Universal Cellular Automata and Class 4

Wolfram has provided a qualitative classification of cellular automata(CA) rules according to which, there exits a class of CA rules (called Class 4) which exhibit complex pattern formation and long-lived dynamical activity (long transients). These properties of Class 4 CA's has led to the conjecture that Class 4 rules are Universal Turing machines i.e. they are bases for computational universality. We describe an embedding of a ``small'' universal Turing machine due to Minsky, into a cellular automaton rule-table. This produces a collection of $(k=18,r=1)$ cellular automata, all of which are computationally universal. However, we observe that these rules are distributed amongst the various Wolfram classes. More precisely, we show that the identification of the Wolfram class depends crucially on the set of initial conditions used to simulate the given CA. This work, among others, indicates that a description of complex systems and information dynamics may need a new framework for non-equilibrium statistical mechanics.Comment: Latex, 10 pages, 5 figures uuencode

Complete Sequencing of pNDM-HK Encoding NDM-1 Carbapenemase from a Multidrug-Resistant Escherichia coli Strain Isolated in Hong Kong

BACKGROUND: The emergence of plasmid-mediated carbapenemases, such as NDM-1 in Enterobacteriaceae is a major public health issue. Since they mediate resistance to virtually all β-lactam antibiotics and there is often co-resistance to other antibiotic classes, the therapeutic options for infections caused by these organisms are very limited. METHODOLOGY: We characterized the first NDM-1 producing E. coli isolate recovered in Hong Kong. The plasmid encoding the metallo-β-lactamase gene was sequenced. PRINCIPAL FINDINGS: The plasmid, pNDM-HK readily transferred to E. coli J53 at high frequencies. It belongs to the broad host range IncL/M incompatibility group and is 88803 bp in size. Sequence alignment showed that pNDM-HK has a 55 kb backbone which shared 97% homology with pEL60 originating from the plant pathogen, Erwina amylovora in Lebanon and a 28.9 kb variable region. The plasmid backbone includes the mucAB genes mediating ultraviolet light resistance. The 28.9 kb region has a composite transposon-like structure which includes intact or truncated genes associated with resistance to β-lactams (bla(TEM-1), bla(NDM-1), Δbla(DHA-1)), aminoglycosides (aacC2, armA), sulphonamides (sul1) and macrolides (mel, mph2). It also harbors the following mobile elements: IS26, ISCR1, tnpU, tnpAcp2, tnpD, ΔtnpATn1 and insL. Certain blocks within the 28.9 kb variable region had homology with the corresponding sequences in the widely disseminated plasmids, pCTX-M3, pMUR050 and pKP048 originating from bacteria in Poland in 1996, in Spain in 2002 and in China in 2006, respectively. SIGNIFICANCE: The genetic support of NDM-1 gene suggests that it has evolved through complex pathways. The association with broad host range plasmid and multiple mobile genetic elements explain its observed horizontal mobility in multiple bacterial taxa

A novel IS26 structure is surrounding blaCTX-M genes in different plasmids of German clinical isolates of Escherichia coli

This report focuses on the molecular characterization of 22 extended-spectrum beta-lactamase (ESBL) producing E. coli isolates collected in a German university hospital, during a period of nine months in 2006. Relationship analysis of clinical isolates was done via pulsed-field gel-electrophoresis, mulit-locus sequence typing, plasmid profiling and additionally PCR for blaESBL detection and phylogroups. After conjugal transfer plasmid isolation and subsequent PCR for blaESBL detection and incompatibility groups were performed. Using one-primer-walking, up to 3600 bp upstream and downstream of different blaCTX-M genes could be sequenced. Beta-Lactamases found were TEM-1 (n=14), SHV-5 (n=1) and a wide variety of CTX-M types (n=21) as CTX-M-15 (n=12), CTX-M-1 (n=4), CTX-M-14 (n=2), CTX-M-9 (n=1), CTX-M-3 (n=1) as well as one new type CTX-M-65 (n=1). In 18 isolates blaESBL genes were located on conjugative plasmids in sizes between 40 and 180 kbp belonging to incompatibility groups FII (n=9), N (n=5) andI1 (n=4). Thereby blaCTX-M were found to be associated with the commonly known elements ISEcp1, IS26 and IS903-D, but with unusual spacer sequences for ISEcp1 in two isolates. These insertion sequences connected to blaCTX-M as well as other genes were located between two IS26 elements in a composition that have not been described yet. The results reveal the emergence of blaESBL, preferentially blaCTX-M, located on different plasmids harboured by genotypic different E. coli strains. The identical gene arrangement in blaCTX-M neighbourhood in plasmids of different incompatibility groups indicates a main role of IS26 in distribution of mobile resistance elements between different plasmids

Complete sequence and molecular epidemiology of IncK epidemic plasmid encoding bla(CTX-M-14)

Antimicrobial drug resistance is a global challenge for the 21st century with the emergence of resistant bacterial strains worldwide. Transferable resistance to beta-lactam antimicrobial drugs, mediated by production of extended-spectrum beta-lactamases (ESBLs), is of particular concern. In 2004, an ESBL-carrying IncK plasmid (pCT) was isolated from cattle in the United Kingdom. The sequence was a 93,629-bp plasmid encoding a single antimicrobial drug resistance gene, bla(CTX-M-14). From this information, PCRs identifying novel features of pCT were designed and applied to isolates from several countries, showing that the plasmid has disseminated worldwide in bacteria from humans and animals. Complete DNA sequences can be used as a platform to develop rapid epidemiologic tools to identify and trace the spread of plasmids in clinically relevant pathogens, thus facilitating a better understanding of their distribution and ability to transfer between bacteria of humans and animals