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Search Results: 1 - 10 of 368915 matches for " Benjamin L. de Bivort "
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Growth and Asymmetry of Soil Microfungal Colonies from “Evolution Canyon,” Lower Nahal Oren, Mount Carmel, Israel
Shmuel Raz, John H. Graham, Ayelet Cohen, Benjamin L. de Bivort, Isabella Grishkan, Eviatar Nevo
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0034689
Abstract: Background Fluctuating asymmetry is a contentious indicator of stress in populations of animals and plants. Nevertheless, it is a measure of developmental noise, typically obtained by measuring asymmetry across an individual organism's left-right axis of symmetry. These individual, signed asymmetries are symmetrically distributed around a mean of zero. Fluctuating asymmetry, however, has rarely been studied in microorganisms, and never in fungi. Objective and Methods We examined colony growth and random phenotypic variation of five soil microfungal species isolated from the opposing slopes of “Evolution Canyon,” Mount Carmel, Israel. This canyon provides an opportunity to study diverse taxa inhabiting a single microsite, under different kinds and intensities of abiotic and biotic stress. The south-facing “African” slope of “Evolution Canyon” is xeric, warm, and tropical. It is only 200 m, on average, from the north-facing “European” slope, which is mesic, cool, and temperate. Five fungal species inhabiting both the south-facing “African” slope, and the north-facing “European” slope of the canyon were grown under controlled laboratory conditions, where we measured the fluctuating radial asymmetry and sizes of their colonies. Results Different species displayed different amounts of radial asymmetry (and colony size). Moreover, there were highly significant slope by species interactions for size, and marginally significant ones for fluctuating asymmetry. There were no universal differences (i.e., across all species) in radial asymmetry and colony size between strains from “African” and “European” slopes, but colonies of Clonostachys rosea from the “African” slope were more asymmetric than those from the “European” slope. Conclusions and Significance Our study suggests that fluctuating radial asymmetry has potential as an indicator of random phenotypic variation and stress in soil microfungi. Interaction of slope and species for both growth rate and asymmetry of microfungi in a common environment is evidence of genetic differences between the “African” and “European” slopes of “Evolution Canyon.”
Isotemporal classes of n-gons
Benjamin de Bivort
Mathematics , 2005,
Abstract: Here I present the present the first major result of a novel form of network analysis - a temporal interpretation. Treating numerical edges labels as the time at which an interaction occurs between the two vertices comprising that edge generates a number of intriguing questions. For example, given the structure of a graph, how many ``fundamentally'' different temporally non-isomorphic forms are there, across all possible edge labelings. Specifically, two networks, N and M, are considered to be in the same isotemporal class if there exists a function alpha(N)->M that is a graph isomorphism and preserves all paths in N with strictly increasing edge labels. I present a closed formula for the number of isotemporal classes N(n) of n-gons. This result is strongly tied to number theoretic identities; in the case of $n$ odd, N(n)= 1/n sum_{d|n} (2^{n/d -1}-1)Phi(d), where Phi is the Euler totient function.
Isotemporal classes of diasters, beachballs, and daisies
Benjamin de Bivort
Mathematics , 2013,
Abstract: If the vertices composing a network interact at distinct time points, the temporal ordering of these interactions and the network's graph structure are sufficient to convey the routes by which information can flow in the network. Two networks with real-valued edge labels are temporally isomorphic if there exists a graph isomorphism f:N->M that preserves temporal paths - paths in which sequential edge labels are strictly increasing. An equivalence class of temporally ismorphic networks is known as an isotemporal class. Methods to determine the number of isotemporal classes of a particular graph structure N(G) are non-obvious, and refractory to traditional techniques such as P\'olya enumeration (P\'olya, 1937). Here, I present a simple formula for the number of isotemporal classes of diasters, graphs composed of a vertex of degree a+1 connected to a vertex of degree b+1, with all other vertices of degree 1 (denoted D(a,b)). In particular, N(D(a,b)))=ab+a+b+1 if a is not equal to b, and N(D(a,a)))=(1/2) (a^2+3a+2) otherwise. This formula is then extended to five additional types of pseudograph by application of a theorem that states N(G) is preserved between two graph types if edge adjacencies and automorphisms are preserved, and provided that any two networks are members of the same isotemporal class if and only if they are isomorphic by transpositions of sequential edge labels on non-adjacent edges.
Behavioral individuality reveals genetic control of phenotypic variability
Julien F. Ayroles,Sean M. Buchanan,Chelsea Jenney,Kyobi Skutt-Kakaria,Jennifer Grenier,Andrew G. Clark,Daniel L. Hartl,Benjamin L. de Bivort
Quantitative Biology , 2014,
Abstract: Variability is ubiquitous in nature and a fundamental feature of complex systems. Few studies, however, have investigated variance itself as a trait under genetic control. By focusing primarily on trait means and ignoring the effect of alternative alleles on trait variability, we may be missing an important axis of genetic variation contributing to phenotypic differences among individuals. To study genetic effects on individual-to-individual phenotypic variability (or intragenotypic variability), we used a panel of Drosophila inbred lines and focused on locomotor handedness, in an assay optimized to measure variability. We discovered that some lines had consistently high levels of intragenotypic variability among individuals while others had low levels. We demonstrate that the degree of variability is itself heritable. Using a genome-wide association study (GWAS) for the degree of intragenotypic variability as the phenotype across lines, we identified several genes expressed in the brain that affect variability in handedness without affecting the mean. One of these genes, Ten-a, implicated a neuropil in the central complex of the fly brain as influencing the magnitude of behavioral variability, a brain region involved in sensory integration and locomotor coordination. We have validated these results using genetic deficiencies, null alleles, and inducible RNAi transgenes. This study reveals the constellation of phenotypes that can arise from a single genotype and it shows that different genetic backgrounds differ dramatically in their propensity for phenotypic variability. Because traditional mean-focused GWASs ignore the contribution of variability to overall phenotypic variation, current methods may miss important links between genotype and phenotype.
Neuronal control of locomotor handedness in Drosophila
Sean Buchanan,Jamey Kain,Benjamin de Bivort
Quantitative Biology , 2014,
Abstract: Handedness in humans - better performance using either the left or right hand - is personally familiar, moderately heritable, and regulated by many genes, including those involved in general body symmetry. But behavioral handedness, i.e. lateralization, is a multifaceted phenomenon. For example, people display clockwise or counter-clockwise biases in their walking behavior that is uncorrelated to their hand dominance, and lateralized behavioral biases have been shown in species as disparate as mice (paw usage), octopi (eye usage), and tortoises (side rolled on during righting). However, the mechanisms by which asymmetries are instilled in behavior are unknown, and a system for studying behavioral handedness in a genetically tractable model system is needed. Here we show that Drosophila melanogaster flies exhibit striking variability in their left-right choice behavior during locomotion. Very strongly biased "left-handed" and "right-handed" individuals are common in every line assayed. The handedness of an individual persists for its lifetime, but is not passed on to progeny, suggesting that mechanisms other than genetics determine individual handedness. We use the Drosophila transgenic toolkit to map a specific set of neurons within the central complex that regulates the strength of behavioral handedness within a line. These findings give insights into choice behaviors and laterality in a simple model organism, and demonstrate that individuals from isogenic populations reared under experimentally identical conditions nevertheless display idiosyncratic behaviors.
Empirical Multiscale Networks of Cellular Regulation
Benjamin de Bivort ,Sui Huang,Yaneer Bar-Yam
PLOS Computational Biology , 2007, DOI: 10.1371/journal.pcbi.0030207
Abstract: Grouping genes by similarity of expression across multiple cellular conditions enables the identification of cellular modules. The known functions of genes enable the characterization of the aggregate biological functions of these modules. In this paper, we use a high-throughput approach to identify the effective mutual regulatory interactions between modules composed of mouse genes from the Alliance for Cell Signaling (AfCS) murine B-lymphocyte database which tracks the response of ~15,000 genes following chemokine perturbation. This analysis reveals principles of cellular organization that we discuss along four conceptual axes. (1) Regulatory implications: the derived collection of influences between any two modules quantifies intuitive as well as unexpected regulatory interactions. (2) Behavior across scales: trends across global networks of varying resolution (composed of various numbers of modules) reveal principles of assembly of high-level behaviors from smaller components. (3) Temporal behavior: tracking the mutual module influences over different time intervals provides features of regulation dynamics such as duration, persistence, and periodicity. (4) Gene Ontology correspondence: the association of modules to known biological roles of individual genes describes the organization of functions within coexpressed modules of various sizes. We present key specific results in each of these four areas, as well as derive general principles of cellular organization. At the coarsest scale, the entire transcriptional network contains five divisions: two divisions devoted to ATP production/biosynthesis and DNA replication that activate all other divisions, an “extracellular interaction” division that represses all other divisions, and two divisions (proliferation/differentiation and membrane infrastructure) that activate and repress other divisions in specific ways consistent with cell cycle control.
Leg-tracking and automated behavioral classification in Drosophila
Jamey Kain,Chris Stokes,Quentin Gaudry,Xiangzhi Song,James Foley,Rachel Wilson,Benjamin de Bivort
Quantitative Biology , 2012, DOI: 10.1038/ncomms2908
Abstract: Here we present the first method for tracking each leg of a fruit fly behaving spontaneously upon a trackball, in real time. Legs were tracked with infrared-fluorescent dye invisible to the fly, and compatible with two-photon microscopy and controlled visual stimuli. We developed machine learning classifiers to identify instances of numerous behavioral features (e.g. walking, turning, grooming) thus producing the highest resolution ethological profiles for individual flies.
Multiethnic Genetic Association Studies Improve Power for Locus Discovery
Sara L. Pulit,Benjamin F. Voight,Paul I. W. de Bakker
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0012600
Abstract: To date, genome-wide association studies have focused almost exclusively on populations of European ancestry. These studies continue with the advent of next-generation sequencing, designed to systematically catalog and test low-frequency variation for a role in disease. A complementary approach would be to focus further efforts on cohorts of multiple ethnicities. This leverages the idea that population genetic drift may have elevated some variants to higher allele frequency in different populations, boosting statistical power to detect an association. Based on empirical allele frequency distributions from eleven populations represented in HapMap Phase 3 and the 1000 Genomes Project, we simulate a range of genetic models to quantify the power of association studies in multiple ethnicities relative to studies that exclusively focus on samples of European ancestry. In each of these simulations, a first phase of GWAS in exclusively European samples is followed by a second GWAS phase in any of the other populations (including a multiethnic design). We find that nontrivial power gains can be achieved by conducting future whole-genome studies in worldwide populations, where, in particular, African populations contribute the largest relative power gains for low-frequency alleles (<5%) of moderate effect that suffer from low power in samples of European descent. Our results emphasize the importance of broadening genetic studies to worldwide populations to ensure efficient discovery of genetic loci contributing to phenotypic trait variability, especially for those traits for which large numbers of samples of European ancestry have already been collected and tested.
Establishment of a community managed marine reserve in the Bay of Ranobe, southwest Madagascar
Elise M. S. Belle,Gerard W. Stewart,Benjamin De Ridder,Roberto J.-L. Komeno
Madagascar Conservation & Development , 2009,
Abstract: The Bay of Ranobe, in southwest Madagascar, once noted for its high biodiversity and fish abundance, is under increasing pressure from overfishing, pollution, sedimentation and tourism. The declining health of the coral reef is reflected in fishery productivity and survey data on biological diversity. Sustainable conservation requires the engagement of all interested parties and the integration of their needs into resource management. The British NGO ReefDoctor has adopted this approach in establishing the first community-protected site in the Bay of Ranobe, the Massif des Roses. This is a large coral patch with a high percentage of live coral cover (38 % ) and important fish diversity compared to other sites surveyed in the lagoon. Since 25 May 2007 it has been legally recognised as a community managed marine reserve under temporary protection where fishing is banned. Tourists must now pay an entry fee to visit the site, with the proceeds contributing to the funding of community projects. In conjunction with the protection of this site, ReefDoctor has worked with local people, regional and local government, tour operators and hotels, and conservation organisations to set up ‘FIMIHARA’, an association representative of local people responsible for the management of this site and the development of sustainable conservation initiatives in the Bay of Ranobe. This paper explains the approach taken by ReefDoctor, by setting up and working with FIMIHARA, to protect the Massif des Roses site and develop other conservation initiatives and community projects in the Bay of Ranobe. RéSUMé: La baie de Ranobe, au sud - ouest de Madagascar, autrefois remarquable pour sa biodiversité et l’abondance de la pêche, est de plus en plus menacée par la surpêche, la sédimentation, la pollution et le tourisme. Le déclin de l’état de santé du récif corallien se reflète dans la diminution de la productivité des pêcheries et dans les suivis de la biodiversité marine. La situation est à présent critique car les ressources marines associées au récif assurent la subsistance des populations c tières vivant le long de la baie. Nous considérons ici qu’une protection pérenne nécessite un engagement concret de toutes les parties prenantes - en particulier des communautés locales - et que leurs besoins soient intégrés dans la gestion des ressources. L’ONG ReefDoctor a mis en oeuvre cette approche lors de la création de la première réserve marine dans la baie de Ranobe gérée par la communauté locale, le Massif des Roses. Cette réserve est constituée d’un grand massif de corail largement cou
Observation of a phononic Mollow triplet in a hybrid spin-nanomechanical system
Benjamin Pigeau,Sven Rohr,Laure Mercier de Lépinay,Arnaud Gloppe,Vincent Jacques,Olivier Arcizet
Physics , 2015, DOI: 10.1038/ncomms9603
Abstract: Reminiscent of the bound character of a qubit's dynamics confined on the Bloch sphere, the observation of a Mollow triplet in the resonantly driven qubit fluorescence spectrum represents one of the founding signatures of Quantum Electrodynamics. Here we report on its observation in a hybrid spin-nanomechanical system, where a Nitro-gen Vacancy spin qubit is magnetically coupled to the vibrations of a Silicon Carbide nanowire. A resonant microwave field turns the originally parametric hybrid interac-tion into a resonant process, where acoustic phonons are now able to induce transitions between the dressed qubit states, leading to synchronized spin-oscillator dynamics. We further explore the vectorial character of the hybrid coupling to the bidimensional de-formations of the nanowire. The demonstrated microwave assisted synchronization of the spin-oscillator dynamics opens novel perspectives for the exploration of spin-dependent forces, the key-ingredient for quantum state transfer.
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