Selected papers from the Fourth Annual q-bio Conference on Cellular Information Processing.

Abstract:

:This special issue consists of 11 original papers that elaborate on work presented at the Fourth Annual q-bio Conference on Cellular Information Processing, which was held on the campus of St John's College in Santa Fe, New Mexico, USA, 11-14 August 2010. Now in its fourth year, the q-bio conference has changed considerably over time. It is now well established and a major event in systems biology. The 2010 conference saw attendees from all continents (except Antarctica!) sharing novel results and participating in lively discussions at both the oral and poster sessions. The conference was oversubscribed and grew to 27 contributed talks, 16 poster spotlights and 137 contributed posters. We deliberately decreased the number of invited speakers to 21 to leave more space for contributed presentations, and the attendee feedback confirmed that the choice was a success. Although the q-bio conference has grown and matured, it has remained true to the original goal of being an intimate and dynamic event that brings together modeling, theory and quantitative experimentation for the study of cell regulation and information processing. Funded in part by a grant from NIGMS and by DOE funds through the Los Alamos National Laboratory Directed Research and Development program, the conference has continued to exhibit youth and vigor by attracting (and partially supporting) over 100 undergraduate, graduate and postdoctoral researchers. The associated q-bio summer school, which precedes the conference each year, further emphasizes the development of junior scientists and makes q-bio a singular event in its impact on the future of quantitative biology. In addition to an increased international presence, the conference has notably diversified its demographic representation within the USA, including increased participation from the southeastern corner of the country. One big change in the conference this year is our new publication partner, Physical Biology. Although we are very grateful to our previous partner, IET Systems Biology, for their help over the years in publicizing the work presented at the conference, we felt that the changing needs of our participants required that we find a new partner. We are thrilled that Physical Biology is publishing the q-bio proceedings this year. It has been a great collaboration, as evidenced by the high quality of this special issue. What's next for q-bio? We are happy to report that NIGMS has recently extended the q-bio conference grant for the next three years, ensuring strong support for junior researchers who need financial assistance to participate in the event. The conference will retain its emphasis on cellular information processing, but will also build connections to other areas of modern biology and biotechnology, focusing specifically on ecology and evolutionary biology next year. Indeed, to fully understand biological information processing systems, they must be studied in their ecological contexts. We will continue to honor distinguished contributors to the field in our opening banquets; the tradition started with Howard Berg, Bruce Alberts and Michael Savageau in previous years, and continues with Dennis Bray at the upcoming 2011 event. Starting in 2011, the conference will also venture into exploration of the social aspects of science. The future is bright for q-bio! We will see you at the Fifth Annual q-bio Conference on 10-13 August 2011, in Santa Fe, New Mexico, USA and at the Sixth Annual q-bio Conference in early August 2012.

journal_name

Phys Biol

journal_title

Physical biology

authors

Nemenman I,Faeder JR,Hlavacek WS,Jiang Y,Wall ME,Zilman A

doi

10.1088/1478-3975/8/5/050301

subject

Has Abstract

pub_date

2011-10-01 00:00:00

pages

050301

issue

5

eissn

1478-3967

issn

1478-3975

journal_volume

8

pub_type

  • Roadmap on multiscale coupling of biochemical and mechanical signals during development.

    abstract::How interactions between mechanics and biochemistry lead to the emergence of complex cell and tissue organization is an old question that has recently attracted renewed interest from biologists, physicists, mathematicians and computer scientists. Rapid advances in optical physics, microscopy and computational image an...

    journal_title:Physical biology

    pub_type: 杂志文章

    doi:10.1088/1478-3975/abd0db

    authors: Lenne PF,Munro E,Heemskerk I,Warmflash A,Bocanegra-Moreno L,Kishi K,Kicheva A,Long Y,Fruleux A,Boudaoud A,Saunders TE,Caldarelli P,Michaut A,Gros J,Maroudas-Sacks Y,Keren K,Hannezo E,Gartner ZJ,Stormo BS,Gladfelter

    更新日期:2020-12-04 00:00:00

  • Caenorhabditis elegans vulval cell fate patterning.

    abstract::The spatial patterning of three cell fates in a row of competent cells is exemplified by vulva development in the nematode Caenorhabditis elegans. The intercellular signaling network that underlies fate specification is well understood, yet quantitative aspects remain to be elucidated. Quantitative models of the netwo...

    journal_title:Physical biology

    pub_type: 杂志文章

    doi:10.1088/1478-3975/9/4/045001

    authors: Félix MA

    更新日期:2012-08-01 00:00:00

  • Helices in peptoids of alpha- and beta-peptides.

    abstract::Peptoids of alpha- and beta-peptides (alpha- and beta-peptoids) can be obtained by shifting the amino acid side chains from the backbone carbon atoms of the monomer constituents to the peptide nitrogen atoms. They are, therefore, N-substituted poly-glycines and poly-beta-alanines, respectively. Due to the substituted ...

    journal_title:Physical biology

    pub_type: 杂志文章,评审

    doi:10.1088/1478-3975/3/1/S01

    authors: Baldauf C,Günther R,Hofmann HJ

    更新日期:2006-02-02 00:00:00

  • Host-to-host variation of ecological interactions in polymicrobial infections.

    abstract::Host-to-host variability with respect to interactions between microorganisms and multicellular hosts are commonly observed in infection and in homeostasis. However, the majority of mechanistic models used to analyze host-microorganism relationships, as well as most of the ecological theories proposed to explain coevol...

    journal_title:Physical biology

    pub_type: 杂志文章

    doi:10.1088/1478-3975/12/1/016003

    authors: Mukherjee S,Weimer KE,Seok SC,Ray WC,Jayaprakash C,Vieland VJ,Swords WE,Das J

    更新日期:2014-12-04 00:00:00

  • Effect of co-transporter blockers on non-synaptic epileptiform activity-computational simulation.

    abstract::The important role of cation-chloride co-transporters in epilepsy is being supported by an increasing number of investigations. However, enormous complexity is involved since the action of these co-transporters has effects on the ionic homeostasis influencing directly the neuronal excitability and the tissue propensit...

    journal_title:Physical biology

    pub_type: 杂志文章

    doi:10.1088/1478-3975/10/5/056008

    authors: Lopes MR,Santos LE,Rodrigues AM,Duarte MA,Infantosi AF,Scorza FA,Arida RM,Madureira AP,da Silveira GA,dos Santos IC,Cavalheiro EA,de Almeida AC

    更新日期:2013-10-01 00:00:00

  • Modeling the bacterial flagellum by an elastic network of rigid bodies.

    abstract::Bacteria such as Escherichia coli propel themselves by rotating a bundle of helical filaments, each driven by a rotary motor embedded in the cell membrane. Each filament is an assembly of thousands of copies of the protein flagellin which assumes two different states. We model the filament by an elastic network of rig...

    journal_title:Physical biology

    pub_type: 杂志文章

    doi:10.1088/1478-3975/8/4/046009

    authors: Speier C,Vogel R,Stark H

    更新日期:2011-08-01 00:00:00

  • Membrane potentials, oxidative stress and the dispersal response of bacterial biofilms to 405 nm light.

    abstract::The majority of chronic infections are caused by biofilms, which have higher levels of antibiotic resistance than planktonic growth. Violet-blue 405 nm light has recently emerged as a novel bactericide, but limited studies have been conducted on its effectiveness against biofilms. We found that in response to 405 nm l...

    journal_title:Physical biology

    pub_type: 杂志文章

    doi:10.1088/1478-3975/ab759a

    authors: Blee JA,Roberts IS,Waigh TA

    更新日期:2020-03-04 00:00:00

  • Genome-scale estimate of the metabolic turnover of E. coli from the energy balance analysis.

    abstract::In this article the notion of metabolic turnover is revisited in the light of recent results of out-of-equilibrium thermodynamics. By means of Monte Carlo methods we perform an exact sampling of the enzymatic fluxes in a genome scale metabolic network of E. coli in stationary growth conditions from which we infer the ...

    journal_title:Physical biology

    pub_type: 杂志文章

    doi:10.1088/1478-3975/13/1/016003

    authors: De Martino D

    更新日期:2016-01-29 00:00:00

  • A model for the integration of conflicting exogenous and endogenous signals by dendritic cells.

    abstract::Cells of the immune system are confronted with opposing pro- and anti-inflammatory signals. Dendritic cells (DC) integrate these cues to make informed decisions whether to initiate an immune response. Confronted with exogenous microbial stimuli, DC endogenously produce both anti- (IL-10) and pro-inflammatory (TNFα) cu...

    journal_title:Physical biology

    pub_type: 杂志文章

    doi:10.1088/1478-3975/aaaa0a

    authors: Marcou Q,Carmi-Levy I,Trichot C,Soumelis V,Mora T,Walczak AM

    更新日期:2018-05-16 00:00:00

  • Reaction schemes, escape times and geminate recombinations in particle-based spatial simulations of biochemical reactions.

    abstract::Modeling the spatiotemporal dynamics of biochemical reaction systems at single-molecule resolution has become feasible with the increase of computing power and is applied especially to cellular signal transduction. For an association reaction the two molecules have to be in contact. Hence, a physically faithful model ...

    journal_title:Physical biology

    pub_type: 杂志文章

    doi:10.1088/1478-3975/10/4/046005

    authors: Klann M,Koeppl H

    更新日期:2013-08-01 00:00:00

  • FACS-sorted particles reduce the data variance in optical tweezers-assisted dynamic force spectroscopy measurements.

    abstract::By combining optical tweezers-assisted dynamic force spectroscopy experiments with fluorescence activated cell sorting (FACS), we demonstrate a new approach to reducing the data variance in measuring receptor-ligand interactions on a single molecule level by ensuring similar coating densities. Therefore, the carboxyfl...

    journal_title:Physical biology

    pub_type: 杂志文章

    doi:10.1088/1478-3975/10/4/046004

    authors: Stangner T,Singer D,Wagner C,Gutsche C,Ueberschär O,Hoffmann R,Kremer F

    更新日期:2013-08-01 00:00:00

  • On the general concept of buoyancy in sedimentation and ultracentrifugation.

    abstract::Gravity or ultracentrifuge settling of colloidal particles and macromolecules usually involves several disperse species, either because natural and industrial colloids display a large size polydispersity, or because additives are put in on purpose to allow for density-based fractionation of the suspension. Such 'macro...

    journal_title:Physical biology

    pub_type: 杂志文章

    doi:10.1088/1478-3975/10/4/045005

    authors: Piazza R,Buzzaccaro S,Secchi E,Parola A

    更新日期:2013-08-01 00:00:00

  • Effect of ribosome shielding on mRNA stability.

    abstract::Based on the experimental evidence that translating ribosomes stabilize the mRNAs, we introduce and study a theoretical model for the dynamic shielding of mRNA by ribosomes. We present an improved fitting of published decay assay data in E. coli and show that only one third of the decay patterns are exponential. Our n...

    journal_title:Physical biology

    pub_type: 杂志文章

    doi:10.1088/1478-3975/10/4/046008

    authors: Deneke C,Lipowsky R,Valleriani A

    更新日期:2013-08-01 00:00:00

  • 'Dicty dynamics': Dictyostelium motility as persistent random motion.

    abstract::We model the motility of Dictyostelium cells in a systematic data-driven manner. We deduce a minimal dynamical model that reproduces the statistical features of experimental trajectories. These are trajectories of the centroid of the cell perimeter, which is more sensitive to pseudopod activity than the usual tracking...

    journal_title:Physical biology

    pub_type: 杂志文章

    doi:10.1088/1478-3975/8/4/046006

    authors: Li L,Cox EC,Flyvbjerg H

    更新日期:2011-08-01 00:00:00

  • Tactile interactions lead to coherent motion and enhanced chemotaxis of migrating cells.

    abstract::When motile cells come into contact with one another their motion is often considerably altered. In a process termed contact inhibition of locomotion (CIL) cells reshape and redirect their movement as a result of cell-cell contact. Here we describe a mathematical model that demonstrates that CIL alone is sufficient to...

    journal_title:Physical biology

    pub_type: 杂志文章

    doi:10.1088/1478-3975/10/4/046002

    authors: Coburn L,Cerone L,Torney C,Couzin ID,Neufeld Z

    更新日期:2013-08-01 00:00:00

  • Non-random distribution of vacuoles in Schizosaccharomyces pombe.

    abstract::A central question in eukaryotic cell biology asks, during cell division, how is the growth and distribution of organelles regulated to ensure each daughter cell receives an appropriate amount. For vacuoles in budding yeast, there are well described organelle-to-cell size scaling trends as well as inheritance mechanis...

    journal_title:Physical biology

    pub_type: 杂志文章

    doi:10.1088/1478-3975/aba510

    authors: Chadwick WL,Biswas SK,Bianco S,Chan YM

    更新日期:2020-10-09 00:00:00

  • Impact of charge variation on the encapsulation of nanoparticles by virus coat proteins.

    abstract::Electrostatic interaction is the driving force for the encapsulation by virus coat proteins of nanoparticles such as quantum dots, gold particles and magnetic beads for, e.g., imaging and therapeutic purposes. In recent experimental work, Daniel et al (2010 ACS Nano 4 3853-60) found the encapsulation efficiency to sen...

    journal_title:Physical biology

    pub_type: 杂志文章

    doi:10.1088/1478-3975/9/6/066004

    authors: Lin HK,van der Schoot P,Zandi R

    更新日期:2012-12-01 00:00:00

  • A minimal model for household effects in epidemics.

    abstract::Shelter-in-place and other confinement strategies implemented in the current COVID-19 pandemic have created stratified patterns of contacts between people: close contacts within households and more distant contacts between the households. The epidemic transmission dynamics is significantly modified as a consequence. W...

    journal_title:Physical biology

    pub_type: 杂志文章

    doi:10.1088/1478-3975/abb209

    authors: Huber G,Kamb M,Kawagoe K,Li LM,Veytsman B,Yllanes D,Zigmond D

    更新日期:2020-10-21 00:00:00

  • Environmental selection of the feed-forward loop circuit in gene-regulation networks.

    abstract::Gene-regulation networks contain recurring elementary circuits termed network motifs. It is of interest to understand under which environmental conditions each motif might be selected. To address this, we study one of the most significant network motifs, a three-gene circuit called the coherent feed-forward loop (FFL)...

    journal_title:Physical biology

    pub_type: 杂志文章

    doi:10.1088/1478-3975/2/2/001

    authors: Dekel E,Mangan S,Alon U

    更新日期:2005-06-01 00:00:00

  • Spin symmetry transitions make DNA strands separate. New insight into the mechanism of transcription.

    abstract::The DFT:B3LYP (6-31G** basis set) method, including the hyperfine and spin-orbit couplings (HFC and SOC, respectively), is used to study the separation of two complementary trinucleotide sequences, (dC-dG-dA)-(dG-dC-dT), upon the action of two Mg(2+) cofactors (a simplified model). The computations reveal a crossing o...

    journal_title:Physical biology

    pub_type: 杂志文章

    doi:10.1088/1478-3975/12/6/066017

    authors: Tulub AA,Stefanov VE

    更新日期:2015-12-10 00:00:00

  • Capacitance fluctuations causing channel noise reduction in stochastic Hodgkin-Huxley systems.

    abstract::Voltage-dependent ion channels determine the electric properties of axonal cell membranes. They not only allow the passage of ions through the cell membrane, but also contribute to an additional charging of the cell membrane resulting in the so-called capacitance loading. The switching of the channel gates between an ...

    journal_title:Physical biology

    pub_type: 杂志文章

    doi:10.1088/1478-3975/3/4/002

    authors: Schmid G,Goychuk I,Hänggi P

    更新日期:2006-11-22 00:00:00

  • Current trends and future requirements for the mass spectrometric investigation of microbial, mammalian and plant metabolomes.

    abstract::The functional levels of biological cells or organisms can be separated into the genome, transcriptome, proteome and metabolome. Of these the metabolome offers specific advantages to the investigation of the phenotype of biological systems. The investigation of the metabolome (metabolomics) has only recently appeared ...

    journal_title:Physical biology

    pub_type: 杂志文章,评审

    doi:10.1088/1478-3975/5/1/011001

    authors: Dunn WB

    更新日期:2008-02-20 00:00:00

  • A topological study of repetitive co-activation networks in in vitro cortical assemblies.

    abstract::To address the issue of extracting useful information from large data-set of large scale networks of neurons, we propose an algorithm that involves both algebraic-statistical and topological tools. We investigate the electrical behavior of in vitro cortical assemblies both during spontaneous and stimulus-evoked activi...

    journal_title:Physical biology

    pub_type: 杂志文章

    doi:10.1088/1478-3975/12/1/016007

    authors: Pirino V,Riccomagno E,Martinoia S,Massobrio P

    更新日期:2015-01-05 00:00:00

  • Estimation of mean first passage time for bursty gene expression.

    abstract::Gene expression is an intrinsically noisy process, typically, producing mRNAs and proteins in bursts. An important description of such stochastic processes can be done in terms of the mean first passage time (MFPT), i.e., the time taken by mRNAs/proteins to reach a particular threshold. We study the role of burstiness...

    journal_title:Physical biology

    pub_type: 杂志文章

    doi:10.1088/1478-3975/13/3/036004

    authors: Shreshtha M,Surendran A,Ghosh A

    更新日期:2016-05-20 00:00:00

  • Motions of leaves and stems, from growth to potential use.

    abstract::The study on aerial plant organs (leaves and stems) motions is reviewed. The history of observations and studies is put in the perspective of the ideas surrounding them, leading to a presentation of the current classification of these motions. After showing the shortcomings of such a classification, we present, follow...

    journal_title:Physical biology

    pub_type: 历史文章,杂志文章,评审

    doi:10.1088/1478-3975/aa5945

    authors: Rivière M,Derr J,Douady S

    更新日期:2017-08-21 00:00:00

  • Requirements for efficient cell-type proportioning: regulatory timescales, stochasticity and lateral inhibition.

    abstract::The proper functioning of multicellular organisms requires the robust establishment of precise proportions between distinct cell types. This developmental differentiation process typically involves intracellular regulatory and stochastic mechanisms to generate cell-fate diversity as well as intercellular signaling mec...

    journal_title:Physical biology

    pub_type: 杂志文章

    doi:10.1088/1478-3975/13/2/026007

    authors: Pfeuty B,Kaneko K

    更新日期:2016-05-11 00:00:00

  • Epithelial-to-mesenchymal transition: lessons from development, insights into cancer and the potential of EMT-subtype based therapeutic intervention.

    abstract::Epithelial-to-mesenchymal transition (EMT) is a fundamental developmental process wherein polarized epithelial cells lose their junctional architecture and apical-basal polarity to become motile mesenchymal cells, and there is emerging evidence for its role in propagating tumor dissemination. While many multifaceted n...

    journal_title:Physical biology

    pub_type: 杂志文章,评审

    doi:10.1088/1478-3975/ab157a

    authors: Antony J,Thiery JP,Huang RY

    更新日期:2019-05-07 00:00:00

  • Regulation of tumor invasion by interstitial fluid flow.

    abstract::The importance of the tumor microenvironment in cancer progression is undisputed, yet the significance of biophysical forces in the microenvironment remains poorly understood. Interstitial fluid flow is a nearly ubiquitous and physiologically relevant biophysical force that is elevated in tumors because of tumor-assoc...

    journal_title:Physical biology

    pub_type: 杂志文章,评审

    doi:10.1088/1478-3975/8/1/015012

    authors: Shieh AC,Swartz MA

    更新日期:2011-02-01 00:00:00

  • Topographical and mechanical characterization of living eukaryotic cells on opaque substrates: development of a general procedure and its application to the study of non-adherent lymphocytes.

    abstract::The mechanical behavior of living murine T-lymphocytes was assessed by atomic force microscopy (AFM). A robust experimental procedure was developed to overcome some features of lymphocytes, in particular their spherical shape and non-adherent character. The procedure included the immobilization of the lymphocytes on a...

    journal_title:Physical biology

    pub_type: 杂志文章

    doi:10.1088/1478-3975/12/2/026005

    authors: Daza R,Cruces J,Arroyo-Hernández M,Marí-Buyé N,De la Fuente M,Plaza GR,Elices M,Pérez-Rigueiro J,Guinea GV

    更新日期:2015-03-19 00:00:00

  • FtsZ rings and helices: physical mechanisms for the dynamic alignment of biopolymers in rod-shaped bacteria.

    abstract::In many bacterial species, the protein FtsZ forms a cytoskeletal ring that marks the future division site and scaffolds the division machinery. In rod-shaped bacteria, most frequently membrane-attached FtsZ rings or ring fragments are reported and occasionally helices. By contrast, axial FtsZ clusters have never been ...

    journal_title:Physical biology

    pub_type: 杂志文章

    doi:10.1088/1478-3975/9/1/016009

    authors: Fischer-Friedrich E,Friedrich BM,Gov NS

    更新日期:2012-02-01 00:00:00