bluuebunny/crossref_metadata_2025 huggingface dataset:
Mitochondrial dysfunction is an early event in aldosterone-induced podocyte injury
Authors: Su Min , Dhoopun Asish-Roopchand , Yuan Yanggang , Huang Songming , Zhu Chunhua , Ding Guixia , Liu Bicheng , Yang Tianxin , Zhang Aihua
Published: June 2013

We previously showed that mitochondrial dysfunction (MtD) is involved in an aldosterone (Aldo)-induced podocyte injury. Here, the potential role of MtD in the initiation of podocyte damage was investigated. We detected the dynamic changes of urinary protein, urinary F2-isoprostane and renal malondialdehyde levels, kidney ultrastructure morphology, mitochondrial DNA (mtDNA) copy number, mitochondrial membrane potential (ΔΨm), and nephrin and podocin expressions in Aldo-infused mice. Aldo infusion first induced renal oxidative stress, as evidenced by increased levels of urinary F2-isoprostane and renal malondialdehyde, and MtD, as demonstrated by reduced mtDNA, ΔΨm, and ATP production. Later, at 5 days after Aldo infusion, proteinuria and podocyte injury began to appear. In cultured podocytes, Aldo or hydrogen peroxide (H2O2) induced MtD after 2–8 h of treatment, whereas the podocyte damage, as shown by decreased nephrin and podocin expressions, occurred later after 12 h of treatment. Thus Aldo treatment both in vitro and in vivo indicated that MtD occurred before podocyte damage. Additionally, MtDNA depletion by ethidium bromide or mitochondrial transcription factor A (TFAM) RNAi induced MtD, further promoting podocyte damage. TFAM expression was found to be reduced in Aldo-infused mice and Aldo-treated podocytes. Adenoviral vector-mediated overexpression of TFAM prevented Aldo-induced MtD and protected against podocyte injury. Together, these findings support MtD as an early event in podocyte injury, and manipulation of TFAM may be a novel strategy for treatment of glomerular diseases such as podocytopathy.
Modulation of central gustatory coding by temperature
Authors: Wilson David M. , Lemon Christian H.
Published: June 2013

Changes in oral temperature can influence taste perception, indicating overlap among mechanisms for taste and oral somesthesis. Medullary gustatory neurons can show cosensitivity to temperature, albeit how these cells process combined taste and thermal input is poorly understood. Here, we electrophysiologically recorded orosensory responses (spikes) from 39 taste-sensitive neurons in the nucleus tractus solitarii of anesthetized mice during oral delivery of tastants adjusted to innocuous cool (16 and 18°C), room (22°C, baseline), and warm (30 and 37°C) oral temperatures. Stimuli included (in mM) 100 sucrose, 30 NaCl, 3 HCl, 3 quinine, an umami mixture, and water. Although cooled water excited few cells, water warmed to 30 and 37°C significantly excited 33% and 64% of neurons, respectively. Warmth induced responses of comparable magnitude to room temperature tastants. Furthermore, warming taste solutions influenced the distribution of gustatory responses among neurons and increased ( P < 0.05) neuronal breadth of tuning across taste qualities. The influence of warmth on response magnitude was stimulus specific. Across neurons, warming facilitated responses to sucrose and umami in a superadditive manner, as these responses exceeded ( P < 0.05) the arithmetic sum of activity to warming alone and the taste stimulus tested at room temperature. Superadditive increases ( P < 0.05) in responding were also noted in some cells for warmed HCl. Yet warming induced only simple additive or subtractive effects on responses to quinine and NaCl. Data show temperature is a parameter of gustatory processing, like taste quality and concentration, in medullary circuits for taste.
Human Neurotropic JC Virus and Its Association with Brain Tumors
Authors: Khalili Kamel
Published: June 2013

JC virus (JCV) is a human polyomavirus known as the causative agent of the fatal demyelinating disease, Progressive Multifocal Leukoencephalopathy (PML). Further, in experimental animals this virus causes a broad range of tumors of central nervous system origin. Recent studies have suggested the association of JCV with several human tumors most notably malignant brain tumors of childhood, medulloblastoma. The development of tumors by JCV is most likely through mechanisms involving inactivation of tumor suppressors and de‐regulation of signaling pathways such as Wnt by the viral early protein, T‐antigen. The neurotropic nature of JCV along with the overwhelming evidence for its oncogenic potential in laboratory animals and its detection in significant numbers of human medulloblastomas invite the re‐evaluation of the role for JCV in the development of human brain tumors.
Multi‐Resolution and Wavelet Representations for Identifying Signatures of Disease
Authors: Sajda Paul , Laine Andrew , Zeevi Yehoshua
Published: June 2013

Identifying physiological and anatomical signatures of disease in signals and images is one of the fundamental challenges in biomedical engineering. The challenge is most apparent given that such signatures must be identified in spite of tremendous inter and intra‐subject variability and noise. Crucial for uncovering these signatures has been the development of methods that exploit general statistical properties of natural signals. The signal processing and applied mathematics communities have developed, in recent years, signal representations which take advantage of Gabor‐type and wavelet‐type functions that localize signal energy in a joint time‐frequency and/or space‐frequency domain. These techniques can be expressed as multi‐resolution transformations, of which perhaps the best known is the wavelet transform. In this paper we review wavelets, and other related multi‐resolution transforms, within the context of identifying signatures for disease. These transforms construct a general representation of signals which can be used in detection, diagnosis and treatment monitoring. We present several examples where these transforms are applied to biomedical signal and imaging processing. These include computer‐aided diagnosis in mammography, real‐time mosaicking of ophthalmic slit‐lamp imagery, characterization of heart disease via ultrasound, predicting epileptic seizures and signature analysis of the electroencephalogram, and reconstruction of positron emission tomography data.
Near‐Infrared Diffuse Optical Tomography
Authors: Hielscher A. H. , Bluestone A. Y. , Abdoulaev G. S. , Klose A. D. , Lasker J. , Stewart M. , Netz U. , Beuthan J.
Published: June 2013

Diffuse optical tomography (DOT) is emerging as a viable new biomedical imaging modality. Using near‐infrared (NIR) light, this technique probes absorption as well as scattering properties of biological tissues. First commercial instruments are now available that allow users to obtain cross‐sectional and volumetric views of various body parts. Currently, the main applications are brain, breast, limb, joint, and fluorescence/bioluminescence imaging. Although the spatial resolution is limited when compared with other imaging modalities, such as magnetic resonance imaging (MRI) or X‐ray computerized tomography (CT), DOT provides access to a variety of physiological parameters that otherwise are not accessible, including sub‐second imaging of hemodynamics and other fast‐changing processes. Furthermore, DOT can be realized in compact, portable instrumentation that allows for bedside monitoring at relatively low cost. In this paper, we present an overview of current state‐of‐the ‐art technology, including hardware and image‐reconstruction algorithms, and focus on applications in brain and joint imaging. In addition, we present recent results of work on optical tomographic imaging in small animals.
Delivery of High‐Quality Biomarker Assays
Authors: Swanson Brian N.
Published: June 2013

Biomarker measurements now support key decisions throughout the drug development process, from lead optimization to regulatory approvals. They are essential for documenting exposure‐response relationships, specificity and potency toward the molecular target, untoward effects, and therapeutic applications. In a broader sense, biomarkers constitute the basis of clinical pathology and laboratory medicine. The utility of biomarkers is limited by their specificity and sensitivity toward the drug or disease process and by their overall variability. Understanding and controlling sources of variability is not only imperative for delivering high‐quality assay results, but ultimately for controlling the size and expense of research studies. Variability in biomarker measurements is affected by: biological and environmental factors (e.g., gender, age, posture, diet and biorhythms), sample collection factors (e.g., preservatives, transport and storage conditions, and collection technique), and analytical factors (e.g., purity of reference material, pipetting precision, and antibody specificity). The quality standards for biomarker assays used in support of nonclinical safety studies fall under GLP (FDA) regulations, whereas, those assays used to support human diagnostics and healthcare are established by CLIA (CMS) regulations and accrediting organizations such as the College of American Pathologists. While most research applications of biomarkers are not regulated, biomarker laboratories in all settings are adopting similar laboratory practices in order to deliver high‐quality data. Because of the escalation in demand for biomarker measurements, the highly‐parallel (multi‐plexed) assay platforms that have fueled the rise of genomics will likely evolve into the analytical engines that drive the biomarker laboratories of tomorrow.
Calcified Nanostructured Silicon Wafer Surfaces for Biosensing: Effects of Surface Modification on Bioactivity
Authors: Weis Robert P. , Montchamp Jean-Luc , Coffer Jeffery L. , Attiah Darlene Gamal , Desai Tejal A.
Published: June 2013

The growth of known biologically‐relevant mineral phases on semiconducting surfaces is one strategy to explicitly induce bioactivity in such materials, either for sensing or drug delivery applications. In this work, we describe the use of a spark ablation process to fabricate deliberate patterns of Ca10(PO4)6(OH)2 on crystalline Si (calcified nanoporous silicon). These patterns have been principally characterized by scanning electron microscopy in conjunction with elemental characterization by energy dispersive x‐ray analysis. This is followed by a detailed comparison of the effects of fibroblast adhesion and proliferation onto calcified nanoporous Si, calcified nanoporous Si derivatized with alendronate, as well as control samples of an identical surface area containing porous SiO2. Fibroblast adhesion and proliferation assays demonstrate that a higher density of cells grow on the Ca3(PO4)2 /porous Si/ SiO2 structures relative to the alendronate‐modified surfaces and porous Si/SiOM2 samples.
Plasma Homocysteine and Oxidative Stress in Cardiovascular Disease
Authors: Moselhy S. S. , Demerdash S. H.
Published: June 2013

Hyperhomocysteinemia (Hhcy) has been associated with pathological and stressfull conditions and is a risk factor for cardiovascular disease (CVD). The aim of this study was to evaluate the correlation between plasma homocysteine (hcy) and lipid peroxidation in patient with CVD. This study was carried out on 40 patients with CVD as well as 15 healthy volunteers of comparable age and gender as control group. The patients were divided into 2 groups as follows: group I, included 20 patients with acute myocardial infarction and group II, included 20 patients with atherosclerotic coronary artery disease with no evidence of previous myocardial infarction . Plasma hcy, nitric oxide (NO) and malondialdhyde (MDA) [as index of lipid peroxidation] were measured in all groups. In addition serum total‐cholesterol, HDL, LDL and triglycerides were evaluated. Results obtained showed that, there was a significant elevation in the levels of plasma hcy, NO and MDA in groups I and II as compared to control group. There was a strong positive correlation between plasma hcy and MDA (r = 0.59, p < 0.001). Also NO was positively correlated with both hcy (r = 0.49, p < 0.001) and MDA (r = 0.51, p < 0.001) . Serum total cholesterol, LDL, and triglycerids were also significantly elevated while serum HDL was significantly decreased in groups I and II as compared to control group. It can be concluded that, hyperhomocysteinemia is a possible factor in free radical generation and therefore cardiovascular diseases.
Use of Markers for the Detection and Treatment of Lung Cancer
Authors: Vourlekis Jason S. , Szabo Eva
Published: June 2013

The unacceptably high morbidity and mortality associated with the diagnosis of lung cancer mandates new approaches toward the early detection and treatment of this disease. Enhanced understanding of the molecular biology of the carcinogenic process is identifying many potential markers of risk of lung cancer occurrence as well as of poor prognosis. Identification of high risk populations who are at greatest risk of being diagnosed with and dying from lung cancer would allow delivery of more intensive screening and interventions to the individuals who are most likely to benefit from such strategies. This review examines the current status of markers of lung cancer risk, early detection, and prognosis, and their applicability to current standards of clinical care.
Near‐Infrared Fluorescence Optical Imaging and Tomography
Authors: Gurfinkel Michael , Ke Shi , Wen Xiaoxia , Li Chun , Sevick-Muraca Eva M.
Published: June 2013

The advent of recent advances in near‐infrared laser diodes and fast electro‐optic detection has spawned a new research field of diagnostic spectroscopy and imaging based on targeting and reporting exogenous fluorescent agents. This review seeks to concisely address the physics, instrumentation, advancements in tomography, and near‐infrared fluorescent contrast agent development that promises selective and specific molecular targeting of diseased tissues. As an example of one area of the field, recent work focusing on pharmacokinetic analysis of fluorophores targeting the epidermal growth factor receptor (EGFR) is presented in a human breast cancer xenograft mouse model to demonstrate specificity of molecularly targeted contrast agents. Finally, a critical evaluation of the limitations and the opportunities for future translation of fluorescence‐enhanced optical imaging of deep tissues is presented.
Single‐Cell Elastography: Probing for Disease with the Atomic Force Microscope
Authors: Costa Kevin D.
Published: June 2013

The atomic force microscope (AFM) is emerging as a powerful tool in cell biology. Originally developed for high‐resolution imaging purposes, the AFM also has unique capabilities as a nano‐indenter to probe the dynamic viscoelastic material properties of living cells in culture. In particular, AFM elastography combines imaging and indentation modalities to map the spatial distribution of cell mechanical properties, which in turn reflect the structure and function of the underlying cytoskeleton. Such measurements have contributed to our understanding of cell mechanics and cell biology and appear to be sensitive to the presence of disease in individual cells. This chapter provides a background on the principles and practice of AFM elastography and reviews the literature comparing cell mechanics in normal and diseased states, making a case for the use of such measurements as disease markers. Emphasis is placed on the need for more comprehensive and detailed quantification of cell biomechanical properties beyond the current standard methods of analysis. A number of technical and practical hurdles have yet to be overcome before the method can be of clinical use. However, the future holds great promise for AFM elastography of living cells to provide novel biomechanical markers that will enhance the detection, diagnosis, and treatment of disease.
The Use of Urine Proteomic and Metabonomic Patterns for the Diagnosis of Interstitial Cystitis and Bacterial Cystitis
Authors: Van Que N. , Klose John R. , Lucas David A. , Prieto DaRue A. , Luke Brian , Collins Jack , Burt Stanley K. , Chmurny Gwendolyn N. , Issaq Haleem J. , Conrads Thomas P. , Veenstra Timothy D. , Keay Susan K.
Published: June 2013

The advent of systems biology approaches that have stemmed from the sequencing of the human genome has led to the search for new methods to diagnose diseases. While much effort has been focused on the identification of disease‐specific biomarkers, recent efforts are underway toward the use of proteomic and metabonomic patterns to indicate disease. We have developed and contrasted the use of both proteomic and metabonomic patterns in urine for the detection of interstitial cystitis (IC). The methodology relies on advanced bioinformatics to scrutinize information contained within mass spectrometry (MS) and high‐resolution proton nuclear magnetic resonance (1H‐NMR) spectral patterns to distinguish IC‐affected from non‐affected individuals as well as those suffering from bacterial cystitis (BC). We have applied a novel pattern recognition tool that employs an unsupervised system (self‐organizing‐type cluster mapping) as a fitness test for a supervised system (a genetic algorithm). With this approach, a training set comprised of mass spectra and 1H‐NMR spectra from urine derived from either unaffected individuals or patients with IC is employed so that the most fit combination of relative, normalized intensity features defined at precise m/z or chemical shift values plotted in n‐space can reliably distinguish the cohorts used in training. Using this bioinformatic approach, we were able to discriminate spectral patterns associated with IC‐affected, BC‐affected, and unaffected patients with a success rate of approximately 84%.
Novel Approaches to Visualization and Data Mining Reveals Diagnostic Information in the Low Amplitude Region of Serum Mass Spectra from Ovarian Cancer Patients
Authors: Johann Donald J. , McGuigan Michael D. , Tomov Stanimire , Fusaro Vincent A. , Ross Sally , Conrads Thomas P. , Veenstra Timothy D. , Fishman David A. , Whiteley Gordon R. , Petricoin Emanuel F. , Liotta Lance A.
Published: June 2013

The ability to identify patterns of diagnostic signatures in proteomic data generated by high throughput mass spectrometry (MS) based serum analysis has recently generated much excitement and interest from the scientific community. These data sets can be very large, with high‐resolution MS instrumentation producing 1–2 million data points per sample. Approaches to analyze mass spectral data using unsupervised and supervised data mining operations would greatly benefit from tools that effectively allow for data reduction without losing important diagnostic information. In the past, investigators have proposed approaches where data reduction is performed by a priori “peak picking” and alignment/warping/smoothing components using rule‐based signal‐to‐noise measurements. Unfortunately, while this type of system has been employed for gene microarray analysis, it is unclear whether it will be effective in the analysis of mass spectral data, which unlike microarray data, is comprised of continuous measurement operations. Moreover, it is unclear where true signal begins and noise ends. Therefore, we have developed an approach to MS data analysis using new types of data visualization and mining operations in which data reduction is accomplished by culling via the intensity of the peaks themselves instead of by location. Applying this new analysis method on a large study set of high resolution mass spectra from healthy and ovarian cancer patients, shows that all of the diagnostic information is contained within the very lowest amplitude regions of the mass spectra. This region can then be selected and studied to identify the exact location and amplitude of the diagnostic biomarkers.
HLA B‐27 Subtypes in Turkish Patients with Spondyloarthropathy and Healthy Controls
Authors: Oguz Fatma Savran , Ocal Lale , Diler Ali Sarper , Ozkul Hilmi , Asicioglu Faruk , Kasapoglu Esen , Bozkurt Gokay , Konice Meral , Carin Mahmut
Published: June 2013

The frequency and the distribution of HLA‐B27 subtypes in spondylarthropathy (SpA) patients and controls were investigated in a sample Turkish population. B27 subtyping was performed by PCR‐SSP method in two groups: 49 unrelated HLA‐B27 positive Turkish patients with the diagnosis of SpA according to the European Spondyloarthropathy Study Group Criteria, and 55 HLA‐B27 positive healthy controls. The frequency of HLA‐B∗27 was 2.6% in the Turkish population, and B∗2705 was the predominant allele among patients with SpA. The difference was mainly between male patients and male controls The proportion of B∗2705 among B27‐positive patients and controls was significantly different (P = 0.02). Our study supports other reports from different populations which showed that B∗2705 and B∗2702 were more frequent in Caucasian patients with SpA.
Advancement of Biomarker Discovery and Validation through the HUPO Plasma Proteome Project
Authors: Omenn Gilbert S.
Published: June 2013

The Human Proteome Organization (HUPO) Plasma Proteome Project has mounted a Pilot Phase focussed on key problems essential for standardization of specimen collection, specimen handling, choice of fractionation and analysis technologies, and search engines and databases for protein identifications. This international collaboration will lay the groundwork for many large‐scale clinical and epidemiological studies of health and disease.
Diagnostic Proteomics: Serum Proteomic Patterns for the Detection of Early Stage Cancers
Authors: Yu Li-Rong , Zhou Ming , Conrads Thomas P. , Veenstra Timothy D.
Published: June 2013

The ability to interrogate thousands of proteins found in complex biological samples using proteomic technologies has brought the hope of discovering novel disease‐specific biomarkers. While most proteomic technologies used to discover diagnostic biomarkers are quite sophisticated, "proteomic pattern analysis" has emerged as a simple, yet potentially revolutionary, method for the early diagnosis of diseases. Utilizing this technology, hundreds of clinical samples can be analyzed per day and several preliminary studies suggest proteomic pattern analysis has the potential to be a novel, highly sensitive diagnostic tool for the early detection of cancer.
Disturbances of Haemostasis in Diabetes Mellitus
Authors: Fattah Mohamed A. , Shaheen Mohamed H. , Mahfouz M. Hesham
Published: June 2013

Diabetes mellitus is associated with disturbances in haemostasis that could contribute to the development of thrombotic complications.The present study was undertaken to determine the behavior of coagulation variables and fibrinolytic system in diabetes mellitus. Forty five diabetic patients and forty five matched controls were evaluated by doing the following haemostatic parameter, prothrombin time, partial thromboplastin time, thrombin time, coagulation factors assay II, VII, IX, & plasma fibrinogen, ADP‐induced platelet aggregation, protein C, a2‐ antiplasmin, PAI and FDPs. Generally diabetic patients have high levels of fibrinogen, a2‐ antiplasmin, & PAI and lower level of protein C. Other haemostatic parameters did not show statistically significant difference between diabetic patients and control group. Significantally elevated levels of PAI, a2‐ antiplasmin together with low protein C level in diabetic patients may result in the disturbance of haemostatic balance favoring thrombotic events. Conclusion: High levels of plasma fibrinogen, a2A‐ antiplasmin with low plasma protein C activity could lead to a prothrombotic tendency in insulin dependent diabetic patients. Moreover, in non‐insulin dependent diabetic patients, the above mentioned parameters together with high levels of ADP‐induced platelet aggregation and plasminogen activator inhibitor may increase the risk of thrombotic complications. Obesity can be considered as an additional risk factor for development of thrombosis in diabetic patients.
Genetic Variability of Apolipoprotein E in Different Populations from Venezuela
Authors: Fernández-Mestre M. T. , Yehirobi Castro , Montagnani S. , Balbas O. , Layrisse Z.
Published: June 2013

The genetic variation at the Apolipoprotein E locus (APOE) is an important determinant of plasma lipids and has been implicated in various human pathological conditions. The objective of the present study was to estimate the distribution of APOE alleles in five Venezuelan communities: two Amerindian tribes (Bari and Yucpa), one Negroid population from Curiepe, one Caucasoid population from Colonia Tovar and the mestizo urban population living in Caracas. The APOE*3 allele was the most common allele in all populations studied. However, a significant increase in the APOE*2 allele frequency in the Mestizo (18.96%) and Negroid (16.25%) populations was found. Similar to results reported in other Native American populations we have found that the APOE*2 allele is completely absent in the Bari and Yucpa Amerindians. Frequencies found in the Colonia Tovar population are in agreement with those reported in the population of Germany, indicating a high degree of relatedness. The results support the notion that the distribution of the APOE alleles shows ethnic variability.
Polymorphisms at the Ligand Binding Site of the Vitamin D Receptor Gene and Osteomalacia
Authors: Ak Duygu Gezen , Kahraman Hakkí , Dursun Erdinç , Duman Belgin Süsleyici , Erensoy Nevin , Alagöl Faruk , Tanakol Refik , Yılmazer Selma
Published: June 2013

Vitamin D receptor (VDR) gene polymorphisms have been suggested as possible determinants of bone mineral density (BMD) and calcium metabolism. In this study, our aim was to determine whether there is an association between VDR gene polymorphism and osteomalacia or not. We determined ApaI and TaqI polymorphisms in the vitamin D receptor gene in 24 patients with osteomalacia and 25 age‐matched healthy controls. Serum calcium, phosphorus, ALP, PTH, 25OHD levels were also examined. We used PCR and RFLP methods to test for an association between osteomalacia and polymorphisms within, intron 8 and exon 9 of the VDR gene. When the control and patients were compared for their ApaI and TaqI genotypes there was no relationship between VDR gene allelic polymorphisms and osteomalacia. Whereas a nearly significant difference for A allele was found in the allellic distribution of the patients (p = 0.08). Also no association between biochemical data and VDR gene polymorphisms was observed.
Complement Protein Isoforms in CSF as Possible Biomarkers for Neurodegenerative Disease
Authors: Finehout Erin J. , Franck Zsofia , Lee Kelvin H.
Published: June 2013

It has been suggested that the activation of the complement system is involved in the pathogenesis of several neurodegenerative diseases including Alzheimer’s disease (AD), Parkinson’s disease (PD), and multiple sclerosis (MS). Here, the CSF expression levels of complement proteins C3b, C4b, factor B, and factor H were compared between normal subjects and patients diagnosed with AD, PD, MS, and neurosyphilis. The CSF proteins were initially separated using two‐dimensional gel electrophoresis, which allowed the comparison of some of the individual complement isoforms. Patients with AD, PD, and MS all showed more than one complement isoform with a significant change (p < 0.05) in CSF expression level compared to normal
subjects. PD patients were found to have the greatest number of significantly changed isoforms, all showing a decreased expression
level in PD CSF. The complement isoforms examined were able to distinguish between some, but not all, of the diseases
studied. The data suggest that when investigating a protein as a possible biomarker, it may be useful to compare individual protein
isoform expression levels in addition to the more commonly measured total protein expression level.
Protein Analysis in Human Cerebrospinal Fluid: Physiological Aspects, Current Progress and Future Challenges
Authors: Hühmer Andreas F. , Biringer Roger G. , Amato Heidi , Fonteh Alfred N. , Harrington Michael G.
Published: June 2013

The introduction of lumbar puncture into clinical medicine over 100 years ago marks the beginning of the study of central nervous system diseases using the human cerebrospinal fluid (CSF). Ever since, CSF has been analyzed extensively to elucidate the physiological and biochemical bases of neurological disease. The proximity of CSF to the brain makes it a good target for studying the pathophysiology of brain functions, but the barrier function of the CSF also impedes its diagnostic value. Today, measurements to determine alterations in the composition of CSF are central in the differential diagnosis of specific diseases of the central nervous system (CNS). In particular, the analysis of the CSF protein composition provides crucial information in the diagnosis of CNS diseases. This enables the assessment of the physiology of the blood‐CSF barrier and of the immunology of intrathecial responses. Besides those routine measurements, protein compositional studies of CSF have been extended recently to many other proteins in the expectation that comprehensive analysis of lower abundance CSF proteins will lead to the discovery of new disease markers. Disease marker discovery by molecular profiling of the CSF tissue has the enormous potential of providing many new disease relevant molecules. New developments in protein profiling techniques hold promise for the discovery and validation of relevant disease markers. In this review, we summarize the current efforts and progress in CSF protein profiling measurements using conventional and current protein analysis tools. We also discuss necessary development in methodology in order to have the highest impact on the study of the molecular composition of CSF proteins.
A Comprehensive Candidate Gene Study on Bronchial Asthma and Juvenile Idiopathic Arthritis
Authors: Schubert K. , von Bonnsdorf H. , Burke M. , Ahlert I. , Braun S. , Berner R. , Deichmann K. A. , Heinzmann A.
Published: June 2013

Bronchial asthma and juvenile idiopathic arthritis (JIA) are complex genetic diseases. As both represent chronic inflammatory diseases it is likely that they are at least partially influenced by the same genetic variants. One goal in dissecting the genetics of complex diseases is to identify a genetic risk profile. Therefore it is necessary to genotype polymorphisms in many different pathways. Thus we investigated 48 polymorphisms in 24 genes for association with asthma and/or JIA.

Genotpying was performed on 231 asthmatic children, 86 children with JIA and 270 controls. Association analysis was performed by the Armitage’s trend test. Furthermore haplotypes were calculated by FAMHAP.

We found association of polymorphisms within IL-4, CTLA4 and TNFalpha with asthma and/or JIA. Furthermore, the polymorphisms showed an inverse distribution between children with asthma and JIA. However, we were not able to confirm association of most of the previously described candidate genes.

We conclude from our data that it might be very difficult to identify genetic risk profiles for the development of asthma and/or JIA that would be valid across different populations. However, this study adds further evidence that the common genetic background of asthma and JIA is mainly based on polymorphisms in important TH1 and TH2 cytokines.
DHPLC Screening of ATM Gene in Italian Patients Affected by Ataxia‐Telangiectasia: Fourteen Novel ATM Mutations
Authors: Magliozzi Monia , Piane Maria , Torrente Isabella , Sinibaldi Lorenzo , Rizzo Giovanni , Savio Camilla , Lulli Patrizia , De Luca Alessandro , Dallapiccola Bruno , Chessa Luciana
Published: June 2013

The gene for ataxia‐telangiectasia (A‐T:MIM:#208900), ATM, spans about 150~kb of genomic DNA and is composed of 62 coding exons. ATM mutations are found along the entire coding sequence of the gene, without evidence of mutational hot spots. Using DNA as the starting material, we used denaturing high performance liquid chromatography (DHPLC) technique to search for ATM gene mutations. Initially, DHPLC was validated in a retrospective study of 16 positive control samples that included 19 known mutations; 100% of mutations were detected. Subsequently, DHPLC was used to screen for mutations a cohort of 22 patients with the classical form of A‐T. A total of 27 different mutations were identified on 38 of the 44 alleles, corresponding to a 86% detection rate. Fourteen of the mutations were novel. In addition, 15 different variants and polymorphisms of unknown functional significance were found. The high incidence of new and individual A‐T mutations in our cohort of patients demonstrates marked mutational heterogeneity of A‐T in Italy and corroborate the efficiency of DHPLC as a method for the mutation screening of A‐T patients.
BsmI, TaqI, ApaI and FokI Polymorphisms in the Vitamin D Receptor (VDR) Gene and the Risk of Osteoporosis: A Meta‐Analysis
Authors: Zintzaras Elias , Rodopoulou Paraskevi , Koukoulis George N.
Published: June 2013

A meta‐analysis regarding BsmI, TaqI, ApaI and FokI polymorphisms in the vitamin D receptor (VDR) gene and their associations with osteoporosis in females is reported. The meta‐analysis involved 14, seven, seven and three studies for BsmI, TaqI, ApaI and FokI polymorphisms, respectively. The studies were association studies with osteoporotic cases and controls free of osteoporosis that provided the genotype distribution of individual cases and controls. For the BsmI polymorphism, the allele contrast b vs. B showed heterogeneity among studies (p < 0.01, I2 > 50%) and the random effects (RE) pooled odds ratio (OR) was non‐significant: 0.94 [95% confidence interval (CI) 0.63–1.38]. Caucasians, postmenopausal cases and studies with WHO diagnostic criteria showed no association under any genetic contrast. However, in East Asians, the OR for the dominant model [fixed effects OR = 0.14 (95% CI 0.04–0.50) and RE OR = 0.16 (95% CI 0.03–0.84)] was significant, indicating prevention. Overall, for the TaqI, ApaI and FokI polymorphisms, the allele contrast showed heterogeneity and the pooled RE ORs were non‐significant [OR = 1.06 (95% CI 0.71–1.60), OR = 0.99 (95% CI 0.72–1.37) and OR = 1.17 (95% CI 0.76–1.80), respectively]. The allele contrast for Caucasians, East Asians, postmenopausal cases and studies with WHO diagnostic criteria showed no association for TaqI, ApaI, and FokI. The allele contrast of homozygotes, and the recessive and dominant models the results followed the same pattern as the allele contrast. Therefore, the relationship between the VDR polymorphisms and osteoporosis remains an unresolved issue and other probable genetic‐environmental risk factors interacting with the above polymorphisms should be investigated.
HPV Infection in Men
Authors: Palefsky Joel M.
Published: June 2013

While much is known about the natural history of cervical human papillomavirus (HPV) infection and its consequences, including cervical intraepithelial neoplasia and cervical cancer, relatively little is known about the natural history of anogenital HPV infection and diseases in men. In part this reflects difficulties in penile sampling and visual assessment of penile lesions. Anal HPV infection and disease also remain poorly understood. Although HPV is transmitted sexually and infects the genitals of both sexes, the cervix remains biologically more vulnerable to malignant transformation than does the penis or anus in men. An understanding of male HPV infection is therefore important in terms of reducing transmission of HPV to women and improving women′s health. However, it is also important due to the burden of disease in men, who may develop both penile and anal cancer, particularly among HIV‐positive men who have sex with men. Improved sampling techniques of the male genitalia and cohort studies in progress should provide important information on the natural history of anogenital HPV infection and disease in men, including risk factors for HPV acquisition and transmission. The impact of HPV vaccination in women on male anogenital HPV infection will also need to be assessed.
Cancer Diagnosis, Risk Assessment and Prediction of Therapeutic Response by Means of DNA Methylation Markers
Authors: Fiegl Heidi , Elmasry Karim
Published: June 2013

Epigenetic alterations are heritable changes in gene expression without an accompanying change in primary DNA sequence. Two major mechanisms that cause epigenetic changes are post‐translational histone modifications and DNA methylation at cytosine bases within a CpG dinucleotide. Epigenetic defects have turned out to be one of the most common molecular alterations in human neoplasia. Promoter hypermethylation is associated with loss of expression of tumour suppressor genes in cancer. The analysis of aberrant DNA methylation is gaining strength in the fields of cancer risk assessment, diagnosis, and therapy monitoring in different cancer types. These issues are discussed in this review.
Loss of Imprinting of IGF2 as an Epigenetic Marker for the Risk of Human Cancer
Authors: Cui Hengmi
Published: June 2013

IGF2 is the first gene discovered to be imprinted and expressed exclusively from the paternal allele in both human and mouse. IGF2 is also the first imprinted gene displaying loss of imprinting (LOI) or aberrant imprinting in human cancers. Evidently, LOI or reactivation of the maternal allele of IGF2 is associated with an increase of IGF2 expression that may subsequently play an important role in the onset of human cancers. The most important discovery was the association of LOI of IGF2 with the risk of developing human colorectal cancer. LOI occurs not only in colon cancer tissues, but also in matched normal tissues and peripheral blood cells. A pilot study indicated a significant relationship between LOI of IGF2 and family history as well as personal history of colorectal cancer, suggesting that LOI of IGF2 might be a valuable biomolecular marker of predicting an individual′s risk for colon cancer. A recent epigenetic progenitor model suggested that human cancers might have a common basis that involves an epigenetic disruption of progenitor cells mediated by “tumor progenitor genes” and proposed that non‐neoplastic but epigenetically disrupted progenitor cells might be an important target for cancer risk assessment and prevention.
Papillomavirus Life Cycle Organization and Biomarker Selection
Authors: Doorbar John
Published: June 2013

Human papillomaviruses (HPVs) are a diverse group of viruses that cause epithelial lesions of varying severity. Of the 100 or so types that have been identified, around 40 can infect the cervix, with a subset of these causing lesions that can progress to high‐grade neoplasia and cervical cancer. These high‐risk types are prevalent in the general population, and can predispose to the development of cancer in women who cannot resolve their infection. Virus infection usually leads to the establishment of productive flat warts, or to maintenance of the viral genome in an asymptomatic or latent state. Virus synthesis depends on the ordered expression of viral gene products as the infected basal cell migrates towards the epithelial surface. E7 is expressed in the lower epithelial layers, and is followed eventually by the expression of E4 and L1 closer to the epithelial surface. This ordered pattern changes in characteristic ways during neoplastic progression and latency, and can be irreversibly fixed following integration of the viral genome into the host cell chromosome. Our understanding of expression patterns and their significance, is beginning to explain the nature of disease progression, and offers a rational basis for the selection of biomarkers that may be used to predict disease status and prognostic outcome.
A Mononucleotide Markers Panel to Identify hMLH1/hMSH2 Germline Mutations
Authors: Pedroni M. , Roncari B. , Maffei S. , Losi L. , Scarselli A. , Di Gregorio C. , Marino M. , Roncucci L. , Benatti P. , Ponti G. , Rossi G. , Menigatti M. , Viel A. , Genuardi M. , de Leon M. Ponz
Published: June 2013

Hereditary NonPolyposis Colorectal Cancer (Lynch syndrome) is an autosomal dominant disease caused by germline mutations in a class of genes deputed to maintain genomic integrity during cell replication, mutations result in a generalized genomic instability, particularly evident at microsatellite loci (Microsatellite Instability, MSI). MSI is present in 85–90% of colorectal cancers that occur in Lynch Syndrome. To standardize the molecular diagnosis of MSI, a panel of 5 microsatellite markers was proposed (known as the “Bethesda panel”). Aim of our study is to evaluate if MSI testing with two mononucleotide markers, such as BAT25 and BAT26, was sufficient to identify patients with hMLH1/hMSH2 germline mutations. We tested 105 tumours for MSI using both the Bethesda markers and the two mononucleotide markers BAT25 and BAT26. Moreover, immunohistochemical evaluation of MLH1 and MSH2 proteins was executed on the tumours with at least one unstable microsatellite, whereas germline hMLH1/hMSH2 mutations were searched for all cases showing two or more unstable microsatellites.

The Bethesda panel detected more MSI(+) tumors than the mononucleotide panel (49.5% and 28.6%, respectively). However, the mononucleotide panel was more efficient to detect MSI(+) tumours with lack of expression of Mismatch Repair proteins (93% vs 54%). Germline mutations were detected in almost all patients whose tumours showed MSI and no expression of MLH1/MSH2 proteins. No germline mutations were found in patients with MSI(+) tumour defined only through dinucleotide markers. In conclusion, the proposed mononucleotide markers panel seems to have a higher predictive value to identify hMLH1 and hMSH2 mutation‐positive patients with Lynch syndrome. Moreover, this panel showed increased specificity, thus improving the cost/effectiveness ratio of the biomolecular analyses.
The Epidemiology of Human Papillomavirus Infection and Cervical Cancer
Authors: Bosch F. Xavier , de Sanjosé Silvia
Published: June 2013

Cervical cancer has been recognized as a rare outcome of a common Sexually Transmitted Infection (STI). The etiologic association is restricted to a limited number of viral types of the family of the Human Papillomaviruses (HPVs). The association is causal in nature and under optimal testing systems, HPV DNA can be identified in all specimens of invasive cervical cancer. As a consequence, it has been claimed that HPV infection is a necessary cause of cervical cancer. The evidence is consistent worldwide and implies both the Squamous Cell Carcinomas (SCC), the adenocarcinomas and the vast majority (i.e. > 95%) of the immediate precursors, namely High Grade Squamous Intraepithelial Lesions (HSIL)/Cervical Intraepithelial Neoplasia 3 (CIN3)/Carcinoma in situ. Co‐factors that modify the risk among HPV DNA positive women include the use of oral contraceptives (OC) for five or more years, smoking, high parity (five or more full term pregnancies) and previous exposure to other sexually transmitted diseases such as Chlamydia Trachomatis (CT) and Herpes Simplex Virus type 2 (HSV‐2). Women exposed to the Human Immunodeficiency Virus (HIV) are at high risk for HPV infection, HPV DNA persistency and progression of HPV lesions to cervical cancer.
Systemic Mastocytosis Presenting with a Prominent B Lymphocyte Proliferation in the Bone Marrow and Extensive Fibrosis of the Spleen
Authors: Neşe Nalan , Çağcaron;ırgan Seçkin , Ertan Yešim , Sönmez Ayhan , Soydan Saliha , Hekimgil Mine
Published: June 2013

Systemic mastocytosis is a disease characterized by multifocal mast cell proliferation in the bone marrow or other extracutaneous organs. Because of loosely scattered and hypo‐/agranular mast cells, the diagnosis is sometimes very difficult. In the bone marrow, mast cell infiltration may be associated with prominent lymphoid infiltration leading to a misdiagnosis of a low grade non‐Hodgkin lymphoma.

A 49‐year‐old woman presented with right arm and leg pain, psychiatric symptoms, and diarrhea for four years. Physical examination and laboratory investigation revealed hepatosplenomegaly, anemia, mild thrombocytosis, mild leucocytosis and lymphocytosis. In the bone marrow biopsy, there was a prominent B lymphocyte proliferation reminiscent of a low grade non‐Hodgkin lymphoma/leukemia and there were some spindle cells aggregates in paratrabecular location. The consecutive bone marrow biopsies were similar to the first. The subsequent splenectomy specimen exhibited striking fibrosis. In the lymph node sections, there was marginal zone hyperplasia.

Multifocal accumulations of mast cells were strongly positive with mast cell tryptase and CD117 on immunohistochemical staining, though no metachromasia was identified in Giemsa and Toluidine Blue stained aspirates and tissue sections, probably due to hypo‐/agranulation of mast cells.

The case was presented to emphasize the importance of the antibody to mast cell tryptase in the diagnosis of mastocytosis and to discuss problems of differential diagnosis of systemic mastocytosis.
Proteomics as a Tool for Biomarker Discovery
Authors: Kohn Elise C. , Azad Nilofer , Annunziata Christina , Dhamoon Amit S. , Whiteley Gordon
Published: June 2013

Novel technologies are now being advanced for the purpose of identification and validation of new disease biomarkers. A reliable and useful clinical biomarker must a) come from a readily attainable source, such as blood or urine, b) have sufficient sensitivity to correctly identify affected individuals, c) have sufficient specificity to avoid incorrect labeling of unaffected persons, and d) result in a notable benefit for the patient through intervention, such as survival or life quality improvement. Despite these critical descriptors, the few available FDA‐approved biomarkers for cancer do not completely fit this definition and their benefits are limited to a small number of cancers. Ovarian cancer exemplifies the need for a diagnostic biomarker of early stage disease. Symptoms are present but not specific to the disease, delaying diagnosis until an advanced and generally incurable stage in over 70% of affected women. As such, diagnostic intervention in the form of oopherectomy can be performed in the appropriate at‐risk population if identified such as with a new accurate, sensitive, and specific biomarker. If early stage disease is identified, the requirement for survival and life quality improvement will be met. One of the new technologies applied to biomarker discovery is tour‐de‐force analysis of serum peptides and proteins. Optimization of mass spectrometry techniques coupled with advanced bioinformatics approaches has yielded informative biomarker signatures discriminating presence of cancer from unaffected in multiple studies from different groups. Validation and randomized outcome studies are needed to determine the true value of these new biomarkers in early diagnosis, and improved survival and quality of life.