bluuebunny/crossref_metadata_2025 huggingface dataset:
In Vivo DNA Binding of Bacteriophage GA-1 Protein p6
Authors: Alcorlo Martín , Salas Margarita , Hermoso José M.
Published: September 2007

Bacteriophage GA-1 infects
Bacillus
sp. strain G1R and has a linear double-stranded DNA genome with a terminal protein covalently linked to its 5′ ends. GA-1 protein p6 is very abundant in infected cells and binds DNA with no sequence specificity. We show here that it binds in vivo to the whole viral genome, as detected by cross-linking, chromatin immunoprecipitation, and real-time PCR analyses, and has the characteristics of a histone-like protein. Binding to DNA of GA-1 protein p6 shows little supercoiling dependency, in contrast to the ortholog protein of the evolutionary related
Bacillus subtilis
phage φ29. This feature is a property of the protein rather than the DNA or the cellular background, since φ29 protein p6 shows supercoiling-dependent binding to GA-1 DNA in
Bacillus
sp. strain G1R. GA-1 DNA replication is impaired in the presence of the gyrase inhibitors novobiocin and nalidixic acid, which indicates that, although noncovalently closed, the viral genome is topologically constrained in vivo. GA-1 protein p6 is also able to bind φ29 DNA in
B. subtilis
cells; however, as expected, the binding is less supercoiling dependent than the one observed with the φ29 protein p6. In addition, the nucleoprotein complex formed is not functional, since it is not able to transcomplement the DNA replication deficiency of a φ29
sus6
mutant. Furthermore, we took advantage of φ29 protein p6 binding to GA-1 DNA to find that the viral DNA ejection mechanism seems to take place, as in the case of φ29, with a right to left polarity in a two-step, push-pull process.
Array-Based Genomic Comparative Hybridization Analysis of Field Strains ofMycoplasma hyopneumoniae
Authors: Madsen Melissa L. , Oneal Michael J. , Gardner Stuart W. , Strait Erin L. , Nettleton Dan , Thacker Eileen L. , Minion F. Chris
Published: September 2007

Mycoplasma hyopneumoniaeis the causative agent of porcine enzootic pneumonia and a major factor in the porcine respiratory disease complex. A clear understanding of the mechanisms of pathogenesis does not exist, although it is clear thatM. hyopneumoniaeadheres to porcine ciliated epithelium by action of a protein called P97. Previous studies have shown variation in the gene encoding the P97 cilium adhesin in different strains ofM. hyopneumoniae, but the extent of genetic variation among field strains across the genome is not known. SinceM. hyopneumoniaeis a worldwide problem, it is reasonable to expect that a wide range of genetic variability may exist given all of the different breeds and housing conditions. This variation may impact the overall virulence of a single strain. Using microarray technology, this study examined the potential variation of 14 field strains compared to strain 232, on which the array was based. Genomic DNA was obtained, amplified with TempliPhi, and labeled indirectly with Alexa dyes. After genomic hybridization, the arrays were scanned and data were analyzed using a linear statistical model. The results indicated that genetic variation could be detected in all 14 field strains but across different loci, suggesting that variation occurs throughout the genome. Fifty-nine percent of the variable loci were hypothetical genes. Twenty-two percent of the lipoprotein genes showed variation in at least one field strain. A permutation test identified a location in theM. hyopneumoniaegenome where there is spatial clustering of variability between the field strains and strain 232.
Nutritional Cues ControlPseudomonas aeruginosaMulticellular Behavior in Cystic Fibrosis Sputum
Authors: Palmer Kelli L. , Aye Lindsay M. , Whiteley Marvin
Published: September 2007

The sputum (mucus) layer of the cystic fibrosis (CF) lung is a complex substrate that providesPseudomonas aeruginosawith carbon and energy to support high-density growth during chronic colonization. Unfortunately, the CF lung sputum layer has been difficult to mimic in animal models of CF disease, and mechanistic studies ofP. aeruginosaphysiology during growth in CF sputum are hampered by its complexity. In this study, we performed chromatographic and enzymatic analyses of CF sputum to develop a defined,syntheticCFsputummedium (SCFM) that mimics the nutritional composition of CF sputum. Importantly,P. aeruginosadisplays similar phenotypes during growth in CF sputum and in SCFM, including similar growth rates, gene expression profiles, carbon substrate preferences, and cell-cell signaling profiles. Using SCFM, we provide evidence that aromatic amino acids serve as nutritional cues that influence cell-cell signaling and antimicrobial activity ofP. aeruginosaduring growth in CF sputum.
Identification of Harpins in
Pseudomonas syringae
pv. tomato DC3000, Which Are Functionally Similar to HrpK1 in Promoting Translocation of Type III Secretion System Effectors
Authors: Kvitko Brian H. , Ramos Adela R. , Morello Joanne E. , Oh Hye-Sook , Collmer Alan
Published: September 2007

Harpins are a subset of type III secretion system (T3SS) substrates found in all phytopathogenic bacteria that utilize a T3SS.
Pseudomonas syringae
pv. tomato DC3000 was previously reported to produce two harpins, HrpZ1 and HrpW1. DC3000 was shown here to deploy two additional proteins, HopAK1 and HopP1, which have the harpin-like properties of lacking cysteine, eliciting the hypersensitive response (HR) when partially purified and infiltrated into tobacco leaves, and possessing a two-domain structure similar to that of the HrpW1 class of harpins. Unlike the single-domain harpin HrpZ1, the two-domain harpins have C-terminal enzyme-like domains: pectate lyase for HopAK1 and lytic transglycosylase for HopP1. Genetic techniques to recycle antibiotic markers were applied to DC3000 to generate a quadruple harpin gene polymutant. The polymutant was moderately reduced in the elicitation of the HR and translocation of the T3SS effector AvrPto1 fused to a Cya translocation reporter, but the mutant was unaffected in the secretion of AvrPto1-Cya. The DC3000
hrpK1
gene encodes a putative translocator in the HrpF/NopX family and was deleted in combination with the four harpin genes. The
hrpK1
quadruple harpin gene polymutant was strongly reduced in HR elicitation, virulence, and translocation of AvrPto1-Cya into plant cells but not in the secretion of representative T3SS substrates in culture. HrpK1, HrpZ1, HrpW1, and HopAK1, but not HopP1, were independently capable of restoring some HR elicitation to the
hrpK1
quadruple harpin gene polymutant, which suggests that a consortium of semiredundant translocators from three protein classes cooperate to form the
P. syringae
T3SS translocon.
Evidence that Bacterial ABC-Type Transporter Imports Free EDTA for Metabolism
Authors: Zhang Hua , Herman Jacob P. , Bolton Harvey , Zhang Zhicheng , Clark Sue , Xun Luying
Published: September 2007

EDTA, a common chelating agent, is becoming a major organic pollutant in the form of metal-EDTA complexes in surface waters, partly due to its recalcitrance to biodegradation. Even an EDTA-degrading bacterium, BNC1, does not degrade stable metal-EDTA complexes. In the present study, an ABC-type transporter was identified for possible uptake of EDTA because the transporter genes and the EDTA monooxygenase gene were expressed from a single operon in BNC1. The ABC-type transporter had a periplasmic-binding protein (EppA) that should confer the substrate specificity for the transporter; therefore, EppA was produced in
Escherichia coli
, purified, and characterized. EppA was shown to bind free EDTA with a dissociation constant as low as 25 nM by using isothermal titration calorimetry. When unstable metal-EDTA complexes, e.g., (Mg-EDTA)
2−
, were added to the EppA solution, binding was also observed. However, experimental data and theoretical analysis supported EppA binding only of free EDTA. When stable metal-EDTA complexes, e.g., (Cu-EDTA)
2−
, were titrated into the EppA solution, no binding was observed. Since EDTA monooxygenase in the cytoplasm uses some of the stable metal-EDTA complexes as substrates, we suggest that the lack of EppA binding and EDTA uptake are responsible for the failure of BNC1 cells to degrade the stable complexes.
The Division Inhibitor EzrA Contains a Seven-Residue Patch Required for Maintaining the Dynamic Nature of the Medial FtsZ Ring
Authors: Haeusser Daniel P. , Garza Anna Cristina , Buscher Amy Z. , Levin Petra Anne
Published: September 2007

The essential cytoskeletal protein FtsZ assembles into a ring-like structure at the nascent division site and serves as a scaffold for the assembly of the prokaryotic division machinery. We previously characterized EzrA as an inhibitor of FtsZ assembly inBacillus subtilis. EzrA interacts directly with FtsZ to prevent aberrant FtsZ assembly and cytokinesis at cell poles. EzrA also concentrates at the cytokinetic ring in an FtsZ-dependent manner, although its precise role at this position is not known. Here, we identified a conserved patch of amino acids in the EzrA C terminus that is essential for localization to the FtsZ ring. Mutations in this patch (designated the “QNR patch”) abolish EzrA localization to midcell but do not significantly affect EzrA's ability to inhibit FtsZ assembly at cell poles.ezrAQNR patch mutant cells exhibit stabilized FtsZ assembly at midcell and are significantly longer than wild-type cells, despite lacking extra FtsZ rings. These results indicate that EzrA has two distinct activities in vivo: (i) preventing aberrant FtsZ ring formation at cell poles through inhibition of de novo FtsZ assembly and (ii) maintaining proper FtsZ assembly dynamics within the medial FtsZ ring, thereby rendering it sensitive to the factors responsible for coordinating cell growth and cell division.
Regulation of Expression of the Fibronectin-Binding Protein BBK32 in
Borrelia burgdorferi
Authors: He Ming , Boardman Bethany K. , Yan Dalai , Yang X. Frank
Published: September 2007

The BBK32 protein binds to host extracellular ligand fibronectin and contributes to the pathogenesis of
Borrelia burgdorferi
. Here we showed that expression of the BBK32 gene is influenced by multiple environmental factors and that its regulation is governed by the response regulator Rrp2 and RpoN-RpoS (σ
54
-σ
S
) sigma cascade in
B. burgdorferi
.
Phosphate-Controlled Regulator for the Biosynthesis of the Dalbavancin Precursor A40926
Authors: Alduina Rosa , Piccolo Luca Lo , D'Alia Davide , Ferraro Clelia , Gunnarsson Nina , Donadio Stefano , Puglia Anna Maria
Published: September 2007

The actinomycete
Nonomuraea
sp. strain ATCC 39727 produces the glycopeptide A40926, the precursor of the novel antibiotic dalbavancin. Previous studies have shown that phosphate limitation results in enhanced A40926 production. The A40926 biosynthetic gene (
dbv
) cluster, which consists of 37 genes, encodes two putative regulators, Dbv3 and Dbv4, as well as the response regulator (Dbv6) and the sensor-kinase (Dbv22) of a putative two-component system. Reverse transcription-PCR (RT-PCR) and real-time RT-PCR analysis revealed that the
dbv14
-
dbv8
and the
dbv30
-
dbv35
operons, as well as
dbv4
, were negatively influenced by phosphate. Dbv4 shows a putative helix-turn-helix DNA-binding motif and shares sequence similarity with StrR, the transcriptional activator of streptomycin biosynthesis in
Streptomyces griseus
. Dbv4 was expressed in
Escherichia coli
as an N-terminal His
6
-tagged protein. The purified protein bound the
dbv14
and
dbv30
upstream regions but not the region preceding
dbv4
. Bbr, a Dbv4 ortholog from the gene cluster for the synthesis of the glycopeptide balhimycin, also bound to the
dbv14
and
dbv30
upstream regions, while Dbv4 bound appropriate regions from the balhimycin cluster. Our results provide new insights into the regulation of glycopeptide antibiotics, indicating that the phosphate-controlled regulator Dbv4 governs two key steps in A40926 biosynthesis: the biosynthesis of the nonproteinogenic amino acid 3,5-dihydroxyphenylglycine and critical tailoring reactions on the heptapeptide backbone.
The Complete Genome Sequence of
Campylobacter jejuni
Strain 81116 (NCTC11828)
Authors: Pearson Bruce M. , Gaskin Duncan J. H. , Segers Ruud P. A. M. , Wells Jerry M. , Nuijten Piet J. M. , van Vliet Arnoud H. M.
Published: September 2007

Campylobacter jejuni
is a major human enteric pathogen that displays genetic variability via genomic reorganization and phase variation. This variability can adversely affect the outcomes and reproducibility of experiments.
C. jejuni
strain 81116 (NCTC11828) has been suggested to be a genetically stable strain (G. Manning, B. Duim, T. Wassenaar, J. A. Wagenaar, A. Ridley, and D. G. Newell, Appl. Environ. Microbiol. 67:1185-1189, 2001), is amenable to genetic manipulation, and is infective for chickens. Here we report the finished annotated genome sequence of
C. jejuni
strain 81116.
Work And Peak Torque During Eccentric Exercise Do Not Predict Changes In Markers Of Muscle Damage
Authors: Chapman Dale W , Newton Michael J , Zainuddin Zanial , Sacco Paul , Nosaka Kazunori
Published: September 2007

Objectives:Large inter-subject variability in responses to eccentric exercise has been reported. This study investigated the hypothesis that the variability of changes in indirect markers of exercise-induced muscle damage (EIMD) would be explained by work performed and/or torque generated during eccentric exercise.Methods:Subjects (n=53) performed 60 maximal eccentric actions of the elbow flexors on an isokinetic dynamometer that forcibly extended the elbow joint from 60° to 180° at a constant velocity (90°·s-1). Markers of EIMD included maximal voluntary isometric contraction torque at 90° elbow flexion (MVC), range of motion, plasma creatine kinase activity and muscle soreness. Measurements were taken 2 days before, immediately after, and 1-4 days post-exercise. Pearson’s correlation coefficient was used to examine relationships between exercise parameters (total work, change in total work, torque produced during exercise, change in peak torque) and markers of EIMD.Results:Large inter-subject variability was evident for both work and torque during exercise, and changes in all markers of EIMD. Contrary to the hypothesis, total work (normalised for individual pre-exercise MVC) did not correlate significantly with any markers of EIMD, with the exception of MVC (r = 0.3). Total work performed and changes in total work showed higher correlations with some markers, but no r-values exceeded 0.4. Normalised exercise torque and the changes in peak torque during exercise were not correlated with changes in MVC, nor other markers.Conclusion:These results suggest the large inter-subject variability in responses to eccentric exercise is not associated with work performed or torque generated during eccentric exercise.
Epstein–Barr virus-associated tumours: an update for the attention of the working pathologist
Authors: Delecluse H-J , Feederle R , O’Sullivan B , Taniere P
Published: September 2007

Epstein–Barr virus (EBV) is a herpesvirus associated with approximately 1% of tumours worldwide. EBV is the epitome of B lymphotropic viruses, but the spectrum of tumours it is associated with extends to T lymphocyte and NK cell malignancies, various types of carcinomas and smooth muscle tumours. Ubiquitous EBV infection in humans implies that most individuals carry EBV-infected cells. Therefore, mere detection of the virus in individuals with a tumour is not sufficient for establishing a causal relationship between both events, but instead requires unequivocal detection of viral nucleic acids or viral proteins in the tumour cells. Recent controversies about EBV infection in several carcinomas mainly resulted from such technical issues. The gold standard remains in situ EBER detection, but detection of EBNA1 would be an interesting alternative. EBV detection can be helpful for diagnostic, prognostic and therapeutic purposes. The rate of EBV association with entities such as NK/T cell tumours of the nasal type is so high that absence of detection of the virus in such a lesion should cast doubt of the accuracy of the diagnosis. Similarly, diagnosis of EBV-associated follicular pseudo-tumour obviously requires detection of the virus. EBV-positive common gastric adenocarcinomas seem to have a better prognosis than their EBV-negative counterparts and identification of the virus in B cell lymphoproliferations in immunocompromised individuals will guide therapeutic options. In conclusion, EBV-associated tumours are common enough to be relevant for the pathologist in everyday practice, but there is a need to facilitate detection of the virus (eg EBNA1 antibody).
Mucinous breast lesions: diagnostic challenges
Authors: Tan P H , Tse G M K , Bay B H
Published: September 2007

Breast lesions with mucin represent a broad spectrum of entities, ranging from benign fibrocystic changes with luminal mucin to mucocele-like lesions (MLL), which can be associated with banal epithelial alterations, atypical ductal hyperplasia or ductal carcinoma in situ. Occasionally invasive mucinous carcinoma can be identified in contiguity with MLL. Diagnostic challenges are enumerated, histological differentials are discussed, and a practical approach towards resolving some of these issues is provided. In addition to these lesions with abundant extracellular mucin, there are also conditions that feature stromal mucinous or myxoid material, as well as rare entities that demonstrate both epithelial extracellular and stromal mucin.
Nestin expression in different tumours and its relevance to malignant grade
Authors: Yang X H , Wu Q L , Yu X B , Xu C X , Ma B F , Zhang X M , Li S N , Lahn B T , Xiang A P
Published: September 2007

Background:

Nestin, an intermediate filament (IF) protein, is expressed in proliferating progenitor cells of developmental and regenerating tissues, and is identified as a neuroepithelial precursor cell marker. Recently, nestin was detected in some neoplasms such as glioma, ependymoma, melanoma, rhabdomyosarcoma, gastrointestinal stromal tumour (GIST), and testicular stromal tumour. Moreover, the expression intensity of nestin exhibited significant correlation with the malignant grade of glioma.

Aims:

To detect the expression of nestin in different tumours and to analyse the relationship between the expression of nestin and the malignant grade of the tumours.

Methods:

Formalin-fixed and paraffin-embedded surgical samples of neoplastic tissues were obtained from the Department of Pathology of Sun Yat-sen University. Histological analysis and immunohistochemical staining for nestin were performed. Histoscores were analysed by semi-quantitative evaluation.

Results:

Nestin was expressed predominantly in the cytoplasm of angiosarcoma, pancreatic adenocarcinoma and GIST samples, and some tumour cells expressed in the nucleus. There was a statistically significant difference between the histoscore of nestin in high malignant GIST (2.2366 (0.6920)) and that in low malignant GIST (1.3783 (0.4268)) (p = 0.003); and also between that in high malignant angiosarcoma (1.9188 (0.2069)) and that in low malignant angiosarcoma (0.6474 (0.3273)) (p = 0.000). Cavernous angioma did not express nestin. The histoscore of nestin in high malignant pancreatic adenocarcinoma (7/14) was 1.1767 (0.4676), and that in low malignant pancreatic adenocarcinoma (3/8) was 0.6577 (0.0056) (no significant difference, p = 0.112).

Conclusions:

Results suggest that the expression of nestin may play an important role in the development of some neoplasms such as GIST and angiosarcoma.
PAIRING IN NON-FERMI LIQUID IN TERMS OF THE BETHE-SALPETER EQUATION
Authors: Malozovsky Y. M. , Fan J. D.
Published: September 2007

Pairing between two fermionic excitations in a non-Fermi liquid is considered in terms of the Bethe-Salpeter equation. We consider the pairing in a Fermi system with vanishing spectral weight. It is well known that the quasiparticle pole in the single-particle Green's function in a Non-Fermi liquid is absent or weak. The examples of such systems can be viewed as the "Marginal" Fermi liquid and Luttinger liquid. Another example that has also been considered is the Fermi system with pseudogap behavior in the spectral weight. Although the pairing between two excitations in a non-Fermi liquid is, in general, absent, nevertheless we show that the Cooper's type of pairing can occur and the conditions for such a kind of pairing are discussed. The results have also been applied to the systems with smeared or non-monotonic Fermi distribution. A system that transits from Fermi-type to Bose-type behavior can serve as an example of such systems as discussed.
DEPENDENCE OF MAGNETIC SUSCEPTIBILITY ON THE NEXT NEAREST HOPPING TERM FOR HIGH TC CUPRATES
Authors: EOM JAE-GON , EOM JAE-HYEON , SALK SUNG-HO SUCK
Published: September 2007

In view of increasing emphasis on the use of next-nearest hopping t' term in the t - J Hamiltonian, we examine its effect on the spin susceptibility and its correlation with the structure of phase diagram. We find from this study that the resonance peak of spin susceptibility rapidly decreases with hole concentration in the overdoped region at which the spin singlet pairing order diminishes. It is shown that the doping dependence of resonance energy in both underdoped and overdoped regions is in agreement with observations.
VORTEX DOPING INTO FINITE-SIZED SUPERCONDUCTING NETWORKS
Authors: ISHIDA TAKEKAZU , MATSUSHIMA YOSHIAKI , SHIMIZU MAKOTO , KATO MASARU , HAYASHI MASAHIKO , EBISAWA HIROMICHI , SATOH KAZUO , YOTSUYA TSUTOMU , SATO OSAMU
Published: September 2007

Superconducting finite-sized Pb square networks with 10×10 square holes fabricated by electron beam lithography have been investigated in view of vortex doping into superconducting networks. Vortex images observed by a SQUID microscope were compared with predictions from the Ginzburg-Landau theory. Exactly reversed pattern was confirmed to appear both in the vortex-doping x into an empty network and in the antivortex doping 1- x into a fully occupied network ( x =1/4). We also confirmed a checker-board crystal of vortices at half filling both theoretically and experimentally.
STRUCTURE AND SUPERCONDUCTIVITY OF GaSr2(Tm,Ca)Cu2Oz CUPRATE DOPED WITH COBALT
Authors: LEE H. K. , KIM Y. I.
Published: September 2007

To address the structural mechanisms associated with T c variations induced by Co doping, two samples of the nominal composition ( Ga 1-x Co x) Sr 2( Tm 0.6 Ca 0.4) Cu 2 O z with x = 0.5 and 0.7 have been prepared and studied by using neutron powder diffraction and transport measurements. In contrast to the x = 0.5 sample, which shows superconductivity around 35 K, the x = 0.7 sample does not exhibit superconductivity. The neutron powder diffraction studies indicate that both samples exhibit the 1212 structure with space group Ima2 and the Co atoms exclusively substitute for the Cu atoms located on the chain sites of the 123 parent structure. The depression in Tc of the x = 0.7 sample, compared to that of the x = 0.5 sample, is discussed in connection with oxygen content, disorder, and change in hole concentration on the superconducting planes.
EFFECT OF Ca CONTENT ON THE STRUCTURE AND TRANSPORT PROPERTIES IN La0.7Ca0.3-xMnO3 MANGANITES
Authors: XIE Q. Y. , LU X. M. , ZHI S. S. , YOU B. , JIANG Z. S. , ZHANG T.
Published: September 2007

With varying the content of Ca , single phase of La 0.7 Ca 0.3-x MnO 3 ( LCMO ) with Pnma symmetry have been studied. There is no phase transition detected with varing the content of Ca . The divergence of Mn-O1(ax) and Mn-O2(eq) values indicates the occurrence of lattice distortions. No marked variations of Mn-O1-Mn and Mn-02-Mn bond angles are observed. The insulator-metal transition temperature T MI of samples shifts to lower values with increasing vacancy content. At low temperature region, a large MR (30∼45%) is observed. We attribute it to the grain boundary tunnel effect.
PHENOMENOLOGICAL EQUATIONS FOR THE MAGNETIC PROPERTIES OF La0.7-xNdxPb0.3MnO3 COMPOUNDS
Authors: OU C. R. , YOUNG S. L. , CHEN H. Z. , KAO M. C. , LIN C. H. , SHEN C. Y. , HORNG LANCE , LIN C. C. , SHI J. B.
Published: September 2007

Polycrystalline single phase oxides, La 0.7-x Nd x Pb 0.3) MnO 3 (0.3≤x≤0.7), have been synthesized by a standard ceramic fabrication method. A phenomenological model is proposed to describe the magnetization process, and to fit the experiment data of hysteresis loops under different composition ratio. The magnetic hysteresis behavior can be modeled by the formula of [Formula: see text]. The resulted model can satisfy the experiment data ranging from 0.005T to 5T. Explanations on the fitting coefficients of these compounds are addressed.
LOCALIZATION ON SNOWFLAKE DOMAINS
Authors: DAUDERT BRITTA , LAPIDUS MICHEL L.
Published: September 2007

The geometric features of the square and triadic Koch snowflake drums are compared using a position entropy defined on the grid points of the discretizations (prefractals) of the two domains. Weighted graphs using the geometric quantities are created and random walks on the two prefractals are performed. The aim is to understand if the existence of narrow channels in the domain may cause the "localization" of eigenfunctions.
Biotechnology in Japan
Authors: Venning Maurice , Yukawa Takao
Published: September 2007

The article discusses the Japanese Biotechnology market which lists human health, agri-food, bioprocess, environment, biotools and bioinformatics as the main industries. It shows a map of structural reorganization in Japan. It also discusses the areas of improvement of the Japanese market.
Alternative Medicine — Electronic Three-dimensional Atlas of Acupuncture
Authors: Nowinski Wieslaw. L , Thirunavuukarasuu A.
Published: September 2007

Electronic Three-Dimensional Atlas of Acupuncture.
Overview of the BMS Industry
Authors: Sheo S. Rai
Published: September 2007

This articles is about the efforts of Singapore government in the biomedical sector.
BOOM TIME for Biomedical Sciences in Singapore: A Perspective from an Educational Institute
Authors: Lau Lionel
Published: September 2007

This article is a perspective from an educational institute. It states how Singapore is shaping its educational focus on the boom in biomedical sciences.
SINGAPORE: MOVING WITH TIMES, COMBINING IT AND RESEARCH
Authors: Breen Stephen
Published: September 2007

The article is about the use of software in the Singapore biomed research industry.
Agriculture — Forest Biotechnology is Beginning to Take Root
Authors: Hong Yan
Published: September 2007

With the increasing loss of forests, the need for their renewal by natural means is imminent. Thanks to the Kyoto treaty demanding reduction in greenhouse gases, plantations of fast growing and high yielding tree species have thrived around the world. In the past few years, there has been a lot of progress in the area of forest biotechnology. Genetic modification (GM) has introduced desirable traits such as insect tolerance, herbicide resistance, sterility, better pulping quality and fast growth. The plantation of GM trees, however, raises the concerns of possible damage to the environment, impact to biodiversity and possible gene flow into natural forests. These issues need to be addressed before there is any wide acceptance of GM trees. Other non-GM biotechnology techniques such as mass propagation of elite tree individuals through meristematic propagation or somatic embryogenesis are more acceptable and have been widely used.
Long-term Prospects of the BIOTECHNOLOGY INDUSTRY
Authors: Hyeon Byung-Hwan
Published: September 2007

The article is a short overview of the long term prospects of the biotechnology industry.
CURRENT STATUS OF BIOTECHNOLOGY-RELATED LAWS AND REGULATIONS
Authors: Hyeon Byung-Hwan
Published: September 2007

This article uplift's the laws and regulations based on biotechnology.
QUINTILES — THE MOST EXPERIENCED CLINICAL DEVELOPMENT ORGANIZATION IN ASIA
Authors: Tharmaratnam Anand , Stibilj Michael , Sivalingam Bhavani , DeSilva Yutaka
Published: September 2007

The article is a short overview of Clinical Development Organization in Asia.
MANAGING CLINICAL TRIALS IN ASIA
Authors: Lim Bee-Koong
Published: September 2007

This article explains about the needs of rapid growth for managing Clinical Trails in Asia.
Agriculture
Authors: Choi Yang Do
Published: September 2007

Progress of Crop Functional Genomics Program in Korea.
ANGIS and BioManager
Authors: Reeves Peter , Cattley Sonia
Published: September 2007

This article deals about the web-based bioinformatics system to provide seamless workstation.
BIOINFORMATICS AND MARSUPIAL GENOMICS
Authors: Papenfuss Tony
Published: September 2007

This article reveals several marsupial immunogenetics projects.
Taiwan Bioinformatics Institute and the GMBD Bioinformatics Core
Authors: Chang I-Shou , Lyu Ping-Chiang , Hwang Jenn-Kang , Sun H. Sunny , Hsiung Chao A.
Published: September 2007

This article explans how the bioinformatics services are crucial to growth and success of genomic medicine research in Taiwan.
KOREAN SOCIETY FOR BIOINFORMATICS (KSBI)
Authors: Lee Kwang Hyung , Lee Doheon , Kim Chul Min , Park Jong , Nam Hong Gil , No Kyoung Tai , Lee Sang Joo , Yoo Jong Shin , Kang Suki , Kim Dongsup , Hahn Jang-Ho , Han Hyun-Woo , Im Seok-Ki , Shin Hyun-Kyu , Kang Bong Joong , Lee Sang Yup
Published: September 2007

This article gives the brief description of the Korean Society for Bioinformatics.
BIC: Resource Unit of NUS Bioinformatics Programme
Authors: De Silva Mark , Lim Kuan Siong
Published: September 2007

This article deals about the resource unit of NUS Bioinformatics Programme.
Computational Biology in NUS School of Computing
Authors: Wong Limsoon
Published: September 2007

This article delivers about the number of advanced computational biology courses in NUS.
The MSc in Bioinformatics Program at NTU
Authors: Schmidt Bertil , Chee Keong-Kwoh
Published: September 2007

This article gives the course overview of MSc in Bioinformatics Program at NTU.
Convergence for Life Sciences
Authors: Lim Teck-Sin
Published: September 2007

This article deals with the multidisciplinary industry of Life Sciences that facing increasing pressure convergence.
Aging is associated with myocardial insulin resistance and mitochondrial dysfunction
Authors: Bhashyam Siva , Parikh Pratik , Bolukoglu Hakki , Shannon Alexander H. , Porter James H. , Shen You-Tang , Shannon Richard P.
Published: September 2007

Aging is associated with insulin resistance, often attributable to obesity and inactivity. Recent evidence suggests that skeletal muscle insulin resistance in aging is associated with mitochondrial alterations. Whether this is true of the senescent myocardium is unknown. Twelve young (Y, 4 years old) and 12 old (O, 11 years old) dogs, matched for body mass, were instrumented with left-ventricular pressure gauges, aortic and coronary sinus catheters, and flow probes on left circumflex artery. Before surgery, all dogs participated in a 6-wk exercise program. Dogs underwent measurements of hemodynamics and plasma substrates before and during a 2-h hyperinsulinemic-euglycemic clamp to measure whole body and myocardial glucose and nonesterified fatty acid uptake. Following the protocol, myocardial and skeletal samples were obtained to measure components of the insulin-signaling cascade and mitochondrial structure. There was no difference in plasma glucose (Y, 90 ± 4 mg/dl; O, 87 ± 4 mg/dl), but old dogs had higher ( P < 0.02) nonesterified fatty acids (Y, 384 ± 48 μmol/l; O, 952 ± 97 μmol/l) and plasma insulin (Y, 39 ± 11 pmol/l; O, 108 ± 18 pmol/l). Old dogs had impaired total body glucose disposition (Y, 11.5 ± 1 mg·kg−1·min−1; O, 8.0 ± 0.5 mg·kg−1·min−1; P < 0.05) and insulin-stimulated myocardial glucose uptake (Y, 3.5 ± 0.3mg·min−1·g−1; O, 1.8 ± 0.3 mg·min−1·g−1; P < 0.05). The impaired insulin action was associated with altered insulin signaling and glucose transporter (GLUT4) translocation. There were myocardial mitochondrial structural changes observed in association with decreased expression of uncoupling protein-3. Aging is associated with both whole body and myocardial insulin resistance, independent of obesity and inactivity, but involving altered mitochondrial structure and impaired cellular insulin action.
Hypertension-induced remodeling of cardiac excitation-contraction coupling in ventricular myocytes occurs prior to hypertrophy development
Authors: Chen-Izu Ye , Chen Ling , Bányász Tamás , McCulle Stacey L. , Norton Byron , Scharf Steven M. , Agarwal Anuj , Patwardhan Abhijit , Izu Leighton T. , Balke C. William
Published: September 2007

Hypertension is a major risk factor for developing cardiac hypertrophy and heart failure. Previous studies show that hypertrophied and failing hearts display alterations in excitation-contraction (E-C) coupling. However, it is unclear whether remodeling of the E-C coupling system occurs before or after heart disease development. We hypothesized that hypertension might cause changes in the E-C coupling system that, in turn, induce hypertrophy. Here we tested this hypothesis by utilizing the progressive development of hypertensive heart disease in the spontaneously hypertensive rat (SHR) to identify a window period when SHR had just developed hypertension but had not yet developed hypertrophy. We found the following major changes in cardiac E-C coupling during this window period. 1) Using echocardiography and hemodynamics measurements, we found a decrease of left ventricular ejection fraction and cardiac output after the onset of hypertension. 2) Studies in isolated ventricular myocytes showed that myocardial contraction was also enhanced at the same time. 3) The action potential became prolonged. 4) The E-C coupling gain was increased. 5) The systolic Ca2+transient was augmented. These data show that profound changes in E-C coupling already occur at the onset of hypertension and precede hypertrophy development. Prolonged action potential and increased E-C coupling gain synergistically increase the Ca2+transient. Functionally, augmented Ca2+transient causes enhancement of myocardial contraction that can partially compensate for the greater workload to maintain cardiac output. The increased Ca2+signaling cascade as a molecular mechanism linking hypertension to cardiac hypertrophy development is also discussed.
Hemodynamics and muscle sympathetic nerve activity after 8 h of sustained hypoxia in healthy humans
Authors: Tamisier Renaud , Hunt Brian E. , Gilmartin Geoffrey S. , Curley Mathew , Anand Amit , Weiss J. Woodrow
Published: September 2007

Hemodynamics, muscle sympathetic nerve activity (MSNA), and forearm blood flow were evaluated in 12 normal subjects before, during (1 and 7 h), and after ventilatory acclimatization to hypoxia achieved with 8 h of continuous poikilocapnic hypoxia. All results are means ± SD. Subjects experienced mean oxygen saturation of 84.3 ± 2.3% during exposure. The exposure resulted in hypoxic acclimatization as suggested by end-tidal CO2 [44.7 ± 2.7 (pre) vs. 39.5 ± 2.2 mmHg (post), P < 0.001] and by ventilatory response to hypoxia [1.2 ± 0.8 (pre) vs. 2.3 ± 1.3 l·min−1·1% fall in saturation−1 (post), P < 0.05]. Subjects exhibited a significant increase in heart rate across the exposure that remained elevated even upon return to room air breathing compared with preexposure (67.3 ± 15.9 vs. 59.8 ± 12.1 beats/min, P < 0.008). Although arterial pressure exhibited a trend toward an increase across the exposure, this did not reach significance. MSNA initially increased from room air to poikilocapnic hypoxia (26.2 ± 10.3 to 32.0 ± 10.3 bursts/100 beats, not significant at 1 h of exposure); however, MSNA then decreased below the normoxic baseline despite continued poikilocapnic hypoxia (20.9 ± 8.0 bursts/100 beats, 7 h Hx vs. 1 h Hx; P < 0.008 at 7 h). MSNA decreased further after subjects returned to room air (16.6 ± 6.0 bursts/100 beats; P < 0.008 compared with baseline). Forearm conductance increased after exposure from 2.9 ± 1.5 to 4.3 ± 1.6 conductance units ( P < 0.01). These findings indicate alterations of cardiovascular and respiratory control following 8 h of sustained hypoxia producing not only acclimatization but sympathoinhibition.
Doxorubicin-induced cardiotoxicity: direct correlation of cardiac fibroblast and H9c2 cell survival and aconitase activity with heat shock protein 27
Authors: Turakhia Samir , Venkatakrishnan C. D. , Dunsmore Kathy , Wong Hector , Kuppusamy Periannan , Zweier Jay L. , Ilangovan Govindasamy
Published: September 2007

The use of doxorubicin (Dox) and its derivatives as chemotherapeutic drugs to treat patients with cancer causes dilated cardiomyopathy and congestive heart failure due to Dox-induced cardiotoxicity. In this work, using heat shock factor-1 wild-type (HSF-1+/+) and HSF-1 knockout (HSF-1−/−) mouse fibroblasts and embryonic rat heart-derived cardiac H9c2 cells, we show that the magnitude of protection from Dox-induced toxicity directly correlates with the level of the heat shock protein 27 (HSP27). Western blot analysis of normal and heat-shocked cells showed the maximum expression of HSP27 in heat-shocked cardiac H9c2 cells and no HSP27 in HSF-1−/−cells (normal or heat-shocked). Correspondingly, the cell viability, measured [with (3,4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay] after treatment with various concentrations of Dox, was the highest in heat-shocked H9c2 cells and the lowest in HSF-1−/−cells. Depleting HSP27 in cardiac H9c2 cells by small interfering (si)RNA also reduced the viability against Dox, confirming that HSP27 does protect cardiac cells against the Dox-induced toxicity. The cells that have lower HSP27 levels such as HSF-1−/−, were found to be more susceptible for aconitase inactivation. Based on these results we propose a novel mechanism that HSP27 plays an important role in protecting aconitase from Dox-generated O2•−, by increasing SOD activity. Such a protection of aconitase by HSP27 eliminates the catalytic recycling of aconitase released Fe(II) and its deleterious effects in cardiac cells.
Development of progressive aortic vasculopathy in a rat model of aging
Authors: Miller Steven J. , Watson William C. , Kerr Kimberly A. , Labarrere Carlos A. , Chen Neal X. , Deeg Mark A. , Unthank Joseph L.
Published: September 2007

Recent studies have established that age is the major risk factor for vascular disease. Numerous aberrant changes occur in vascular structure and function during aging, and animal models are the primary means to determine the underlying mechanisms of age-mediated vascular pathology. The Fischer 344/Brown Norway F1 hybrid (F344xBN) rat thoracic aorta has been shown to display age-related pathology similar to what occurs in humans. This study utilized the F344xBN rat aorta and both morphometric and global gene expression analyses to identify appropriate time points to study vascular aging and to identify molecules associated with the development and progression of vascular pathology. In contrast to some previous studies that indicated age-related abrupt changes, a progressive increase in intimal and medial thickness, as well as smooth muscle cell-containing intimal protrusions, was observed in thoracic aorta. This structural vascular pathology was associated with a progressive, but nonlinear, increase in global differential gene expression. Gene products with altered mRNA and protein expression included inflammation-related molecules: specifically, the adhesion molecules ICAM-1 and VCAM-1 and the bone morphogenic proteins osteopontin and bone sialoprotein-1. Intimal-associated macrophages were found to increase significantly in number with age. Both systemic and tissue markers of oxidant stress, serum 8-isoprostane and 3-nitrotyrosine, respectively, were also found to increase during aging. The results demonstrate that major structural abnormalities and altered gene expression develop after 6 mo and that the progressive pathological development is associated with increased inflammation and oxidant stress.
Growth-related oncogene-α induces endothelial dysfunction through oxidative stress and downregulation of eNOS in porcine coronary arteries
Authors: Bechara Carlos , Wang Xinwen , Chai Hong , Lin Peter H. , Yao Qizhi , Chen Changyi
Published: September 2007

Growth-related oncogene-α (GRO-α) is a member of the CXC chemokine family, which is involved in the inflammatory process including atherosclerosis. We hypothesized that GRO-α may affect endothelial functions in both porcine coronary arteries and human coronary artery endothelial cells (HCAECs). Vasomotor function was analyzed in response to thromboxane A2 analog U-46619 for contraction, bradykinin for endothelium-dependent vasorelaxation, and sodium nitroprusside (SNP) for endothelium-independent vasorelaxation. In response to 10−6M bradykinin, GRO-α (50 and 100 ng/ml) significantly reduced endothelium-dependent vasorelaxation by 34.73 and 48.8%, respectively, compared with controls ( P < 0.05). There were no changes in response to U-46619 or SNP between treated and control groups. With the lucigenin-enhanced chemiluminescence assay, superoxide anion production in GRO-α-treated vessels (50 and 100 ng/ml) was significantly increased by 50 and 86%, respectively, compared with controls ( P < 0.05). With real-time PCR analysis, endothelial nitric oxide synthase (eNOS) mRNA levels in porcine coronary arteries and HCAECs after GRO-α treatment were significantly decreased compared with controls ( P < 0.05). The eNOS protein levels by both immunohistochemistry and Western blot analyses were also decreased in GRO-α-treated vessels. Antioxidant seleno-l-methionine and anti-GRO-α antibody effectively blocked these effects of GRO-α on both porcine coronary arteries and HCAECs. In addition, GRO-α immunoreactivity was substantially increased in the atherosclerotic regions compared with nonatherosclerotic regions in human coronary arteries. Thus GRO-α impairs endothelium-dependent vasorelaxation in porcine coronary arteries through a mechanism of overproduction of superoxide anion and downregulation of eNOS. GRO-α may contribute to human coronary artery disease.
Characterization and mechanism of P2X receptor-mediated increase in cardiac myocyte contractility
Authors: Shen Jian-Bing , Shutt Robin , Pappano Achilles , Liang Bruce T.
Published: September 2007

Cardiac P2X purinergic receptors can mediate an increase in myocyte contractility and a potentially important role in the heart. The P2X4receptor (P2X4R) is an important subunit of native cardiac P2X receptors. With transgenic mice with cardiac-specific overexpression of P2X4R (Tg) used as a model, the objectives here were to characterize the P2X receptor-mediated cellular contractile and Ca2+transient effects and to determine the mechanism underlying the receptor-induced increase in myocyte contractility. In response to the agonist 2-methylthioATP (2-meSATP), Tg myocytes showed an increased intracellular Ca2+transient, as defined by fura 2 fluorescence ratio, and an enhanced contraction shortening that were unaccompanied by cAMP accumulation or L-type Ca2+channel activation. The increased Ca2+transient was not associated with any alteration in action potential duration, resting membrane potential, or diastolic fluorescence ratio or rates of rise and decline of the Ca2+transient. Simultaneous Ca2+transient and contraction measurements did not show any agonist-mediated change in myofilament Ca2+sensitivity. However, activation of the overexpressed P2X4receptor caused an enhanced SR Ca2+loading, as evidenced by a 2-meSATP-evoked increase in the caffeine-induced inward current and Ca2+transient. Similar data were obtained in wild-type mouse ventricular myocytes. Thus an increased SR Ca2+content, occurring in the absence of cAMP accumulation or L-type Ca2+channel activation, is the principal mechanism by which cardiac P2X receptor mediates a stimulatory effect on cardiac myocyte contractility.
Chronic high blood flow potentiates shear stress-induced release of NO in arteries of aged rats
Authors: Yan Changdong , Huang An , Kaley Gabor , Sun Dong
Published: September 2007

Aging impairs shear-stress-dependent dilation of arteries via increased superoxide production, decreased SOD activity, and decreased activation of endothelial nitric oxide (NO) synthase (eNOS). In the present study, we investigated whether chronic increases in shear stress, elicited by increases in blood flow, would improve vascular endothelial function of aged rats. To this end, second-order mesenteric arteries of young (6 mo) and aged (24 mo) male Fischer-344 rats were selectively ligated for 3 wk to elevate blood flow in a first-order artery [high blood flow (HF)]. An in vitro study was then conducted on first-order arteries with HF and normal blood flow (NF) to assess shear stress (1, 10, and 20 dyn/cm2)-induced release of NO into the perfusate. In HF arteries of both age groups, shear stress-induced NO production increased significantly. In 24-mo-old rats, the reduced shear stress-induced NO production in NF arteries was normalized by HF to a level similar to that in NF arteries of 6-mo-old rats. The increased NO production in HF arteries of 24-mo-old rats was associated with increased shear stress-induced dilation, expression of eNOS protein, and shear stress-induced eNOS phosphorylation. Wortmannin, a phosphatidylinositol 3-kinase inhibitor, reduced shear stress-induced eNOS phosphorylation and vasodilation. Superoxide production decreased significantly in HF compared with NF arteries in 24-mo-old rats. The decreased superoxide production was associated with significant increases in CuZn-SOD and extracellular SOD protein expressions and total SOD activity. These results suggest that stimulation with chronic HF restores shear-stress-induced activation of eNOS and antioxidant ability in aged arteries.
Surrounding tissues affect the passive mechanics of the vessel wall: theory and experiment
Authors: Liu Yi , Dang Charles , Garcia Marisa , Gregersen Hans , Kassab Ghassan S.
Published: September 2007

The stress and strain in the vessel wall are important determinants of vascular physiology and pathophysiology. Vessels are constrained radially by the surrounding tissue. The hypothesis in this work is that the surrounding tissue takes up a considerable portion of the intravascular pressure and significantly reduces the wall strain and stress. Ten swine of either sex were used to test this hypothesis. An impedance catheter was inserted into the carotid or femoral artery, and after mechanical preconditioning pressure-cross-sectional area relations were obtained with the surrounding tissue intact and dissected away (untethered), respectively. The radial constraint of the surrounding tissue was quantified as an effective perivascular pressure on the outer surface of the vessel, which was estimated as 50% or more of the intravascular pressure. For carotid arteries at pressure of 100 mmHg, the circumferential wall stretch ratio in the intact state was ∼20% lower than in the untethered state and the average circumferential stress was reduced by ∼70%. For femoral arteries, the reductions were ∼15% and 70%, respectively. These experimental data support the proposed hypothesis and suggest that in vitro and in vivo measurements of the mechanical properties of vessels must be interpreted with consideration of the constraint of the surrounding tissue.