Synchronous vs. asynchronous dynamics of diffusion-controlled reactions

An analytical method based on the classical ruin problem is developed to compute the mean reaction time between two walkers undergoing a generalized random walk on a 1d lattice. At each time step, either both walkers diffuse simultaneously with probability $p$ (synchronous event) or one of them diffuses while the other remains immobile with complementary probability (asynchronous event). Reaction takes place through same site occupation or position exchange. We study the influence of the degree of synchronicity $p$ of the walkers and the lattice size $N$ on the global reaction's efficiency. For odd $N$, the purely synchronous case ($p=1$) is always the most effective one, while for even $N$, the encounter time is minimized by a combination of synchronous and asynchronous events. This new parity effect is fully confirmed by Monte Carlo simulations on 1d lattices as well as for 2d and 3d lattices. In contrast, the 1d continuum approximation valid for sufficiently large lattices predicts a monotonic increase of the efficiency as a function of $p$. The relevance of the model for several research areas is briefly discussed.Comment: 21 pages (including 12 figures and 4 tables), uses revtex4.cls, accepted for publication in Physica

Genomics of lipid metabolism: Identifying novel causal pathways and new therapeutic targets for reducing risk of coronary heart disease

Coronary heart disease (CHD) is one of the leading causes of death worldwide; mortality rates are expected to continue to rise over the coming decades. Circulating lipids have been shown to be strongly and linearly associated with risk of CHD; however, despite considerable efforts to demonstrate causality, available evidence is conflicting and insufficient. Study of the underlying metabolic pathways implicated in the association between lipids and CHD would help to disentangle and elucidate these complex relationships. Direct infusion high-resolution mass spectrometry was performed on 5,551 participants from the Pakistan Risk of Myocardial Infarction Study; raw data were then processed, cleaned, and normalized to extract signals corresponding to 444 known lipid metabolites. Cross-correlations of lipid metabolites and their correlations with circulating lipids were examined, and the association of principal components of lipid metabolites with CHD risk factors was assessed. Genome-wide analyses were conducted to analyze the association of each lipid metabolite with 7.2 million genotyped and imputed single nucleotide polymorphisms (SNPs). Following conditional analyses on the lead SNP within each loci, we identified genome-wide significant associations at 148 independent metabolic loci and 54 novel loci. We then used functional annotation to link the variants associated with each metabolite to the most probable causal genes, and two-sample Mendelian randomization to examine the causal effect of lipid metabolites on risk of CHD. Analyses of circulating lipid metabolites in large epidemiological studies could lead to enhanced understanding of mechanisms for CHD development and identification of novel causal pathways and new therapeutic targets

MmeI: a minimal Type II restriction-modification system that only modifies one DNA strand for host protection

MmeI is an unusual Type II restriction enzyme that is useful for generating long sequence tags. We have cloned the MmeI restriction-modification (R-M) system and found it to consist of a single protein having both endonuclease and DNA methyltransferase activities. The protein comprises an amino-terminal endonuclease domain, a central DNA methyltransferase domain and C-terminal DNA recognition domain. The endonuclease cuts the two DNA strands at one site simultaneously, with enzyme bound at two sites interacting to accomplish scission. Cleavage occurs more rapidly than methyl transfer on unmodified DNA. MmeI modifies only the adenine in the top strand, 5′-TCCRAC-3′. MmeI endonuclease activity is blocked by this top strand adenine methylation and is unaffected by methylation of the adenine in the complementary strand, 5′-GTYGGA-3′. There is no additional DNA modification associated with the MmeI R-M system, as is required for previously characterized Type IIG R-M systems. The MmeI R-M system thus uses modification on only one of the two DNA strands for host protection. The MmeI architecture represents a minimal approach to assembling a restriction-modification system wherein a single DNA recognition domain targets both the endonuclease and DNA methyltransferase activities

Fifteen new risk loci for coronary artery disease highlight arterial-wall-specific mechanisms

Coronary artery disease (CAD) is a leading cause of morbidity and mortality worldwide. Although 58 genomic regions have been associated with CAD thus far, most of the heritability is unexplained, indicating that additional susceptibility loci await identification. An efficient discovery strategy may be larger-scale evaluation of promising associations suggested by genome-wide association studies (GWAS). Hence, we genotyped 56,309 participants using a targeted gene array derived from earlier GWAS results and performed meta-analysis of results with 194,427 participants previously genotyped, totaling 88,192 CAD cases and 162,544 controls. We identified 25 new SNP-CAD associations (P < 5 × 10(-8), in fixed-effects meta-analysis) from 15 genomic regions, including SNPs in or near genes involved in cellular adhesion, leukocyte migration and atherosclerosis (PECAM1, rs1867624), coagulation and inflammation (PROCR, rs867186 (p.Ser219Gly)) and vascular smooth muscle cell differentiation (LMOD1, rs2820315). Correlation of these regions with cell-type-specific gene expression and plasma protein levels sheds light on potential disease mechanisms

High-resolution structure of the M14-type cytosolic carboxypeptidase from <em>Burkholderia cenocepacia </em>refined exploiting <em>PDB_REDO </em>strategies

A potential cytosolic metallocarboxypeptidase from Burk­holderia cenocepacia has been crystallized and a synchrotron-radiation microfocus beamline allowed the acquisition of diffraction data to 1.9 Å resolution. The asymmetric unit comprises a tetramer containing over 1500 amino acids, and the high-throughput automated protocols embedded in PDB_REDO were coupled with model–map inspections in refinement. This approach has highlighted the value of such protocols for efficient analyses. The subunit is constructed from two domains. The N-terminal domain has previously only been observed in cytosolic carboxypeptidase (CCP) proteins. The C-terminal domain, which carries the Zn(2+)-containing active site, serves to classify this protein as a member of the M14D subfamily of carboxypeptidases. Although eukaryotic CCPs possess deglutamylase activity and are implicated in processing modified tubulin, the function and substrates of the bacterial family members remain unknown. The B. cenocepacia protein did not display deglutamylase activity towards a furylacryloyl glutamate derivative, a potential substrate. Residues previously shown to coordinate the divalent cation and that contribute to peptide-bond cleavage in related enzymes such as bovine carboxypeptidase are conserved. The location of a conserved basic patch in the active site adjacent to the catalytic Zn(2+), where an acetate ion is identified, suggests recognition of the carboxy-terminus in a similar fashion to other carboxypeptidases. However, there are significant differences that indicate the recognition of substrates with different properties. Of note is the presence of a lysine in the S1′ recognition subsite that suggests specificity towards an acidic substrate

Structure of the type III secretion and substrate-binding domain of Yersinia YopH phosphatase

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/72457/1/j.0950-382x.2001.02711.x.pd

Reaction Kinetics in Restricted Spaces

Reactions in restricted spaces rarely get stirred vigorously by convection and are thus controlled by diffusion. Furthermore, the compactness of the Brownian motion leads to both anomalous diffusion and anomalous reaction kinetics. Elementary binary reactions of the type A + A → Products, A + B → Products, and A + C → C + Products are discussed theoretically for both batch and steady‐state conditions. The anomalous reaction orders and time exponents (for the rate coefficients) are discussed for various situations. Global and local rate laws are related to particle distribution functions. Only Poissonian distributions guarantee the classical rate laws. Reactant self‐organization leads to interesting new phenomena. These are demonstrated by theory, simulations, and experiments. The correlation length of reactant production affects the self‐ordering length scale. These effects are demonstrated experimentally, including the stability of reactant segregation observed in chemical reactions in one‐dimensional spaces, e.g., capillaries and microcapillaries. The gap between the reactant A (cation) and B (anion) actually increases in time and extends over millimeters. Excellent agreement is found among theory, simulation, and experiment for the various scaling exponents.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/101785/1/199100016_ftp.pd

Antisense RNA associated with biological regulation of a restriction–modification system

Restriction–modification systems consist of a modification enzyme that methylates a specific DNA sequence and a restriction endonuclease that cleaves DNA lacking this epigenetic signature. Their gene expression should be finely regulated because their potential to attack the host bacterial genome needs to be controlled. In the EcoRI system, where the restriction gene is located upstream of the modification gene in the same orientation, we previously identified intragenic reverse promoters affecting gene expression. In the present work, we identified a small (88 nt) antisense RNA (Rna0) transcribed from a reverse promoter (PREV0) at the 3′ end of the restriction gene. Its antisense transcription, as measured by transcriptional gene fusion, appeared to be terminated by the PM1,M2 promoter. PM1,M2 promoter-initiated transcription, in turn, appeared to be inhibited by PREV0. Mutational inactivation of PREV0 increased expression of the restriction gene. The biological significance of this antisense transcription is 2-fold. First, a mutation in PREV0 increased restriction of incoming DNA. Second, the presence of the antisense RNA gene (ecoRIA) in trans alleviated cell killing after loss of the EcoRI plasmid (post-segregational killing). Taken together, these results strongly suggested the involvement of an antisense RNA in the biological regulation of this restriction–modification system

Rare and common genetic determinants of metabolic individuality and their effects on human health

Garrod’s concept of ‘chemical individuality’ has contributed to comprehension of the molecular origins of human diseases. Untargeted high-throughput metabolomic technologies provide an in-depth snapshot of human metabolism at scale. We studied the genetic architecture of the human plasma metabolome using 913 metabolites assayed in 19,994 individuals and identified 2,599 variant–metabolite associations (P < 1.25 × 10−11) within 330 genomic regions, with rare variants (minor allele frequency ≤ 1%) explaining 9.4% of associations. Jointly modeling metabolites in each region, we identified 423 regional, co-regulated, variant–metabolite clusters called genetically influenced metabotypes. We assigned causal genes for 62.4% of these genetically influenced metabotypes, providing new insights into fundamental metabolite physiology and clinical relevance, including metabolite-guided discovery of potential adverse drug effects (DPYD and SRD5A2). We show strong enrichment of inborn errors of metabolism-causing genes, with examples of metabolite associations and clinical phenotypes of non-pathogenic variant carriers matching characteristics of the inborn errors of metabolism. Systematic, phenotypic follow-up of metabolite-specific genetic scores revealed multiple potential etiological relationships