Extraction and isolation of glycoproteins and proteoglycans

A number of diverse approaches have been devised to bring about the efficient extraction and isolation of glycoproteins and proteoglycans from biological tissues. Many of these approachs are general procedures that can also be used for the extraction of nonglycoproteins from cells or tissues. Others, such as lectin affinity chromatography, take advantage of specialized structures found only on discrete sub-classes of glycoproteins. Unfortunately, the development of a protocol suitable for the purification of a given glycoprotein of interest remains largely empirical. This article presents a general overview of some of the potential strategies that can be utilized in the development of new isolation procedures and attempts to point out some of the possible pitfalls that may be encountered.     

Ontologies for molecular biology and bioinformatics

About five years ago, ontology was almost unknown in bioinformatics, even more so in molecular biology. Nowadays, many bioinformatics articles mention it in connection with text mining, data integration or as a metaphysical cure for problems in standardisation of nomenclature and other applications. This article attempts to give an account of what concept ontologies in the domain of biology and bioinformatics are; what they are not; how they can be constructed; how they can be used; and some fallacies and pitfalls creators and users should be aware of.     

AN INTRODUCTION TO MORPHOMETRIC CYTOLOGY AND ITS APPLICATION TO BOTANICAL RESEARCH

Morphometric cytology is the study which quantifies dimensions of cells and tissues through the observations of two-dimensional sections. Useful parameters such as volumes, surface areas, numbers of particles, etc. can be determined from sections of plant materials. This paper introduces botanists to the basic concepts of morphometry as well as demonstrates their application. A section is included which outlines some of the pitfalls encountered in non-random sampling of micrographs, artifacts due to shrinkage, section thickness, and specimen contrast. This article is designed to be a teaching tool which hopefully will stimulate botanists to apply these techniques in the future.     

Atomistic Simulation of New Materials: Pitfalls and Promises

Abstract

In this paper, we discuss some of the pitfalls that may be encountered using atomistic computer simulations of complex inorganic materials. The examples discussed are intended to illustrate the promising role that computer simulations can play in solid state chemistry, providing the pitfalls are avoided.     

Are caveolae involved in clathrin-independent endocytosis?

In addition to endocytosing molecules via clathrin-coated pits, cells also internalize membrane and fluid by a clathrin-independent endocytic mechanism. In this article we search for the equivalent of clathrin-coated pits in clathrin-independent endocytosis, and discuss some pitfalls in the interpretation of electron micrographs. We also discuss how the early steps in clathrin-independent endocytosis might be analysed morphologically, and we argue that caveolae are not involved in clathrin-independent endocytosis.     

State-of-the-art cytology of pleural fluid,focusing on the diagnosis of mesothelioma

Mesothelioma has always been a challenging diagnosis to render in body cavity cytology samples. This review is a timely update on pleural fluid cytology and ancillary studies that should be considered in the diagnosis of mesothelial proliferations, specifically mesotheliomas. Information about new diagnostic approaches and ancillary studies in mesothelioma was obtained from the peer-reviewed literature and the authors' experiences. Although the morphological diagnosis of mesothelioma is fraught with numerous challenges given the overlap with other diagnostic entities, there are a variety of immunohistochemical and fluorescence in situ hybridization studies available to help in determining mesothelial origin and in distinguishing malignant proliferations from the more common benign or reactive mesothelial proliferations. Although ancillary studies can be helpful, there are important pitfalls to be aware of when interpreting these cases, and this review highlights some of the challenges that require caution.     

What is a Hospital? Future Roles and Prospects for Success: The Business of Medicine: A Course for Physician Leaders

As hospitals consolidate and take on more financial and clinical risk, they face numerous obstacles. While the past can provide answers to solving many of the challenges, some issues are new and require innovative approaches. This article, from a speech delivered to The Business of Medicine: A Course for Physician Leaders symposium presented by Yale-New Haven Hospital and the Medical Directors Leadership Council at Yale University in November 2012, discusses the models for these hospital organizations and the pitfalls they will face in coordinating care. The insights will help these systems overcome potential problems and enhance their chances of success.     

How microbial ancient DNA, found in association with human remains, can be interpreted

The analysis of the DNA of ancient micro-organisms in archaeological and palaeontological human remains can contribute to the understanding of issues as different as the spreading of a new disease, a mummification process or the effect of diets on historical human populations. The quest for this type of DNA, however, can represent a particularly demanding task. This is mainly due to the abundance and diffusion of bacteria, fungi, yeasts, algae and protozoans in the most diverse environments of the present-day biosphere and the resulting difficulty in distinguishing between ancient and modern DNA. Nevertheless, at least under some special circumstances, by using rigorous protocols, which include an archaeometric survey of the specimens and evaluation of the palaeoecological consistency of the results of DNA sequence analysis, glimpses of the composition of the original microbial flora (e.g. colonic flora) can be caught in ancient human remains. Potentials and pitfalls of this research field are illustrated by the results of research works performed on prehistoric, pre-Columbian and Renaissance human mummies.     

Proteomic analysis in the identification of allergenic molecules

Conventional and innovative strategies can be exploited to identify and characterize new allergenic proteins. With the aim of obtaining suggestions for future improvements, this article describes our attempt to understand and describe some of the advantages and pitfalls of the methodologies and procedures often used in this field. The analysis includes the protein extract preparation, starting from the allergenic source, the separation of the proteins contained in a mixture and the detection, identification and characterization of IgE-binding molecules. Classic and emerging proteomic technologies, including mass spectrometry-based methodologies, Edman degradation procedure, microarray-based techniques and bioinformatics search strategies, have been explored. A comparative analysis of biochemistry-based proteomics and molecular biology strategies has also been given.     

Proteomic analysis in the identification of allergenic molecules

Conventional and innovative strategies can be exploited to identify and characterize new allergenic proteins. With the aim of obtaining suggestions for future improvements, this article describes our attempt to understand and describe some of the advantages and pitfalls of the methodologies and procedures often used in this field. The analysis includes the protein extract preparation, starting from the allergenic source, the separation of the proteins contained in a mixture and the detection, identification and characterization of IgE-binding molecules. Classic and emerging proteomic technologies, including mass spectrometry-based methodologies, Edman degradation procedure, microarray-based techniques and bioinformatics search strategies, have been explored. A comparative analysis of biochemistry-based proteomics and molecular biology strategies has also been given.     

Orthognathic surgery in cleft patients

LEARNING OBJECTIVES: After studying this article, the participant should be able to: 1. Identify the skeletal changes in the cleft patient that necessitate surgery. 2. Describe the orthodontic principles that precede surgical treatment. 3. Demonstrate the surgical principles involved in cleft orthognathic surgery and how to avoid common pitfalls particular to cleft orthognathic surgery. 4. Anticipate when dentoalveolar distraction can help in the treatment of problems not easily treated with conventional orthognathic techniques. SUMMARY: This CME article covers the basic multidisciplinary approach to the treatment of patients requiring a combined orthodontic orthognathic approach to their skeletally based malocclusion. The dentoskeletal abnormalities are described for these patients, as are the fundamental orthodontic principles in the presurgical treatment of these patients. The basic surgical principles are discussed in general, and the reader is provided with advice on avoiding common pitfalls. Specific attention is given to the more recent advances in dentoalveolar distraction in cases of large defects that would have been difficult to treat using conventional orthognathic surgery. Videos are provided to illustrate the general principles in treating the cleft orthognathic patient and to illustrate the treatment of large defects using dentoalveolar distraction.     

Catches in pitfall traps in relation to mean densities of carabid beetles

Summary Based on continuous pitfall catches summed over the whole activity period for the carabid beetles Pterostichus versicolor Sturm and Calathus melanocephalus L., a satisfactorily linear relationship is presented between the mean densities in several habitats and in different years and the numbers of beetles trapped. This means that with the help of continuous pitfall sampling a reliable relative measure of the sizes of carabid populations can be obtained.Simulation experiments show that for individuals of P. versicolor the distances covered each day should be represented by strips of some width instead of by lines to obtain numbers trapped that equal the field data. The influence on numbers trapped of the high mobility of beetles in unfavorable habitats is probably not significant. Simulation experiments with C. melanocephalus indicate that a much lower capture efficiency than for P. versicolor has to be programmed to fit the simulation results with the field data.The catch from different types of pitfalls is not always proportional to trap perimeter due to different vegetation cover of the immediate trap surroundings and to different kinds of roofs placed over the pitfalls. For the same species the capture efficiency of a pitfall can also change throughout the season.Simulation experiments show that the number and shape of the pitfalls need not influence the catches, provided that the traps keep the same total perimeter and are broadly spaced.Remodelling of some data from the literature reveals that the linear relationship between mean densities and year-catches in pitfalls is probably a general one among carabid species. This leads to the hypothesis that carabid beetles have to work through a fixed reproductive program each year by means of an almost constant total amount of locomotory activity which is realized step by step during spells of suitable weather.Some recommendations are given for intraspecific and interspecific comparisons of pitfall catches between sites and years.Communication no. 196 of the Biological Station of the Agricultural University (Wageningen), Wijster (Drenthe), The Netherlands     

Reporting of lipidomics data should be standardized

This article highlights, to our opinion, some of the most pertinent issues related to producing high quality lipidomics data. These issues include pitfalls related to sample collection and storage, lipid extraction, the use of shotgun and LC-MS-based lipidomics approaches, and the identification, annotation and quantification of lipid species. We hope that highlighting these issues will help stimulate efforts to implement reporting standards for dissemination of lipidomics data. This article is part of a Special Issue entitled: BBALIP_Lipidomics Opinion Articles edited by Sepp Kohlwein.     

Redox-based regulation of signal transduction: principles, pitfalls, and promises

Oxidants are produced as a by-product of aerobic metabolism, and organisms ranging from prokaryotes to mammals have evolved with an elaborate and redundant complement of antioxidant defenses to confer protection against oxidative insults. Compelling data now exist demonstrating that oxidants are used in physiological settings as signaling molecules with important regulatory functions controlling cell division, migration, contraction, and mediator production. These physiological functions are carried out in an exquisitely regulated and compartmentalized manner by mild oxidants, through subtle oxidative events that involve targeted amino acids in proteins. The precise understanding of the physiological relevance of redox signal transduction has been hampered by the lack of specificity of reagents and the need for chemical derivatization to visualize reversible oxidations. In addition, it is difficult to measure these subtle oxidation events in vivo. This article reviews some of the recent findings that illuminate the significance of redox signaling and exciting future perspectives. We also attempt to highlight some of the current pitfalls and the approaches needed to advance this important area of biochemical and biomedical research.     

Commercial antibodies: the good, bad, and really ugly

The range of antibodies available commercially grows ever larger. Perhaps as a consequence, quality control is not always what it could and should be. Investigators must be aware of potential pitfalls and take steps to assure themselves that the specificity of each antibody is as advertised. Additionally, companies should provide the necessary information about the antigen and antibody to investigators, including references, so that the appropriate controls can be included.     

Plant cell culture initiation

The use of cultured plant cells in either organized or unorganized form has increased vey considerably in the last 10–15 yr. Many new technologies have been developed and applications in both fundamental and applied research have led to the development of some powerful tools for improving our knowledge of botanical systems and for gaining external influence over some of the key processes involved in inter-and intracellular organization. This is particularly the case when cell culture techniques are combined with those for the genetic modification of plant cells. Being able to regenerate whole plants that have gained or lost the expression of one or more specific genes has revolutionized the way in which we approach scientific questions and has opened up many additional possibilities for the molecular dissection of plants. The success or fall of all plant cell culture technologies lies with culture initiation. The choice of plant material, its physiologival state and cultivation history, the media used, and their means of preparation are just some of the factors that can greatly influence whether the desired end result will be achieved. In this article are described some of the practical aspects involved in successful plant cell culture initiation and the choices that have to be made. Attention is given to some of the pitfalls that can occur and how to avoid them. A good start is half the work     

Précautions,pièges et artefacts en TEP/TDM au 18FDG : généralités et cas particulier des pathologies de l’abdomen et du pelvis

The PET-CT with ¹⁸F-FDG is a complex technique imaging combining the acquisition of scintigraphic and CT images. CT is often performed with the addition of product oral or intravenous contrast (PDCI) to facilitate localization and characterization of the lesion. All these steps can be a source of artifacts. Furthermore, ¹⁸F-FDG is a non-specific tracer and may accumulate in malignant cells but also inflammatory, benign tumor or just in certain physiologically consuming glucose areas. All these elements are important to consider in order to optimize the interpretation of PET-CT and in this article, we will try to illustrate potential pitfalls and artifacts that could lead to misinterpretation in abdominal and pelvic imaging.     

Pharmacogenetic testing, informed consent and the problem of secondary information

Numerous benefits for patients have been predicted if prescribing decisions were routinely accompanied by pharmacogenetic testing. So far, little attention has been paid to the possibility that the routine application of this new technology could result in considerable harm to patients. This article emphasises that pharmacogenetic testing shares both the opportunities and the pitfalls with 'conventional' disease-genetic testing. It demonstrates that performing pharmacogenetic tests as well as interpreting the results are extraordinarily complex issues requiring a high level of expertise. It further argues that pharmacogenetic testing can have a huge impact on clinical decisions and may influence the therapeutic strategy as well as the clinical monitoring of a patient. This view challenges the predominant paradigm that pharmacogenetic testing will predict patients' responses to medicines, but that it will not provide any other significant disease-specific predictive information about the patient or family members. The article also questions published proposals to reduce the consent procedure for pharmacogenetic testing to a simple statement that the physician wishes to test a sample of the patient's DNA to see if a drug will be safe or whether it will work, and presents an alternative model that is better suited to protect patient's interests and to obtain meaningful informed consent. The paper concludes by outlining conditions for the application of pharmacogenetic testing in clinical practice in a way that can make full use of its potential benefits while minimising possible harm to patients and their families.