BOOK REVIEWS

Book reviewed in this article:
YEASTS: CHARACTERISTICS AND IDENTIFICATION (1983). J.A. Barnett, R.W. Payne & D. Yarrow. 812 pp. Cambridge: The University Press. pD75.00.     

Book Reviews

Book reviewed in this article:
MICROBIAL GENETICS APPLIED TO1987). By Venetia A. Saun-ders & Jon R. Saunders.
BIOSENSORS(1987). Edited by M. Akhtar, C.R.Lowe & I.J. Higgins.
MICROBES IN THE SEA (1987). Edited by Michael A. Sleigh.
DICTIONARY OF MICROBIOLOGY AND MOLECULAR BIOLOGY 2nd edition (1987). By Paul Singleton & Diana Sainsbury.
Escherichia coli AND Salmonella typhimurium: CELLULAR AND MOLECULAR BIOLOGY (1987). Edited by F.C. Neidhardt, J.L.Ingraham, K.B. Low, B. Magasanik, M. Schaechter & H.E. Umbarger.
BACTERIA-HOST CELL INTERACTION (1988). Edited by M.A. Horowitz
IMMUNOLOGICAL TECHNIQUES IN MICROBIOLOGY (1987). Edited by J.M. Grange, A. Fox & N.L. Morgan.
FOOD BEVERAGE MYCOLOGY 2nd edn.(1987).Edited by Larry R. Beuchat.
MOLECULAR PARADIGMS FOR ERADICATING PARASITES (1987).:Edited by Austin J. MacInnes.
DEVELOPMENTS IN FOOD MICROBIOLOGY-3 (1988).Edited by R.K. Robinson.
A LARVA MINUTE-THE MOLECULAR BIOLOGY OF BACULOVIRUSES. Current Topics on Microbiology and Immunology 131.Edited by W. Doerfler & P. Bohm.
FERMENTED FOOD OF THE WORLD. A DICTIONARY AND GUIDE (1987). By Geoffrey Campbell-Platt.     

Book Reviews

Book reviewed in this article:
FOOD MICROSCOPY (1979). Edited by J. C. Vaughan.
A GUIDE TO IDENTIFYING AND CLASSIFYING YEASTS (1979) J. A. Barnett, R. W. Payne and D. Yarrow.
CURRENT PROCEDURES IN CLINICAL BACTERIOLOGY (1978). P. D. Ellner.
YEAR BOOK OF PATHOLOGY AND CLINICAL PATHOLOGY (1979). Edited by F. A. Carone and R. B. Conn.
METHODS IN MICROBIOLOGY Volume 12 (1979). Edited by T. Bergan and J. R. Norris.
THE BACTERIA—A TREATISE ON STRUCTURE AND FUNCTION, VOLUME VII (1979). MECHANISMS OF ADAPTATION. Editor-in-Chief, L. C. Gunsalus.
PROCEEDINGS IN LIFE SCIENCES—MICROBIAL ECOLOGY (1978). Proceedings of the 1st International Microbial Ecology Symposium, 1977. Edited by M. W. Loutit and J. A. R. Miles.     

Can genetic bar-coding be used to identify aquatic Ranunculus L. subgenus Batrachium (DC) A. Gray? A test using some species from the British Isles

Aquatic Batrachium Ranunculus species are a key component of river macrophyte communities selected for protection under European Union legislation. The group's simplified morphology and variable taxonomic interpretation often makes identification to species level very difficult. A genetic approach was trialled as an alternative, more reliable, means of identification. DNA barcoding using four markers (chloroplast and nuclear) was tested. The chloroplast sequence trnH-psbA worked best and allowed identification of three out of five species while nuclear sequences supported the identification of two hybrids. This method is amenable to simplification through techniques such as PCR-RFLP or RT-PCR. It has the potential to provide easy, rapid and inexpensive identification of Batrachium Ranunculus species.     

Use of a spectrophotometric bioassay for determination of microbial sensitivity to manuka honey

The antimicrobial activity of manuka honey has been well documented (Molan, 1992a,b,c, 1997) [Molan, P.C., 1992. The antibacterial activity of honey. 1: the nature of the antibacterial activity. Bee World 73 (1) 5-28; Molan, P.C., 1992. The antibacterial activity of honey. 2: variation in the potency of the antibacterial activity. Bee World 73 (2) 59-76; Molan, P.C., 1992. Medicinal uses for honey. Beekeepers Quarterly 26; Molan, P.C., 1997. Finding New Zealand honeys with outstanding antibacterial and antifungal activity. New Zealand Beekeeper 4 (10) 20-26]. The current bioassays for determining this antimicrobial effect employ a well diffusion (Ahn and Stiles, 1990) [Ahn, C., Stiles, M.E., 1990. Antibacterial activity of lactic acid bacteria isolated from vacuum-packed meats. Journal of Applied Bacteriology 69, 302-310], (Weston et al., 1999) [Weston, R.J., Mitchell, K.R., Allen, K.L., 1999. Antibacterial phenolic components of New Zealand manuka honey. J. Food Chem. 64, 295-301] or disc diffusion (Taormina et al., 2001) [Taormina, Peter J., Niemira, Brendan A., Beuchat, Larry R., 2001. Inhibitory activity of honey against food borne pathogens as influenced by the presence of hydrogen peroxide and level of antioxidant power. Int. J. Food Microbiol. 69, 217-225] assay using zones of inhibition as indicators of bacterial susceptibility. The development of a 24-h spectrophotometric assay employing 96-well microtiter plates, that is more sensitive and more amenable to statistical analysis than the assays currently employed, was undertaken. This simple and rapid assay permits extensive kinetic studies even in the presence of low honey concentrations, and is capable of detecting inhibitory levels below those recorded for well or disc diffusion assays. In this paper, we compare the assay to both well and disc diffusion assays. The results we obtained for the spectrophotometric method MIC values show that this method has greater sensitivity than the standard well and disc diffusion assays. In addition, inter- and intra-assay variance for this method was investigated, demonstrating the methods reproducibility and repeatability.     

Searching for Genomic Region of High-Fat Diet-Induced Type 2 Diabetes in Mouse Chromosome 2 by Analysis of Congenic Strains

SMXA-5 mice are a high-fat diet-induced type 2 diabetes animal model established from non-diabetic SM/J and A/J mice. By using F2 intercross mice between SMXA-5 and SM/J mice under feeding with a high-fat diet, we previously mapped a major diabetogenic QTL (T2dm2sa) on chromosome 2. We then produced the congenic strain (SM.A-T2dm2sa (R0), 20.8–163.0 Mb) and demonstrated that the A/J allele of T2dm2sa impaired glucose tolerance and increased body weight and body mass index in the congenic strain compared to SM/J mice. We also showed that the combination of T2dm2sa and other diabetogenic loci was needed to develop the high-fat diet-induced type 2 diabetes. In this study, to narrow the potential genomic region containing the gene(s) responsible for T2dm2sa, we constructed R1 and R2 congenic strains. Both R1 (69.6–163.0 Mb) and R2 (20.8–128.2 Mb) congenic mice exhibited increases in body weight and abdominal fat weight and impaired glucose tolerance compared to SM/J mice. The R1 and R2 congenic analyses strongly suggested that the responsible genes existed in the overlapping genomic interval (69.6–128.2 Mb) between R1 and R2. In addition, studies using the newly established R1A congenic strain showed that the narrowed genomic region (69.6–75.4 Mb) affected not only obesity but also glucose tolerance. To search for candidate genes within the R1A genomic region, we performed exome sequencing analysis between SM/J and A/J mice and extracted 4 genes (Itga6, Zak, Gpr155, and Mtx2) with non-synonymous coding SNPs. These four genes might be candidate genes for type 2 diabetes caused by gene-gene interactions. This study indicated that one of the genes responsible for high-fat diet-induced diabetes exists in the 5.8 Mb genomic interval on mouse chromosome 2.     

Reconstructing a Thauera genome from a hydrogenotrophic-denitrifying consortium using metagenomic sequence data

Here, shotgun metagenomic sequencing was conducted to reveal the hydrogen-oxidizing autotrophic-denitrifying metabolism in an enriched Thauera-dominated consortium. A draft genome named Thauera R4 of over 90 % completeness (3.8 Mb) was retrieved mainly by a coverage-defined binning method from 3.5 Gb paired-end Illumina reads. We identified 1,263 genes (accounting for 33 % of total genes in the finished genome of Thauera aminoaromatica MZ1T) with average nucleotide identity of 87.6 % shared between Thauera R4 and T. aminoaromatica MZ1T. Although Thauera R4 and T. aminoaromatica shared quite similar nitrogen metabolism and a high nucleotide similarity (98.8 %) in their 16S ribosomal RNA genes, they showed different functional potentials in several important environmentally relevant processes. Unlike T. aminoaromatica MZ1T, Thauera R4 carries an operon of [NiFe]-hydrogenase (EC 1.12.99.6) catalyzing molecular hydrogen oxidation in nitrate-rich solution. Moreover, Thauera R4 is a mixtrophic bacterium possessing key enzymes for autotrophic CO₂-fixation and heterotrophic acetate assimilation metabolism. This Thauera R4 bin provides another genetic reference to better understand the niches of Thauera and demonstrates a model pipeline to reveal functional profiles and reconstruct novel and dominant genomes from a simplified mixed culture in environmental studies.     

A new shuttle vector for gene expression in biopolymer-producing Ralstonia eutropha

Ralstonia eutropha (formerly Alcaligenes eutrophus) is a fascinating microorganism with a great scientific importance and an immense commercial potential. A new genetic transformation system for the organism would greatly facilitate the biological study and molecular engineering of this organism. We report here a versatile gene expression method for the genetic engineering of R. eutropha. This method, based on a simplified electroporation protocol, uses a recombinant plasmid, pBS29-P2, containing a Pseudomonas syringae promoter (P2) and two antibiotic-resistance markers (i.e., genes coding for kanamycin (Km)- and tetracycline (Tc)-resistance). Using this method, we successfully achieved transformation of wild-type R. eutropha and its poly(hydroxyalkanoate)-negative mutant, R. eutropha PHB⁻4, with various pBS29-P2-based recombinants. A transformation frequency as high as 4 × 10³ Km-resistance colonies/μg DNA was obtained per electroporation experiment. We further demonstrated the successful expression of a heterologous gene coding for green-fluorescent-protein by fluorescence measurement. In addition, our results indicated the expression of a truncated but active Streptomyces coelicolor α-galactosidase in R. eutropha.     

Applied Spatial Data Analysis with R. by BIVAND, R. S., PEBESMA, E. J., and GOMEZ-RUBIO, V.

Applied Spatial Data Analysis with R (R. S. Bivand, E. J. Pebesma, and V. Gomez‐Rubio) Jay M. Ver Hoef Bayesian Disease Mapping: Hierarchical Modeling in Spatial Epidemiology (A. B. Lawson) J. Law Disease Surveillance: A Public Health Informatics Approach (J. S. Lombardo and D. L. Buckeridge, editors) Iris Pigeot Survival Analysis for Epidemiologic and Medical Research (S. Selvin) M. G. Valsecchi Survival and Event History Analysis: A Process Point of View (O. O. Aalen, O. Borgan, and H. K. Gjessing) Patricia Grambsch Nonlinear Dimensionality Reduction (J. A. Lee and M. Verleysen) Haonan Wang Model Selection and Model Averaging (G. Claeskens and N. L. Hjort) Thomas M. Loughin Meta‐Analysis of Binary Data Using Profile Likelihood (D. Böhning, R. Kuhnert, and S. Rattanasiri) Eloise Kaizar Wavelet Methods in Statistics with R (G. P. Nason) Jeffrey S. Morris Adaptive Design Theory and Implementation Using SAS and R (M. Chang) Feifang Hu Ecological Models and Data in R (B. M. Bolker) Rachel M. Fewster Applied Multiway Data Analysis (P. M. Kroonenberg) Renato Coppi Brief Reports by the Editor Sampling of Populations: Methods and Applications, 4th edition (P. S. Levy and S. Lemeshow) Applied Survival Analysis: Regression Modeling of Time‐to‐Event Data, 2nd edition (D. W. Hosmer, S. Lemeshow, and S. May) SAS for Data Analysis: Intermediate Statistical Methods (M. G. Marasinghe and W. J. Kennedy) Advances in Mathematical and Statistical Modeling (B. C. Arnold, N. Balakrishnan, J. M. Sarabia, and R. Mínguez, editors) An Introduction to Generalized Linear Models, 3rd edition (A. J. Dobson and A. G. Barnett) Design and Analysis of Bioavailability and Bioequivalence Studies, 3rd edition (S.‐C. Chow and J.‐P. Liu)     

Event-driven simulation of cerebellar granule cells

Around half of the neurons of a human brain are granule cells (approximately 10(11)granule neurons) [Kandel, E.R., Schwartz, J.H., Jessell, T.M., 2000. Principles of Neural Science. McGraw-Hill Professional Publishing, New York]. In order to study in detail the functional role of the intrinsic features of this cell we have developed a pre-compiled behavioural model based on the simplified granule-cell model of Bezzi et al. [Bezzi, M., Nieus, T., Arleo, A., D'Angelo, E., Coenen, O.J.-M.D., 2004. Information transfer at the mossy fiber-granule cell synapse of the cerebellum. 34th Annual Meeting. Society for Neuroscience, San Diego, CA, USA]. We can use an efficient event-driven simulation scheme based on lookup tables (EDLUT) [Ros, E., Carrillo, R.R., Ortigosa, E.M., Barbour, B., Ags, R., 2006. Event-driven simulation scheme for spiking neural networks using lookup tables to characterize neuronal dynamics. Neural Computation 18 (12), 2959-2993]. For this purpose it is necessary to compile into tables the data obtained through a massive numerical calculation of the simplified cell model. This allows network simulations requiring minimal numerical calculation. There are three major features that are considered functionally relevant in the simplified granule cell model: bursting, subthreshold oscillations and resonance. In this work we describe how the cell model is compiled into tables keeping these key properties of the neuron model.     

Altered expression of Autism-associated genes in the brain of Fragile X mouse model

Autism is a severe neurodevelopmental disorder, which typically emerges in early childhood. Most cases of autism have not been linked to mutations in a specific gene, and the etioloty of the disorder remains to be established [S.S. Moy, J.J. Nadler, T.R. Magnuson, J.N. Crawley, Mouse models of autism spectrum disorders: the challenge for behavioral genetics, Am. J. Med. Genet. 142 (2006) 40-51]. Fragile X syndrome is caused by mutation in the FMR1 gene and is characterized by mental retardation, physical abnormalities, and, in most case, autistic-like behavior [R.J. Hagerman, A.W. Jackson, A. Levitas, B. Rimland, M. Braden, An analysis of autism in fifty males with the Fragile X syndrome, Am. J. Med. Genet. 23 (1986) 359-374, C.E. Bakker, C. Verheij, R. Willemsen, R. van der Helm, F. Oerlemans, M. Vermeij, A. Bygrave, A.T. Hoogeveen, B.A. Oostra, E. Reyniers, K. De Boulle, R. D’Hooge, P. Cras, D. van Velzen, G. Nagels, J.J. Marti, P. De Deyn, J.K. Darby, P.J. Willems, Fmr1 knockout mice: a model to study Fragile X mental retardation, Cell 78 (1994) 23-33]. The FMR1 knockout (KO) mouse is one of the best characterized animal models for human disorders associated with autism [S.S. Moy, J.J. Nadler, T.R. Magnuson, J.N. Crawley, Mouse models of autism spectrum disorders: the challenge for behavioral genetics, Am. J. Med. Genet. 142 (2006) 40-51]. We have used real-time PCR to investigate changes in expression levels of three genes: WNT2, MECP2, and FMR1 in different brain regions of Fagile X mice and litter mate controls. We found major changes in the expression pattern for the three genes examined. FMR1, MECP2, and WNT2 expression were drastically down regulated in the Fragile X mouse brain.     

Structural characterization of saturated branched chain fatty acid methyl esters by collisional dissociation of molecular ions generated by electron ionization

Saturated branched chain fatty acids (BCFA) are present as complex mixtures in numerous biological samples. The traditional method for structure elucidation, electron ionization (EI) mass spectrometry, sometimes does not unambiguously enable assignment of branching in isomeric BCFA. Zirrolli and Murphy (Zirrolli , J. A. , and R. A. Murphy. 1993. Low-energy tandem mass spectrometry of the molecular ion derived from fatty acid methyl esters: a novel method for analysis of branched-chain fatty acids. J. Am. Soc. Mass Spectrom. 4: 223–229.) showed that the molecular ions of four BCFA methyl ester (BCFAME) yield highly characteristic fragments upon collisional dissociation using a triple quadrupole instrument. Here, we confirm and extend these results by analysis using a tabletop 3-D ion trap for activated molecular ion EI-MS/MS to 30 BCFAME. iso-BCFAME produces a prominent ion (30-100% of base peak) for [M-43] (M-C₃H₇), corresponding to the terminal isopropyl moiety in the original iso-BCFAME. Anteiso-FAME yield prominent ions (20-100% of base peak) corresponding to losses on both side of the methyl branch, [M-29] and [M-57], and tend to produce more prominent m/z 115 peaks corresponding to a cyclization product around the ester. Dimethyl and tetramethyl FAME, with branches separated by at least one methylene group, yield fragment on both sides of the sites of methyl branches that are more than 6 C away from the carboxyl carbon. EI-MS/MS yields uniquely specific ions that enable highly confident structural identification and quantification of BCFAME.     

Pressure clamp method to measure transpiration in growing single plant cells : demonstration with sporangiophores of phycomyces

A pressure probe method (pressure clamp) was developed to measure transpiration rates of both growing and nongrowing single plant cells, and represents an improvement over the previous pressure probe method (pressure relaxation), which is restricted to nongrowing plant cells (J.K.E. Ortega, R.G. Keanini, K.J. Manica [1988] Plant Physiol 87: 11-14). The pressure clamp method was used to measure transpiration rates of Phycomyces sporangiophores in two developmental stages: stage III (nongrowing) and stage IV (growing).     

Structural variations in the catalytic and ubiquitin-associated domains of microtubule-associated protein/microtubule affinity regulating kinase (MARK) 1 and MARK2

The microtubule-associated protein (MAP)/microtubule affinity regulating kinase (MARK)/Par-1 phosphorylates microtubule-associated proteins tau, MAP2, and MAP4 and is involved in the regulation of microtubule-based transport. Par-1, a homologue of MARK in Drosophila and Caenorhabditis elegans, is essential for the development of embryonic polarity. Four isoforms of MARK are found in humans. Recently, we reported the crystal structure of the catalytic and ubiquitin-associated domains of MARK2, an isoform enriched in brain (Panneerselvam, S., Marx, A., Mandelkow, E.-M., and Mandelkow, E. (2006) Structure 14, 173-183). It showed that the ubiquitin-associated domain (UBA) domain has an unusual fold and binds to the N-terminal lobe of the catalytic domain. This is at variance with a previous low resolution structure derived from small angle solution scattering (Jaleel, M., Villa, F., Deak, M., Toth, R., Prescott, A. R., Van Aalten, D. M., and Alessi, D. R. (2006) Biochem. J. 394, 545-555), which predicts binding of the UBA domain to the larger, C-terminal lobe. Here we report the crystal structure of the catalytic and UBA domain of another isoform, MARK1. Although the crystal packing of the two isoforms are unrelated, the overall conformations of the molecules are similar. Notably, the UBA domain has the same unusual conformation as in MARK2, and it binds at the same site. Remarkable differences occur in the catalytic domain at helix C, the catalytic loop, and the activation segment.     

PCR-Based Identification of Hyperthermophilic Archaea of the Family Thermococcaceae

A method for rapid detection and identification of hyperthermophilic archaea of the family Thermococcaceae based on PCR amplification of 16S rRNA gene fragments with primers TcPc 173F (5′-TCCCCCATAGGYCTGRGGTACTGGAAGGTC-3′) and TcPc 589R (5′-GCCGTGRGATTTCGCCAGGGACTTACGGGC-3′) was developed and used for identification of new isolates.     

Isolation of glucosinolates and the identification of o-(α-l-rhamnopyranosyloxy)benzylglucosinolate from Reseda odorata

A method has been developed for the quantitative isolation of glucosinolates by ion-exchange chromatography and high voltage electrophoresis avoiding strongly alkaline and acidic conditions. The compounds were identified by ¹H and ¹³C NMR spectroscopy and through the products arising from enzymatic, acid and alkaline hydrolysis. The method is well suited for the isolation and identification of glucosinolates containing aglucone parts which produce non-volatile compounds on enzymatic hydrolysis. The method has been used in the isolation and identification of 2-hydroxy-2-methylpropylglucosinolate from Reseda alba, 2-hydroxy-2-phenylethylglucosinolate from R. luteola and a new glucosinolate, o-(α-l-rhamnopyranosyloxy)benzylglucosinolate, occurring in R. odorata. The glucosinolate content in different parts of this plant has been determined and the metabolism of glucosinolates is briefly discussed.     

Molecular serogrouping of porcine enterotoxigenic Escherichia coli from Australia

Enterotoxigenic Escherichia coli (ETEC) is a common etiological agent of neonatal, pre and post weaning diarrhoea in piglets. One of the most important steps in the diagnosis and epidemiological understanding of this organism is accurate serogrouping. In many instances, however, conventional serogrouping fails to produce accurate identification of serogroups. In this communication we report a modified and simplified molecular serogrouping method (rfb-RFLP) for the accurate identification of the most common porcine ETEC strains that cause neonatal, pre and post weaning diarrhoea in Australia.     

Heteroduplex Panel Analysis, a Novel Method for Genetic Identification of Aspergillus Section Flavi Strains

For genetic identification of Aspergillus Section Flavi isolates and detection of intraspecific variation, we developed a novel method for heteroduplex panel analysis (HPA) utilizing fragments of the internal transcribed spacer (ITS) regions (ITS1-5.8S-ITS2) of the rRNA gene that was PCR amplified with universal primers. The method involves formation of heteroduplexes with a set of reference fragments amplified from Aspergillus flavus, A. parasiticus, A. tamarii, and A. nomius and subsequent minislab vinyl polymer gel electrophoresis. The test panel is compared with species-specific standard panels (F-1, P-1, T-1, and N-1) generated by pairwise reannealing among four reference fragments. Of 90 test panels, 89 succeeded in identifying the species and 74 were identical to one of the four standard panels. Of the 16 new panels, 11 A. flavus/A. oryzae panels were identical and typed as F-2 and 4 of 5 A. nomius panels were typed as N-2 or N-3. The other strain, A. nomius IMI 358749, was unable to identify the species because no single bands were formed with any of the four reference strains. DNA sequencing revealed that our HPA method has the highest sensitivity available and is able to detect as little as one nucleotide of diversity within the species. When Penicillium or non-Section Flavi Aspergillus was subjected to HPA, the resulting bands of heteroduplexes showed apparently lower mobility and poor heteroduplex formation. This indicates that HPA is a useful identification method without morphological observation and is suitable for rapid and inexpensive screening of large numbers of isolates. The HPA typing coincided with the taxonomy of Section Flavi and is therefore applicable as an alternative to the conventional methods (Samson, R. A., E. S. Hoekstra, J. C. Frisvad, and O. Filtenborg, p. 64–97, in Introduction to Food- and Airborne Fungi, 6th ed., 2000).     

濒危植物都支杜鹃雄蕊数目描述的修正

通过对都支杜鹃5个种群（包括模式产地）的雄蕊数目进行统计、对馆藏标本进行查询和对模式标本采集人进行采访,修正了现有文献对都支杜鹃雄蕊数目（一个关键鉴别特征）的描述——应是12~15枚,而非10枚;本文还对同地点栽培的都支杜鹃和云锦杜鹃的形态进行观察,发现都支杜鹃与云锦杜鹃诸多形态特征差异显著,支持都支杜鹃是一个独立的“好种”。