1,026 research outputs found
Simple flexible polymers in a spherical cage
We report the results of Monte Carlo simulations investigating the effect of
a spherical confinement within a simple model for a flexible homopolymer. We
use the parallel tempering method combined with multi-histogram reweighting
analysis and multicanonical simulations to investigate thermodynamical
observables over a broad range of temperatures, which enables us to describe
the behavior of the polymer and to locate the freezing and collapse
transitions. We find a strong effect of the spherical confinement on the
location of the collapse transition, whereas the freezing transition is hardly
effected.Comment: 7 pages, 4 figure
Enhancement of the stability of genetic switches by overlapping upstream regulatory domains
We study genetic switches formed from pairs of mutually repressing operons.
The switch stability is characterised by a well defined lifetime which grows
sub-exponentially with the number of copies of the most-expressed transcription
factor, in the regime accessible by our numerical simulations. The stability
can be markedly enhanced by a suitable choice of overlap between the upstream
regulatory domains. Our results suggest that robustness against biochemical
noise can provide a selection pressure that drives operons, that regulate each
other, together in the course of evolution.Comment: 4 pages, 5 figures, RevTeX
Monotone Grid Drawings of Planar Graphs
A monotone drawing of a planar graph is a planar straight-line drawing of
where a monotone path exists between every pair of vertices of in some
direction. Recently monotone drawings of planar graphs have been proposed as a
new standard for visualizing graphs. A monotone drawing of a planar graph is a
monotone grid drawing if every vertex in the drawing is drawn on a grid point.
In this paper we study monotone grid drawings of planar graphs in a variable
embedding setting. We show that every connected planar graph of vertices
has a monotone grid drawing on a grid of size , and such a
drawing can be found in O(n) time
Complete Genome Sequence of Pelosinus fermentans JBW45, a Member of a Remarkably Competitive Group of Negativicutes in the Firmicutes Phylum.
The genome of Pelosinus fermentans JBW45, isolated from a chromium-contaminated site in Hanford, Washington, USA, has been completed with PacBio sequencing. Nine copies of the rRNA gene operon and multiple transposase genes with identical sequences resulted in breaks in the original draft genome and may suggest genomic instability of JBW45
Transcriptomic and proteomic analyses of Desulfovibrio vulgaris biofilms: carbon and energy flow contribute to the distinct biofilm growth state.
BackgroundDesulfovibrio vulgaris Hildenborough is a sulfate-reducing bacterium (SRB) that is intensively studied in the context of metal corrosion and heavy-metal bioremediation, and SRB populations are commonly observed in pipe and subsurface environments as surface-associated populations. In order to elucidate physiological changes associated with biofilm growth at both the transcript and protein level, transcriptomic and proteomic analyses were done on mature biofilm cells and compared to both batch and reactor planktonic populations. The biofilms were cultivated with lactate and sulfate in a continuously fed biofilm reactor, and compared to both batch and reactor planktonic populations.ResultsThe functional genomic analysis demonstrated that biofilm cells were different compared to planktonic cells, and the majority of altered abundances for genes and proteins were annotated as hypothetical (unknown function), energy conservation, amino acid metabolism, and signal transduction. Genes and proteins that showed similar trends in detected levels were particularly involved in energy conservation such as increases in an annotated ech hydrogenase, formate dehydrogenase, pyruvate:ferredoxin oxidoreductase, and rnf oxidoreductase, and the biofilm cells had elevated formate dehydrogenase activity. Several other hydrogenases and formate dehydrogenases also showed an increased protein level, while decreased transcript and protein levels were observed for putative coo hydrogenase as well as a lactate permease and hyp hydrogenases for biofilm cells. Genes annotated for amino acid synthesis and nitrogen utilization were also predominant changers within the biofilm state. Ribosomal transcripts and proteins were notably decreased within the biofilm cells compared to exponential-phase cells but were not as low as levels observed in planktonic, stationary-phase cells. Several putative, extracellular proteins (DVU1012, 1545) were also detected in the extracellular fraction from biofilm cells.ConclusionsEven though both the planktonic and biofilm cells were oxidizing lactate and reducing sulfate, the biofilm cells were physiologically distinct compared to planktonic growth states due to altered abundances of genes/proteins involved in carbon/energy flow and extracellular structures. In addition, average expression values for multiple rRNA transcripts and respiratory activity measurements indicated that biofilm cells were metabolically more similar to exponential-phase cells although biofilm cells are structured differently. The characterization of physiological advantages and constraints of the biofilm growth state for sulfate-reducing bacteria will provide insight into bioremediation applications as well as microbially-induced metal corrosion
Complete Genome Sequences of Four Escherichia coli ST95 Isolates from Bloodstream Infections
Finished genome sequences are presented for four Escherichia coli strains isolated from bloodstream infections at San Francisco General Hospital. These strains provide reference sequences for four major fimH-identified sublineages within the multilocus sequence type (MLST) ST95 group, and provide insights into pathogenicity and differential antimicrobial susceptibility within this group
Vibrational Enhancement of the Effective Donor - Acceptor Coupling
The paper deals with a simple three sites model for charge transfer phenomena
in an one-dimensional donor (D) - bridge (B) - acceptor (A) system coupled with
vibrational dynamics of the B site. It is found that in a certain range of
parameters the vibrational coupling leads to an enhancement of the effective
donor - acceptor electronic coupling as a result of the formation of the
polaron on the B site. This enhancement of the charge transfer efficiency is
maximum at the resonance, where the effective energy of the fluctuating B site
coincides with the donor (acceptor) energy.Comment: 5 pages, 3 figure
Selection of chromosomal DNA libraries using a multiplex CRISPR system.
The directed evolution of biomolecules to improve or change their activity is central to many engineering and synthetic biology efforts. However, selecting improved variants from gene libraries in living cells requires plasmid expression systems that suffer from variable copy number effects, or the use of complex marker-dependent chromosomal integration strategies. We developed quantitative gene assembly and DNA library insertion into the Saccharomyces cerevisiae genome by optimizing an efficient single-step and marker-free genome editing system using CRISPR-Cas9. With this Multiplex CRISPR (CRISPRm) system, we selected an improved cellobiose utilization pathway in diploid yeast in a single round of mutagenesis and selection, which increased cellobiose fermentation rates by over 10-fold. Mutations recovered in the best cellodextrin transporters reveal synergy between substrate binding and transporter dynamics, and demonstrate the power of CRISPRm to accelerate selection experiments and discoveries of the molecular determinants that enhance biomolecule function
Functional genomics with a comprehensive library of transposon mutants for the sulfate-reducing bacterium Desulfovibrio alaskensis G20.
UnlabelledThe genomes of sulfate-reducing bacteria remain poorly characterized, largely due to a paucity of experimental data and genetic tools. To meet this challenge, we generated an archived library of 15,477 mapped transposon insertion mutants in the sulfate-reducing bacterium Desulfovibrio alaskensis G20. To demonstrate the utility of the individual mutants, we profiled gene expression in mutants of six regulatory genes and used these data, together with 1,313 high-confidence transcription start sites identified by tiling microarrays and transcriptome sequencing (5' RNA-Seq), to update the regulons of Fur and Rex and to confirm the predicted regulons of LysX, PhnF, PerR, and Dde_3000, a histidine kinase. In addition to enabling single mutant investigations, the D. alaskensis G20 transposon mutants also contain DNA bar codes, which enables the pooling and analysis of mutant fitness for thousands of strains simultaneously. Using two pools of mutants that represent insertions in 2,369 unique protein-coding genes, we demonstrate that the hypothetical gene Dde_3007 is required for methionine biosynthesis. Using comparative genomics, we propose that Dde_3007 performs a missing step in methionine biosynthesis by transferring a sulfur group to O-phosphohomoserine to form homocysteine. Additionally, we show that the entire choline utilization cluster is important for fitness in choline sulfate medium, which confirms that a functional microcompartment is required for choline oxidation. Finally, we demonstrate that Dde_3291, a MerR-like transcription factor, is a choline-dependent activator of the choline utilization cluster. Taken together, our data set and genetic resources provide a foundation for systems-level investigation of a poorly studied group of bacteria of environmental and industrial importance.ImportanceSulfate-reducing bacteria contribute to global nutrient cycles and are a nuisance for the petroleum industry. Despite their environmental and industrial significance, the genomes of sulfate-reducing bacteria remain poorly characterized. Here, we describe a genetic approach to fill gaps in our knowledge of sulfate-reducing bacteria. We generated a large collection of archived, transposon mutants in Desulfovibrio alaskensis G20 and used the phenotypes of these mutant strains to infer the function of genes involved in gene regulation, methionine biosynthesis, and choline utilization. Our findings and mutant resources will enable systematic investigations into gene function, energy generation, stress response, and metabolism for this important group of bacteria
The statistical mechanics of complex signaling networks : nerve growth factor signaling
It is becoming increasingly appreciated that the signal transduction systems
used by eukaryotic cells to achieve a variety of essential responses represent
highly complex networks rather than simple linear pathways. While significant
effort is being made to experimentally measure the rate constants for
individual steps in these signaling networks, many of the parameters required
to describe the behavior of these systems remain unknown, or at best,
estimates. With these goals and caveats in mind, we use methods of statistical
mechanics to extract useful predictions for complex cellular signaling
networks. To establish the usefulness of our approach, we have applied our
methods towards modeling the nerve growth factor (NGF)-induced differentiation
of neuronal cells. Using our approach, we are able to extract predictions that
are highly specific and accurate, thereby enabling us to predict the influence
of specific signaling modules in determining the integrated cellular response
to the two growth factors. We show that extracting biologically relevant
predictions from complex signaling models appears to be possible even in the
absence of measurements of all the individual rate constants. Our methods also
raise some interesting insights into the design and possible evolution of
cellular systems, highlighting an inherent property of these systems wherein
particular ''soft'' combinations of parameters can be varied over wide ranges
without impacting the final output and demonstrating that a few ''stiff''
parameter combinations center around the paramount regulatory steps of the
network. We refer to this property -- which is distinct from robustness -- as
''sloppiness.''Comment: 24 pages, 10 EPS figures, 1 GIF (makes 5 multi-panel figs + caption
for GIF), IOP style; supp. info/figs. included as brown_supp.pd
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