It is all about resolution. Meeting report based upon presentations at the 10th International Global BioMillennium 2006 symposium on molecular cell biology (Tbilisi, Georgia)

The 2006 Global BioMillennium Conference took place in Tbilisi, Georgia, on 13-17 July 2006. The Conference was focused on key aspects of gene expression processes. Characteristic of state-of-the-art research in the life sciences, the invited lectures spanned approaches in cell biology, gene expression, and protein function. A particular aspect that is special to the BioMillenium series of conferences (this has been the 10th in this series) is the emphasis on new and emerging technologies; the various experts in the subfields that were covered presented what, in their view, should be critical to enabling future progress.

Molecular imaging programs in the United States: results of a national survey

RATIONALE AND OBJECTIVES

We sought to identify and describe the characteristics of molecular imaging (MI) programs in the United States and to determine the factors considered critical for their future.

MATERIALS AND METHODS

In a cross-sectional study, a validated survey was sent to members of the Society of Chairmen in Academic Radiology Departments (SCARD) in the United States, and 26 variables were studied.

RESULTS

The response rate was 40.3%; 67.9% of the departments surveyed have an MI program. The main focus of 47.4% of departments is oncology. The number of radiologists working for the department was the only variable found to be significantly positively correlated with (1) number of researchers in the MI program, (2) number of MI modalities available, (3) total number of grants, and (4) having ongoing MI clinical trials. These four variables plus the number of federal grants and the space used by MI programs were independent of the geographical region, hospital size (number of beds), and department size (number of radiological examinations per year). All the MI programs received grants during 2005. Only 16.1% have no alliances with industry. Among all the departments, 82% identified staff training and recruitment as the keys for success; 78.57% considered oncology the most important future application of MI and cancer management the hospital service most affected by MI.

CONCLUSION

MI programs are starting to be more widespread throughout the United States, and the trend is for more academic radiology departments to become engaged in MI activities; their development is independent of department characteristics. Radiology departments strongly agreed about the key components for success of MI initiatives and the areas that will be most affected by MI applications.

A survey of single-molecule techniques in chemical biology

Single-molecule methods have revolutionized scientific research by rendering the investigation of once-inaccessible biological processes amenable to scientific inquiry. Several of the more established techniques will be emphasized in this Review, including single-molecule fluorescence microscopy, optical tweezers, and atomic force microscopy, which have been applied to many diverse biological processes. Serving as a taste of all the exciting research currently underway, recent examples will be discussed of translocation of RNA polymerase, myosin VI walking, protein folding, and enzyme activity. We will end by providing an assessment of what the future holds, including techniques that are currently in development.

On microRNA and the need for exploratory experimentation in post-genomic molecular biology

This paper is devoted to an examination of the discovery, characterization, and analysis of the functions of microRNAs, which also serves as a vehicle for demonstrating the importance of exploratory experimentation in current (post-genomic) molecular biology. The material on microRNAs is important in its own right: it provides important insight into the extreme complexity of regulatory networks involving components made of DNA, RNA, and protein. These networks play a central role in regulating development of multicellular organisms and illustrate the importance of epigenetic as well as genetic systems in evolution and development. The examination of these matters yields principled arguments for the historicity of the functions of key biological molecules and for the indispensability of exploratory experimentation in contemporary molecular biology as well as some insight into the complex interplay between exploratory experimentation and hypothesis-driven science. This latter result is not only important for philosophy of science, but also of practical importance for the evaluation of grant proposals, although the elaboration of this latter claim must be left for another occasion.

In search of mitochondrial mechanisms: interfield excursions between cell biology and biochemistry

Developing models of biological mechanisms, such as those involved in respiration in cells, often requires collaborative effort drawing upon techniques developed and information generated in different disciplines. Biochemists in the early decades of the 20th century uncovered all but the most elusive chemical operations involved in cellular respiration, but were unable to align the reaction pathways with particular structures in the cell. During the period 1940-1965 cell biology was emerging as a new discipline and made distinctive contributions to understanding the role of the mitochondrion and its component parts in cellular respiration. In particular, by developing techniques for localizing enzymes or enzyme systems in specific cellular components, cell biologists provided crucial information about the organized structures in which the biochemical reactions occurred. Although the idea that biochemical operations are intimately related to and depend on cell structures was at odds with the then-dominant emphasis on systems of soluble enzymes in biochemistry, a reconceptualization of energetic processes in the 1960s and 1970s made it clear why cell structure was critical to the biochemical account. This paper examines how numerous excursions between biochemistry and cell biology contributed a new understanding of the mechanism of cellular respiration.

The intelligence in developing systems for molecular biology

A report on the 14th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Fortaleza, Brazil, 6-10 August 2006.

A report on the 14th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Fortaleza, Brazil, 6-10 August 2006.

Von vulnerablem Plaque bis Infarktheilung – neue Perspektiven in der Kardiologie mit molekularer Bildgebung

We will witness a change of paradigm in cardiovascular imaging, which is empowered by advances in imaging technology, biochemistry, molecular biology and nanotechnology. Instead of simply following the physical distribution of established contrast agents, we now have the opportunity to noninvasively image biological processes such as enzyme activity, interaction with cell surface markers, gene expression and cell migration. These advancements open up new avenues in basic cardiovascular research and will greatly speed up the pace of discovery. Patient management will profit as well: cardiovascular molecular imaging will strengthen personlized and prophylactic medicine through timely and precise diagnostics. In our review we describe selected molecular imaging strategies in atherosclerosis, myocardial ischemia and healing.

[From cellular biology to molecular biology: Golgi apparatus from the discovery to nowadays]

On April the 9th 1898 Golgi presented the discovery of the Apparato Reticolare Interno or internal reticular apparatus to the Società Medico-Chirurgica in Pavia. The internal reticular apparatus was described as "a fine and elegant network within the cell body" of Purkinje cells. The discovery of this new intracellular structure can be considered a byproduct of Golgi studies devoted to the analysis of the nervous system histology. Golgi and his co-workers detected the internal reticular apparatus in many cell types and described the organelle pleiomorphism due to specific physiological or pathological conditions. However, the real existence of the apparatus was questioned until the organelle was finally identified by electron microscopy in 1954. At this point Golgi apparatus became an actual intracellular structure without any clear function. The involvement in cell secretion processes was verified by using biochemical and molecular investigations from the 1960s. Nowadays, Golgi apparatus is clearly known to be involved in different cell functions as growth, homeostasis and division. The correct execution of these functions lies on the ability to maintain an equilibrated balance between the proteins therein resident. Recently, Golgi apparatus has been involved also in human pathology as mutations in proteins localized in the organelle are linked to some hereditary disorders like the Lowe syndrome. Golgi apparatus has been debated since its discovery. From the Golgi milestones discussed here it is evident that controversies that have arisen were often resolved by information resulting from the application of new technical developments. Indeed the compound dynamic structure and the relevance in cell physiology and in human pathology render Golgi apparatus an open object for future studies. Overall, the history of the Golgi apparatus represents an excellent model not only to follow the transition of the study approaches from cellular biology to molecular cell biology but also to understand the current attention paid to integrate the molecular function and the organelle structure in order to explain what goes wrong in the context of human disease.

Schizophrenia susceptibility genes: in search of a molecular logic and novel drug targets for a devastating disorder

Schizophrenia is a devastating psychiatric disorder that affects approximately one percent of the population worldwide. We argue that the efforts to decipher the genetic causes of schizophrenia have reached another turning point and describe evidence supporting some of the major recent genetic findings in the field. In addition, we identify some general areas of caution in the interpretation of these findings and addresses the promise this recently acquired knowledge holds for the generation of reliable animal models, characterization of genetic interactions, dissection of the disease pathophysiology and development of novel, mechanism-based treatments for the patients.

Application of Molecular Biology and Genetics in Endocrinology

OBJECTIVE

To review the growing impact of molecular biology and genetics on clinical endocrinology.

METHODS

Medical literature, databases, and Web sites describing genetics and genomic medicine with relevance for clinical endocrinology were reviewed.

RESULTS

Many monogenic disorders can now be explained at the molecular level and the diagnosis can be established through mutational analysis. The ability to establish a molecular diagnosis is relevant for carrier detection and genetic counseling. In contrast to the significant advances in monogenic disorders, the current knowledge about the genetic components contributing to the pathogenesis of complex disorders is still relatively modest and is a major focus of current research efforts. Molecular biology already has an important impact on therapy in endocrine disorders. A broad spectrum of recombinant peptides and proteins are used in daily practice, eg, insulin and insulin analogues. Moreover, the increasingly detailed understanding of the molecular pathogenesis of cancer is leading to the development of novel and more specific inhibitors. While genetic testing has many advantages, it is important that physicians and patients are aware of potential limitations. They include, among others, technical limitations and allelic and nonallelic heterogeneity. These limitations need to be discussed in detail with patients and relatives, and it is often useful to involve a genetic counselor before obtaining informed consent by the individuals undergoing testing.

CONCLUSION

Molecular biology and genetics play an increasingly important role for the diagnosis and therapy of endocrine disorders. Challenges for the future include the elucidation of the genetic components contributing to complex disorders, eg, diabetes mellitus type 2, and the development of cheaper and comprehensive DNA sequencing technologies. Lastly, it is important that there is continuing attention directed towards the ethical, social, and legal aspects surrounding genetic medicine.

Enhancing children's intelligence: do the means matter morally?

This article deals with the prospect of genetically enhancing intelligence. We identify and contrast social attitudes (disapproval) to the use of future genetic technology with social attitudes (approval) for environmental methods of enhancing intelligence. Using various forms of the argument that the means by which enhancement is achieved has moral significance, we look for differences that could justify the different attitudes. We find that the different attitudes cannot be ethically justified. We predict that the lack of ethical justification for distinguishing between means of enhancement is likely to result in the eventual acceptance of genetic enhancement of intelligence.

Molecular cardiology and genetics in the 21st century--a primer

The terminology and technology of molecular genetics and recombinant DNA have become an essential part of academic cardiology and will soon be applied at the bedside. The treatise includes a brief summary of the essentials of the DNA molecule, the more common techniques, and their application to genetics and molecular cardiology. It is written to be understood by physicians, scientists, and paramedical personnel who would not necessarily have a background in molecular biology. Inherent in the DNA molecule are three properties fundamental to all of the diagnostic and therapeutic applications, namely, the ability of DNA to separate into single strands, recombine (annealment or hybridization), and the presence of the negative charge enables DNA fragments to be separated easily by electrophoresis. Genetic linkage analysis of a family with an inherited disease enables one to identify the gene without knowing its protein product. Over 50 diseases in cardiology due to single-gene disorders have been identified and multiple mutations have been detected. The new therapeutic frontier will be stem cells and nuclear transfer. Identification of genes responsible for coronary artery disease made possible by genome-wide single nucleotide polymorphism (SNP) mapping techniques paves the way for personalized medicine.

Synthetic biology projects in vitro

Advances in the in vitro synthesis and evolution of DNA, RNA, and polypeptides are accelerating the construction of biopolymers, pathways, and organisms with novel functions. Known functions are being integrated and debugged with the aim of synthesizing life-like systems. The goals are knowledge, tools, smart materials, and therapies.

Recent advances in iron oxide nanocrystal technology for medical imaging

Superparamagnetic iron oxide particles (SPIO and USPIO) have a variety of applications in molecular and cellular imaging. Most of the recent research has concerned cellular imaging with imaging of in vivo macrophage activity. According to the iron oxide nanoparticle composition and size which influence their biodistribution, several clinical applications are possible: detection liver metastases, metastatic lymph nodes, inflammatory and/or degenerative diseases. USPIO are investigated as blood pool agents with T1 weighted sequence for angiography, tumour permeability and tumour blood volume or steady-state cerebral blood volume and vessel size index measurements using T2 weighted sequences. Stem cell migration and immune cell trafficking, as well as targeted iron oxide nanoparticles for molecular imaging studies, are at the stage of proof of concept, mainly in animal models.

PALM reading: Seeing the future of cell biology at higher resolution

The inherent resolution limit of the light microscope has been a limiting factor in investigations of many fields of cell biology. A recent paper in Science by Betzig and coworkers describes a new method that can push the limit significantly lower.

From imaging to understanding: Frontiers in Live Cell Imaging, Bethesda, MD, April 19-21, 2006

A recent meeting entitled Frontiers in Live Cell Imaging was attended by more than 400 cell biologists, physicists, chemists, mathematicians, and engineers. Unlike typical special topics meetings, which bring together investigators in a defined field primarily to review recent progress, the purpose of this meeting was to promote cross-disciplinary interactions by introducing emerging methods on the one hand and important biological applications on the other. The goal was to turn live cell imaging from a "technique" used in cell biology into a new exploratory science that combines a number of research fields.

Breast cancer expression profiling: the impact of microarray testing on clinical decision making

The available clinical prognostic tools show an obvious limitation in predicting the outcome of breast cancer patients, and pathological features cannot classify tumours accurately. Microarray-based molecular classification of breast tumours or selection of gene expression panels to improve risk prediction or treatment outcomes are thought to be theoretically superior to established clinical and pathological criteria, based on guidelines such as the St Gallen and National Institute of Health consensus, or which use specific prognostic tools, such as the Nottingham Prognostic Index or Adjuvant-Online algorithm. Although two diagnostic tests based on gene expression profiling of breast cancer are commercially available, a new molecular classification and molecular forecasting of breast cancer based on expression profiling cannot outperform the standard tumour diagnostic at present. This review focuses on some important problems in the practical application of molecular profiling of breast cancer for clinical purposes.

Nanoparticles and their biological and environmental applications

Nanoparticles exhibit unique physical properties (such as particle aggregation and photoemission, and electrical and heat conductivities) and chemical properties (such as catalytic activity), and hence have received much attention from scientists and researchers in different areas of biological sciences. In this review, we briefly summarize the major types of nanoparticle that have been used so far and discuss the possible applications of these nanoparticles in biological and environmental research, and the potential environmental and health impacts associated with the use of these nanoparticles.

Yeast as a tool to uncover the cellular targets of drugs

Knowledge of the spectrum of cellular proteins targeted by experimental therapeutic agents would greatly facilitate drug development. However, identifying the targets of drugs is a daunting challenge. The yeast Saccharomyces cerevisiae is a valuable model organism for human diseases and pathways because it is genetically tractable and shares many functional homolog with humans. In yeast, it is possible to increase or decrease the expression level of essentially every gene and measure changes in drug sensitivity to uncover potential targets. It is also possible to infer mechanism of action from comparing the changes in mRNA expression elicited by drug treatment with those induced by gene deletions or by other drugs. Proteins that bind drugs directly can be identified using yeast protein chips. This review of the use of yeast for discovering targets of drugs discusses the advantages and drawbacks of each approach and how combining methods may reveal targets more efficiently.

Molecular markers of gliomas: a clinical approach

Over the last decade, the knowledge on the molecular genetic background of gliomas has dramatically increased. This information provides the basis for the molecular target therapies and molecular tests serve to complement the subjective nature of histopathologic criteria and add useful data regarding response to treatments and prognosis. In particular, the use of loss of heterozygosity (LOH) and methylation specific polymerase chain reaction (PCR) (MSP) based testing of gliomas is already in place and used clinically in several centers. This paper provides a brief overview of these molecular genetic aberrations and discusses the clinical utility, as well as the advantages and disadvantages of such approach. Newly developed molecular techniques, such as LOH testing, fluorescence in situ hybridization (FISH), DNA sequencing and MSP, are currently being employed in assessment of gliomas in some laboratories. However, the clinical use of some markers and the context in which the information obtained should be used are still not entirely understood. Therefore, this paper will focus on validation and implementation of molecular testing in gliomas, with emphasis on LOH on chromosomes 1p, 19q, 17p and 10q and O(6)-methylguanine-DNA methyltransferase (MGMT) methylation status.

Diagnostic Molecular Pathology: An Increasingly Indispensable Tool for the Practicing Pathologist

Context.—Diagnostic molecular pathology is rapidly becoming an indispensable tool for anatomic pathologists. Familiarity with some of the technologic principles and current, as well as upcoming, molecular diagnostic applications is greatly advantageous for today's practice of pathology.

Objectives.— To provide a discussion of the most common techniques currently used in molecular pathology laboratories and review their essential applications to diagnosis and management of neoplastic diseases.

Data Sources.—A literature review and illustrative cases from the authors' molecular diagnostic practices.

Conclusions.—Applications such as clonality assays, molecular cytogenetics, and chimerism analysis are providing us with accurate tools to resolve difficult diagnostic and management decisions in hemato-oncology. This should serve as a future model to expand molecular applications into the wider field of solid tumors.

A compilation of molecular biology web servers: 2006 update on the Bioinformatics Links Directory

The Bioinformatics Links Directory is a public online resource that lists the servers published in this and all previously published Nucleic Acids Research Web Server issues together with other useful tools, databases and resources for bioinformatics and molecular biology research. This rich directory of tools and websites can be browsed and searched with all listed links freely accessible to the public. The 2006 update includes the 149 websites highlighted in the July 2006 issue of Nucleic Acids Research and brings the total number of servers listed in the Bioinformatics Links Directory to over 1000 links. To aid navigation through this growing resource, all link entries contain a brief synopsis, a citation list and are classified by function in descriptive biological categories. The most up-to-date version of this actively maintained listing of bioinformatics resources is available at the Bioinformatics Links Directory website, . A complete list of all links listed in this Nucleic Acids Research 2006 Web Server issue can be accessed online at . The 2006 update of the Bioinformatics Links Directory, which includes the Web Server list and summaries, is also available online at the Nucleic Acids Research website, .

Alternative splicing: new insights from global analyses

Recent analyses of sequence and microarray data have suggested that alternative splicing plays a major role in the generation of proteomic and functional diversity in metazoan organisms. Efforts are now being directed at establishing the full repertoire of functionally relevant transcript variants generated by alternative splicing, the specific roles of such variants in normal and disease physiology, and how alternative splicing is coordinated on a global level to achieve cell- and tissue-specific functions. Recent progress in these areas is summarized in this review.

RNA: Networks & Imaging

The past few years have brought about a fundamental change in our understanding and definition of the RNA world and its role in the functional and regulatory architecture of the cell. The discovery of small RNAs that regulate many aspects of differentiation and development have joined the already known non-coding RNAs that are involved in chromosome dosage compensation, imprinting, and other functions to become key players in regulating the flow of genetic information. It is also evident that there are tens or even hundreds of thousands of other non-coding RNAs that are transcribed from the mammalian genome, as well as many other yet-to-be-discovered small regulatory RNAs. In the recent symposium RNA: Networks & Imaging held in Heidelberg, the dual roles of RNA as a messenger and a regulator in the flow of genetic information were discussed and new molecular genetic and imaging methods to study RNA presented.

Future lab-on-a-chip technologies for interrogating individual molecules

Advances in technology have allowed chemical sampling with high spatial resolution and the manipulation and measurement of individual molecules. Adaptation of these approaches to lab-on-a-chip formats is providing a new class of research tools for the investigation of biochemistry and life processes.

[Further development of urology in the tension field of surgical and molecular medicine]

Methods based on molecular biology and molecular medicine now have important practical applications in many areas of theoretical and clinical medicine, and it is no longer possible to imagine life without them. This means that in a largely surgical discipline, such as urology, completely new challenges are coming to the fore, which urology, as an academic and clinical discipline, now has to face up to, and to a much greater degree than hitherto. However, there is less and less freedom of action in any university department of urology, as a result not only of intensified legal outline conditions in the healthcare sector and tight public budgets, but also of faculty- and hospital-specific blocks to innovation. There is an urgent need for the creation of appropriate outline conditions and innovative structures that will allow efficient surgical care and also an efficient way of working scientifically.

Application of encapsulated cell technology for retinal degenerative diseases

Ophthalmic disorders represent a rapidly growing disease area that is associated with the ageing population. Their sight is threatened by age-related macular degeneration, diabetic retinopathy, glaucoma and/or retinitis pigmentosa (RP). Few effective treatments for these disorders are available at present, in part due to lack of effective delivery of therapeutic molecules to the retina. Encapsulated cell technology (ECT) allows the controlled, continuous and long-term administration of protein drugs in the eye, where therapeutic agents are needed, and does not subject the host to the systemic exposure. Furthermore, the implants can be retrieved, providing an added level of safety. Ciliary neurotrophic factor (CNTF) has been shown to protect the retina from degeneration in 13 animal models, and ECT-based delivery of CNTF protected photoreceptors in the rcd1 dog model of RP.

On the complementarity of methods in structural biology

Structural biology has transformed a number of fields of biochemistry and biology. A few examples are the following. The allosteric uptake and release of oxygen from haemoglobin obtained an elegant description from the work of Perutz [Perutz (1970), Nature (London), 227, 726-739; Perutz et al. (1998), Annu. Rev. Biophys. Biomol. Struct. 27, 1-34]. The structure of tRNA highlighted the fact that the two functional facets of the molecule, the anticodon and the 3'-end, which is charged with amino acids, were 75 A apart [Robertus et al. (1974), Nature (London), 250, 546-551; Kim et al. (1974), Science, 185, 435-440]. This had interesting consequences both for charging by tRNA synthetases and for the role of tRNA as the adaptor in protein synthesis on the ribosome. The structure of the ATP synthase illustrated how the enzyme could hydrolyze or synthesize ATP by a rotating mechanism [Abrahams et al. (1994), Nature (London), 370, 621-628]. This transformation is a consequence of the fact that such structural insights on different levels and of different characters can provide a basis for the interpretation or reinterpretation of old observations. In addition, the design of experiments from a structural basis has become more relevant and focused.

Flipping Riboswitches

Riboswitches are common cis-acting regulatory elements in bacteria. They are made of nascent RNA that changes its conformation in response to direct binding of cognate metabolites. The publication of five high-resolution crystal structures provides a comprehensive view of how riboswitches sense their ligands and points to new challenges in this emerging field.

New insights into the molecular biology and targeted therapy of cutaneous T-cell lymphomas

Cutaneous T-cell lymphoma is an extra-nodal non-Hodgkin lymphoma of mature T cells. These tumor cells home to and persist in the skin,producing a broad spectrum of clinical entities. Recent results of basic research on tumor biology and tumor immunology as well as molecular genetics of cutaneous T-cell lymphoma have fostered the development of new therapeutic approaches. Several clinical trials testing these targeted therapies have shown encouraging results. This article provides an overview of recent research developments and therapeutic strategies for cutaneous T-cell lymphoma.