bluuebunny/crossref_metadata_2025 huggingface dataset:
Bisphosphonate-related osteonecrosis of the jaw is associated with polymorphisms of the cytochrome P450 CYP2C8 in multiple myeloma: a genome-wide single nucleotide polymorphism analysis
Authors: Sarasquete Maria E. , García-Sanz Ramon , Marín Luis , Alcoceba Miguel , Chillón Maria C. , Balanzategui Ana , Santamaria Carlos , Rosiñol Laura , de la Rubia Javier , Hernandez Miguel T. , Garcia-Navarro Inmaculada , Lahuerta Juan J. , González Marcos , San Miguel Jesus F.
Published: July 2008

We have explored the potential role of genetics in the development of osteonecrosis of the jaw (ONJ) in multiple myeloma (MM) patients under bisphosphonate therapy. A genome-wide association study was performed using 500 568 single nucleotide polymorphisms (SNPs) in 2 series of homogeneously treated MM patients, one with ONJ (22 MM cases) and another without ONJ (65 matched MM controls). Four SNPs (rs1934951, rs1934980, rs1341162, and rs17110453) mapped within the cytochrome P450-2C gene (CYP2C8) showed a different distribution between cases and controls with statistically significant differences (P = 1.07 × 10−6, P = 4.231 × 10−6, P = 6.22 × 10−6, and P = 2.15 × 10−6, respectively). SNP rs1934951 was significantly associated with a higher risk of ONJ development even after Bonferroni correction (P corrected value = .02). Genotyping results displayed an overrepresentation of the T allele in cases compared with controls (48% vs 12%). Thus, individuals homozygous for the T allele had an increased likelihood of developing ONJ (odds ratio 12.75, 95% confidence interval 3.7-43.5).
spib is required for primitive myeloid development in Xenopus
Authors: Costa Ricardo M. B. , Soto Ximena , Chen Yaoyao , Zorn Aaron M. , Amaya Enrique
Published: July 2008

Vertebrate blood formation occurs in 2 spatially and temporally distinct waves, so-called primitive and definitive hematopoiesis. Although definitive hematopoiesis has been extensively studied, the development of primitive myeloid blood has received far less attention. In Xenopus, primitive myeloid cells originate in the anterior ventral blood islands, the equivalent of the mammalian yolk sac, and migrate out to colonize the embryo. Using fluorescence time-lapse video microscopy, we recorded the migratory behavior of primitive myeloid cells from their birth. We show that these cells are the first blood cells to differentiate in the embryo and that they are efficiently recruited to embryonic wounds, well before the establishment of a functional vasculature. Furthermore, we isolated spib, an ETS transcription factor, specifically expressed in primitive myeloid precursors. Using spib antisense morpholino knockdown experiments, we show that spib is required for myeloid specification, and, in its absence, primitive myeloid cells retain hemangioblast-like characteristics and fail to migrate. Thus, we conclude that spib sits at the top of the known genetic hierarchy that leads to the specification of primitive myeloid cells in amphibians.
High accuracy mass spectrometry analysis as a tool to verify and improve gene annotation using Mycobacterium tuberculosis as an example
Authors: de Souza Gustavo A , Målen Hiwa , Søfteland Tina , Sælensminde Gisle , Prasad Swati , Jonassen Inge , Wiker Harald G
Published: July 2008

Background

While the genomic annotations of diverse lineages of the Mycobacterium tuberculosis complex are available, divergences between gene prediction methods are still a challenge for unbiased protein dataset generation. M. tuberculosis gene annotation is an example, where the most used datasets from two independent institutions (Sanger Institute and Institute of Genomic Research-TIGR) differ up to 12% in the number of annotated open reading frames, and 46% of the genes contained in both annotations have different start codons. Such differences emphasize the importance of the identification of the sequence of protein products to validate each gene annotation including its sequence coding area.

Results

With this objective, we submitted a culture filtrate sample from M. tuberculosis to a high-accuracy LTQ-Orbitrap mass spectrometer analysis and applied refined N-terminal prediction to perform comparison of two gene annotations. From a total of 449 proteins identified from the MS data, we validated 35 tryptic peptides that were specific to one of the two datasets, representing 24 different proteins. From those, 5 proteins were only annotated in the Sanger database. In the remaining proteins, the observed differences were due to differences in annotation of transcriptional start sites.

Conclusion

Our results indicate that, even in a less complex sample likely to represent only 10% of the bacterial proteome, we were still able to detect major differences between different gene annotation approaches. This gives hope that high-throughput proteomics techniques can be used to improve and validate gene annotations, and in particular for verification of high-throughput, automatic gene annotations.
TDAG51 is an ERK signaling target that opposes ERK-mediated HME16C mammary epithelial cell transformation
Authors: Oberst Michael D , Beberman Stacey J , Zhao Liu , Yin Juan Juan , Ward Yvona , Kelly Kathleen
Published: July 2008

Introduction

Signaling downstream of Ras is mediated by three major pathways, Raf/ERK, phosphatidylinositol 3 kinase (PI3K), and Ral guanine nucleotide exchange factor (RalGEF). Ras signal transduction pathways play an important role in breast cancer progression, as evidenced by the frequent over-expression of the Ras-activating epidermal growth factor receptors EGFR and ErbB2. Here we investigated which signal transduction pathways downstream of Ras contribute to EGFR-dependent transformation of telomerase-immortalized mammary epithelial cells HME16C. Furthermore, we examined whether a highly transcriptionally regulated ERK pathway target, PHLDA1 (TDAG51), suggested to be a tumor suppressor in breast cancer and melanoma, might modulate the transformation process.

Methods

Cellular transformation of human mammary epithelial cells by downstream Ras signal transduction pathways was examined using anchorage-independent growth assays in the presence and absence of EGFR inhibition. TDAG51 protein expression was down-regulated by interfering small hairpin RNA (shRNA), and the effects on cell proliferation and death were examined in Ras pathway-transformed breast epithelial cells.

Results

Activation of both the ERK and PI3K signaling pathways was sufficient to induce cellular transformation, which was accompanied by up-regulation of EGFR ligands, suggesting autocrine EGFR stimulation during the transformation process. Only activation of the ERK pathway was sufficient to transform cells in the presence of EGFR inhibition and was sufficient for tumorigenesis in xenografts. Up-regulation of the PHLDA1 gene product, TDAG51, was found to correlate with persistent ERK activation and anchorage-independent growth in the absence or presence of EGFR inhibition. Knockdown of this putative breast cancer tumor-suppressor gene resulted in increased ERK pathway activation and enhanced matrix-detached cellular proliferation of Ras/Raf transformed cells.

Conclusion

Our results suggest that multiple Ras signal transduction pathways contribute to mammary epithelial cell transformation, but that the ERK signaling pathway may be a crucial component downstream of EGFR activation during tumorigenesis. Furthermore, persistent activation of ERK signaling up-regulates TDAG51. This event serves as a negative regulator of both Erk activation as well as matrix-detached cellular proliferation and suggests that TDAG51 opposes ERK-mediated transformation in breast epithelial cells.
Relationships between climate and year-to-year variability in meningitis outbreaks: A case study in Burkina Faso and Niger
Authors: Yaka Pascal , Sultan Benjamin , Broutin Hélène , Janicot Serge , Philippon Solenne , Fourquet Nicole
Published: July 2008

Background

Every year, West Africa is afflicted with Meningococcal Meningitis (MCM) disease outbreaks. Although the seasonal and spatial patterns of disease cases have been shown to be linked to climate, the mechanisms responsible for these patterns are still not well identified.

Results

A statistical analysis of annual incidence of MCM and climatic variables has been performed to highlight the relationships between climate and MCM for two highly afflicted countries: Niger and Burkina Faso. We found that disease resurgence in Niger and in Burkina Faso is likely to be partly controlled by the winter climate through enhanced Harmattan winds. Statistical models based only on climate indexes work well in Niger showing that 25% of the disease variance from year-to-year in this country can be explained by the winter climate but fail to represent accurately the disease dynamics in Burkina Faso.

Conclusion

This study is an exploratory attempt to predict meningitis incidence by using only climate information. Although it points out significant statistical results it also stresses the difficulty of relating climate to interannual variability in meningitis outbreaks.
Efficacy of antidepressants in juvenile depression: meta-analysis
Authors: Tsapakis Evangelia M. , Soldani Federico , Tondo Leonardo , Baldessarini Ross J.
Published: July 2008

Background

The safety of antidepressants in children and adolescents is being questioned and the efficacy of these drugs in juvenile depression remains uncertain

Aims

To assess antidepressant efficacy in juvenile depression

Method

Systematic review and meta-analysis of randomised controlled trials (RCTs) comparing responses to antidepressants, overall and by type, v. placebo in young people with depression

Results

Thirty drug-placebo contrasts in RCTs lasting 8 weeks (median) involved 3069 participants (512 person-years) of average age 13.5 years. Meta-analysis yielded a modest pooled drug/placebo response rate ratio (RR=1.22, 95% CI 1.15–1.31), with little separation between antidepressant types. Findings were similar for response rate differences and corresponding number needed to treat (NNT): overall NNT=9; tricyclic antidepressants NNT=14 > serotonin reuptake inhibitors NNT=9 > other antidepressants NNT=8. Numbers needed to treat decreased with increasing age: children (NNT=21) > mixed ages (NNT=10) > adolescents (NNT=8)

Conclusions

Antidepressants of all types showed limited efficacy in juvenile depression, but fluoxetine might be more effective, especially in adolescents. Studies in children and in severely depressed, hospitalised or suicidal juvenile patients are needed, and effective, safe and readily accessible treatments for juvenile depression are urgently required
Assessing competence in cognitive-behavioural therapy
Authors: Keen Andrew J. A. , Freeston Mark H.
Published: July 2008

Background

Postgraduate courses on cognitive-behavioural therapy (CBT) assess various competencies using essays, case studies and audiotapes or videotapes of clinical work

Aims

To evaluate how reliably a well-established postgraduate course assesses CBT competencies

Method

Data were collected on two cohorts of trainees (n=52). Two examiners marked trainees on: (a) two videotapes of clinical practice; (b) two case studies; and (c) three essays

Results

Essay examinations were more reliable than case studies, which in turn were more reliable than videotaped assessments. The reliability of the latter two assessments was considerably lower than that commonly expected of high-stakes examinations. To assess reliably standard CBT competencies, postgraduate courses would need to examine about 5 essays, 12 case studies and 19 videotapes

Conclusions

Reliable assessment of standard competencies is complex and resource intensive. There would need to be a marked increase in the number of samples of clinical work assessed to be able to make reliable judgements about proficiency
Principal components analysis of a large cohort with Tourette syndrome
Authors: Robertson Mary M. , Althoff Robert R. , Hafez Adam , Pauls David L.
Published: July 2008

Background

Tourette syndrome is a heterogeneous familial disorder for which the genetic mechanisms are unknown. A better characterisation of the phenotype may help identify susceptibility genes

Aims

To extend previous factor-analytic studies of the syndrome

Method

Symptom data from 410 people with Tourette syndrome were included in agglomerative hierarchical cluster and principal components analyses

Results

Five factors were observed, characterised by: (1) socially inappropriate behaviours and other complex vocal tics; (2) complex motor tics; (3) simple tics; (4) compulsive behaviours; and (5) touching self. Individuals with co-occurring attention-deficit hyperactivity disorder had significantly higher factor scores on Factors 1 and 3, whereas individuals with co-occurring obsessive-compulsive disorder and behaviours had significantly higher factor scores for Factors 1–4

Conclusions

These findings add to the growing body of evidence that Tourette syndrome is not a unitary condition and can be disaggregated into more homogeneous symptom components
Brain dopamine response in human opioid addiction
Authors: Daglish Mark R.C. , Williams Tim M. , Wilson Sue J. , Taylor Lindsay G. , Eap Chin B. , Augsburger Marc , Giroud Christian , Brooks David J. , Myles Judy S. , Grasby Paul , Lingford-Hughes Anne R. , Nutt David J.
Published: July 2008

Background

Drugs of dependence cause dopamine release in the rat striatum. Human neuroimaging studies have shown an increase in dopamine in the equivalent region in response to stimulants and other drugs

Aims

We tested whether opioids provoke dopamine release and its relationship to the subjective experience

Method

In two combined studies 14 heroin addicts on methadone maintenance treatment underwent two positron emission tomography brain scans of the dopamine system using [11C]-raclopride following an injection of placebo and either 50 mg intravenous diamorphine or 10 mg subcutaneous hydromorphone in a double-blind, random order design

Results

Both opioids produced marked subjective and physiological effects, but no measurable change in [11C]-raclopride binding

Conclusions

The absence of a dopamine response to opioid agonists contrasts with that found with stimulant drugs and suggests dopamine may not play the same role in addiction to opioids. This questions the role of dopamine in the subjective experience of heroin in opioid addicts
Comparison of antipsychotic medication effects on reducing violence in people with schizophrenia
Authors: Swanson Jeffrey W. , Swartz Marvin S. , Van Dorn Richard A. , Volavka Jan , Monahan John , Stroup T. Scott , McEvoy Joseph P. , Wagner H. Ryan , Elbogen Eric B. , Lieberman Jeffrey A.
Published: July 2008

Background

Violence is an uncommon but significant problem associated with schizophrenia

Aims

To compare antipsychotic medications in reducing violence among patients with schizophrenia over 6 months, identify prospective predictors of violence and examine the impact of medication adherence on reduced violence

Method

Participants (n=1445) were randomly assigned to double-blinded treatment with one of five antipsychotic medications. Analyses are presented for the intention-to-treat sample and for patients completing 6 months on assigned medication

Results

Violence declined from 16% to 9% in the retained sample and from 19% to 14% in the intention-to-treat sample. No difference by medication group was found, except that perphenazine showed greater violence reduction than quetiapine in the retained sample. Medication adherence reduced violence, but not in patients with a history of childhood antisocial conduct. Prospective predictors of violence included childhood conduct problems, substance use, victimisation, economic deprivation and living situation. Negative psychotic symptoms predicted lower violence

Conclusions

Newer antipsychotics did not reduce violence more than perphenazine. Effective antipsychotics are needed, but may not reduce violence unrelated to acute psychopathology
Cognitive-behavioural therapyv.structured care for medically unexplained symptoms: randomised controlled trial
Authors: Sumathipala A. , Siribaddana S. , Abeysingha M. R. N. , De Silva P. , Dewey M. , Prince M. , Mann A. H.
Published: July 2008

Background

A pilot trial in Sri Lanka among patients with medically unexplained symptoms revealed that cognitive-behavioural therapy (CBT) administered by a psychiatrist was efficacious

Aims

To evaluate CBT provided by primary care physicians in a comparison with structured care

Method

A randomised control trial (n=75 in each arm) offered six 30 min sessions of structured care or therapy. The outcomes of the two interventions were compared at 3 months, 6 months, 9 months and 12 months

Results

In each arm, 64 patients (85%) completed the three mandatory sessions. No difference was observed between groups in mean scores on the General Health Questionnaire or the Bradford Somatic Inventory, or in number of complaints or patient-initiated consultations at 3 months. For both groups, all outcome measures improved at 3 months, and remained constant in the follow-up assessments

Conclusions

Cognitive–behavioural therapy given by primary care physicians after a short course of training is no more efficacious than structured care. Natural remission is an unlikely explanation for improvements in people with chronic medically unexplained symptoms, but lack of a ‘treatment as usual’ arm limits further conclusions. Further research on enhanced structured care, medical assessment and structured care incorporating simple elements of CBT principles is worthy of consideration
Structured risk assessment and violence in acute psychiatric wards: randomised controlled trial
Authors: Abderhalden Christoph , Needham Ian , Dassen Theo , Halfens Ruud , Haug Hans-Joachim , Fischer Joachim E.
Published: July 2008

Background

There is a lack of research on the possible contribution of a structured risk assessment to the reduction of aggression in psychiatric in-patient care

Aims

To assess whether such risk assessments decrease the incidence of violence and coercion

Method

A cluster randomised controlled trial was conducted with 14 acute psychiatric admission wards as the units of randomisation, including a preference arm. The intervention comprised a standardised risk assessment following admission with mandatory evaluation of prevention in high-risk patients

Results

Incidence rates decreased substantially in the intervention wards, whereas little change occurred in the control wards. The adjusted risk ratios suggest a 41% reduction in severe aggressive incidents and a 27% decline in the use of coercive measures. The severity of aggressive incidents did not decrease

Conclusions

Structured risk assessment during the first days of treatment may contribute to reduced violence and coercion in acute psychiatric wards
Flow Cytometric FRET Analysis of erbB Receptor Interaction on a Cell‐by‐Cell Basis
Authors: Diermeier‐Daucher Simone , Hasmann Max , Brockhoff Gero
Published: July 2008

Lateral interaction of c‐erbB family receptors resulting in dimer formation is the key event initiating signal transduction. Consequently cross‐activation and intracellular signaling is triggered with immediate impact on cell proliferation, migration, cell survival, and differentiation. In order to elucidate the connection of signal input (receptor activation) and signal output (altered cellular behavior) we dynamically assessed cell proliferation of BT474 and SK‐BR‐3 breast cancer cell lines. We quantitated c‐erbB2 receptor homodimerization upon treatment with the therapeutic monoclonal anti‐c‐erbB2 antibodies trastuzumab (Herceptin®) and pertuzumab by flow cytometric FRET (FCET) measurements on a cell‐by‐cell basis and calculated the extent of antibody‐induced cell cycle exit. The results confirm that trastuzumab does not decrease c‐erbB2 homodimers despite its strong potency to drive c‐erbB2‐overexpressing cells into quiescence. Pertuzumab, however, is able to prevent c‐erbB2 homodimerization and thereby enhance the antiproliferative effect of trastuzumab when administered in combination.
Multifunctionalized Biocompatible Microspheres for Sensing
Authors: Sánchez‐Martín Rosario M. , Alexander Lois , Bradley Mark
Published: July 2008

We present our achievements in the synthesis and application of multifunctionalized, cross‐linked, polystyrene microspheres, which remarkably and quite generally are taken up by all cell types studied to date. Importantly, the nature of these synthetic beads allows multistep solid‐phase chemistry and the ability to bind essentially any molecule/sensor/nucleic acid to them. These microspheres have a number of advantages over other cellular delivery approaches. First, a diverse range of compounds can be attached to the microspheres, and we have demonstrated that these materials are effectively delivered into cells; second, the cellular cargo can be modulated through modification of bead loading; third, they are large enough to be visualized using standard microscopy techniques; and fourth, their cargos are not diluted within the cell. Populations of cells containing beads can be readily sorted from other cells for subsequent analysis with very high, but controllable, uptake rates, which can be modulated through modulation of the bead size and incubation time. Recent work has focused on the development of these microspheres as sensors for intracellular calcium and pH.
Time‐resolved Microspectrofluorometry and Fluorescence Imaging Techniques: Study of Porphyrin‐mediated Cellular Uptake of Oligonucleotides
Authors: Praus Petr , Kočišová Eva , Mojzeš Peter , Štěpánek Josef , Seksek Olivier , Sureau Franck , Turpin Pierre‐Yves
Published: July 2008

Time‐resolved confocal microspectrofluorometry and fluorescence microscopy imaging were applied to monitor the cellular uptake of fluorescent‐labeled oligonucleotides (ONs) delivered by a porphyrin molecule. The fate of porphyrin–ON complexes inside living cells has also been monitored. Due to intrinsic fluorescence of the porphyrin and sensitivity of its characteristics to microenvironment, multicomponent analysis of time‐resolved fluorescence provides unique information about stability of the porphyrin–ON complexes, ON interactions with their target sequences, and ON and porphyrin distributions after delivery inside the cells. Time‐resolved confocal microspectrofluorometry indeed delivers additional information compared with fluorescence confocal microscopy imaging widely employed to study ON uptake.
Luminescent Lanthanide Complexes as Probes for the Determination of Enzyme Activities
Authors: Spangler Corinna M. , Spangler Christian , Schäerling Michael
Published: July 2008

The determination of enzyme activities and the screening of enzyme regulators is a major task in clinical chemistry and the development of new drugs. A broad variety of enzymatic reactions is associated with the consumption or formation of small molecules like H2O2, ATP, pyrophosphate, or phosphate. Luminescent lanthanide complexes can be applied to monitor these enzymatic conversions and therefore can serve as probes for the determination of enzyme activities. The utility of this concept will be demonstrated by means of some selected examples including europium and terbium complexes. Accordingly, this new approach could be already implemented for the determination of glucose oxidase, catalase, and peroxidase activity. In particular, enzymes that catalyze phosphorylation or dephosphorylation reactions came to the fore of interest because of their high relevance as drug targets. These include (protein) kinases, adenylyl cyclases, phosphodiesterases, phosphatases, and ATPases. The development and design of fluorescent lanthanide complexes should lead to probes with optimized selectivity and response times that can be applied for high‐throughput screening of enzyme inhibitors and for real‐time monitoring of enzyme kinetics. In contrast to other assays for enzyme activity determination, this method does not require the use of radioactively labelled substrates or the accomplishment of rather complex and expensive immunoassays.
Lanthanide Bimetallic Helicates forin VitroImaging and Sensing
Authors: Bünzli Jean‐Claude G. , Chauvin Anne‐Sophie , Vandevyver Caroline D.B. , Bo Song , Comby Steve
Published: July 2008

As the need for targeting luminescent biolabels increases, for mapping selected analytes, imaging of cells and organs, and tracking in cellulo processes, lanthanide bimetallic helicates are emerging as versatile bioprobes. The wrapping of three ligand strands around two metallic centers by self‐assembly affords robust molecular edifices with tunable chemical and photophysical properties. In addition, heterometallic helical chelates can be assembled leading to bioprobes with inherent chiral properties. In this paper, we review the literature demonstrating that neutral [Ln2(LCX)3] (x = 1–3) helicates represent a viable alternative to existing chelating agents for bio‐analyses, while featuring specific enhanced properties. These bimetallic chelates self‐assemble in water, and at physiological pH the 2:3 (Ln:LCX) complex is by far the dominant species, conditional stability constants logβ23 being in the range 23–30. The metal ions are 9‐coordinate and lie in sites with slightly distorted D3 symmetry. Efficient protection from water interaction by the tightly wrapped ligand strands results in sizeable photophysical properties, with quantum yields up to 24% for EuIII and 11% for TbIII, while the luminescence of several other visible and/or near‐infrared emitting LnIII ions is also sensitized. Noncytotoxicity for all the helicates is established for several living cell lines including HeLa, HaCat, MCF‐7, 5D10, and Jurkat. We present new data pertaining to the live cell imaging ability of [Eu2(LC1)3] and compare the three systems with x = 1–3 with respect to thermodynamic stability, photophysics, cell‐permeation ability, and targeting capability for sensing in cellulo processes. Prospects of derivatization for characterizing specific biological interactions are discussed.
Fluorescence Measurements on Functionalized Polymer Surfaces—Problems and Troubleshooting
Authors: Hoffmann Katrin , Mix Renate , Resch‐Genger Ute , Friedrich Joerg F.
Published: July 2008

Plasma‐chemically tailor‐made polymer surfaces are of ever‐increasing importance to control surface properties in material science, as well as for (bio)analytical and biomedical applications. For the characterization of such systems, sensitive fluorescence techniques are attractive tools. To underline the potential and drawbacks of these strategies, this article addresses different problems that complicate fluorometric analysis. To overcome some of these limitations, such as nonspecific adsorption of unreacted fluorescent probes, we discuss potential troubleshooting, including the use of a chromogenic and fluorogenic pyrylium dye for the detection of amino functionalities at polypropylene surfaces.
Standardization of Fluorescence Measurements: Criteria for the Choice of Suitable Standards and Approaches to Fit‐for‐Purpose Calibration Tools
Authors: Resch‐Genger Ute , Hoffmann Katrin , Hoffmann Angelika
Published: July 2008

This report summarizes problems associated with the comparability of measurements of photoluminescence and procedures for the characterization of relevant instruments, focusing on physical and chemical fluorescence standards. To provide recommendations on selecting and using such standards, we derive general and scope‐specific requirements and quality criteria for suitable devices and materials and briefly address metrological requirements linked to the realization of comparable measurements. Special emphasis is dedicated to liquid and solid chromophore‐based fluorescence standards developed or currently tested by us.
Sensitive Terbium Probes for Luminescent Determination of both Alkaline Phosphatase and Codeine Phosphate
Authors: Duerkop Axel , Aleksandrova Darya , Scripinets Yuliya , Yegorova Alla , Vityukova Ekateryna
Published: July 2008

New terbium complexes of 2‐oxo‐4‐hydroxy‐quinoline‐3‐carboxylic acid derivatives are reported for determination of alkaline phosphatase (aPase) and codeine phosphate (CP). Complexation with terbium occurs by way of the oxygen atoms of the 4‐hydroxyl group and the carbonyl group of the 3‐carboxy function, respectively. The complexes are highly luminescent and do not require luminescence enhancers. The excitation maxima of the terbium chelates are at 320 nm. The assay is based on the quenching of the hypersensitive 545‐nm luminescence of the terbium complexes with the ligands 4‐hydroxy‐1‐methyl‐2‐oxo‐1,2‐dihydro‐quinoline‐3‐carboxylic acid (5‐ethyl‐[1,3,4]thiadiazol‐2‐yl)‐amide (L1) and 1‐ethyl‐4‐hydroxy‐2‐oxo‐1,2‐dihydro‐quinoline‐3‐carboxylic acid (4‐trifluoromethyl‐phenyl)‐amide (L2) by phosphate ions. The assays require equimolar (1.0 μM) concentrations of Tb3+ and of the ligand at pH 8.0 (Tris–HCl buffer). The luminescence quenching is proportional to the concentration of aPase and CP within the range of 0.1–70 mU mL−1 and 0.3–20 μg mL−1, respectively. The detection limits were 0.05 mU mL−1 = 40.0 pmol L−1 of aPase and 0.120 μg mL−1 of CP.
Investigating Transcriptional Regulation by Fluorescence Spectroscopy, from Traditional Methods to State‐of‐the‐Art Single‐Molecule Approaches
Authors: Zorrilla Silvia , Lillo M. Pilar , Chaix Denis , Margeat Emmanuel , Royer Catherine A. , Declerck Nathalie
Published: July 2008

Gene expression regulation, in particular at the level of transcription, has been demonstrated to play a key role in the development of human diseases, including cancer, and in bacteria it is crucial for proliferation as well as for pathogenicity. Transcriptional regulation is based on complex networks of interactions, including those of the regulatory proteins with the operator DNAs, which are further modulated by ligands. Thus, understanding transcriptional regulation mechanisms requires a thorough analysis of the physical parameters underlying the interactions involved. Among the panoply of methods available, fluorescence spectroscopy–based approaches have been widely used for the assessment of the thermodynamics and structural dynamics of biomolecular interactions. Here we will discuss the application of three fluorescence spectroscopy methods—fluorescence anisotropy and fluorescence correlation and cross‐correlation spectroscopy—for the investigation of protein–DNA, protein–protein, and protein–ligand interactions. The weaknesses and the strengths of each method will be highlighted on the basis of our experience in the analysis of the interactions of bacterial repressors implicated in transcriptional regulation in bacilli.
Subpicosecond Transient Signal Spectroscopy of Prodan in Dimethylformamide Solution
Authors: Erostyák János , Myllyperkiö Pasi , Buzády Andrea , Korppi‐Tommola Jouko
Published: July 2008

We report a pump–probe experiment revealing the temporal evolution of subpicosecond evolution of Prodan's excited‐state absorption in dimethylformamide. Also, we present calculation of the first spectral moment of this spectral band and estimation of different relaxation components on the subpicosecond time scale.
Excitation Energy Transfer and Trapping in Dye‐Loaded Solid Particles
Authors: Rodríguez Hernán B. , San Román Enrique
Published: July 2008

The photophysics of several systems composed of a single dye or pairs of dyes attached to solid particles has been studied in the dry solid state at high dye concentrations taking into account light scattering and inner filter effects. Interaction among dye molecules and singlet‐singlet energy transfer are relevant in these conditions, as has been demonstrated for pairs of dyes with suitable spectral overlap. For single dyes, after correction for radiative energy transfer, fluorescence quenching is observed as the surface concentration increases. This effect is explained by two different trapping models. Irrespective of the nature of the traps, concentration quenching may be of static (trap absorption) and dynamic (energy transfer) nature. The unraveling of energy trapping mechanisms is a key to the development of efficient photoactive solid materials.
Characterization of Water‐soluble Luminescent Quantum Dots by Fluorescence Correlation Spectroscopy
Authors: Dong Chaoqing , Huang Xiangyi , Ren Jicun
Published: July 2008

Quantum dots (QDs) are nanoscale inorganic particles generally composed of II–VI and III–V elements. Recently, QDs have received great interest in biological applications because of their unique and fascinating optical properties. In this short review, we introduce the synthesis of luminescent QDs in the aqueous phase and characterize certain fundamental parameters of luminescent QDs synthesized in the aqueous phase by fluorescence correlation spectroscopy (FCS), which include, for example, their dynamic diameters and surface charges. Meanwhile, combining with some ensemble spectroscopy techniques, we applied FCS to investigate the quenching process and mechanism of heavy metal ions (e.g., Ag+) on CdTe QDs, as well as the aggregation and subsequent photoactivation process of 3‐mercaptopropionic acid–capping CdTe QDs induced by laser irradiation. Our preliminary results demonstrate that FCS is a sensitive and efficient tool to characterize fluorescent nanoparticles, such as QDs, at the single‐molecule detection level.
Luminescent Amino‐functionalized or Erbium‐doped Silica Spheres for Biological Applications
Authors: Enrichi Francesco
Published: July 2008

This work presents the morphological and optical properties of luminescent silica spheres, discussing applications in bioimaging and biosensing. The spheres are obtained by the hydrolysis and condensation of tetraethylorthosilicate (TEOS) and can be synthesized by following either a basic or an acidic route. Luminescence emission is induced after incorporation of aminopropyltriethoxysilane (APTES) during synthesis or by introducing an optically active element, such as erbium, or other rare‐earth elements. The luminescence properties of APTES‐functionalized silica spheres have been investigated and optimized by varying the annealing temperature. On the other hand, erbium incorporation in silica spheres was also studied and the corresponding Er3+ luminescence emission at 1.54 μm was evaluated for intensity and lifetime. The basic pH environment in the synthesis allows good control of the size of the spheres (∼200 nm in diameter), whereas the acidic route produces a wide dispersion in particle size (200–5000 nm). Both these approaches, however, can be followed to obtain an efficient photoluminescence (PL) emission for the APTES‐functionalized silica spheres after 400–600°C thermal treatment. If Er(NO3)3 is introduced in the basic solution, a rapid precipitation of Er(OH)3 occurs, but erbium can be easily and efficiently incorporated in the acid‐synthesized spheres, showing high PL intensity at 1.54 μm with lifetime of 3.9 ms. Finally, I discuss perspectives for the applications of these luminescent silica spheres, in particular as biological markers for bioimaging and biosensing.
Time‐Gated Luminescence Microscopy
Authors: Connally Russell E. , Piper James A.
Published: July 2008

Autofluorescent algal samples were spiked with europium beads for analysis on a novel all‐solid‐state, time‐gated luminescence (TGL) microscope. Pulsed UV excitation (365 nm) was provided by a high‐power UV‐LED source fitted to an Olympus BX51 microscope. An “Impactron” electron multiplying charge‐coupled‐device (CCD) camera acquired images in delayed luminescence mode. Second, we evaluated sensitivity of the instrument by acquiring images of immunofluorescently labeled Giardia cysts with a single‐exposure period of 3 ms. The camera was triggered 3 μs after the LED had extinguished to yield a 14‐fold increase in signal‐to‐noise ratio within a single 33 ms capture cycle. This novel instrument could be switched instantly from prompt epifluorescence mode to TGL mode for suppression of short‐lived fluorescence.
Fluorescent Probes and Labels for Biomedical Applications
Authors: Patsenker Leonid , Tatarets Anatoliy , Kolosova Olga , Obukhova Olena , Povrozin Yevgeniy , Fedyunyayeva Iryna , Yermolenko Inna , Terpetschnig Ewald
Published: July 2008

Fluorescence probes and labels have become indispensable tools for clinical diagnostics, high‐throughput screening, and other biomedical applications. We have developed several classes of new squaraine‐based red and near‐infrared (NIR) probes and labels (SETA and Square series), naphthalimide‐based fluorescence lifetime dyes (SeTau series), and cyanine‐ and squaraine‐based quenchers (SQ series). This report discusses the spectral and photophysical properties of these new markers. In particular, the red and NIR dyes of the SETA and Square series are extremely bright, with photostabilities that are unmatched by any other dyes in the same spectral region.
Toward Single‐metal‐ion Sensing by Förster Resonance Energy Transfer
Authors: Sutter Jens U. , Macmillan Alexander M. , Birch David J. S. , Rolinski Olaf J.
Published: July 2008

Here we describe progress toward our objective of detecting single nonfluorescent hydrated metal ions. Single‐ion detection represents detection and spectroscopy at the ultimate sensitivity level of approximately 1.6 × 10−24 M. Achieving this goal would provide a breakthrough in analytical science and allow much more detailed insight into sensor–ion interaction than that available with conventional bulk detection methods. We combine recent advances in confocal microscopy with the sensitivity and the noninvasive nature of fluorescence by analyzing Förster resonance energy transfer between sensor fluorophores and transition metal ions.
Two‐photon Excitation Fluorescence Bioassays
Authors: Hänninen Pekka , Soukka Jori , Soini Juhani T.
Published: July 2008

Application of two‐photon excitation of fluorescence in microscopy is one of the major discoveries of the “renaissance” of light microscopy that started in the 1980s. The technique derives its advantages from the biologically “smooth” wavelength of the excitation light and the confinement of the excitation. Difficult, and seemingly nontransparent, samples may be imaged with the technique with good resolution. Although the bioresearch has been concentrating mostly on the positive properties of the technique for imaging, the same properties may be applied successfully to nonimaging bioassays. This article focuses on the development path of two‐photon excitation–based assay system.
Ordered Self‐assembly of Protonated Porphyrin Induced by the Aqueous Environment of Biomimetic Systems
Authors: Andrade Suzana M. , Costa Sílvia M. B.
Published: July 2008

Water‐soluble ionic porphyrins show an interesting self‐association pattern in acidic conditions under which highly ordered aggregates are stabilized. Herein we give an overview of the template effect of biological interfaces in tetrakis(4‐sulfonatophenyl)porphyrin TSPP self‐aggregation, in which we point out the possibility of tuning this process by screening the charge repulsion through ionic strength and pH. We give special emphasis to the use of fluorescence lifetime imaging microscopy and of fluorescence correlation spectroscopy to visualize and characterize these molecular aggregates.
Nano‐ and Microparticles of Organic Fluorescent Dyes
Authors: Fery‐Forgues Suzanne , Abyan Mouhammad , Lamere Jean‐François
Published: July 2008

Organic nanostructured materials are of increasing interest for applications in the fields of bioanalysis, photocatalysis, photonics, and organic light‐emitting diodes. However, their preparation is still difficult to control and their optical properties are inadequately known. A solvent‐exchange process called the “reprecipitation method” was used here to prepare nano‐ and microcrystals from fluorescent dyes belonging, for example, to the coumarin and nitrobenzoxadiazole (NBD) series. Typically, the dyes were dissolved in a hydrophilic organic solvent and then suddenly placed in an aqueous environment, where they spontaneously produce molecular assemblies. According to the self‐association properties of the dyes and to the experimental conditions used, the nano‐ and microcrystals obtained exhibited different sizes and shapes, as observed by fluorescence and electron microscopy. In some cases, the crystal habit was controlled by adding some additives to the reprecipitation medium. The overall optical properties of the free‐standing particles in suspension were generally quite close to those of the dissolved dyes. However, strong distortions of the absorption and emission spectra were observed for crystals grown in the presence of ionic additives. Under the fluorescence microscope, individual microcrystals may show peculiar emission characteristics, displaying bright and dark zones, or behaving like tiny optical fibers.
Processing and Characterization of Gold Nanoparticles for Use in Plasmon Probe Spectroscopy and Microscopy of Biosystems
Authors: Chen Yu , Preece Jon A. , Palmer Richard E.
Published: July 2008

Noble metal nanoparticles have great potential for applications in biochemical sensing and biological imaging because of their unique optical properties originating from the excitation of local surface plasmon resonances. We investigated gold nanoparticles with controlled size, shape, and passivating agents, along with a new process of guided self‐assembly to create two‐dimensional nanostructures from such nanoparticles.
Fluorescent Silica Nanoparticles
Authors: Mader Heike , Li Xiaohua , Saleh Sayed , Link Martin , Kele Peter , Wolfbeis Otto S.
Published: July 2008

We report on the preparation of fluorescent silica nanoparticles (NPs). They have been prepared by (a) modification of the NPs by amino groups and subsequent introduction of amino‐reactive fluorophores of various color and (b) by modification of the NPs by either azido groups or alkyne groups and subsequent conjugation to fluorophores by so‐called click chemistry, which is a novel approach toward modifying silica NPs. The new NPs were characterized in terms of size and spectral properties.
Single‐bead, Single‐molecule, Single‐cell Fluorescence
Authors: Hintersteiner Martin , Auer Manfred
Published: July 2008

According to many current reports, the pharmaceutical business will hit a wall over the next few years. The generic competition is expected to wipe out a double‐digit billion‐dollar amount from top companies' annual sales between 2007 and 2012 (Wall Street Journal, online, December 6, 2007). The industry's science engine has stalled, new blockbusters are lacking, and patent expirations are a big problem. Also, the U.S. Food and Drug Administration is pulling back on approvals, requesting larger safety studies. Among the different approaches taken throughout the industry to improve productivity and to reduce the attrition rate of compounds in the drug discovery process, an extended application of quantitative biology and biophysical methods is ranked very high. Fluorescence spectroscopy and imaging represented the main detection technologies for assays and screening methods in recent years. Today, label‐free detection methods, such as isothermal titration calorimetry, differential scanning calorimetry, tandem mass spectrometry (MSn), light scattering, or interferometry, start to provide viable alternative readouts for physicochemical characterization of leads and hit list triaging. However, the multidimensional nature of fluorescence along with its high sensitivity and single‐molecule resolution remains an unparalleled source of molecular parameters to extract all different kinds of information on molecules and ligand–protein complexes in solution. Although fluorescence‐based methods are currently applied throughout the different stages of the industrial drug discovery process, they are usually applied in an unconnected way. We have developed a fully integrated hit and lead discovery process combining bead‐based synthesis and screening methods with confocal fluorescence microspectroscopy. The primary on‐bead screening process provides fluorescent ligands that after a multistep characterization process ultimately leads to fully mechanistically characterized cellularly validated binders and inhibitors of target protein interactions. The unlabeled small‐molecular inhibitors represent chemical starting points in drug discovery and target validation.
Perspectives for Improved and More Accurate Classification of Thyroid Epithelial Tumors
Authors: Eszlinger Markus , Krohn Knut , Hauptmann Steffen , Dralle Henning , Giordano Thomas J. , Paschke Ralf
Published: July 2008

Context: Histologic examination of thyroid nodules is the current standard to distinguish benign from malignant thyroid epithelial tumors and to classify histologic subtypes. This review analyzes the problems in histological differential diagnosis as well as contradictions between histology and molecular data and describes possibilities to combine histology with molecular data in an effort to more accurately classify thyroid epithelial tumors.

Evidence Acquisition: Published literature, addressing the current recommendations for thyroid tumor classification, as well as literature on the application of histology and molecular studies on the etiology of thyroid tumors is analyzed.

Evidence Synthesis: The current histologic criteria to classify thyroid tumors, especially follicular-patterned tumors, are hampered by considerable interobserver variability. The detection of somatic mutations via genotyping and the definition of potentially informative gene expression signatures by microarray analyses, which can distinguish cancer subtypes as well as low- and high-risk cohorts, have recently demonstrated significant diagnostic potential. Moreover, in a routine diagnostic setting, micro-RNA profiling appears most promising due to their relative stability and the high accuracy of their expression profiles.

Conclusions: It is very likely that molecular definitions of thyroid tumors mentioned in the current World Health Organization classification will be further developed, leading to future progress in defining thyroid tumor types by an integrated histologic and molecular approach. These integrated classifications need to be evaluated for their specific impact on thyroid tumor diagnosis and prognosis.
Anti-Mullerian Hormone and Inhibin B in the Definition of Ovarian Aging and the Menopause Transition
Authors: Sowers Mary Fran R. , Eyvazzadeh Aimee D. , McConnell Daniel , Yosef Matheos , Jannausch Mary L. , Zhang Daowen , Harlow Sioban , Randolph John F.
Published: July 2008

Context/Objective: The objective of the study was to determine whether anti-Mullerian hormone (AMH) and inhibin B are viable endocrine biomarkers for framing the menopause transition from initiation to the final menstrual period (FMP).

Design: We assayed AMH, inhibin B, and FSH in 300 archival follicular phase specimens from 50 women with six consecutive annual visits commencing in 1993 when all women were in the pre- and perimenopausal menopause stages. Subsequently each woman had a documented FMP. The assay results were fitted as individual-woman profiles and then related to time to FMP and age at FMP as outcomes.

Results: Based on annual values from six time points prior to the FMP, logAMH longitudinal profiles declined and were highly associated with a time point 5 yr prior to FMP [including both observed and values below detection (P < 0.0001 and P = 0.0001, respectively)]. Baseline AMH profiles were also associated with age at FMP (P = 0.035). Models of declining loginhibin B profiles (including both observed and values below detection) were associated with time to FMP (P < 0.0001 and P = 0.0003, respectively). There was no significant association of loginhibin B profiles with age at FMP.

Conclusions: AMH, an endocrine marker that reflects the transition of resting primordial follicles to growing follicles, declined to a time point 5 yr prior to the FMP; this may represent a critical biological juncture in the menopause transition. Low and nondetectable levels inhibin B levels also were observed 4–5 yr prior to the FMP but were less predictive of time to FMP or age at FMP.