bluuebunny/crossref_metadata_2025 huggingface dataset:
The Mechanisms of Catalysis by Metallo β‐Lactamases
Authors: Page Michael I. , Badarau Adriana
Published: June 2008

Class B β‐lactamases or metallo‐β‐lactamases (MBLs) require zinc ions to catalyse the hydrolysis of β‐lactam antibiotics such as penicillins, cephalosporins, carbapenems, and cephamycins. There are no clinically useful inhibitors against MBLs which are responsible for the resistance of some bacteria to antibiotics. There are two metal‐ion binding sites that have different zinc ligands but the exact roles of the metal‐ion remain controversial, and distinguishing between their relative importance is complex. The metal‐ion can act as a Lewis acid by co‐ordination to the β‐lactam carbonyl oxygen to facilitate nucleophilic attack and stabilise the negative charge developed on this oxygen in the tetrahedral intermediate anion. The metal‐ion also lowers the pKa of the directly co‐ordinated water molecule so that the metal‐bound hydroxide ion is a better nucleophile than water and is used to attack the β‐lactam carbonyl carbon. An intrinsic property of binuclear metallo hydrolytic enzymes that depend on a metal‐bound water both as the attacking nucleophile and as a ligand for the second metal‐ion is that this water molecule, which is consumed during hydrolysis of the substrate, has to be replaced to maintain the catalytic cycle. With MBL this is reflected in some unusual kinetic profiles.
Fuzzy Boundary and Fuzzy Semiboundary
Authors: Athar M. , Ahmad B.
Published: June 2008

We present several properties of fuzzy boundary and fuzzy
semiboundary which have been supported by examples. Properties of
fuzzy semi‐interior, fuzzy semiclosure, fuzzy boundary, and fuzzy
semiboundary have been obtained in product‐related spaces. We give
necessary conditions for fuzzy continuous (resp., fuzzy
semicontinuous, fuzzy irresolute) functions. Moreover, fuzzy
continuous (resp., fuzzy semicontinuous, fuzzy irresolute)
functions have been characterized via fuzzy‐derived (resp., fuzzy‐semiderived) sets.
On the Design and Exploitation of User′s Personal and Public Information for Semantic Personal Digital Photograph Annotation
Authors: Sarin Supheakmungkol , Nagahashi Toshinori , Miyosawa Tadashi , Kameyama Wataru
Published: June 2008

Automating the process of semantic annotation of digital personal photographs is a crucial step towards efficient and effective management of this increasingly high volume of content. However, this is still a highly challenging task for the research community. This paper proposes a novel solution. Our solution integrates all contextual information available to and from the users, such as their daily emails, schedules, chat archives, web browsing histories, documents, online news, Wikipedia data, and so forth. We then analyze this information and extract important semantic terms, using them as semantic keyword suggestions for their photos. Those keywords are in the form of named entities, such as names of people, organizations, locations, and date/time as well as high frequency terms. Experiments conducted with 10 subjects and a total of 313 photos proved that our proposed approach can significantly help users with the annotation process. We achieved a 33% gain in annotation time as compared to manual annotation. We also obtained very positive results in the accuracy rate of our suggested keywords.
Global Transcriptional Analysis of Yeast Cell Death Induced by Mutation of Sister Chromatid Cohesin
Authors: Ren Qun , Yang Hui , Gao Bifeng , Zhang Zhaojie
Published: June 2008

Cohesin is a protein complex that regulates sister chromatid cohesin during cell division. Malfunction in chromatid cohesin results in chromosome missegregation and aneuploidy. Here, we report that mutations of MCD1 and PDS5, two major components of cohesin in budding yeast, cause apoptotic cell death, which is characterized by externalization of phosphatidylserine at cytoplasmic membrane, chromatin condensation and fragmentation, and ROS production. Microarray analysis suggests that the cell death caused by mutation of MCD1 or PDS5 is due to the internal stress response, contrasting to the environmental or external stress response induced by external stimuli, such as hydrogen peroxide. A common feature shared by the internal stress response and external stress response is the response to stimulus, including response to DNA damage, mitochondria functions, and oxidative stress, which play an important role in yeast apoptotic cell death.
Photonic Integration on the Hybrid Silicon Evanescent Device Platform
Authors: Park Hyundai , Fang Alexander W. , Liang Di , Kuo Ying-Hao , Chang Hsu-Hao , Koch Brian R. , Chen Hui-Wen , Sysak Matthew N. , Jones Richard , Bowers John E.
Published: June 2008

This paper reviews the recent progress of hybrid silicon evanescent devices. The hybrid silicon evanescent device structure consists of III‐V epitaxial layers transferred to silicon waveguides through a low‐temperature wafer bonding process to achieve optical gain, absorption, and modulation efficiently on a silicon photonics platform. The low‐temperature wafer bonding process enables fusion of two different material systems without degradation of material quality and is scalable to wafer‐level bonding. Lasers, amplifiers, photodetectors, and modulators have been demonstrated with this hybrid structure and integration of these individual components for improved optical functionality is also presented. This approach provides a unique way to build photonic active devices on silicon and should allow application of silicon photonic integrated circuits to optical telecommunication and optical interconnects.
Antigen-Induced Immunomodulation in the Pathogenesis of Atherosclerosis
Authors: Milioti Natalia , Bermudez-Fajardo Alexandra , Penichet Manuel L. , Oviedo-Orta Ernesto
Published: June 2008

Atherosclerosis is a chronic inflammatory disorder characterised by the accumulation of monocytes/macrophages, smooth muscle cells, and lymphocytes within the arterial wall in response to the release of proinflammatory molecules. Such accumulation results in the formation of the atherosclerotic plaque, which would eventually evolve to complications such as total artery occlusion, rupture, calcification, or aneurysm. Although the molecular mechanism responsible for the development of atherosclerosis is not completely understood, it is clear that the immune system plays a key role in the development of the atherosclerotic plaque and in its complications. There are multiple antigenic stimuli that have been associated with the pathogenesis of atherosclerosis. Most of these stimuli come from modified self-molecules such as oxidised low-density lipoproteins (oxLDLs), beta2glycoprotein1 (2GP1), lipoprotein a (LP(a)), heat shock proteins (HSPs), and protein components of the extracellular matrix such as collagen and fibrinogen in the form of advanced glycation-end (AGE) products. In addition, several foreign antigens including bacteria such as Porphyromonas gingivalis and Chlamydia pneumoniae and viruses such as enterovirus and cytomegalovirus have been associated with atherosclerosis as potentially causative or bystander participants, adding another level of complexity to the analysis of the pathophysiology of atherosclerosis. The present review summarises the most important scientific findings published within the last two decades on the importance of antigens, antigen stimulation, and adaptive immune responses in the development of atherosclerotic plaques.
Diabetes Alters Contraction‐Induced Mitogen Activated Protein Kinase Activation in the Rat Soleus and Plantaris
Authors: Katta A. , Preston D. L. , Karkala S. K. , Asano S. , Meduru S. , Mupparaju S. P. , Yokochi E. , Rice Kevin M. , Desai D. H. , Blough E. R.
Published: June 2008

The prescription of anaerobic exercise has recently been advocated for the management of diabetes; however exercise‐induced signaling in diabetic muscle remains largely unexplored. Evidence from exercise studies in nondiabetics suggests that the extracellular‐signal‐regulated kinases (Erk1/2), p38, and c‐JUN NH2‐terminal kinase (Jnk) mitogen‐activated protein kinases (MAPKs) are important regulators of muscle adaptation. Here, we compare the basal and the in situ contraction‐induced phosphorylation of Erk1/2‐ p38‐ and Jnk‐MAPK and their downstream targets (p90rsk and MAPKAP‐K2) in the plantaris and soleus muscles of normal and obese (fa/fa) Zucker rats. Compared to lean animals, the time course and magnitude of Erk1/2, p90rsk and p38 phosphorylation to a single bout of contractile stimuli were greater in the plantaris of obese animals. Jnk phosphorylation in response to contractile stimuli was muscle‐type dependent with greater increases in the plantaris than the soleus. These results suggest that diabetes alters intramuscular signaling processes in response to a contractile stimulus.
Screening for PPAR Responsive Regulatory Modules in Cancer
Authors: Heinäniemi Merja , Carlberg Carsten
Published: June 2008

Peroxisome proliferator‐activated receptors (PPARs) have via their large set of target genes a critical impact on numerous diseases including cancer. Cancer development involves numerous regulatory cascades that drive the progression of the malignancy of the cells. On a genomic level, these pathways converge on regulatory modules, some of which contain colocalizing PPAR binding sites (PPREs). We developed an in silico screening method that incorporates experiment‐ and informatics‐derived evidence for a more reliable prediction of PPREs and PPAR target genes. This method is based on DNA‐binding data of PPAR subtypes to a panel of DR1‐type PPREs and tracking the enrichment of binding sites from multiple species. The ability of PPARγ to induce cellular differentiation and the existence of FDA‐approved PPARγ agonists encourage the exploration of possibilities to activate or inactivate PPRE containing modules to arrest cancer progression. Recent advances in genomic techniques combined with computational analysis of binding modules are discussed in the review with the example of our recent screen for PPREs on human chromosome 19.
Micro‐Optoelectromechanical Tilt Sensor
Authors: Constandinou Timothy G. , Georgiou Julius
Published: June 2008

This paper presents a novel hybrid CMOS/MEMS tilt sensor with a 5∘resolution over a 300∘range. The device uses a MEMS‐based semicircular mass suspended from a rigid body, projecting a shadow onto the CMOS‐based optical sensor surface. A one‐dimensional photodiode array arranged as a uniformly segmented ring is then used to determine the tilt angle by detecting the position of the semicircular mass. The complete sensor occupies an area of under 2.5 mm × 2.5 mm.
Radiation Safety and Future Innovative Diagnostic Modalities
Authors: Radmayr Christian
Published: June 2008

One must demand an accurate, safe, radiation-free, and noninvasive method for reflux examination as the ideal possibility for reflux screening. Of course the available different imaging modalities are far from this ideal situation, but minimal radiation exposure is indeed a permanent objective. Additionally since all of these studies might be quite stressful to the child and the family, a specially designed and equipped environment is obligatory for the comfort of all involved. An absolute ideal modality in the diagnosis of VUR would be the definition of a certain marker in serum or urine that could identify children with VUR without the need for any interventional screening modality. Therefore more and more efforts have to be made in the future to investigate different markers for this purpose. Since reflux is one of the most frequent congenital conditions pediatric urologist have to deal with potential risks that might lead to renal insufficiency, noninvasive and radiation-free modalities should become the methods of choice, hopefully in the near future.
Stability of the Cauchy-Jensen Functional Equation in "Equation missing" -Algebras: A Fixed Point Approach
Authors: Park Choonkil , An Jong Su
Published: June 2008

we prove the Hyers-Ulam-Rassias stability of "Equation missing"-algebra homomorphisms and of generalized derivations on "Equation missing"-algebras for the following Cauchy-Jensen functional equation "Equation missing", which was introduced and investigated by Baak (2006). The concept of Hyers-Ulam-Rassias stability originated from the stability theorem of Th. M. Rassias that appeared in (1978).
Polymorphisms in DNA Repair Genes, Smoking, and Pancreatic Adenocarcinoma Risk
Authors: McWilliams Robert R. , Bamlet William R. , Cunningham Julie M. , Goode Ellen L. , de Andrade Mariza , Boardman Lisa A. , Petersen Gloria M.
Published: June 2008

Base excision repair and nucleotide excision repair are vital responses to multiple types of DNA damage, including damage from tobacco exposure. Single-nucleotide polymorphisms (SNP) in these pathways may affect DNA repair capacity and therefore influence risk for cancer development. We performed a clinic-based, case-control study comprising 481 consecutive patients with confirmed pancreatic adenocarcinoma and 625 healthy controls. Allele and genotype frequencies for 16 SNPs in DNA repair genes ERCC1, XPD/ERCC2, XPC, XPF/ERCC4, OGG1, and XRCC1 were compared after adjusting for age, sex, and smoking history. Subgroup analysis by sex and smoking history was performed. Carriers of one or two XPF/ERCC4 minor alleles at R415Q had decreased risk of pancreatic adenocarcinoma compared with those who had two major alleles [odds ratio (OR), 0.59; 95% confidence interval (95% CI), 0.40–0.85]. Heavy smokers (>40 pack-years) had increased risk for cancer if they were carriers of at least one minor allele for XPD/ERCC2 at D312N (OR, 2.78; 95% CI, 1.28–6.04) or D711D (OR, 2.19; 95% CI, 1.01–4.73). No other significant differences in risk were identified. Minor alleles in DNA repair genes XPF/ERCC4 and XPD/ERCC2 were associated with altered risk for pancreatic cancer. [Cancer Res 2008;68(12):4928–35]
Hepatitis B Core-Related Antigen Assay Is Useful for Monitoring the Antiviral Effects of Nucleoside Analogue Therapy
Authors: Tanaka Eiji , Matsumoto Akihiro , Yoshizawa Kaname , Maki Noboru
Published: June 2008

Objective: The clinical significance of the hepatitis B virus core-related antigen (HBcrAg) assay in monitoring the antiviral effects of lamivudine is reviewed. Methods: The HBcrAg assay simultaneously measured serum levels of hepatitis B core (HBc) and e (HBe) antigens using monoclonal antibodies which recognize common epitopes of these two denatured antigens. Results: Although serum HBcrAg levels correlated linearly with those of hepatitis B virus (HBV) DNA in natural course, the decrease in HBcrAg was significantly slower than in HBV DNA after initiation of lamivudine administration. We analyzed the clinical significance of HBV DNA and HBcrAg levels to predict the occurrence of lamivudine resistance. HBV DNA measurement may be useful to identify patients who are at high risk of developing lamivudine resistance, and HBcrAg measurement may help to detect patients who are at low risk of drug resistance. The measurement of HBcrAg was also found to be a useful prognosticator for reactivation of hepatitis after cessation of lamivudine administration. Conclusion: The HBcrAg assay is indeed useful for monitoring the antiviral effects of lamivudine, and we propose that it be adopted as a serum marker which reflects the amount of HBV covalently closed circular DNA in hepatocytes.
Technique for the Early Detection of Drug-Resistant HBV DNA during Antiviral Therapy
Authors: Yeon Jong Eun
Published: June 2008

Early detection of antiviral resistant mutants is of clinical importance in patients receiving antiviral treatment. The ideal assay is sensitive, specific, accurate, reproducible and easy to perform, attains a high throughput and is able to detect mixed and novel mutations. Advantages and disadvantages of sequencing, line probe assay, DNA chip technology, peptide nucleic acid cramping, fluorescent biprobe hybridization and a new technique based on matrix-assisted laser desorption/ionization time-of-flight mass-spectrometric analysis will be discussed.
A New Prognostic Staging System for Hepatocellular Carcinoma: Value of the Biomarker Combined Japan Integrated Staging Score
Authors: Kitai Satoshi , Kudo Masatoshi , Minami Yasunori , Ueshima Kazuomi , Chung Hobyung , Hagiwara Satoru , Inoue Tatsuo , Ishikawa Emi , Takahashi Shunsuke , Asakuma Yutaka , Haji Seiji , Osaki Yukio , Oka Hiroko , Seki Toshihito , Kasugai Hiroshi , Sasaki Yo , Matsunaga Takashi
Published: June 2008

Objectives: The Japan Integrated Staging (JIS) score has been reported to have good stratification ability in patients with hepatocellular carcinoma (HCC). However, the JIS score could not estimate malignant grade of HCC. The aim of this study was to evaluate the performance of a new staging system: the biomarker combined JIS (bm-JIS) which includes three tumor markers: α-fetoprotein (AFP), Lens culinaris agglutinin-reactive AFP and des-γ-carboxy prothrombin with the conventional JIS score. Methods: A total of 1,924 HCC patients were included in this study. We compared their overall survival, the stratification ability and suitability as a prognostic model according to the bm-JIS score and the conventional JIS score. Results: There were significant differences between the survival curves for all bm-JIS scores. For the conventional JIS scores of 0, 1, 2 and 3, the survival curves differed greatly according to the bm-JIS score (p < 0.0001). The independent homogenizing ability and the stratification value of the JIS score and the bm-JIS score determined by the likelihood ratio test using the Cox proportional hazard regression model showed the bm-JIS score to have a higher value(χ2 = 717.348) than the JIS score (χ2 = 668.91). Conclusions: The bm-JIS score showed superior stratification ability and thus was found to be a better predictor of the prognosis than the conventional JIS score, especially for the patients with good prognosis.
Differential Diagnosis of Hepatic Tumors: Value of Contrast-Enhanced Harmonic Sonography Using the Newly Developed Contrast Agent, Sonazoid
Authors: Hatanaka Kinuyo , Kudo Masatoshi , Minami Yasunori , Ueda Taisuke , Tatsumi Chie , Kitai Satoshi , Takahashi Shunsuke , Inoue Tatsuo , Hagiwara Satoru , Chung Hobyung , Ueshima Kazuomi , Maekawa Kiyoshi
Published: June 2008

Objective: To clarify the value of contrast-enhanced harmonic ultrasonography (US) with Sonazoid, a second-generation US contrast agent, in the differential diagnosis of liver tumors compared to dynamic CT. Methods: A total of 249 hepatic nodules in 214 patients were studied; these included 177 hepatocellular carcinomas (HCCs), 42 liver metastases, 20 liver hemangiomas, 6 dysplastic nodules and 4 focal nodular hyperplasias (FNHs). After the injection of Sonazoid, nodules were scanned using real-time contrast-enhanced harmonic US in the vascular phases, i.e. the early and late vascular phases, and the Kupffer phase. Results: Six enhancement patterns were identified to be significant for the differential diagnosis of hepatic tumors. In HCCs, the presence of intratumoral vessels supplied from the periphery and fast washout (sensitivity, 96.6%; specificity, 94.4%) were the most typical characteristics. In metastases, the presence of rim-like enhancement with peripheral tumor vessels (sensitivity, 88.1%; specificity, 100%) was the typical pattern. In hemangiomas, the presence of intratumoral hypoperfusion images with globular or cotton wool-like pooling, which continue to the late vascular phase (sensitivity, 90.0%; specificity, 99.6%), was typical. In dysplastic nodules, the presence of portal enhancement without arterial supply in the early vascular phase and the presence of intratumoral uptake in the Kupffer phase (sensitivity, 83.3%; specificity, 100%) were the most typical patterns. In FNHs, the presence of a spoke-wheel pattern in the early vascular phase with dense staining in the late vascular phase, and positive uptake within the nodule in the Kupffer phase (sensitivity, 100%; specificity, 100%) were the most typical patterns. Conclusion: Contrast-enhanced harmonic US with Sonazoid allowed intimate vascular and Kupffer imaging and, therefore, is useful for the differential diagnosis of hepatic tumors.
Usefulness of a New Immunoradiometric Assay of HCV Core Antigen to Predict Virological Response during PEG-IFN/RBV Combination Therapy for Chronic Hepatitis with High Viral Load of Serum HCV RNA Genotype 1b
Authors: Sasase Noriko , Kim Soo Ryang , Kim Ke Ih , Taniguchi Miyuki , Imoto Susumu , Mita Keiji , Hotta Hak , Shouji Ikuo , El-Shamy Ahmed , Kawada Norifumi , Kudo Masatoshi , Hayashi Yoshitake
Published: June 2008

We investigated the clinical usefulness of a new immunoradiometric (IRM) assay of hepatitis C virus (HCV) core antigen in predicting virological response during pegylated interferon plus ribavirin (PEG-IFN/RBV) combination therapy for chronic hepatitis with high viral loads of serum HCV RNA genotype 1b. Thirty-nine patients received a regimen of PEG-IFNα-2b (1.5 µg/kg/week s.c.) in combination with RBV (600–1,000 mg/day). Of the 39 patients, 18 (46.2%) achieved sustained virological response (SVR), 11 (28.2%) attained partial response (PR) and 10 (25.6%) showed no response (NR). Four weeks after the start of therapy, 1- and 2-log reductions in the amount of HCV core antigen were observed in 20 (2/10) and 0% (0/10) showing NR, 91 (10/11) and 63.6% (7/11) with PRs, and 88.9 (16/18) and 55.6% (10/18) of patients with SVR, respectively. The 1- and 2-log reductions 4 weeks after the start of therapy were not a definingcondition for PR and SVR. The amount of HCV core antigen was significantly different between SVR and PR patients on days 1 and 7, and between patients with NR and SVR at all points of time. In conclusion, this new IRM assay is useful in predicting virological response during PEG-IFN/RBV therapy.
Elevated Serum ALT Levels during Pegylated Interferon Monotherapy May Be Caused by Hepatic Iron Overload
Authors: Nagashima Miki , Kudo Masatoshi , Chung Hobyung , Ishikawa Emi , Inoue Tatsuo , Nakatani Tatsuya , Dote Kensaku
Published: June 2008

Objective: Persistently elevated serum alanine aminotransferase (ALT) levels have been observed in chronic hepatitis C (CHC) patients during pegylated interferon (PEG-IFN) therapy. We investigated whether elevated serum ALT levels during PEG-IFN therapy are associated with iron overload. Methods: Sixty-three CHC patients treated with PEG-IFNα-2a monotherapy were evaluated. The associations between elevated serum ALT levels (≧70 IU/l) were investigated before and 24 weeks after therapy. We classified patients as follows: patients with no elevated serum ALT levels (group NE: n = 35), patients with elevated serum ALT levels (group E: n = 28), and patients with no elevated serum ALT level and negative HCV RNA (group NE–: n = 24), and patients with elevated serum ALT level and negative HCV RNA (group E–: n = 19). We also compared total iron score (TIS) and fibrosis stage in liver specimens obtained before and during therapy from 3 patients with elevated serum ALT levels. Results: Serum ferritin levels were significantly increased after 24 weeks compared to baseline levels in group E (218 ± 273 vs. 438 ± 308 ng/ml; p < 0.0001) and group E– (146 ± 152 vs. 410 ± 291 ng/ml; p < 0.0001). Serum ALT and ferritin levels were significantly correlated after 24 weeks. The liver specimens revealed that TIS and fibrosis progressed during therapy. Conclusion: Our findings suggest that the elevation in serum ALT levels during therapy is caused by iron overload which may be induced by PEG-IFNα-2a.
Comparative Genomic Hybridisation Arrays: High-Throughput Tools to Determine Targeted Therapy in Breast Cancer
Authors: Tan David S.P. , Reis-Filho Jorge S.
Published: June 2008

Microarray-based comparative genomic hybridisation (aCGH) is contributing to the molecular characterisation of solid malignancies. This technique provides tremendous opportunities for translational research by facilitating detailed analysis of entire cancer genomes in a single experiment with unprecedented resolution. Apart from providing data to help catalogue the molecular genetic profiles of breast cancers and breast cancer cell lines, aCGH has also proven to be a useful technique for the identification of novel therapeutic targets. However, aCGH alone does not provide all lines of evidence required for the identification of ‘amplicon drivers’ and ‘druggable targets’. This can be more effectively achieved by integrating data from aCGH, expression profiling and RNA interference experiments. In this review, we discuss the techniques available for aCGH analysis and possible approaches for using aCGH as a tool for the identification of novel therapeutic targets.
Understanding the Molecular Basis of Histologic Grade
Authors: Ignatiadis M. , Sotiriou C.
Published: June 2008

Histologic grading in breast cancer is based on the evaluation of 3 morphologic features (tubule formation, nuclear pleomorphism and mitotic count), is essentially describing proliferation and differentiation in breast cancer, and is considered an important prognostic factor for this disease. It has been suggested that histologic grade 1 and 3 breast tumors are 2 different diseases that may have distinct molecular origins, pathogenesis and natural history. Different single markers like Ki-67, thymidine labeling index and S phase fraction/flow cytometry have been studied as markers of proliferation, but none of them, with the possible exception of Ki-67, is currently employed routinely in clinical practice. The advent of the powerful microarray technology has enabled scientists to comprehensively study proliferation in breast cancer on a genome-wide scale. A gene expression grade index (GGI) was developed that challenges the existence and clinical relevance of an intermediate grade 2 classification. The GGI could reclassify patients with histologic grade 2 tumors into 2 groups with high versus low risks of recurrence. GGI has also been used to define 2 clinically relevant subgroups in estrogen receptor-positive breast carcinomas. Finally, in the largest meta-analysis of publicly available gene expression and clinical data, 4 stable molecular subgroups of breast cancer have been identified, namely ER–/HER–, HER2+ and ER+/HER2–, which was divided into 2 subgroups (ER+/low proliferation and ER+/high proliferation). In this same meta-analysis, proliferation was shown to be the common driving force responsible for the performance of various breast cancer prognostic signatures.
Is ‘Basal-Like’ Carcinoma of the Breast a Distinct Clinicopathological Entity? A Critical Review with Cautionary Notes
Authors: Moinfar Farid
Published: June 2008

This review deals with studies that have used cDNA microarrays and immunohistochemistry to identify a subtype of breast carcinoma known as basal-like carcinoma. The key breast carcinoma studies are critically discussed to highlight methodological problems in cohort selection, definitions, interpretation of results and statistical analysis. The review concludes that basal-like carcinomas do not reflect a single, biologically uniform group of breast cancers, but show significant variations in their phenotypes, grades, immunoprofiles and clinical behavior, just as a wide range of subtypes and behaviors is observed among epithelial/luminal-derived breast carcinomas. Well-designed studies with comparison of low-grade nonbasal versus low-grade basal and high-grade nonbasal versus high-grade basal carcinomas are necessary before one can be convinced that this subtype represents a distinct clinicopathological entity.
An improved method for generating BAC DNA suitable for FISH
Authors: Roohi J. , Cammer M. , Montagna C. , Hatchwell E.
Published: June 2008

Fluorescence in situ hybridization (FISH) is commonly used to identify chromosomal aberrations such as translocations, deletions, duplications, gene fusions, and aneuploidies. It relies on the hybridization of fluorescently labeled DNA probes onto denatured metaphase chromosomes or interphase nuclei. These probes are often generated from DNA sequences cloned within bacterial artificial chromosomes (BACs). Growing these BACs in adequate amounts for FISH can be demanding. We describe FISH performed with bacteriophage Phi29 DNA polymerase amplified BAC DNA. Generating this material required significantly smaller cultures and less time than standard methods. The FISH results obtained were comparable with those obtained from standard BAC DNA. We believe this method of BAC DNA generation is useful for the entire FISH community as it improves considerably on prior methods.
Microarray mRNA expression analysis of Fanconi anemia fibroblasts
Authors: Galetzka D. , Weis E. , Rittner G. , Schindler D. , Haaf T.
Published: June 2008

Fanconi anemia (FA) cells are generally hypersensitive to DNA cross-linking agents, implying that mutations in the different FANC genes cause a similar DNA repair defect(s). By using a customized cDNA microarray chip for DNA repair- and cell cycle-associated genes, we identified three genes, cathepsin B (CTSB), glutaredoxin (GLRX), and polo-like kinase 2 (PLK2), that were misregulated in untreated primary fibroblasts from three unrelated FA-D2 patients, compared to six controls. Quantitative real-time RT PCR was used to validate these results and to study possible molecular links between FA-D2 and other FA subtypes. GLRX was misregulated to opposite directions in a variety of different FA subtypes. Increased CTSB and decreased PLK2 expression was found in all or almost all of the analyzed complementation groups and, therefore, may be related to the defective FA pathway. Transcriptional upregulation of the CTSB proteinase appears to be a secondary phenomenon due to proliferation differences between FA and normal fibroblast cultures. In contrast, PLK2 is known to play a pivotal role in processes that are linked to FA defects and may contribute in multiple ways to the FA phenotype: PLK2 is a target gene for TP53, is likely to function as a tumor suppressor gene in hematologic neoplasia, and Plk2–/– mice are small because of defective embryonal development.
Characterization of a familial small supernumerary marker chromosome in a patient with adult-onset tongue cancer
Authors: Bakshi S.R. , Dave B.J. , Sanger W. , Brahmbhatt M.M. , Trivedi P.J. , Kakadia P.M. , Patel S.J.
Published: June 2008

Cytogenetic analysis in peripheral blood lymphocytes of a 50-year-old female with tongue cancer showed the presence of one to three copies of a small supernumerary marker chromosome (sSMC) in a mosaic state. Family studies also revealed the marker in mosaic form in four (age <29 years) of eleven clinically normal individuals studied from her family of 16 individuals spanning three generations. Due to the extremely small size of the marker chromosome, identification by classical cytogenetics was not informative. Multicolor FISH followed by whole chromosome painting identified the marker as a derivative of chromosome 21. This is the first report of sSMC21 in an adult-onset tongue cancer patient and some of her family members with no clinical symptoms.
Cytogenetic studies and karyotype nomenclature of three wild canid species: maned wolf (Chrysocyon brachyurus), bat-eared fox (Otocyon megalotis) and fennec fox (Fennecus zerda)
Authors: Pieńkowska-Schelling A. , Schelling C. , Zawada M. , Yang F. , Bugno M. , Ferguson-Smith M.
Published: June 2008

We have analysed the chromosomes of three wild and endangered canid species: the maned wolf (Chrysocyon brachyurus), the bat-eared fox (Otocyon megalotis) and the fennec fox (Fennecuszerda) using classical and molecular cytogenetic methods. For the first time detailed and encompassing descriptions of the chromosomes are presented including the chromosomal assignment of nucleolar organizer regions and the 5S rRNA gene cluster. We propose a karyotype nomenclature with ideograms including more than 300 bands per haploid set for each of these three species which will form the basis for further research. In addition, we propose four basic different patterns of karyotype organization in the family Canidae. A comparison of these patterns with the most recent molecular phylogeny of Canidae revealed that the karyotype evolution of a species is not always strongly connected with its phylogenetic position. Our findings underline the need and justification for basic cytogenetic work in rare and exotic species.
Non-homologous sex chromosomes in two species of the genus Eigenmannia (Teleostei: Gymnotiformes)
Authors: Henning F. , Trifonov V. , Ferguson-Smith M.A. , de Almeida-Toledo L.F.
Published: June 2008

The Neotropical genus Eigenmannia is a fish group with unknown species diversity where representatives possess a broad range of chromosomal sex determining systems namely XY/XX, X1X2Y/X1X1X2X2, ZZ/ZW as well as homomorphic sex chromosomes. To test the homology of two heteromorphic XY sex chromosome systems present in two sympatric populations, reciprocal cross-species FISH experiments were performed using probes derived by microdissection of X and Y chromosomes present in analyzed specimens of Eigenmannia virescens and Eigenmannia sp.2, respectively. While X and Y paint probes hybridized to species-specific sex chromosomes, in reciprocal cross-FISH both probes hybridized exclusively to autosomes. The result suggests multiple independent origins of the XY systems in the analyzed populations.
Genomes, diversity and resistance gene analogues in Musa species
Authors: Azhar M. , Heslop-Harrison J.S.
Published: June 2008

Resistance genes (R genes) in plants are abundant and may represent more than 1% of all the genes. Their diversity is critical to the recognition and response to attack from diverse pathogens. Like many other crops, banana and plantain face attacks from potentially devastating fungal and bacterial diseases, increased by a combination of worldwide spread of pathogens, exploitation of a small number of varieties, new pathogen mutations, and the lack of effective, benign and cheap chemical control. The challenge for plant breeders is to identify and exploit genetic resistances to diseases, which is particularly difficult in banana and plantain where the valuable cultivars are sterile, parthenocarpic and mostly triploid so conventional genetic analysis and breeding is impossible. In this paper, we review the nature of R genes and the key motifs, particularly in the Nucleotide Binding Sites (NBS), Leucine Rich Repeat (LRR) gene class. We present data about identity, nature and evolutionary diversity of the NBS domains of Musa R genes in diploid wild species with the Musa acuminata (A), M. balbisiana (B), M. schizocarpa (S), M. textilis (T), M. velutina and M. ornata genomes, and from various cultivated hybrid and triploid accessions, using PCR primers to isolate the domains from genomic DNA. Of 135 new sequences, 75% of the sequenced clones had uninterrupted open reading frames (ORFs), and phylogenetic UPGMA tree construction showed four clusters, one from Musa ornata, one largely from the B and T genomes, one from A and M. velutina, and the largest with A, B, T and S genomes. Only genes of the coiled-coil (non-TIR) class were found, typical of the grasses and presumably monocotyledons. The analysis of R genes in cultivated banana and plantain, and their wild relatives, has implications for identification and selection of resistance genes within the genus which may be useful for plant selection and breeding and also for defining relationships and genome evolution patterns within the genus using the multi-copy and variable resistance genes.
Comparative Efficacy of Two Microdoses of a Potentized Homeopathic Drug, Arsenicum Album, to Ameliorate Toxicity Induced by Repeated Sublethal Injections of Arsenic Trioxide in Mice
Authors: Banerjee Pathikrit , Bhattacharyya Soumya Sundar , Pathak Surajit , Naoual Boujedaini , Belon Philippe , Khuda-Bukhsh Anisur Rahman
Published: June 2008

Objectives: To evaluate the efficacy of 2 potentized homeopathic remedies of Arsenicum Album (Ars Alb) – 6C and 30C – in combating chronic arsenic toxicity induced by repeated sublethal injections in mice (Mus musculus). Methods: Mice were randomized and divided into sets: (1) normal (control 1); (2) normal + succussed alcohol (control 2); (3) As2O3 (0.016%) injected at 1 ml/100 g body weight every 7 days (treated); (4) As2O3 injected + succussed alcohol (positive control); (5) As2O3 injected + Ars Alb 6C (drug-fed); (6) As2O3 injected + Ars Alb 30C (drug-fed). Cytogenetical endpoints like chromosome aberrations, micronuclei, mitotic index, sperm head abnormality and biochemical protocols like acid and alkaline phosphatases, aspartate and alanine aminotransferases, reduced glutathione, lipid peroxidation, catalase and succinate dehydrogenase were studied at 30, 60, 90 and 120 days. Results: Compared to controls, chromosome aberrations, micronuclei, sperm head abnormality frequencies and activities of acid and alkaline phosphatases, aspartate and alanine aminotransferases and lipid peroxidation were reduced in both drug-fed series, while mitotic index and activities of glutathione, catalase and succinate dehydrogenase were increased. Ars Alb 30C showed marginally better efficacy than Ars Alb 6C. Conclusion: Both remedies indicated potentials of use against arsenic intoxication.
Neural Stem Cells Improve Learning and Memory in Rats with Alzheimer’s Disease
Authors: Wu Shuliang , Sasaki Akira , Yoshimoto Reiko , Kawahara Yumi , Manabe Tomotaka , Kataoka Katsuko , Asashima Makoto , Yuge Louis
Published: June 2008

Objective: We investigated whether neural stem cells (NSC) with transgenic expression of human nerve growth factor (hNGF) transplanted into the brain could offer a therapeutic option for the treatment of Alzheimer’s disease (AD). Methods: We infused okadaic acid into rat lateral ventricles to establish a chronic AD animal model. In addition, NSC were stably transduced with hNGF and enhanced green fluorescent protein (eGFP) genes (NSC-hNGF-eGFP) by using a recombination adeno-associated virus serotype 2 (rAAV2) vector. These genetically modified stem cells were grafted into the cerebral cortex of AD rats. Results: AD model rats showed significant damage in learning and memory function, with the formation of senile plaques and neurofibrillary tangles in the cerebral cortex. The transferred hNGF gene conferred stable and high levels of protein expression in NSC in vitro. Moreover, the NSC-hNGF-eGFP, but not the NSC, survived, integrating into the host brain and enhancing cognitive performance after transplantation. Conclusion: The injection of okadaic acid into rat lateral ventricles constitutes a promising animal model for investigating selective aspects of AD. rAAV2-mediated hNGF delivery can render long-term and stable transduction of hNGF in NSC. NSC-hNGF-eGFP transplantation may offer a viable therapeutic approach for treatment of AD.
SOX Gene Expression in Human Osteoarthritic Cartilage
Authors: Haag Jochen , Gebhard Pia M. , Aigner Thomas
Published: June 2008

Objective: While the developmental role of the SOX transcription factors in fetal chondrocyte differentiation is well documented, much less is known about the expression of SOX family members in normal and osteoarthritic adult cartilage. Therefore, the aim of the present study was to present a thorough analysis of SOX gene expression in normal and osteoarthritic human adult cartilage. Methods: RNA from normal and osteoarthritic knee cartilage from human adults was analyzed by gene expression profiling using GeneChip technology (Affymetrix) and quantitative real time PCR. Results: Most members of the SOX transcription factor family showed no or very low expression levels in normal and osteoarthritic cartilage from adults. In contrast, SOX9 expression was fairly high in normal cartilage, amounting to approximately 20% of GAPDH levels. SOX9 transcript levels were substantially reduced in osteoarthritis. SOX6 levels were reduced, albeit starting from a low basis expression in normal tissue. Conclusion: The presented data indicate that the role of the SOX transcription factor family in adult human cartilage is most probably restricted to a few members, with SOX9 being the most prominent. Furthermore, the reduction of SOX9 and SOX6 transcript levels in osteoarthritic chondrocytes might be responsible for the loss of phenotypic stability of osteoarthritic chondrocytes.
Presence of Low Dose of Fludarabine in Cultures Blocks Regulatory T Cell Expansion and Maintains Tumor-Specific Cytotoxic T Lymphocyte Activity Generated with Peripheral Blood Lymphocytes
Authors: Hegde Upendra , Chhabra Arvind , Chattopadhyay Subhasis , Das Raja , Ray Swagatam , Chakraborty Nitya G.
Published: June 2008

Background: For tumor vaccine-based immunotherapy of cancer, the expansion of tumor antigen-specific cytotoxic T lymphocytes (CTL) in the patients by blocking induced regulatory T (Treg) cells is the most important objective now. Fludarabine (FLU), a known anticancer drug, has been shown to downregulate Treg cells in vivo in chronic leukemia patients. Melanoma tumor antigen Mart-127–35-specific CD8+ CTLs generated in vitrowith total peripheral blood lymphocytes (PBL) lose their activity within 14–21 days with concomitant expansion of Treg cells. When CD4+ cells are removed from PBL and CTL are generated with purified CD8+ cells, the CTL survive and maintain their activity for a significantly longer period. Methods: We used a low dose of FLU in the cultures in Mart-1-specific CTL generation assays with total PBL. Blood samples were taken from HLA-A2-positive melanoma patients and normal donors. Autologous matured dendritic cells pulsed with Mart-127–35 peptide were used to generate CTL responses using purified CD8+ cells or total PBL. Results: The presence of FLU in the cultures with PBL helped to generate a significantly higher number of antigen-specific CTLs as detected by Mart-1 HLA-A2 tetramer staining. Specificity of such CTLs was determined by IFN-γ secretion or by cytotoxicity against the target cells bearing the specific antigen. The presence of FLU stopped the expansion of IL-10-producing CD4+ Treg cells in the cultures with PBL. Analyses of expanded CD4+ cells isolated from PBL in vitro cocultures with FLU showed a Th1 type of function. Those cells secreted higher amounts of IFN-γ and very low levels of IL-10, or no IL-10 at all, upon restimulation. Conclusion: The observations of the study are as important for adaptive immunotherapy of cancer as they are for vaccine-based approaches.
Elevated chromosome translocation frequencies in New Zealand nuclear test veterans
Authors: Wahab M.A. , Nickless E.M. , Najar-M’Kacher R. , Parmentier C. , Podd J.V. , Rowland R.E.
Published: June 2008

In 1957/58 the British Government conducted a series of nuclear tests in the mid-Pacific codenamed Operation Grapple, which involved several naval vessels from Britain and New Zealand. Two New Zealand frigates with 551 personnel onboard were stationed at various distances between 20 and 150 nautical miles from ground zero. In the present study we applied the cytomolecular technique mFISH (multicolour fluorescent in situ hybridisation) to investigate a potential link between chromosome abnormalities and possible past radiation exposure in New Zealand nuclear test veterans who participated in Operation Grapple. Compared to age matched controls, the veterans showed significantly higher (P < 0.0001) frequencies of chromosomal abnormalities (275 translocations and 12 dicentrics in 9,360 cells vs. 96 translocations and 1 dicentric in 9,548 cells in the controls), in addition to a significant excess of CCRs (complex chromosomal rearrangements) in the veterans. A Kolmogorov-Smirnoff test showed that the distributions of translocations for the two groups were significantly different.
Impairment of gastric acid secretion and increase of embryonic lethality in Foxq1-deficient mice
Authors: Goering W. , Adham I.M. , Pasche B. , Männer J. , Ochs M. , Engel W. , Zoll B.
Published: June 2008

The mouse Foxq1 gene, also known as Hfh1, encodes a winged helix/forkhead transcription factor. In adult mice, Foxq1 is highly expressed in kidney and stomach. Here, we report that Foxq1 is expressed during prenatal and postnatal stomach development and the transcripts are restricted to acid secreting parietal cells. Mice homozygous for a deletion of the Foxq1 locus on a 129/Sv × C57BL/6J hybrid genetic background display variable phenotypes consistent with requirement of the gene during embryogenesis. Approximately 50% of Foxq1–/– embryos die in utero. Surviving homozygous mutants are normal and fertile, and have a silky shiny coat. Although the parietal cell development is not affected in the absence of Foxq1, there is a lack of gastric acid secretion in response to various secretagogue stimuli. Ultrastructural analysis suggests that the gastric acid secretion defect in Foxq1-deficient mice might be due to impairment in the fusion of cytoplasmic tubulovesicles to the apical membrane of secretory canaliculi.
X chromosome inactivation in nuclear transfer ES cells
Authors: Shibata S. , Wakayama T. , Yokota T.
Published: June 2008

Nuclear transfer ES (ntES) cells are established from cloned blastocysts generated by somatic cell nuclear transfer and are expected to be an important resource for regenerative medicine. However, cloned mammals, generated by similar methods, show various abnormalities, which suggest disordered gene regulation. Random X chromosome inactivation (XCI) has been observed to take place in cloned female mouse embryos, but XCI does not necessarily occur according to Xce strength, a genetic element that determines the likelihood of each X chromosome to be inactivated. This observation suggests incomplete reprogramming of epigenetic marks related to XCI. Here, we investigated XCI in ntES cell lines, which were established using differentiated embryoid bodies that originated from a female mouse ES cell line. We examined Xist RNA localization, histone modifications in the Xist locus, and XCI choice. We did not find substantial differences between the ntES lines and their parental ES line. This suggests that the Xist locus and the epigenetic marks involved in XCI are reprogrammed by nuclear transfer and subsequent ntES cell establishment. In contrast to skewed XCI in cloned mice, our observations indicate that normal XCI choice takes place in ntES cells, which supports the goal of safe therapeutic cloning for clinical use.
The horse pseudoautosomal region (PAR): characterization and comparison with the human, chimp and mouse PARs
Authors: Raudsepp T , Chowdhary B.P.
Published: June 2008

The pseudoautosomal region (PAR) is a genomic segment on mammalian sex chromosomes where sequence homology mimics that seen between autosomal homologues. The region is essential for pairing and proper segregation of sex chromosomes during male meiosis. As yet, only human/chimp and mouse PARs have been characterized. The two groups of species differ dramatically in gene content and size of the PAR and therefore do not provide clues about the likely evolution and constitution of PAR among mammals. Here we characterize the equine PAR by i) isolating and arranging 71 BACs containing 129 markers (110 STS and 19 genes) into two contigs spanning the region, ii) precisely localizing the pseudoautosomal boundary (PAB), and iii) describing part of the contiguous X- and Y-specific regions. We also report the discovery of an approximately 200 kb region in the middle of the PAR that is present in the male-specific region of the Y (MSY) as well. Such duplication is a novel observation in mammals. Further, comparison of the equine PAR with the human counterpart shows that despite containing orthologs from an additional 1 Mb region beyond the human PAR1, the equine PAR is around 0.9 Mb smaller than the size of the human PAR. We theorize that the PAR varies in size and gene content across evolutionarily closely as well as distantly related mammals. Although striking differences like those observed between human and mouse may be rare, variations similar to those seen between horse and human may be prevalent among mammals.