baro- and electro-diffusion coefficients depend on the choice of the thermodynamic system, prediction for the total diffusive mass flux is invariant.