Calibration of a fuzzy cellular automata model of urban dynamics in Saudi Arabia

An urban cellular automata model has been designed, developed and tested for the city of Riyadh in Saudi Arabia as a research project. The model uses fuzzy set theory to capture the uncertainty associated with the transition rules and employs two automated methods of calibration: a genetic algorithm and simulated annealing. This paper describes the results of the calibration process for three time periods: 1987–1997, 1997–2005 and 1987–2005, which are characterised by different patterns of urban development. Nine different scenarios have been devised to capture the effect of different primary drivers to development including transport, urban agglomeration and topography and their interactions. The results showed that the genetic algorithm produces a better calibrated model than parallel simulated annealing. The model that contains all primary drivers and all interactions produced the best performing calibrated model overall.     

Uromycladium tepperianum, the gall rust fungus from Falcataria moluccana in Malaysia and Indonesia

Batai (Falcataria moluccana) is a valuable tree species for forest plantations in Malaysia and Indonesia. Since 1993, a gall rust disease has caused severe damage to all growth stages, from seedlings in the nursery to mature trees in the field. To identify the fungus causing gall rust disease on F. moluccana in Malaysia and Indonesia, study of the mode of infection and changes in the anatomy of infected cells were carried out in the anatomy laboratory. The disease in Malaysia and Indonesia is caused by Uromycladium tepperianum. The fungus produces three longitudinally ridged teliospores on each head, with spores measuring 13–20 μm wide and 17–28 μm long. The fungus is microcyclic, completing its entire life cycle on F. moluccana. This study confirmed that the teliospores themselves cannot infect the host. Under favorable conditions, about 10 h after inoculation, teliospores germinate to produce basidiospores that form penetration pegs about 6 h later, and it is this peg which penetrates the host cells directly through the epidermis. Pycnia, recognized as small brown pustules, break through the epidermis about 7 days after inoculation.     

A Thr357 to Ser polymorphism in homozygous and compound heterozygous subjects causes absent or reduced P2X7 function and impairs ATP-induced mycobacterial killing by macrophages

The P2X(7) receptor is a ligand-gated cation channel that is highly expressed on mononuclear leukocytes and that mediates ATP-induced apoptosis and killing of intracellular pathogens. There is a wide variation in P2X(7) receptor function between subjects, explained in part by four loss-of-function polymorphisms (R307Q, E496A, I568N, and a 5'-intronic splice site polymorphism), as well as rare mutations. In this study, we report the allele frequencies of 11 non-synonymous P2X(7) polymorphisms and describe a fifth loss-of-function polymorphism in the gene (1096C --> G), which changes Thr(357) to Ser (T357S) with an allele frequency of 0.08 in the Caucasian population. P2X(7) function was measured by ATP-induced ethidium(+) influx into peripheral blood lymphocytes and monocytes and, when compared with wild-type subjects, was reduced to 10-65% in heterozygotes, 1-18% in homozygotes, and 0-10% in compound heterozygotes carrying T357S and a second loss-of-function polymorphism. Overexpression of the T357S mutant P2X(7) in either HEK-293 cells or Xenopus oocytes gave P2X(7) function of approximately 50% that of wild-type constructs. Differentiation of monocytes to macrophages, which also up-regulates P2X(7), restored P2X(7) function to near normal in cells heterozygous for T357S and to a value 50-65% of wild-type in cells homozygous for T357S or compound heterozygous for T357S/E496A. However, macrophages from subjects that are compound heterozygous for either T357S/R307Q or T357S/stop codon had near-to-absent P2X(7) function. These functional deficits induced by T357S were paralleled by impaired ATP-induced apoptosis and mycobacteria killing in macrophages from these subjects. Lymphocytes, monocytes, and macrophages from subjects homozygous for T357S or compound heterozygous for T357S and a second loss-of-function allele have reduced or absent P2X(7) receptor function.     

Highly specific antibodies for co-detection of human choline kinase α1 and α2 isoforms

Background

Choline kinase is the first enzyme in the CDP-choline pathway that synthesizes phosphatidylcholine, the major phospholipid in eukaryotic cell membranes. In humans, choline kinase exists as three isoforms (CKα1, α2, and β). Specific inhibition of CKα has been reported to selectively kill tumoral cells. Monoclonal and polyclonal antibodies against CKα used in previous studies to detect the level of this isozyme in different cellular or biochemical contexts were able to detect either the α1 or the α2 isoform.

Methodology/Principal Findings

In this study, an antiserum against CKα was produced by immunizing rabbits with denatured, purified recombinant CKα2 full-length protein. This antiserum was highly specific for CKα when tested with extracts from different cell lines, and there was no cross reactivity with purified CKβ and other related proteins like human ethanolamine kinases (EK) and yeast choline or ethanolamine kinases. The antiserum simultaneously detected both CKα1 and α2 isoforms in MCF-7 and HepG2 cell extracts, but not in HeLa, HCT-116, and mouse embryonic stem cell extracts. Subsequent protein dot blot assay of total CKα in a human normal/tumor protein array of 30 tissue samples by using the antiserum showed that CKα was not overexpressed in all tumor tissues when compared to their normal counterparts. Most striking differences between tumor and normal CKα expression levels were observed in kidney (11-fold higher in tumor) and liver (15-fold lower in tumor) samples.

Conclusion/Significance

Apart from its high sensitivity and specificity, the antiserum produced in this work, which does not require further purification, has the advantage of co-detecting both α1 and α2 isoforms in cell extracts for direct comparison of their expression levels.     

Methylated DNA/RNA in Body Fluids as Biomarkers for Lung Cancer

DNA/RNA methylation plays an important role in lung cancer initiation and progression. Liquid biopsy makes use of cells, nucleotides and proteins released from tumor cells into body fluids to help with cancer diagnosis and prognosis. Methylation of circulating tumor DNA (ctDNA) has gained increasing attention as biomarkers for lung cancer. Here we briefly introduce the biological basis and detection method of ctDNA methylation, and review various applications of methylated DNA in body fluids in lung cancer screening, diagnosis, prognosis, monitoring and treatment prediction. We also discuss the emerging role of RNA methylation as biomarkers for cancer.     

Mapping and validation of QTL which confer partial resistance to broadly virulent post-2000 North American races of stripe rust in hexaploid wheat

A mapping population of 186 recombinant inbred lines developed from a cross between UC1110, an adapted California spring wheat, and PI610750, a synthetic derivative from CIMMYT’s Wide Cross Program, was evaluated for its response to current California races of stripe rust (Puccinia striiformis f. sp. tritici) in replicated field trials over four seasons (2007–2010) in the northern Sacramento Valley. A genetic map was constructed consisting of 1,494 polymorphic probes (SSRs, DArTs, and ESTs) mapped to 558 unique loci, and QTL analysis revealed the presence of four stripe rust resistance QTL segregating in this population, two from UC1110 (on chromosomes 3BS and 2BS) and two from PI610750 (5AL and 2AS). The two QTL of largest effects (on 3BS and 5AL) were validated in independent populations and their intervals narrowed to 2.5 and 5.3 cM, respectively. The 3BS QTL was shown, by allelism test and genotype, to carry a gene different from the Yr30/Sr2 complex. Mapped position also suggests that the 3BS QTL is associated with a gene different from either Yrns-B1 or YrRub, two stripe rust resistance genes mapped to this region in other studies. The 5AL QTL carries a previously unreported partial stripe rust resistance gene, designated here as Yr48. This paper discusses the individual contributions to resistance of these four QTL, their epistatic interactions, and their potential in durable resistance breeding strategies based on combinations of partial resistance genes.     

Essential role of EGFR in cardioprotection and signaling responses to A1 adenosine receptors and ischemic preconditioning

Transactivation of epidermal growth factor receptor (EGFR) may contribute to specific protective responses (e.g. mediated by δ-opioid, bradykinin, or muscarinic receptors). No studies have assessed EGFR involvement in cardioprotection mediated by adenosine receptors (ARs), and the role of EGFR in ischemic preconditioning (IPC) is unclear. We tested EGFR, matrix metalloproteinase (MMP), and heparin-binding EGF (HB-EGF) dependencies of functional protection via A(1)AR agonism or IPC. Pretreatment of mouse hearts with 100 nM of A(1)AR agonist 2-chloro-N(6)-cyclopentyladenosine (CCPA) or IPC (3 × 1.5-min ischemia/2-min reperfusion) substantially improved recovery from 25-min ischemia, reducing left ventricular diastolic dysfunction up to 50% and nearly doubling pressure development and positive change in pressure over time (+dP/dt). Benefit with both CCPA and IPC was eliminated by inhibitors of EGFR tyrosine kinase (0.3 μM AG1478), MMP (0.3 μM GM6001), or HB-EGF ligand (0.3 ng/ml CRM197), none of which independently altered postischemic outcome. Phosphorylation of myocardial EGFR, Erk1/2, and Akt increased two- to threefold during A(1)AR agonism, with responses blocked by AG1478, GM6001, and CRM197. Studies in HL-1 myocytes confirm A(1)AR-dependent Erk1/2 phosphorylation is negated by AG1478 or GM6001, and reduced with CRM197 (as was Akt activation). These data collectively reveal that A(1)AR- and IPC-mediated functional protection is entirely EGFR and MMP dependent, potentially involving the HB-EGF ligand. Myocardial survival kinase activation (Erk1/2, Akt) by A(1)AR agonism is similarly MMP/HB-EGF/EGFR dependent. Thus MMP-mediated EGFR activation appears essential to cardiac protection and signaling via A(1)ARs and preconditioning.