Whole Genome Amplification * Edited by S. Hughes and R. Lasken * Scion Publishing Ltd, Bloxham, UK; * 2005; ISBN 1-904842-07-0; 193 pp.; * Paperback.

With increasingly powerful methods of genomic analysis becomingavailable in the last few years, the availability of genomicDNA in sufficient quantities can become a limiting factor. Thisrequirement for the unlimited supply of DNA has acceleratedthe development of reliable methods of amplifying the wholegenome. This book outlines various methodologies that could be adoptedto enhance and optimise ‘Whole Genome Amplification’(WGA). Each chapter contains a concise introduction that leadsthe reader into the practical approaches of the     

Reactions of PTIO and carboxy-PTIO with *NO, *NO2, and O2-*

Nitronyl nitroxides, such as derivatives of 2-phenyl-4,4,5,5,-tetramethylimidazoline-1-oxyl 3-oxide (PTIOs), react with *NO to form the corresponding imino nitroxides (PTIs) and *NO2. PTIOs are considered as monitors of *NO, stoichiometric sources of *NO2, biochemical and physiological effectors, specific tools for the elimination of *NO, and potential therapeutic agents. However, a better understanding of the chemical properties of PTIOs, especially following their reaction with *NO, is necessary to resolve many of the reported discrepancies surrounding the effects of PTIOs and to better characterize their potential therapeutic activity. We have generated electrochemically the oxidized and reduced forms of PTIO and carboxy-PTIO (C-PTIO), characterized their absorption spectra, and determined the reduction potentials for the oxoammonium/nitroxide and nitroxide/hydroxylamine couples. The rate constants for the reaction of *NO2 with PTIO and C-PTIO to form the corresponding oxoammonium cations (PTIO+s) and nitrite were determined to be (1.5 - 2) x 10(7) m-1 s-1. We have also shown that the reactions of PTIO+s with *NO form PTIOs and NO2-. The rate constants for these reactions are approximately 30-fold higher than those for the reactions of PTIOs with *NO or O2-*. The present results show that (i) the reaction of PTIOs with *NO forms solely PTIs and NO2- where [NO2-]/[PTI] varies between 1 and 2 depending on the steady-state concentrations of *NO. Consequently, quantitation of *NO is valid only at sufficiently low fluxes of *NO; (ii) the reaction of PTIOs with *NO can be used as a valid source of *NO2 only when the latter is effectively scavenged by an appropriate reductant; and (iii) the formation of peroxynitrite cannot be efficiently inhibited by PTIOs even under relatively low fluxes of *NO and O2-* and millimolar levels of PTIOs.     

The Evolution of the Genome * Edited by T. Ryan Gregory * Elsevier Academic Press, Inc., London, UK; 2005; ISBN 0-12-301463-8; 768 pp.; {pound}39.99; Hardback.

The Evolution of the Genome is an ambitious project that aimsto compress a wealth of information about all kinds of genomes,and combine this with a perspective on how genomes evolve. Itis easy for volumes such as this to fall into the trap of becominglittle more than an almanac of useful facts and figures andwhilst this is something that the editor is amply qualifiedto do, the resulting tome is in fact a surprisingly interestingread, mixing evolutionary theory and conundrums, with insightsinto some of the mechanisms of genome change. The book is split into five roughly symmetrical parts, each     

Photocyclization of trans-1-(1'-naphthyl)-2-(3-hydroxyphenyl)ethene: evidence for adiabatic 1trans*-->1cis* photoisomerization.

The photochemistry of trans- and cis-1-(1'-naphthyl)-2-(3-hydroxyphenyl)ethene in cyclohexane and acetonitrile was examined. In cyclohexane fluorescence is the main deactivation channel for the 1trans* isomer while photocyclization is the main reaction of the 1cis* isomer. The weighty formation of hydroxychrysene following one photon absorption by the trans isomer furnished evidence of an adiabatic 1trans*-->1cis* isomerization. The photoreactivity data in acetonitrile indicated the influence of solvent polarity on the shape of the excited state surface.     

XML for Bioinformatics * Ethan Cerami * Berlin: Springer-Verlag; * ISBN: 0-387-23028-9; 304pp.; * 2005; {pound}42.50

Not until I received this book to review, did I realize thatI had another book on my shelf, ‘Web Services Essentials’,by the same author. This was a good omen. The Essentials bookwas where I first cut my teeth on notions such as XML-RPC, SOAP,WSDLs,     

Glycoconjugated hypocrellin: photosensitized generation of free radicals (O2*-, *OH, and GHB*-) and singlet oxygen (1O2).

To improve water solubility and specific affinity for malignant tumors, glycoconjugated hypocrellin B (GHB) has been synthesized. Illumination of deoxygenated DMSO solution containing GHB generates a strong electron paramagnetic resonance (EPR) signal. The EPR signal is assigned to the semiquinone anion radical of GHB (GHB*-) based on a series of experimental results. Spectrophotometric measurements show that the absorption bands at 645 nm and 502 nm (pH 8.0) or 505 nm (pH 11.0) arise from the semiquinone anion radical (GHB*-) and hydroquinone (GHBH2) of GHB, respectively. GHBH2 is readily formed via the decay of GHB*- in water-contained solution. The increase of pH value of the reaction media promotes this process. When oxygen is present, superoxide anion radical (O2*-) is formed, via the electron transfer from GHB*-, the precursor, to ground state molecular oxygen. Hydroxyl radical can be readily detected by DMPO spin trapping when aerobic aqueous solution containing GHB is irradiated. As compared with the parent compound, hypocrellin B (HB), the efficiency of O2* and *OH generation by GHB photosensitization is enhanced significantly. Singlet oxygen (1O2) can be produced via the energy transfer from triplet GHB to ground state oxygen molecules, with a decreased quantum yield, i.e., 0.19. These findings suggest that the new GHB possesses an enhanced type I process and a decreased type II process as compared with hypocrellin B.     

Erratum: Ochnaflavone inhibits TNF‐α‐induced human VSMC proliferation via regulation of cell cycle,ERK1/2, and MMP‐9. S.‐J. Suh,U.‐H. Jin,S.‐H. Kim,H.‐W. Chang,J.‐K. Son,S.H. Lee,K.‐H. Son,C.‐H. Kim

During the corresponding author's transfer from Dongguk University to Sungkyunkwan University in March 2006, data from the previous University was transferred to the corresponding author's new computer. During this data transfer there was a mixing of EMSA data from experiments involving Quercetin (QC), Ochnaflavone (OC), Tanshinone (TS), Crytotanshinone (CT), BMK, and natural extracts. The mixed EMSA data was inadvertently incorporated in more than one publication. Figure 6 has been corrected to new data with re‐confirmation. J. Cell. Biochem. 108: 337, 2009. © 2009 Wiley‐Liss, Inc.

6. Effect of OC on the TNF‐α‐induced DNA binding activities of MMP‐9, NF‐κB, and AP‐1 motif in HASMC. Cells were pretreated with indicated OC for 40 min in serum‐free medium, were incubated with TNF‐α (100 ng/ml) for 24 h. Nuclear extracts were analyzed by EMSA for the activated NF‐κB (A) and AP‐1 (B) using radiolabeled oligonucleotide probes, respectively. Indicated values are means of three triplicate experiments.     

Developmental profiles of three embryo-lethal maize mutants lacking leaf primordia: ptd*-1130, cp*-1418, and bno*-747B

The defective kernel (dek) mutants of maize are altered in both their embryo and endosperm development. Earlier studies have indicated that some of the dek mutants are unable to form shoot apical meristems or leaf primoirda. We have examined three embryo lethal dek mutants of this type, ptd*-1130, cp*-1418, and bno*-747B, to obtain a developmental profile for each. Allelism tests show that these three mutants are not allelic. Embryos were examined in early, mid-, and late kernel development as well as at kernel maturity by dissection and sectioning procedures and also at kernel maturity by scanning electron microscopy. All three mutants lag behind normal embryos in their rate of development. Embryos of ptd*-1130 reached the transition stage by early kernel development and progressed no further but underwent cell enlargement and necrosis during late kernel development. Embryos of cp*-1418 reached an early coleoptilar stage by midkernel development. They subsequently increased in size but did not form any leaf primordia. At kernel maturity, they no longer had a shoot apical meristem but often had a well formed root meristem. They appeared to remain healthy and did not become necrotic. Embryos of bno*747B reached the early coleoptilar stage by early kernel development but progressed no further. By kernel maturity, they had grown into masses of irregularly shaped embryonic tissue that no longer resembled any normal embryo stage but were not necrotic. None of these three mutants responded to attempts to support continued embryo development when cultured, but all three mutants formed callus on N6 and MS media supplemented with 2,4-D. These results indicate that these mutants are all uniformly blocked at specific stages early in embryonic development, have different subsequent developmental fates, and represent three different genes performing unique functions that are essential for embryogenesis.     

Analysis of HLA DR2&;DQ6 (DRB1*1501, DQA1*0102, DQB1*0602) Haplotypes in Iranian Patients with Multiple Sclerosis

Multiple sclerosis (MS) is prototype of inflammatory demyelinating disease of the central nervous system .The etiology of MS remains unclear, but according to current data the disease develops in genetically susceptible individuals and may require additional environmental triggers. The human leukocyte antigen (HLA) class II alleles (DRB1*1501, DQA1*0102, DQB1*0602) may have the strongest genetic effect in MS. In this study, the role of these alleles were investigated in 183 Iranian patients with multiple sclerosis and compared with 100 healthy individuals. HLA typing for DRB1*1501, DQA1*0102, DQB1*0602 was performed by polymerase chain reaction (PCR) amplification with sequence-specific primers (PCR-SSP) method. The results show that, HLA DR B1*1501 was significantly more frequent among MS patients (46% vs. 20%, PV = 0.0006) but DQA1*0102 haplotype was negatively associated with MS (30% vs. 50%, PV = 0.0049) and no significant association was found with DQB1*0602 and MS patients in comparison with control group (24% and 30%, PV = 0.43). No significant correlation was observed among these alleles with sex, type of disease; initial symptoms, expanded disability status scale (EDSS), as well as age at onset and familial MS. This study therefore indicates that there is no association of above HLA haplotypes with clinical presentation, disease duration, and disability in Iranian patients with MS which is in line with other previous studies in different ethnic groups.     

Erratum to Wang X,et al. Cell Cycle Volume 5, Issue 6; pp. 635-640

In the paper “Differential Subcellular Localizations of Two Human Sgo1 Isoforms” by Xiaoxing Wang, Yali Yang and Wei Dai (Cell Cycle, 5:6, 635-640, March 2006), following changes should be made:

In page 638, the sentence “this notion is supported by the observation that kinetochore recruitments of CENP-E and CENP-F are compromised after Sgo1 deletion (Marko Kallio, unpublished data)” should be revised as “this notion is supported by the observation that kinetochore recruitments of CENP-E 11 and CENP-F (J. Pouwels, A. Kukkonen, M. Kallio, L76, Late Abstracts-The American Society for Cell Biology 45th Annual Meeting, 2005) are compromised after Sgo1 depletion”.

Xiaoxing Wang, Yali Yang, Wei Dai

New York Medical College     

An in vivo pilot study characterizing the new CYP2A6*7, *8, and *10 alleles.

We developed genotyping assays for CYP2A6*7 (Ile471Thr) and CYP2A6*8 (Arg485Leu). We found higher allelic frequencies in Japanese and Chinese versus Caucasians and identified an allele in which both substitutions occur together (CYP2A6*10). We created a homology model for predicting the impact of allelic variants on enzymatic activity and subsequently tested this in vivo in a pilot kinetic study. Consistent with our homology model predictions, we found (i) that CYP2A6*7 produces an enzyme that has decreased (not inactive) activity for metabolizing nicotine and coumarin; (ii) that CYP2A6*8 is unlikely to affect catalytic activity in vivo; and (iii) that having both substitutions together on an allele (CYP2A6*10) dramatically reduces function and may be fully inactive for some substrates. In conclusion, this study identifies, at relatively high frequency in Asians, an allele with decreased activity (may be substrate selective), a fully functional allele, and an allele containing both substitutions in which function is dramatically reduced.     

B3LYP/6-311++G* * study of structure and spin-spin coupling constant in heparin disaccharide

Structures of heparin disaccharide have been analyzed by DFT using the B3LYP/6-311++G( * *) method. The optimized geometries of two forms of this disaccharide, differing in the conformation ((1)C(4) and (2)S(0)) of the IdoA2S residue, confirmed considerable influences of the sulfate and the carboxylate groups upon the pyranose ring geometries. The computed energies showed that disaccharide having the (1)C(4) form of the IdoA2S residue is more stable than that with the (2)S(0) form. Interatomic distances, bond and torsion angles showed that interconversion of the IdoA2S residue results in geometry changes in the GlcN,6S residue as well. Three-bond proton-proton and proton-carbon spin-spin coupling constants computed for both forms agree with the experimental data and indicate that only two chair forms contribute to the conformational equilibrium in disaccharide. Influences of the charged groups upon the magnitudes of spin-spin coupling constants are also discussed.     

Bioinformatics and Computational Biology Solutions Using R and Bioconductor. * Edited by Robert Gentleman, Wolfgang Huber, Vincent J. Carey, Rafael A. Irizarry and Sandrine Dudoit

This book guides through practical bioinformatics data analysisusing the Bioconductor toolkit, which is based on the statisticallanguage R. R itself is an open-source recreation of the languageS-Plus. The Bioconductor is a collection of R-packages for theanalysis of genomic and molecular biological data generatedin high-throughput experiments. High-throughput experimentsare characterized by large amounts of data generated in shortperiods of time on a sizable number of samples. This poses newchallenges to the analysis such as assessing and adjusting fornoise, exploration using cluster-analysis, visualization, andlinking to (or ‘annotating with’) biomedical knowledgebases. The book focuses on gene expression microarrays, the high-throughputtechnology for which statistical methods are best developedtoday. In addition, a     

Essential Bioinformatics * Jin Xiong * Cambridge University Press; ISBN: 0-521-60082-0; 339pp.; 2006; * {pound}65.00 (hardcover); {pound}29.00 (paperback).

Few would argue the need for today's college biology majorsto have basic skills in bioinformatics. Yet, their undergraduatefaculty faces several challenges in providing these skills,particularly at smaller colleges. First, faculty members whoteach bioinformatics have usually been trained in molecularbiology, genetics or biochemistry. Therefore, most do not haveextensive applied mathematics experience beyond statistics.Second, bioinformatics textbooks for undergraduate biology majorsare rare. Most bioinformatics books are geared to researchers,computer programmers or graduate students. Others are simpleuser manuals, with little coverage of critical evaluation ofthe output. Third, most students today have great ‘point-and-click’computing skills, but minimal understanding or patience forcommand-line computing or programming. In light of these challenges to introducing undergraduate studentsto bioinformatics, it was quite a joy to read and review ProfessorJin Xiong's recent book, Essential Bioinformatics. This compact,economical, first edition of     

Effect of some psychotropic drugs on luminol-dependent chemiluminescence induced by O2-, *OH,HOCl

We studied antioxidant activity of six neuroleptics (chlorpromazine, levomepromazine, promethazine, trifluoperazine and thioridazine) and two antidepressants (imipramine and amitriptyline) in the range of concentration of 10(-7)-10(-4) M. We applied luminol-dependent chemiluminescence to test the ability of these drugs to scavenge the biologically relevant oxygen-derived species: hydroxyl radical, superoxide radical, hypochlorous acid in vitro. We found that the phenothiazines were powerful scavengers of hydroxyl and superoxide radicals. Chlorprothixene, amitriptyline and imipramine had no scavenge activity to the superoxide radical. All drugs showed a moderate scavenger effect on hypochloric anion.     

Some Important Developments in Northern Plains Prehistory, 1942-1967*

Abstract

The area of the Northern Plains is defined as by Wedel in his 1961 synthesis. For the period under consideration, the “process” of archeological work is presented in terms of two main areas of growth--the River Basin Survey Program and the opening up of intensive work in Canada. Also for the period considered, the “results 11 of archeological work are presented in terms of the following eight areas of both fact and theory development: 1) The Middle Missouri “Plains Village” development; 2) Paleo-Indian diversity; 3) Meso-Indian gap filling; 4) Projectile points as diagnostics; 5) Functional interpretations; 6) Ecological prespectives; 7)Relationships outsidethePlains; 8) Broad-ranging synthesis. Future developments are seen in the need and possibilities for historic work, preparation of syntheses and the deeper development of micro-analytic approaches.     

Corrigendum to: Kopec, G., J. Allwood,J. Cullen and D. Ralph. 2016. A general nonlinear least squares data reconciliation and estimation method for material flow analysis. Journal of Industrial Ecology 20(5): 1038–1049

Table 2 displays a list of the variables, data points with data quality, and reconciled solution for the MFA in figure 1. Row 3, column 4 Data points (quality) should read 15 (60) | 19 (90) rather than 15 (60) | 18 (90).