Discovery of putative oocyte quality markers by comparative ExacTag proteomics

Purpose: Identification of the biomarkers of oocyte quality, and developmental and reprogramming potential is of importance to assisted reproductive technology in humans and animals. Experimental design: PerkinElmer ExacTag? Kit was used to label differentially proteins in pig oocyte extracts (oocyte proteome) and pig oocyte‐conditioned in vitro maturation media (oocyte secretome) obtained with high‐ and low‐quality oocytes. Results: We identified 16 major proteins in the oocyte proteome that were expressed differentially in high‐ versus low‐quality oocytes. More abundant proteins in the high‐quality oocyte proteome included kelch‐like ECH‐associated protein 1 (an adaptor for ubiquitin‐ligase CUL3), nuclear export factor CRM1 and ataxia‐telangiectasia mutated protein kinase. Dystrophin (DMD) was more abundant in low‐quality oocytes. In the secretome, we identified 110 proteins, including DMD and cystic fibrosis transmembrane conductance regulator, two proteins implicated in muscular dystrophy and cystic fibrosis, respectively. Monoubiquitin was identified in the low‐quality‐oocyte secretome. Conclusions and clinical implications: A direct, quantitative proteomic analysis of small oocyte protein samples can identify potential markers of oocyte quality without the need for a large amount of total protein. This approach will be applied to discovery of non‐invasive biomarkers of oocyte quality in assisted human reproduction and in large animal embryo transfer programs.     

Gastrointestinal fluids proteomics

Seventy million people suffer from diseases of the gastrointestinal tract annually in US, translating to US$85.5 billion in direct healthcare costs. The debilitating effects of these gastrointestinal (GI) diseases can be circumvented with good biomarkers for early detection of these disorders, which will greatly increase the success of curative treatments. GI fluids represent a potential reservoir of biomarkers for early diagnosis of various GI and systemic diseases since these fluids are the most proximal fluid bathing diseased cells. They are anticipated to have proteomes that closely reflect the ensemble of proteins secreted from the respective GI tissues. Most importantly, the disease markers present in GI fluids should be present in higher concentrations than in sera, thus offering greater sensitivity in their detection. However, proteome analysis of GI fluids can be complex mainly due to the dynamic range of protein content and the numerous PTMs of proteins in each specialized GI compartment. This review attempts to discuss the physiology of the various GI fluids, the special technical considerations required for proteome analysis of each fluid, as well as to summarize the current state of knowledge of biomarker discoveries and clinical utility of GI fluids such as salivary, gastric, pancreatic, and biliary secretions.     

Proteomics of human cerebrospinal fluid - the good, the bad, and the ugly

The development of MALDI ESI in the late 1980s has revolutionized the biological sciences and facilitated the emergence of a new discipline called proteomics. Application of proteomics to human cerebrospinal fluid (CSF) has greatly hastened the advancement of characterizing the CSF proteome as well as revealing novel protein biomarkers that are diagnostic of various neurological diseases. While impressive progressions have been made in this field, it has become increasingly clear that proteomics results generated by various laboratories are highly variable. The underlying issues are vast, including limitations and complications with heterogeneity of patients/testing subjects, experimental design, sample processing, as well as current proteomics technology. Accordingly, this review not only summarizes the current status of characterization of the human CSF proteome and biomarker discovery for major neurodegenerative disorders, i.e., Alzheimer's disease and Parkinson's disease, but also addresses a few essential caveats involved in several steps of CSF proteomics that may contribute to the variable/contradicting results reported by different laboratories. The potential future directions of CSF proteomics are also discussed with this analysis.     

Quantitative analysis of sperm rheotaxis using a microfluidic device

Quite puzzling issue in biology is how sperm cells are selected naturally where human sperm has to maintain a correct swimming behavior during the various stages of reproduction process. In nature, sperm has to compete a long journey from cervix to oocyte to stand a chance for fertilization. Although various guidance mechanisms such as chemical and thermal gradients are proposed previously, these mechanisms may only be relevant as sperm reaches very close to the oocyte. Rheotaxis, a phenomenon where sperm cells swim against the flow direction, is possibly the long-range sperm guidance mechanism for successful fertilization. A little is known quantitatively about how flow shear effects may help guide human sperm cells over long distances. Here, we have developed microfluidic devices to quantitatively investigate sperm rheotaxis at various physiological flow conditions. We observed that at certain flow rates sperm actively orient and swim against the flow. Sperm that exhibit positive rheotaxis show better motility and velocity than the control (no-flow condition), however, rheotaxis does not select sperm based on hyaluronic acid (HA) binding potential and morphology. Morphology and HA binding potential may not be a significant factor in sperm transport in natural sperm selection.     

Identification of proteins in human substantia nigra

Characterization of the human brain proteome is a critical area of research. While examination of the human cortex has provided some insight, very little is known about the proteome of the human midbrain, which demonstrates substantial loss of dopaminergic neurons in the substantia nigra pars compacta (SNpc) in Parkinson's disease (PD). Therefore, characterization of this region is essential to a better understanding of the pathogenesis of PD. This dataset paper reports two separate studies, where human SNpc was collected from PD and control subjects and 1263 proteins were identified using MALDI-TOF/TOF as well as linear ion trap MS platforms. With gene ontology analysis, the proteins were categorized according to their biological processes, as well as cellular components. These data were also compared with previous proteomic characterization of the human frontal and temporal cortex, and cerebrospinal fluid to establish shared proteins of relevance. The present dataset is the most extensive survey of the human SNpc proteome, to date. Further characterization of the SNpc proteome will significantly facilitate our understanding of the function and expression of proteins involved in PD, as well as provide potential proteins that may be utilized as biomarkers.     

Recent progress in urinary proteomics

Urinary proteomics has become one of the most attractive subdisciplines in clinical proteomics as the urine is an ideal source for the discovery of noninvasive biomarkers for kidney and nonkidney diseases. This field has been growing rapidly as indicated by >80 original research articles on urinary proteome analyses appearing since 2001, of which 28 (approximately 1/3) had been published within the year 2006. The most common technologies used in recent urinary proteome studies remain gel-based methods (1-DE, 2-DE and 2-D DIGE), whereas LC-MS/MS, SELDI-TOF MS, and CE-MS are other commonly used techniques. In addition, mass spectrometric immunoassay (MSIA) and array technology have also been applied. This review provides an extensive but concise summary of recent applications of urinary proteomics. Proteomic analyses of dialysate and ultrafiltrate fluids derived from renal replacement therapy (or artificial kidney) are also discussed.     

Proteomics in rheumatology: The beginning of a fairy tale?

One of the major challenges in proteome research is to translate its applications to the setting of human diseases. Proteomics in rheumatology is an area with marked potential including applications ranging from diagnostics, over therapeutic monitoring to discovery of new potential therapeutic targets. Biomarkers will be essential to discriminate between clinical similar rheumatic diseases, to monitor disease-states or to install the best appropriate therapy. Especially in the field of rheumatology, analysis of specific genes and/or their expression products by pharmacogenetics/-genomics or pharmacoproteomics could be necessary to enable an effective, patient-tailored therapy. In rheumatology, direct examination of proteins may be of utmost importance, as it is already known that PTMs, such as citrullination of proteins or peptides, may be involved in certain rheumatic diseases. The discovery and validation of antibodies directed against citrullinated proteins/peptides in rheumatic diseases using proteome analysis approaches has been described. Gel-free methods, SELDI-approaches and classic 2-DE approaches have been deployed on body fluids as well as on target tissues in different rheumatic diseases. Proteomics in rheumatology is on the rise and pilot studies have indicated that the application of proteomics-based technologies in rheumatic diseases appears to be an exciting example of translational research.     

Proteome analysis of body fluids for amyotrophic lateral sclerosis biomarker discovery

Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disorder of motor neurons leading to death of the patients, mostly within 2–5 years after disease onset. The pathomechanism of motor neuron degeneration is only partially understood and therapeutic strategies based on mechanistic insights are largely ineffective. The discovery of reliable biomarkers of disease diagnosis and progression is the sine qua non of both the revelation of insights into the ALS pathomechanism and the assessment of treatment efficacies. Proteomic approaches are an important pillar in ALS biomarker discovery. Cerebrospinal fluid is the most promising body fluid for differential proteome analyses, followed by blood (serum, plasma), and even urine and saliva. The present study provides an overview about reported peptide/protein biomarker candidates that showed significantly altered levels in certain body fluids of ALS patients. These findings have to be discussed according to proposed pathomechanisms to identify modifiers of disease progression and to pave the way for the development of potential therapeutic strategies. Furthermore, limitations and advantages of proteomic approaches for ALS biomarker discovery in different body fluids and reliable validation of biomarker candidates have been addressed.     

一种高速缓存方案的实现方法

基于Altera公司的EP2SGX90FF1508C3N和NEC公司的UPD44165364AF5,提出了一种高速缓存方案。本设计采用可编程逻辑器件,灵活性高,可靠性强,可以根据用户的需要进行方便的扩展和升级。深入研究了QDRII SRAM的工作原理和时序原理,提出了比较可靠的读写状态机实现方案。硬件设计经过实际测试,达到了预期的指标,实现了43.2Gb/s的数据吞吐速率,并且成功用于某产品中。     

The untapped potential of proteomic analysis in pediatric pulmonary hypertension

Analysis of the human proteome has become increasingly sophisticated, and offers invaluable potential insight into the pathophysiology of human disease. The increasing standardization of methods, speed, and sophistication of mass spectrometric analysis, availability of reliable antibodies, and dissemination of information among the scientific community has allowed for exponential growth of our knowledge base. The continued effort to provide a molecular explanation for future medical applications based on biomarker discovery is epitomized by the outstanding efforts of the human proteome project, whose goal is to generate a map of the human proteome. However, proteomic analysis is underrepresented in pediatric illness; given the unique challenges of research in the pediatric population, proteomic analysis represents enormous untapped potential, especially in the further elucidation of the pathophysiology of rare diseases such as pulmonary hypertension (PH). In this article, we will describe the unique challenge of pediatric research, the importance of alternative avenues such as proteomics for in-depth analysis of pediatric pathobiology at the cellular level, the specific need for proteomic investigation of pediatric PH, the current status of PH proteomics, and future directions.     

The human synovial fluid proteome: A key factor in the pathology of joint disease

This review aims to summarise our knowledge to date on the protein complement of the synovial fluid (SF). The tissues, structure and pathophysiology of the synovial joint are briefly described. The salient features of the SF proteome, how it is composed and the influence of arthritic disease are highlighted and discussed. The concentrations of proteins that have been detected and quantified in SF are drawn together from the literature on osteoarthritis, rheumatoid arthritis and juvenile idiopathic arthritis. The measurements are plotted to give a perspective on the dynamic range of protein levels within the SF. Approaches to proteomic analysis of SF to date are discussed along with their findings. From the recent literature reviewed within, it is becoming increasingly clear that analysis of the SF proteome as a whole, could deliver the most valuable differential diagnostic fingerprints of a number of arthritic disorders. Further development of proteomic platforms could characterise prognostic profiles to improve the clinician's ability to resolve unremitting disease by existing and novel therapeutics.     

Implementation of Proteomics Biomarkers in Nephrology: From Animal Models to Human Application?

Preclinical animal models are extensively used in nephrology. In this review, the utility of performing proteome analysis of kidney tissue or urine in such models and transfer of the results to human application has been assessed. Analysis of the literature identified 68 relevant publications. Pathway analysis of the reported proteins clearly indicated links with known biological processes in kidney disease providing validation of the observed changes in the preclinical models. However, although most studies focused on the identification of early markers of kidney disease or prediction of its progression, none of the identified makers has made it to substantial validation in the clinic or at least in human samples. Especially in renal disease where urine is an abundant source of biomarkers of diseases of the kidney and the urinary tract, it therefore appears that the focus should be on human material based discovery studies. In contrast, the most valid information of proteome analysis of preclinical models in nephrology for translation in human disease resides in studies focusing on drug evaluation, both efficacy for translation to the clinic and for mechanistic insight.     

Exploring the potential of platelet proteomics in children

Proteomics is a rapidly evolving ‘‘post-genomic’’ science utilizing advanced technologies in protein separation, identification, quantitation and heavily relying on bioinformatics. Proteomic research in pediatrics is important and most of the successes thus far are seen in research that utilize samples that require less invasive procedures and focus on prevailing childhood diseases such as acute lymphoblastic leukaemia and neuroblastoma. Recent advances in proteomics are helping to elucidate platelet processes that are relevant to bleeding and clotting disorders, as well as other important roles of platelets such as in angiogenesis and inflammation. Nevertheless, most of platelet proteome data obtained to date are derived from the adult population and the potential of platelet proteomic application in children has not yet been explored. As it happens in all research fields, there are additional challenges in studying children such as procuring sufficient biological samples and access to less common disease cohorts as compared to in adults. Furthermore, many of the prevalent platelet-mediated diseases in adults, such as coronary heart disease and atherosclerotic lesions, are believed to have origins during childhood. Hence, platelet proteomic research in children may reveal some important information on how platelet plays a role in the pathogenesis of disease. In this article, we refer to the current knowledge from platelet proteomic research strategies in adults and address the specific concerns in the study of pediatric samples.     

Output pressure and efficiency of electrokinetic pumping of non-Newtonian fluids

Theoretical expressions of the flow rate, output pressure and thermodynamic efficiency of electrokinetic pumping of non-Newtonian fluids through cylindrical and slit microchannels are reported. Calculations are carried out in the framework of continuum fluid mechanics. The constitutive model of Ostwald-de Waele (power law) is used to express the fluid shear stress in terms of the velocity gradient. The resulting equations of flow rate and electric current are nonlinear functions of the electric potential and pressure gradients. The fact that the microstructure of non-Newtonian fluids is altered at solid–liquid interfaces is taken into account. In the case of fluids with wall depletion, both the output pressure and efficiency are found to be several times higher than that obtained with simple electrolytes under the same experimental conditions. Apart from potential applications in electrokinetic pumps, these predictions are of interest for the design of microfluidic devices that manipulate non-Newtonian fluids such as polymer solutions and colloidal suspensions. From a more fundamental point of view, the paper discusses a relevant example of nonlinear electrokinetics.     

Challenges and opportunities for cell line secretomes in cancer proteomics

Cancer cell lines are the most widely used experimental models in cancer research. Their advantages of easy growth and manipulation are unfortunately paralleled by their limitations derived from long-term growth in isolation from the rest of the tumor, and hence, lack of tumor microenvironment. We are however currently witnessing novel and transformative advances that are making cell lines more reflective of the human biology and therefore, better experimental models for cancer research. Beyond the experimental model used, the choice of cellular proteome is key in proteomics-based biomarker discovery. Over the last decade, cell line secretomes have been proposed as an alternative for tumor biomarker discovery due to the difficulties posed by plasma in terms of complexity and low abundance of tumor-specific biomarkers. Cell line secretomes are enriched with proteins already linked to tumorigenesis, which also have a good chance of being present in biological fluids. In this review, we will provide an overview of the main technical and biological issues related to cell line secretome analysis, and briefly discuss both the challenges and opportunities in its use for tumor biomarker discovery.     

From flatness, GPI observers, GPI control and flat filters to observer-based ADRC

In this article, we establish the route taken by the author, and his research group, to bring differential flatness to the realm of active disturbance rejection control (ADRC). This avenue entitled: 1) generalized proportional integral observers (GPIO), as natural state and disturbance observers for flat systems, 2) generalized proportional integral (GPI) control, provided with extra integrations, to produce a modular controller known as flat filters (FF’s) and, finally, 3) the establishing of an equivalence of observer based ADRC with FF’s. The context is that of pure integration systems. The obtained controllers depend only on the order of the flat system and they are to be directly used on the basis of the available flat output signal in a universal, modular, fashion. The map is complemented with the relevant references where the intermediate techniques were illustrated and developed, over the years, in connection with laboratory experimental implementations.     

Techniques for Realistic Visualization of Fluids: A Survey

Visualization of fluids has wide applications in science, engineering and entertainment. Various methodologies of visualizing fluids have evolved which emphasize on capturing different aspects of the fluids accurately. In this survey the existing methods for realistic visualization of fluids are reviewed. The approaches are classified based on the key concept they rely on for fluid modeling. This classification allows for easy selection of the method to be adopted for visualization given an application. It also enables identification of alternative techniques for fluid modeling.     

Stable and Fast Fluid–Solid Coupling for Incompressible SPH

The solid boundary handling has been a research focus in physically based fluid animation. In this paper, we propose a novel stable and fast particle method to couple predictive–corrective incompressible smoothed particle hydrodynamics and geometric lattice shape matching (LSM), which animates the visually realistic interaction of fluids and deformable solids allowing larger time steps or velocity differences. By combining the boundary particles sampled from solids with a momentum‐conserving velocity‐position correction scheme, our approach can alleviate the particle deficiency issues and prevent the penetration artefacts at the fluid–solid interfaces simultaneously. We further simulate the stable deformation and melting of solid objects coupled to smoothed particle hydrodynamics fluids based on a highly extended LSM model. In order to improve the time performance of each time step, we entirely implement the unified particle framework on GPUs using compute unified device architecture. The advantages of our two‐way fluid–solid coupling method in computer animation are demonstrated via several virtual scenarios.