CiteULike: madhadron's library [1041 articles]

Evidence from detrital zircons for the existence of continental crust and oceans on the Earth 4.4 Gyr ago.

SA Wilde — 2008-07-22T08:47:40-00:00

Nature, Vol. 409, No. 6817. (11 January 2001), pp. 175-178.

No crustal rocks are known to have survived since the time of the intense meteor bombardment that affected Earth between its formation about 4,550 Myr ago and 4,030 Myr, the age of the oldest known components in the Acasta Gneiss of northwestern Canada. But evidence of an even older crust is provided by detrital zircons in metamorphosed sediments at Mt Narryer and Jack Hills in the Narryer Gneiss Terrane, Yilgarn Craton, Western Australia, where grains as old as approximately 4,276 Myr have been found. Here we report, based on a detailed micro-analytical study of Jack Hills zircons, the discovery of a detrital zircon with an age as old as 4,404+/-8 Myr--about 130 million years older than any previously identified on Earth. We found that the zircon is zoned with respect to rare earth elements and oxygen isotope ratios (delta18O values from 7.4 to 5.0%), indicating that it formed from an evolving magmatic source. The evolved chemistry, high delta18O value and micro-inclusions of SiO2 are consistent with growth from a granitic melt with a delta18O value from 8.5 to 9.5%. Magmatic oxygen isotope ratios in this range point toward the involvement of supracrustal material that has undergone low-temperature interaction with a liquid hydrosphere. This zircon thus represents the earliest evidence for continental crust and oceans on the Earth.

Population Graphs: the graph theoretic shape of genetic structure.

RJ Dyer — 2007-01-11T11:23:34-00:00

Mol Ecol, Vol. 13, No. 7. (July 2004), pp. 1713-1727.

Patterns of intraspecific genetic variation result from interactions among both historical and contemporary evolutionary processes. Traditionally, population geneticists have used methods such as F-statistics, pairwise isolation by distance models, spatial autocorrelation and coalescent models to analyse this variation and to gain insight about causal evolutionary processes. Here we introduce a novel approach (Population Graphs) that focuses on the analysis of marker-based population genetic data within a graph theoretic framework. This method can be used to estimate traditional population genetic summary statistics, but its primary focus is on characterizing the complex topology resulting from historical and contemporary genetic interactions among populations. We introduce the application of Population Graphs by examining the range-wide population genetic structure of a Sonoran Desert cactus (Lophocereus schottii). With this data set, we evaluate hypotheses regarding historical vicariance, isolation by distance, population-level assignment and the importance of specific populations to species-wide genetic connectivity. We close by discussing the applicability of Population Graphs for addressing a wide range of population genetic and phylogeographical problems.

High throughput gene expression measurement with real time PCR in a microfluidic dynamic array.

SL Spurgeon — 2008-07-16T15:12:44-00:00

PLoS ONE, Vol. 3, No. 2. (2008)

We describe a high throughput gene expression platform based on microfluidic dynamic arrays. This system allows 2,304 simultaneous real time PCR gene expression measurements in a single chip, while requiring less pipetting than is required to set up a 96 well plate. We show that one can measure the expression of 45 different genes in 18 tissues with replicates in a single chip. The data have excellent concordance with conventional real time PCR and the microfluidic dynamic arrays show better reproducibility than commercial DNA microarrays.

Plant species radiations: where, when, why?

Hans Peter Linder — 2008-07-16T15:11:49-00:00

Philosophical transactions of the Royal Society of London. Series B, Biological sciences (25 June 2008)

The spatial and temporal patterns of plant species radiations are largely unknown. I used a nonlinear regression to estimate speciation and extinction rates from all relevant dated clades. Both are surprisingly high. A high species richness can be the result of either little extinction, thus preserving the diversity that dates from older radiations (a 'mature radiation'), or a 'recent and rapid radiation'. The analysis of radiations from different regions (Andes, New Zealand, Australia, southwest Africa, tropics and Eurasia) revealed that the diversity of Australia may be largely the result of mature radiations. This is in sharp contrast to New Zealand, where the flora appears to be largely the result of recent and rapid radiations. Mature radiations are characteristic of regions that have been climatically and geologically stable throughout the Neogene, whereas recent and rapid radiations are more typical of younger (Pliocene) environments. The hyperdiverse Cape and Neotropical floras are the result of the combinations of mature as well as recent and rapid radiations. Both the areas contain stable environments (the Amazon basin and the Cape Fold Mountains) as well as dynamic landscapes (the Andes and the South African west coast). The evolution of diversity can only be understood in the context of the local environment.

Stepwise formation of the bacterial flagellar system.

R Liu — 2008-07-16T15:01:33-00:00

Proceedings of the National Academy of Sciences of the United States of America, Vol. 104, No. 17. (24 April 2007), pp. 7116-7121.

Elucidating the origins of complex biological structures has been one of the major challenges of evolutionary studies. The bacterial flagellum is a primary example of a complex apparatus whose origins and evolutionary history have proven difficult to reconstruct. The gene clusters encoding the components of the flagellum can include >50 genes, but these clusters vary greatly in their numbers and contents among bacterial phyla. To investigate how this diversity arose, we identified all homologs of all flagellar proteins encoded in the complete genome sequences of 41 flagellated species from 11 bacterial phyla. Based on the phylogenetic occurrence and histories of each of these proteins, we could distinguish an ancient core set of 24 structural genes that were present in the common ancestor to all Bacteria. Within a genome, many of these core genes show sequence similarity only to other flagellar core genes, indicating that they were derived from one another, and the relationships among these genes suggest the probable order in which the structural components of the bacterial flagellum arose. These results show that core components of the bacterial flagellum originated through the successive duplication and modification of a few, or perhaps even a single, precursor gene.

Supertrees Disentangle the Chimeric Origin of Eukaryotic Genomes.

Davide Pisani — 2007-06-10T09:57:27-00:00

Mol Biol Evol (15 May 2007)

Eukaryotes are traditionally considered to be one of the three natural divisions of the tree of life and the sister group of the Archaebacteria. However, eukaryotic genomes are replete with genes of eubacterial ancestry and more than 20 mutually incompatible hypotheses have been proposed to account for eukaryote origins. Here we test the predictions of these hypotheses using a novel supertree-based phylogenetic signal-stripping method, and recover supertrees of life based on phylogenies for up to 5741 single gene families distributed across 185 genomes. Using our signal-stripping method we show that there are three distinct phylogenetic signals in eukaryotic genomes. In order of strength, these link eukaryotes with the Cyanobacteria, the Proteobacteria and the Thermoplasmatales, an Archaebacterial (euryarchaeotes) group. These signals correspond to distinct symbiotic partners involved in eukaryote evolution: plastids, mitochondria, and the elusive host lineage. According to our whole-genome data, eukaryotes are hardly the sister group of the Archaebacteria because up to 83% of eukaryotic genes with a prokaryotic homologue have eubacterial, not archaebacterial, origins. The results reject all but two of the current hypotheses for the origin of eukaryotes: those assuming a sulphur- or hydrogen- dependent syntrophy for the origin of mitochondria.

Genome-Wide Experimental Determination of Barriers to Horizontal Gene Transfer

Rotem Sorek — 2007-11-30T19:08:53-00:00

Science, Vol. 318, No. 5855. (30 November 2007), pp. 1449-1452.

Horizontal gene transfer, in which genetic material is transferred from the genome of one organism to that of another, has been investigated in microbial species mainly through computational sequence analyses. To address the lack of experimental data, we studied the attempted movement of 246,045 genes from 79 prokaryotic genomes into Escherichia coli and identified genes that consistently fail to transfer. We studied the mechanisms underlying transfer inhibition by placing coding regions from different species under the control of inducible promoters. Our data suggest that toxicity to the host inhibited transfer regardless of the species of origin and that increased gene dosage and associated increased expression may be a predominant cause for transfer failure. Although these experimental studies examined transfer solely into E. coli, a computational analysis of gene-transfer rates across available bacterial and archaeal genomes supports that the barriers observed in our study are general across the tree of life. 10.1126/science.1147112

Pattern pluralism and the Tree of Life hypothesis.

WF Doolittle — 2007-09-26T22:20:38-00:00

Proc Natl Acad Sci U S A, Vol. 104, No. 7. (13 February 2007), pp. 2043-2049.

Darwin claimed that a unique inclusively hierarchical pattern of relationships between all organisms based on their similarities and differences [the Tree of Life (TOL)] was a fact of nature, for which evolution, and in particular a branching process of descent with modification, was the explanation. However, there is no independent evidence that the natural order is an inclusive hierarchy, and incorporation of prokaryotes into the TOL is especially problematic. The only data sets from which we might construct a universal hierarchy including prokaryotes, the sequences of genes, often disagree and can seldom be proven to agree. Hierarchical structure can always be imposed on or extracted from such data sets by algorithms designed to do so, but at its base the universal TOL rests on an unproven assumption about pattern that, given what we know about process, is unlikely to be broadly true. This is not to say that similarities and differences between organisms are not to be accounted for by evolutionary mechanisms, but descent with modification is only one of these mechanisms, and a single tree-like pattern is not the necessary (or expected) result of their collective operation. Pattern pluralism (the recognition that different evolutionary models and representations of relationships will be appropriate, and true, for different taxa or at different scales or for different purposes) is an attractive alternative to the quixotic pursuit of a single true TOL.

GENETICS: Paradigm for Life

James Mcinerney — 2007-11-30T12:52:09-00:00

Science, Vol. 318, No. 5855. (30 November 2007), pp. 1390-1391.

10.1126/science.1151657

Robust, Tunable Biological Oscillations from Interlinked Positive and Negative Feedback Loops

Tony Tsai — 2008-07-03T22:13:28-00:00

Science, Vol. 321, No. 5885. (4 July 2008), pp. 126-129.

A simple negative feedback loop of interacting genes or proteins has the potential to generate sustained oscillations. However, many biological oscillators also have a positive feedback loop, raising the question of what advantages the extra loop imparts. Through computational studies, we show that it is generally difficult to adjust a negative feedback oscillator's frequency without compromising its amplitude, whereas with positive-plus-negative feedback, one can achieve a widely tunable frequency and near-constant amplitude. This tunability makes the latter design suitable for biological rhythms like heartbeats and cell cycles that need to provide a constant output over a range of frequencies. Positive-plus-negative oscillators also appear to be more robust and easier to evolve, rationalizing why they are found in contexts where an adjustable frequency is unimportant. 10.1126/science.1156951

Size Limits of Very Small Microorganisms: Proceedings of a Workshop

2008-06-22T11:06:29-00:00

Phylogenetic mapping of bacterial morphology.

JL Siefert — 2008-06-22T11:04:24-00:00

Microbiology (Reading, England), Vol. 144 ( Pt 10) (October 1998), pp. 2803-2808.

The availability of a meaningful molecular phylogeny for bacteria provides a context for examining the historical significance of various developments in bacterial evolution. Herein, the classical morphological descriptions of selected members of the domain Bacteria are mapped upon the genealogical ancestry deduced from comparison of small-subunit rRNA sequences. For the species examined in this study, a distinct pattern emerges which indicates that the coccus shape has arisen and accumulated independently multiple times in separate lineages and typically survived as a persistent end-state morphology. At least two other morphologies persist but have evolved only once. This study demonstrates that although bacterial morphology is not useful in defining bacterial phylogeny, it is remarkably consistent with that phylogeny once it is known. An examination of the experimental evidence available for morphogenesis as well as microbial fossil evidence corroborates these findings. It is proposed that the accumulation of persistent morphologies is a result of the biophysical properties of peptidoglycan and their genetic control, and that an evolved body-plan strategy based on peptidoglycan may have been a fate-sealing step in the evolution of Bacteria. More generally, this study illustrates that significant evolutionary insights can be obtained by examining biological and biochemical data in the context of a reliable phylogenetic structure.

Subdiffraction Multicolor Imaging of the Nuclear Periphery with 3D Structured Illumination Microscopy

Lothar Schermelleh — 2008-06-06T16:49:53-00:00

Science, Vol. 320, No. 5881. (6 June 2008), pp. 1332-1336.

Fluorescence light microscopy allows multicolor visualization of cellular components with high specificity, but its utility has until recently been constrained by the intrinsic limit of spatial resolution. We applied three-dimensional structured illumination microscopy (3D-SIM) to circumvent this limit and to study the mammalian nucleus. By simultaneously imaging chromatin, nuclear lamina, and the nuclear pore complex (NPC), we observed several features that escape detection by conventional microscopy. We could resolve single NPCs that colocalized with channels in the lamin network and peripheral heterochromatin. We could differentially localize distinct NPC components and detect double-layered invaginations of the nuclear envelope in prophase as previously seen only by electron microscopy. Multicolor 3D-SIM opens new and facile possibilities to analyze subcellular structures beyond the diffraction limit of the emitted light. 10.1126/science.1156947

Genetic engineering using homologous recombination.

DL Court — 2006-03-02T23:00:26-00:00

Annu Rev Genet, Vol. 36 (2002), pp. 361-388.

In the past few years, in vivo technologies have emerged that, due to their efficiency and simplicity, may one day replace standard genetic engineering techniques. Constructs can be made on plasmids or directly on the Escherichia coli chromosome from PCR products or synthetic oligonucleotides by homologous recombination. This is possible because bacteriophage-encoded recombination functions efficiently recombine sequences with homologies as short as 35 to 50 base pairs. This technology, termed recombineering, is providing new ways to modify genes and segments of the chromosome. This review describes not only recombineering and its applications, but also summarizes homologous recombination in E. coli and early uses of homologous recombination to modify the bacterial chromosome. Finally, based on the premise that phage-mediated recombination functions act at replication forks, specific molecular models are proposed.

Efficient and seamless DNA recombineering using a thymidylate synthase A selection system in Escherichia coli.

QN Wong — 2007-09-20T09:25:48-00:00

Nucleic Acids Res, Vol. 33, No. 6. (2005)

Lambda-red system-based recombinogenic engineering is a powerful new method to engineer DNA without the need for restriction enzymes or ligases. Here, we report the use of a single selectable marker to enhance the usefulness of this approach. The strategy is to utilize the thymidylate synthase A (thyA) gene, which encodes an enzyme involved in the synthesis of thymidine 5'-triphosphate, for both positive and negative selection. With this approach, we successfully created point mutations in plasmid and bacterial artificial chromosome (BAC) DNA containing the mouse Col10a1 gene. The results showed that the thyA selection system is highly efficient and accurate, giving an average of >90% selection efficiency. This selection system produces DNA that is free from permanent integration of unwanted sequences, thus allowing unlimited rounds of modifications if required.

One step construction of PCR mutagenized libraries for genetic analysis by recombination cloning.

Al-Muataz Khalil — 2007-08-21T18:59:17-00:00

Nucleic Acids Res (15 August 2007)

Recombination cloning encompasses a set of technologies that transfer gene sequences between vectors through site-specific recombination. Due in part to the instability of linear DNA in bacteria, both the initial capture and subsequent transfer of gene sequences is often performed using purified recombination enzymes. However, we find linear DNAs flanked by loxP sites recombine efficiently in bacteria expressing Cre recombinase and the lambda Gam protein, suggesting Cre/lox recombination of linear substrates can be performed in vivo. As one approach towards exploiting this capability, we describe a method for constructing large (>1 x 10(6) recombinants) libraries of gene mutations in a format compatible with recombination cloning. In this method, gene sequences are cloned into recombination entry plasmids and whole-plasmid PCR is used to produce mutagenized plasmid amplicons flanked by loxP. The PCR products are converted back into circular plasmids by transforming Cre/Gam-expressing bacteria, after which the mutant libraries are transferred to expression vectors and screened for phenotypes of interest. We further show that linear DNA fragments flanked by loxP repeats can be efficiently recombined into loxP-containing vectors through this same one-step transformation procedure. Thus, the approach reported here could be adapted as general cloning method.

Identification and analysis of recombineering functions from Gram-negative and Gram-positive bacteria and their phages

Simanti Datta — 2008-02-05T19:12:08-00:00

Proceedings of the National Academy of Sciences, Vol. 105, No. 5. (5 February 2008), pp. 1626-1631.

We report the identification and functional analysis of nine genes from Gram-positive and Gram-negative bacteria and their phages that are similar to lambda (lambda) bet or Escherichia coli recT. Beta and RecT are single-strand DNA annealing proteins, referred to here as recombinases. Each of the nine other genes when expressed in E. coli carries out oligonucleotide-mediated recombination. To our knowledge, this is the first study showing single-strand recombinase activity from diverse bacteria. Similar to bet and recT, most of these other recombinases were found to be associated with putative exonuclease genes. Beta and RecT in conjunction with their cognate exonucleases carry out recombination of linear double-strand DNA. Among four of these foreign recombinase/exonuclease pairs tested for recombination with double-strand DNA, three had activity, albeit barely detectable. Thus, although these recombinases can function in E. coli to catalyze oligonucleotide recombination, the double-strand DNA recombination activities with their exonuclease partners were inefficient. This study also demonstrated that Gam, by inhibiting host RecBCD nuclease activity, helps to improve the efficiency of lambda Red-mediated recombination with linear double-strand DNA, but Gam is not absolutely essential. Thus, in other bacterial species where Gam analogs have not been identified, double-strand DNA recombination may still work in the absence of a Gam-like function. We anticipate that at least some of the recombineering systems studied here will potentiate oligonucleotide and double-strand DNA-mediated recombineering in their native or related bacteria. 10.1073/pnas.0709089105

A recombineering based approach for high-throughput conditional knockout targeting vector construction.

W Chan — 2007-09-07T16:23:30-00:00

Nucleic Acids Res, Vol. 35, No. 8. (2007)

Functional analysis of mammalian genes in vivo is primarily achieved through analysing knockout mice. Now that the sequencing of several mammalian genomes has been completed, understanding functions of all the genes represents the next major challenge in the post-genome era. Generation of knockout mutant mice has currently been achieved by many research groups but only by making individual knockouts, one by one. New technological advances and the refinements of existing technologies are critical for genome-wide targeted mutagenesis in the mouse. We describe here new recombineering reagents and protocols that enable recombineering to be carried out in a 96-well format. Consequently, we are able to construct 96 conditional knockout targeting vectors simultaneously. Our new recombineering system makes it a reality to generate large numbers of precisely engineered DNA constructs for functional genomics studies.

Recombineering linear DNA that replicate stably in E. coli

Yaw-Shin Ooi — 2008-01-02T00:03:30-00:00

Plasmid, Vol. In Press, Corrected Proof

The advent of recombineering technology in Escherichia coli has revolutionized the way recombinant DNA molecules are constructed. We present a novel application of recombineering to linearize DNA by capping their ends with individual telomeres derived from bacteriophage N15, which exists as a linear prophage in E. coli. The N15 telomerase occupancy site was recombined into circular DNA and resolved into individual telomeres by the phage N15 protelomerase enzyme. We demonstrate this technique by assembling linear BACs that replicate stably in their host strain E. coli DH10B. Correct linearization of the BACs was confirmed by restriction mapping using pulsed field gel electrophoresis. The linear BAC DNA can be easily purified using standard plasmid isolation methods and resist degradation from RecBCD nuclease in vitro and in vivo owing to the presence of telomeres. Transfection of a linear 100 kb BAC containing the human [beta]-globin gene cluster into HT1080 cells produced accurately spliced transcripts, demonstrating that the linear DNA will be useful for subsequent functional studies. This novel recombineering technique may be particularly useful for building large linear constructs for assembling artificial chromosomes with telomeres, and may provide a unique means to clone and study large linear viral genomes that contain hairpin ends.

Recombineering: in vivo genetic engineering in E. coli, S. enterica, and beyond.

JA Sawitzke — 2007-11-13T03:09:22-00:00

Methods Enzymol, Vol. 421 (2007), pp. 171-199.

"Recombineering," in vivo genetic engineering with short DNA homologies, is changing how constructs are made. The methods are simple, precise, efficient, rapid, and inexpensive. Complicated genetic constructs that can be difficult or even impossible to make with in vitro genetic engineering can be created in days with recombineering. DNA molecules that are too large to manipulate with classical techniques are amenable to recombineering. This technology utilizes the phage lambda homologous recombination functions, proteins that can efficiently catalyze recombination between short homologies. Recombineering can be accomplished with linear PCR products or even single-stranded oligos. In this chapter we discuss methods of and ways to use recombineering.

Stars of the terrestrial deep subsurface: A novel star-shaped bacterial morphotype from a South African platinum mine

G Wanger — 2008-05-25T05:48:48-00:00

Geobiology, Vol. 6, No. 3. (June 2008), pp. 325-330.

Archaea with square cells.

AE Walsby — 2006-04-11T17:56:50-00:00

Trends Microbiol, Vol. 13, No. 5. (May 2005), pp. 193-195.

Two groups of microbiologists have independently isolated 'Walsby's square bacterium' from salt crystallizer ponds; its growth depends on pyruvate. Genetic analysis shows that the squares, discovered 25 years ago on the Sinai Peninsula, are archaea rather than bacteria. These transparent tile-like cells might have been dismissed as surface artefacts of salt crystals but for their gas vesicles--structures peculiar to prokaryotic organisms. Paradoxically, the square archaea are the dominant microorganisms in some hypersaline environments and might be globally important.

A square bacterium

AE Walsby — 2008-06-17T14:29:54-00:00

Nature, Vol. 283, No. 5742. (3 January 1980), pp. 69-71.

Modular construction of plasmids through ligation-free assembly of vector components with oligonucleotide linkers

Jonathan Vroom — 2008-06-10T18:19:30-00:00

Biotechniques, Vol. 44 (June 2008), pp. 924-926.

joined in any order. In this case, we assembled plasmids with up to four PCR fragments. Using Pfu DNA polymerase (Stratagene, La Jolla, CA, USA) and standard We have developed a modular method of plasmid construction that can join multiple DNA components in a single reaction. A nicking enzyme is used to create 5′ and 3′ overhangs on PCR-generated DNA components. Without the use of ligase or restriction enzymes, compo- nents are joined using oligonucleotide linkers that recognize the overhangs. By specifying the sequences of the linkers, desired components can be assembled in any combination and order to generate different plasmid vectors.

Critical factors influencing the occurrence of Vibrio cholerae in the environment of Bangladesh.

A Huq — 2008-06-01T12:51:27-00:00

Applied and environmental microbiology, Vol. 71, No. 8. (August 2005), pp. 4645-4654.

The occurrence of outbreaks of cholera in Africa in 1970 and in Latin America in 1991, mainly in coastal communities, and the appearance of the new serotype Vibrio cholerae O139 in India and subsequently in Bangladesh have stimulated efforts to understand environmental factors influencing the growth and geographic distribution of epidemic Vibrio cholerae serotypes. Because of the severity of recent epidemics, cholera is now being considered by some infectious disease investigators as a "reemerging" disease, prompting new work on the ecology of vibrios. Epidemiological and ecological surveillance for cholera has been under way in four rural, geographically separated locations in Bangladesh for the past 4 years, during which both clinical and environmental samples were collected at biweekly intervals. The clinical epidemiology portion of the research has been published (Sack et al., J. Infect. Dis. 187:96-101, 2003). The results of environmental sampling and analysis of the environmental and clinical data have revealed significant correlations of water temperature, water depth, rainfall, conductivity, and copepod counts with the occurrence of cholera toxin-producing bacteria (presumably V. cholerae). The lag periods between increases or decreases in units of factors, such as temperature and salinity, and occurrence of cholera correlate with biological parameters, e.g., plankton population blooms. The new information on the ecology of V. cholerae is proving useful in developing environmental models for the prediction of cholera epidemics.

Pathogenicity islands and phages in Vibrio cholerae evolution.

SM Faruque — 2008-06-01T12:50:39-00:00

Trends in microbiology, Vol. 11, No. 11. (November 2003), pp. 505-510.

The identification of accessory genetic elements (plasmids, phages and chromosomal 'pathogenicity islands') encoding virulence-associated genes has facilitated our efforts to understand the origination of pathogenic microorganisms. Toxigenic Vibrio cholerae, the etiologic agent of cholera, represents a paradigm for this process in that this organism evolved from environmental nonpathogenic V. cholerae by acquisition of virulence genes. The major virulence genes in V. cholerae, which are clustered in several chromosomal regions, appear to have been recently acquired from phages or through undefined horizontal gene transfer events. Evidence is accumulating that the interactions of phages with each other can also influence the emergence of pathogenic clones of V. cholerae. Therefore, to track the evolution of pathogens from their nonpathogenic progenitors, it is also crucial to identify and characterize secondary genetic elements that mediate lateral transfer of virulence genes in trans. Understanding the evolutionary events that lead to the emergence of pathogenic clones might provide new approaches to the control of cholera and other infectious diseases.

Detection and transformation of genome segments that differ within a coastal population of Vibrio cholerae strains.

MC Miller — 2008-06-01T12:50:04-00:00

Applied and environmental microbiology, Vol. 73, No. 11. (June 2007), pp. 3695-3704.

Vibrio cholerae is an autochthonous member of diverse aquatic ecosystems around the globe. Collectively, the genomes of environmental V. cholerae strains comprise a large repository of encoded functions which can be acquired by individual V. cholerae lineages through uptake and recombination. To characterize the genomic diversity of environmental V. cholerae, we used comparative genome hybridization to study 41 environmental strains isolated from diverse habitats along the central California coast, a region free of endemic cholera. These data were used to classify genes of the epidemic V. cholerae O1 sequenced strain N16961 as conserved, variably present, or absent from the isolates. For the most part, absent genes were restricted to large mobile elements and have known functions in pathogenesis. Conversely, genes present in some, but not all, California isolates were in smaller contiguous clusters and were less likely to be near genes with functions in DNA mobility. Two such clusters of variable genes encoding different selectable metabolic phenotypes (mannose and diglucosamine utilization) were transformed into the genomes of environmental isolates by chitin-dependent competence, indicating that this mechanism of general genetic exchange is conserved among V. cholerae. The transformed DNA had an average size of 22.7 kbp, demonstrating that natural competence can mediate the movement of large chromosome fragments. Thus, whether variable genes arise through the acquisition of new sequences by horizontal gene transfer or by the loss of preexisting DNA though deletion, natural transformation provides a mechanism by which V. cholerae clones can gain access to the V. cholerae pan-genome.

Growth of walled cells: from shells to vesicles.

A Boudaoud — 2008-06-01T12:43:26-00:00

Physical review letters, Vol. 91, No. 1. (4 July 2003)

The growth of isolated walled cells is investigated. Examples of such cells range from bacteria to giant algae, and include cochlear hair, plant root hair, fungi, and yeast cells. They are modeled as elastic shells containing a liquid. Cell growth is driven by fluid pressure and is is similar to a plastic deformation of the wall. The requirement of mechanical equilibrium leads to two new scaling laws for cell size that are in quantitative agreement with the compiled biological data. Given these results, possible shapes for growing cells are computed by analogy with those of vesicle membranes.

Biophysical characterization of changes in amounts and activity of Escherichia coli cell and compartment water and turgor pressure in response to osmotic stress.

DS Cayley — 2008-06-01T12:27:43-00:00

Biophysical journal, Vol. 78, No. 4. (April 2000), pp. 1748-1764.

To obtain turgor pressure, intracellular osmolalities, and cytoplasmic water activity of Escherichia coli as a function of osmolality of growth, we have quantified and analyzed amounts of cell, cytoplasmic, and periplasmic water as functions of osmolality of growth and osmolality of plasmolysis of nongrowing cells with NaCl. The effects are large; NaCl (plasmolysis) titrations of cells grown in minimal medium at 0.03 Osm reduce cytoplasmic and cell water to approximately 20% and approximately 50% of their original values, and increase periplasmic water by approximately 300%. Independent analysis of amounts of cytoplasmic and cell water demonstrate that turgor pressure decreases with increasing osmolality of growth, from approximately 3.1 atm at 0.03 Osm to approximately 1.5 at 0.1 Osm and to less than 0.5 atm above 0.5 Osm. Analysis of periplasmic membrane-derived oligosaccharide (MDO) concentrations as a function of osmolality, calculated from literature analytical data and measured periplasmic volumes, provides independent evidence that turgor pressure decreases with increasing osmolality, and verifies that cytoplasmic and periplasmic osmolalities are equal. We propose that MDO play a key role in periplasmic volume regulation at low-to-moderate osmolality. At high growth osmolalities, where only a small amount of cytoplasmic water is observed, the small turgor pressure of E. coli demonstrates that cytoplasmic water activity is only slightly less than extracellular water activity. From these findings, we deduce that the activity of cytoplasmic water exceeds its mole fraction at high osmolality, and, therefore, conclude that the activity coefficient of cytoplasmic water increases with increasing growth osmolality and exceeds unity at high osmolality, presumably as a consequence of macromolecular crowding. These novel findings are significant for thermodynamic analyses of effects of changes in growth osmolality on biopolymer processes in general and osmoregulatory processes in particular in the E. coli cytoplasm.

Themes and variations in prokaryotic cell division.

W Margolin — 2008-06-01T12:26:09-00:00

FEMS microbiology reviews, Vol. 24, No. 4. (October 2000), pp. 531-548.

Perhaps the biggest single task facing a bacterial cell is to divide into daughter cells that contain the normal complement of chromosomes. Recent technical and conceptual breakthroughs in bacterial cell biology, combined with the flood of genome sequence information and the excellent genetic tools in several model systems, have shed new light on the mechanism of prokaryotic cell division. There is good evidence that in most species, a molecular machine, organized by the tubulin-like FtsZ protein, assembles at the site of division and orchestrates the splitting of the cell. The determinants that target the machine to the right place at the right time are beginning to be understood in the model systems, but it is still a mystery how the machine actually generates the constrictive force necessary for cytokinesis. Moreover, although some cell division determinants such as FtsZ are present in a broad spectrum of prokaryotic species, the lack of FtsZ in some species and different profiles of cell division proteins in different families suggests that there are diverse mechanisms for regulating cell division.

The evaluation of the rates of biological processes from tracer kinetic data : II. RNA metabolism in growing bacteria

Arthur Koch — 2008-05-22T08:38:55-00:00

Journal of Theoretical Biology, Vol. 18, No. 1. (January 1968), pp. 105-132.

Because messenger RNA continuously breaks down to form nucleotides that are reutilized for synthesis of all forms of RNA, analysis of the kinetics of uptake of precursors into the nucleic acids of cells is complicated. Our theoretical work (Koch, 1962) is now extended to evaluate the effects of recycling for the case of growing cells. Equations are derived for several different assumptions about the turnover of the intermediate pool of RNA precursors. Even if one assumes the pool infinitesimal, the equations apply to uptake at times greater than a minute for Escherichia coli. The effective turnover rate constant of messenger is smaller than the true turnover rate constant by a factor which is the ratio of the rate at which molecules enter the intermediate pool from the exogenous source to the total rate at which molecules enter the pool from all sources. The initial lag in the incorporation of isotope into total nucleic acids can be used to measure the velocity of synthesis of the pool from all sources if the pool size is known. If the pool size is unknown, it may be estimated from the lag time extrapolated from uptake measurements at intermediate times. Short lag times, however, do not necessarily reflect a small pool. The pool may be large and it may communicate with a bypass or with the external medium but still give rise to a short lag because of the initial rapid uptake of precursor into messenger. The percentage of the isotope in particular classes of nucleic acid relative to the total nucleic acids is a quantity that can be measured. These measurements can be used to measure both the rate of synthesis and the amount of labile RNA in the cells.

Evaluation of the rates of biological processes from tracer kinetic data : III. The net synthesis lemma and exchangeable pools

Arthur Koch — 2008-05-22T08:38:33-00:00

Journal of Theoretical Biology, Vol. 32, No. 3. (September 1971), pp. 429-450.

Equations are developed for total isotope incorporation into the sum of all species of RNA in growing bacterial cultures. The model is approximate in that it considers only one intermediate pool, only one messenger fraction and only one intermediate on the path of the biosynthesis of the ribosome. However, there is no mathematical approximation involved in the treatment as there was in the previous paper. With the aid of a computer, the conditions necessary to observe linear uptake with no lag were determined. It is concluded that exchange of exogenous isotopic precursor across the cell membrane, together with the existence of a turning over class of RNA, accounts for the observed smaller lag in isotope incorporation than that predicted from the size of the intermediate pool. The effect of amino acid starvation and turnover of precursors of ribosomal and transfer RNA is discussed. With the computer program, data from the literature are used to estimate the turnover rate of messenger RNA.

Nuclear Physics: A Course Given by Enrico Fermi at the University of Chicago

Enrico Fermi — 2008-05-21T09:25:58-00:00

(15 August 1974)

This volume presents, with some amplification, the notes on the lectures on nuclear physics given by Enrico Fermi at the University of Chicago in 1949. "The compilers of this publication may be warmly congratulated. . . . The scope of this course is amazing: within 240 pages it ranges from the general properties of atomic nuclei and nuclear forces to mesons and cosmic rays, and includes an account of fission and elementary pile theory. . . . The course addresses itself to experimenters rather than to specialists in nuclear theory, although the latter will also greatly profit from its study on account of the sound emphasis laid everywhere on the experimental approach to problems. . . . There is a copious supply of problems."—_Proceedings of the Physical Society _ "Only a relatively few students are privileged to attend Professor Fermi's brilliant lectures at the University of Chicago; it is therefore a distinct contribution to the followers of nuclear science that his lecture material has been systematically organized in a publication and made available to a much wider audience."—_Nucelonics _

Stochastic Receptor Expression Allows Sensitive Bacteria to Evade Phage Attack. Part II: Theoretical Analyses

E Chapman-Mcquiston — 2008-05-14T21:44:56-00:00

Biophys. J., Vol. 94, No. 11. (1 June 2008), pp. 4537-4548.

Stochastic gene expression in bacteria can create a diverse protein distribution. Most of the current studies have focused on fluctuations around the mean, which constitutes the majority of a bacterial population. However, when the bacterial population is subject to a severe selection pressure, it is the properties of the minority cells that determine the fate of the population. The central question is whether phenotype heterogeneity, such as a spread in the expression level of a critical protein, is sufficient to account for the persistence of the bacteria under the selection. A related question is how long such persistence can last before genetic mutation becomes significant. In this work, survival statistics of a bacterial population with a diverse phage-receptor number distribution is theoretically investigated when the cells are subject to phage pressures. The calculations are compared with our experimental observations presented in Part I in this issue. The fundamental basis of our analysis is the Berg-Purcell theoretical result for the reaction rate between a phage particle and a bacterium with a discrete number of receptors, and the observation that most phage-resistant mutants isolated in laboratory cultures are defective in phage binding. It is shown that a heterogeneous bacterial population is significantly more fit compared to a homogeneous population when confronting a phage attack. 10.1529/biophysj.107.121723

Stochastic Receptor Expression Allows Sensitive Bacteria to Evade Phage Attack. Part I: Experiments

E Chapman-Mcquiston — 2008-05-14T21:39:56-00:00

Biophys. J., Vol. 94, No. 11. (1 June 2008), pp. 4525-4536.

It has long been suspected that population heterogeneity, either at a genetic level or at a protein level, can improve the fitness of an organism under a variety of environmental stresses. However, quantitative measurements to substantiate such a hypothesis turn out to be rather difficult and have rarely been performed. Herein, we examine the effect of expression heterogeneity of lambda-phage receptors on the response of an Escherichia coli population to attack by a high concentration oflambda -phage. The distribution of the phage receptors in the population was characterized by flow cytometry, and the same bacterial population was then subjected to different phage pressures. We show that a minority population of bacteria that produces the receptor slowly and at low levels determines the long-term survivability of the bacterial population and that phage-resistant mutants can be efficiently isolated only when the persistent phage pressure >1010 viruses/cm3 is present. Below this phage pressure, persistors instead of mutants are dominant in the population. 10.1529/biophysj.107.120212

The Four Basic Mechanisms of Fitness and Complexity Increase in Evolution

Yong Fu — 2008-05-13T10:35:21-00:00

(10 May 2008)

The generation, selection, and preservation of the patterns are the essence of evolution. Complete probing of the entire configuration space is critical for the fitness and complexity increase in evolution. The bias in pattern generation is unfavourable for configuration space probing. Therefore, the pattern generation underlying evolution should be as diverse as possible to achieve complete probing. One of the missions of evolution is to minimize the bias in pattern generation. Natural selection is to couple the fate of pattern with the survival of its output, i.e. its host evolutionary entity. This responsibility is the driving force of fitness and complexity increase. Therefore, another mission of evolution is to enhance the efficiency and resolving power of natural selection. During evolution, the selected patterns are inevitably subjected to various deleterious influences, which may compromise the benefit resulting from selection, or even destroy the selected patterns. The third mission of evolution is to preserve the generated and selected patterns from various influences except the coupled selection to the host evolutionary entity. Nonbiotic evolution cannot fulfil these missions because of the primitive mode of nonbiotic evolution. Special mechanisms emerge during the origin of life to perform these missions and thus account for the fitness and complexity of life.

Single-cell protein induction dynamics reveals a period of vulnerability to antibiotics in persister bacteria

Orit Gefen — 2008-04-22T17:45:58-00:00

Proceedings of the National Academy of Sciences (21 April 2008), 0711712105.

Phenotypic variability in populations of cells has been linked to evolutionary robustness to stressful conditions. A remarkable example of the importance of cell-to-cell variability is found in bacterial persistence, where subpopulations of dormant bacteria, termed persisters, were shown to be responsible for the persistence of the population to antibiotic treatments. Here, we use microfluidic devices to monitor the induction of fluorescent proteins under synthetic promoters and characterize the dormant state of single persister bacteria. Surprisingly, we observe that protein production does take place in supposedly dormant bacteria, over a narrow time window after the exit from stationary phase. Only thereafter does protein production stop, suggesting that differentiation into persisters fully develops over this time window and not during starvation, as previously believed. In effect, we observe that exposure of bacteria to antibiotics during this time window significantly reduces persistence. Our results point to new strategies to fight persistent bacterial infections. The quantitative measurement of single-cell induction presented in this study should shed light on the processes leading to the dormancy of subpopulations in different systems, such as in subpopulations of viable but nonculturable bacteria, or those of quiescent cancer cells. 10.1073/pnas.0711712105

Evolution of the genetic code. From the CG- to the CGUA-alphabet, from RNA double helix to DNA

Denis Semenov — 2008-05-07T07:56:11-00:00

(5 May 2008)

A hypothesis of the evolution of the genetic code is proposed, the leading mechanism of which is the nucleotide spontaneous damage leading to AT-enrichment of the genome. The hypothesis accounts for stability of the genetic code towards point mutations, the presence of code dialects, emergence of stop codons, emergence of the DNA double helix and the symmetry of the genetic code table. The assumption of the originally triplet structure of the genetic code has been substantiated. A hypothesis concerning the primary structure of the first gene and the first protein has been proposed.

Noisy translation of a single gene: fluctuations in protein synthesis from a single template

Ashok Garai — 2008-03-14T13:36:30-00:00

(11 Mar 2008)

We introduce some new quantitative measures of fluctuations in the process of synthesis of proteins from a single messenger RNA (mRNA) template. We calculate the statistical distributions of these fluctuating quantities and extract the strength of the corresponding translational noise. For these calculations we use a model that captures both the mechano-chemistry of each individual ribosome as well as their steric interactions in ribosome traffic on the same mRNA track. By comparing our results for a specific gene of the Escherichia coli bacteria with those for the corresponding homogeneous mRNA template, we demonstrate the effects of the sequence inhomogeneities of real genes on the fluctuations and noise. We also suggest in-vitro laboratory experiments for testing our theoretical predictions.

Bounding the Size and Probability of Epidemics on Networks

Joel Miller — 2008-05-07T07:30:00-00:00

(1 May 2008)

We consider an infectious disease spreading along the edges of a network which may have significant clustering. The individuals in the population have heterogeneous infectiousness and/or susceptibility. We define the out-transmissibility of a node to be the marginal probability that it would infect a randomly chosen neighbor given its infectiousness and the distribution of susceptibility. For a given distribution of out-transmissibility, we find the conditions which give the upper [or lower] bounds on size and probability of an epidemic, under weak assumptions on the transmission properties, but very general assumptions on the network. We find similar bounds for a given distribution of in-transmissibility (the marginal probability of being infected by a neighbor). We also find conditions giving global upper bounds on size and probability. The distributions leading to these bounds are network-independent. In the special case of networks with high girth (locally tree-like), we are able to prove stronger results. In general the probability and size of epidemics are maximal when the population is homogeneous and minimal when the variance of in- or out-transmissibility is maximal.

Signaling cascades as cellular devices for spatial computations

Jörg Stelling — 2008-02-26T13:07:15-00:00

Journal of Mathematical Biology

Abstract Signaling networks usually include protein-modification cycles. Cascades of such cycles are the backbones of multiple signaling pathways. Protein gradients emerge from the spatial separation of opposing enzymes, such as kinases and phosphatases, or guanine nucleotide exchange factors (GEFs) and GTPase activating proteins (GAPs) for GTPase cycles. We show that different diffusivities of an active protein form and an inactive form leads to spatial gradients of protein abundance in the cytoplasm. For a cascade of cycles, using a discrete approximation of the space, we derive an analytical expression for the spatial gradients and show that it converges to an exact solution with decreasing the size of the quantization. Our results facilitate quantitative analysis of the dependence of spatial gradients on the network topology and reaction kinetics. We demonstrate how different cascade designs filter and process the input information to generate precise, complex spatial guidance for multiple GTPase effector processes. Thus, protein-modification cascades may serve as devices to compute complex spatial distributions of target proteins within intracellular space.

In Search of the Biological Significance of Modular Structures in Protein Networks

Zhi Wang — 2008-05-05T09:15:46-00:00

PLoS Computational Biology, Vol. 3, No. 6. (2007), e107.

Bacterial morphogenesis: learning how cells make cells.

FM Harold — 2008-05-05T08:24:54-00:00

Current opinion in microbiology, Vol. 10, No. 6. (December 2007), pp. 591-595.

Bacteria furnish tractable models for complex biological processes, and morphogenesis is now taking its turn. We can already explain in general terms how such elementary forms as rods and cocci are produced, and the shapes of several individual organisms are coming into focus. In most bacteria shape is maintained by the cell wall, specifically the peptidoglycan layer, which has the attributes of a strong stiff fabric. Compliance of that fabric with turgor pressure is an important aspect of morphogenesis. The shape of the wall sacculus is determined by the way it is deposited, which is controlled by a cytoskeleton made up of two molecular families. One, related to the eukaryotic tubulins, is responsible for the construction of the septum and the poles. The other, related to eukaryotic actins, localizes peptidoglycan synthesis in the lateral walls of rod-shaped cells. Just how the cytoskeleton itself is organized remains to be discovered, but it seems likely that, as in eukaryotes, the cytoskeleton is produced by self-organized assembly, guided by the fabric of the cell.

The Cell Wall of Lactic Acid Bacteria: Surface Constituents and Macromolecular Conformations

Prisca Schar-Zammaretti — 2008-05-01T08:09:51-00:00

Biophys. J., Vol. 85, No. 6. (1 December 2003), pp. 4076-4092.

A variety of strains of the genus Lactobacillus was investigated with respect to the structure, softness, and interactions of their outer surface layers in order to construct structure-property relations of the Gram-positive bacterial cell wall. The role of the conformational properties of the constituents of the outer cell-wall layers and their spatial distribution on the cell wall is emphasized. Atomic force microscopy was used to resolve the surface structure, interactions, and softness of the bacterial cell wall at nanometer-length scales and upwards. The pH-dependence of the electrophoretic mobility and a novel interfacial adhesion assay were used to analyze the average physicochemical properties of the bacterial strains. The bacterial surface is smooth when a compact layer of globular proteins constitutes the outer surface, e.g., the S-layer of L. crispatus DSM20584. In contrast, for two other S-layer containing strains (L. helveticus ATCC12046 and L. helveticus ATCC15009), the S-layer is covered by polymeric surface constituents which adopt a much more extended conformation and which confer a certain roughness to the surface. Consequently, the S-layer is important for the overall surface properties of L. crispatus, but not for the surface properties of L. helveticus. Both surface proteins (L. crispatus DSM20584) and (lipo)teichoic acids (L. johnsonii ATCC332) confer hydrophobic properties to the bacterial surface whereas polysaccharides (L. johnsonii DSM20533 and L. johnsonii ATCC 33200) render the bacterial surface hydrophilic. Using the interfacial adhesion assay, it was demonstrated that hydrophobic groups within the cell wall adsorb limited quantities of hydrophobic compounds. The present work demonstrates that the impressive variation in surface properties displayed by even a limited number of genetically-related bacterial strains can be understood in terms of established colloidal concepts, provided that sufficiently detailed structural, chemical, and conformational information on the surface constituents is available.

A generic mechanism for adaptive growth rate regulation

Chikara Furusawa — 2008-04-28T14:37:16-00:00

(25 Apr 2007)

How can a microorganism adapt to a variety of environmental conditions despite there exists a limited number of signal transduction machineries? We show that for any growing cells whose gene expression is under stochastic fluctuations, adaptive cellular state is inevitably selected by noise, even without specific signal transduction network for it. In general, changes in protein concentration in a cell are given by its synthesis minus dilution and degradation, both of which are proportional to the rate of cell growth. In an adaptive state with a higher growth speed, both terms are large and balanced. Under the presence of noise in gene expression, the adaptive state is less affected by stochasticity since both the synthesis and dilution terms are large, while for a non-adaptive state both the terms are smaller so that cells are easily kicked out of the original state by noise. Hence, escape time from a cellular state and the cellular growth rate are negatively correlated. This leads to a selection of adaptive states with higher growth rates, and model simulations confirm this selection to take place in general. The results suggest a general form of adaptation that has never been brought to light - a process that requires no specific machineries for sensory adaptation. The present scheme may help explain a wide range of cellular adaptive responses including the metabolic flux optimization for maximal cell growth.

Feed-forward loop circuits as a side effect of genome evolution.

OX Cordero — 2007-06-19T12:03:45-00:00

Mol Biol Evol, Vol. 23, No. 10. (October 2006), pp. 1931-1936.

In this article, we establish a connection between the mechanics of genome evolution and the topology of gene regulation networks, focusing in particular on the evolution of the feed-forward loop (FFL) circuits. For this, we design a model of stochastic duplications, deletions, and mutations of binding sites and genes and compare our results with yeast network data. We show that the mechanics of genome evolution may provide a mechanism of FFL circuit generation. Our simulations result in overrepresentation of FFL circuits as well as in their clustering around few regulator pairs, in concordance with data from transcription networks. The mechanism here proposed and the analysis of the yeast data show that regulator duplication could have played an important role in FFL evolution.

Network topology and the evolution of dynamics in an artificial genetic regulatory network model created by whole genome duplication and divergence.

P Dwight Kuo — 2008-04-27T12:56:02-00:00

Bio Systems, Vol. 85, No. 3. (September 2006), pp. 177-200.

Topological measures of large-scale complex networks are applied to a specific artificial regulatory network model created through a whole genome duplication and divergence mechanism. This class of networks share topological features with natural transcriptional regulatory networks. Specifically, these networks display scale-free and small-world topology and possess subgraph distributions similar to those of natural networks. Thus, the topologies inherent in natural networks may be in part due to their method of creation rather than being exclusively shaped by subsequent evolution under selection. The evolvability of the dynamics of these networks is also examined by evolving networks in simulation to obtain three simple types of output dynamics. The networks obtained from this process show a wide variety of topologies and numbers of genes indicating that it is relatively easy to evolve these classes of dynamics in this model.

An evolutionary and functional assessment of regulatory network motifs.

A Mazurie — 2005-08-30T19:52:35-00:00

Genome Biol, Vol. 6, No. 4. (2005)

BACKGROUND: Cellular functions are regulated by complex webs of interactions that might be schematically represented as networks. Two major examples are transcriptional regulatory networks, describing the interactions among transcription factors and their targets, and protein-protein interaction networks. Some patterns, dubbed motifs, have been found to be statistically over-represented when biological networks are compared to randomized versions thereof. Their function in vitro has been analyzed both experimentally and theoretically, but their functional role in vivo, that is, within the full network, and the resulting evolutionary pressures remain largely to be examined. RESULTS: We investigated an integrated network of the yeast Saccharomyces cerevisiae comprising transcriptional and protein-protein interaction data. A comparative analysis was performed with respect to Candida glabrata, Kluyveromyces lactis, Debaryomyces hansenii and Yarrowia lipolytica, which belong to the same class of hemiascomycetes as S. cerevisiae but span a broad evolutionary range. Phylogenetic profiles of genes within different forms of the motifs show that they are not subject to any particular evolutionary pressure to preserve the corresponding interaction patterns. The functional role in vivo of the motifs was examined for those instances where enough biological information is available. In each case, the regulatory processes for the biological function under consideration were found to hinge on post-transcriptional regulatory mechanisms, rather than on the transcriptional regulation by network motifs. CONCLUSION: The overabundance of the network motifs does not have any immediate functional or evolutionary counterpart. A likely reason is that motifs within the networks are not isolated, that is, they strongly aggregate and have important edge and/or node sharing with the rest of the network.

Symbiotic gut microbes modulate human metabolic phenotypes.

M Li — 2008-02-24T21:53:59-00:00

Proc Natl Acad Sci U S A, Vol. 105, No. 6. (12 February 2008), pp. 2117-2122.

Humans have evolved intimate symbiotic relationships with a consortium of gut microbes (microbiome) and individual variations in the microbiome influence host health, may be implicated in disease etiology, and affect drug metabolism, toxicity, and efficacy. However, the molecular basis of these microbe-host interactions and the roles of individual bacterial species are obscure. We now demonstrate a"transgenomic" approach to link gut microbiome and metabolic phenotype (metabotype) variation. We have used a combination of spectroscopic, microbiomic, and multivariate statistical tools to analyze fecal and urinary samples from seven Chinese individuals (sampled twice) and to model the microbial-host metabolic connectivities. At the species level, we found structural differences in the Chinese family gut microbiomes and those reported for American volunteers, which is consistent with population microbial cometabolic differences reported in epidemiological studies. We also introduce the concept of functional metagenomics, defined as "the characterization of key functional members of the microbiome that most influence host metabolism and hence health." For example, Faecalibacterium prausnitzii population variation is associated with modulation of eight urinary metabolites of diverse structure, indicating that this species is a highly functionally active member of the microbiome, influencing numerous host pathways. Other species were identified showing different and varied metabolic interactions. Our approach for understanding the dynamic basis of host-microbiome symbiosis provides a foundation for the development of functional metagenomics as a probe of systemic effects of drugs and diet that are of relevance to personal and public health care solutions.

Mathematical model of the lac operon: inducer exclusion, catabolite repression, and diauxic growth on glucose and lactose.

P Wong — 2008-04-23T11:35:59-00:00

Biotechnology progress, Vol. 13, No. 2. (r 1997), pp. 132-143.

A mathematical model of the lactose (lac) operon was developed to study diauxic growth on glucose and lactose. The model includes catabolite repression, inducer exclusion, lactose hydrolysis to glucose and galactose, and synthesis and degradation of allolactose. Two models for catabolite repression were tested: (i) cyclic AMP (cAMP) synthesis inversely correlated with the external glucose concentration and (ii) synthesis inversely correlated with the glucose transport rate. No significant differences in the two models were observed. In addition to synthesis, degradation and secretion of cAMP were also included in the model. Two models for the phosphorylation of the glucose produced from lactose hydrolysis were also tested: (i) phosphorylation by intracellular hexokinase and (ii) secretion of glucose and subsequent phosphorylation upon transport back into the cell. The latter model resulted in weak catabolite repression when the glucose produced from lactose was transported out of the cell, whereas the former model showed no catabolite repression during growth on lactose. Parameter sensitivity analysis indicates the importance of key parameters to lac operon expression and cell growth: the lactose and allolactose transformation rates by beta-galactosidase and the glucose concentrations that affect catabolite repression and inducer exclusion. Large values of the allolactose hydrolysis rate resulted in low concentrations of allolactose, low-level expression of the lac operon, and slow growth due to limited import and metabolism of lactose; small values resulted in a high concentration of allolactose, high-level expression of the lac operon, and slow growth due to a limiting concentration of glucose 6-phosphate formed from allolactose. Changes in the rates of all beta-galactosidase-catalyzed reactions showed similar behavior, but had more drastic effects on the growth rate. Changes in the glucose concentration that inhibited lactose transport could extend or contract the diauxic growth period during growth in the presence of glucose and lactose. Moreover, changes in the glucose concentration that affected catabolite repression affected the cAMP levels and lac operon expression, but had a lesser effect on the growth rate.