Mutually exclusive var gene expression in the malaria parasite: multiple layers of regulation

As a major factor in Plasmodium falciparum malaria pathogenesis, the var gene family has been the focus of extensive research, which has contributed to our current understanding of Plasmodium antigenic variation. In recent years, sophisticated molecular tools have enabled the generation of interesting data regarding the regulation of mutually exclusive var expression. Although their results are still inconclusive, these studies have demonstrated the existence of multiple layers of control over gene activation, silencing, memory and 'counting'. This review attempts to summarize recent findings and dissect the different layers of var regulation.     

DNA microarrays in clinical cancer research

The recent sequencing of the human genome, coupled with advances in biotechnology, is enabling the comprehensive molecular "profiling" of human tissues. In particular, DNA microarrays are powerful tools for obtaining global views of human tumor gene expression. Complex information from tumor "expression profiling" studies can, in turn, be used to create novel molecular cancer diagnostics. We discuss the utility of DNA microarray-based tumor profiling in clinical cancer research, highlight some important recent studies, and identify future avenues of research in this evolving field.     

Chalkbrood disease in honey bees

Chalkbrood is a fungal disease of honey bee brood caused by Ascosphaera apis. This disease is now found throughout the world, and there are indications that chalkbrood incidence may be on the rise. In this review we consolidate both historic knowledge and recent scientific findings. We document the worldwide spread of the fungus, which is aided by increased global travel and the migratory nature of many beekeeping operations. We discuss the current taxonomic classification in light of the recent complete reworking of fungal systematics brought on by application of molecular methods. In addition, we discuss epidemiology and pathogenesis of the disease, as well as pathogen biology, morphology and reproduction. New attempts at disease control methods and management tactics are reviewed. We report on research tools developed for identification and monitoring, and also include recent findings on genomic and molecular studies not covered by previous reviews, including sequencing of the A. apis genome and identification of the mating type locus.     

Ceramide in apoptosis: an overview and current perspectives

Recent years have witnessed significant advances in the understanding of the role of ceramide in apoptosis. This review summarizes these recent findings and discusses insights from studies of ceramide metabolism, topology, and effector actions. The recent identification of several genes for enzymes of ceramide metabolism, the development of mass spectrometric methods for ceramide analysis, and the increasing molecular and pharmacological tools to probe ceramide metabolism and function promise an accelerated phase in defining the molecular and biochemical details of the role of ceramide in apoptosis.     

Improvement of alignment accuracy utilizing sequentially conserved motifs

Background  

Multiple sequence alignment algorithms are very important tools in molecular biology today. Accurate alignment of proteins is central to several areas such as homology modelling, docking studies, understanding evolutionary trends and study of structure-function relationships. In recent times, improvement of existing progressing programs and implementation of new iterative algorithms have made a significant change in this field.     

Psychological functioning and aging. Learning from longitudinal studies

Population-based longitudinal studies are very useful tools for investigating the characteristics of the aging process among different geographical and socio-cultural contexts. On the other hand, these kind of projects look at a wide range of key issues of aging. In this review, most recent psychological findings in this field are analysed. The increasing interest in longitudinal studies for psychological variables is shown, as well as explicit links with other areas of study. Finally, main areas of improvement are identified according to future analysis of psychological variables, regarding both conceptual and methodological issues.     

Polar auxin transport – old questions and new concepts?

Polar auxin transport controls multiple aspects of plant development including differential growth, embryo and root patterning and vascular tissue differentiation. Identification of proteins involved in this process and availability of new tools enabling `visualization' of auxin and auxin routes in planta largely contributed to the significant progress that has recently been made. New data support classical concepts, but several recent findings are likely to challenge our view on the mechanism of auxin transport. The aim of this review is to provide a comprehensive overview of the polar auxin transport field. It starts with classical models resulting from physiological studies, describes the genetic contributions and discusses the molecular basis of auxin influx and efflux. Finally, selected questions are presented in the context of developmental biology, integrating available data from different fields.     

Vascular-homing peptides for targeted drug delivery and molecular imaging: Meeting the clinical challenges

The vasculature of each organ expresses distinct molecular signatures critically influenced by the pathological status. The heterogeneous profile of the vascular beds has been successfully unveiled by the in vivo phage display, a high-throughput tool for mapping normal, diseased, and tumor vasculature. Specific challenges of this growing field are targeted therapies against cancer and cardiovascular diseases, as well as novel bioimaging diagnostic tools. Tumor vasculature-homing peptides have been extensively evaluated in several preclinical and clinical studies both as targeted-therapy and diagnosis. To date, results from several Phase I and II trials have been reported and many other trials are currently ongoing or recruiting patients. In this review, advances in the identification of novel peptide ligands and their corresponding receptors on tumor endothelium through the in vivo phage display technology are discussed. Emphasis is given to recent findings in the clinical setting of vascular-homing peptides selected by in vivo phage display for the treatment of advanced malignancies and their altered vascular beds.     

Strategies and methods for studying the rhizosphere—the plant science toolbox

This review summarizes and discusses methodological approaches for studies on the impact of plant roots on the surrounding rhizosphere and for elucidation of the related mechanisms, covering a range from simple model experiments up to the field scale. A section on rhizosphere sampling describes tools and culture systems employed for analysis of root growth, root morphology, vitality testing and for monitoring of root activity with respect to nutrient uptake, water, ion and carbon flows in the rhizosphere. The second section on rhizosphere probing covers techniques to detect physicochemical changes in the rhizosphere as a consequence of root activity. This comprises compartment systems to obtain rhizosphere samples, visualisation techniques, reporter gene approaches and remote sensing technologies for monitoring the conditions in the rhizosphere. Approaches for the experimental manipulation of the rhizosphere by use of molecular and genetic methods as tools to study rhizosphere processes are discussed in a third section. Finally it is concluded that in spite of a wide array of methodological approaches developed in the recent past for studying processes and interactions in the rhizosphere mainly under simplified conditions in model experiments, there is still an obvious lack of methods to test the relevance of these findings under real field conditions or even on the scale of ecosystems. This also limits reliable data input and validation in current rhizosphere modelling approaches. Possible interactions between different environmental factors or plant-microbial interactions (e.g. mycorrhizae) are frequently not considered in model experiments. Moreover, most of the available knowledge arises from investigations with a very limited number of plant species, mainly crops and studies considering also intraspecific genotypic differences or the variability within wild plant species are just emerging.     

An epigenetic view of plant cells cultured in vitro: somaclonal variation and beyond

Epigenetic mechanisms are highly dynamic events that modulate gene expression. As more accurate and powerful tools for epigenetic analysis become available for application in a broader range of plant species, analysis of the epigenetic landscape of plant cell cultures may turn out to be crucial for understanding variant phenotypes. In vitro plant cell and tissue culture methodologies are important for many ongoing plant propagation and breeding programmes as well as for cutting-edge research in several plant model species. Although it has long been known that in vitro conditions induce variation at several levels, most studies using such conditions rely on the assumption that in vitro cultured plant cells/tissues mostly conform genotypically and phenotypically. However, when large-scale clonal propagation is the aim, there has been a concern in confirming true-to-typeness using molecular markers for evaluating stability. While in most reports genetic variation has been found to occur at relatively modest frequencies, variation in DNA methylation patterns seems to be much more frequent and in some cases it has been directly implicated in phenotypic variation. Recent advances in the field of epigenetics have uncovered highly dynamic mechanisms of chromatin remodelling occurring during cell dedifferentiation and differentiation processes on which in vitro adventitious plant regeneration systems are based. Here, an overview of recent findings related to developmental switches occurring during in vitro culture is presented. Additionally, an update on the detection of epigenetic variation in plant cell cultures will be provided and discussed in the light of recent progress in the plant epigenetics field.     

Molecular approaches to the study of evolution and phylogeny of the Nemertina

Molecular biological tools currently available to us are revolutionizing the way in which we can address questions in evolutionary biology. The purpose of this article is to provide an overview of molecular techniques and applications available to biologists who are interested in evolutionary studies but who have little acquaintance with molecular biology. In evolutionary biology, techniques designed to determine degree of nucleic acid similarity are in common use and will be dealt with first. Another approach, namely gene expression studies, has strong implications for evolutionary biology but generally requires substantial familiarity with molecular biological tools. Expression studies provide powerful tools for discerning processes of speciation, as in the selection of genetic variants, as well as discerning lineages, e.g., expression of specific homeobox genes during segment formation. For investigations where either nucleic acid identity or gene expression are the ultimate goal, detailed information, protocols and appropriate controls are beyond the scope of this work but, where possible, recent review articles are cited.     

The octanoylated energy regulating hormone ghrelin: An expanded view of ghrelin’s biological interactions and avenues for controlling ghrelin signaling

Ghrelin is a small peptide hormone that requires a unique post-translational modification, serine octanoylation, to bind and activate the GHS-R1a receptor. Initially demonstrated to stimulate hunger and appetite, ghrelin-dependent signaling is implicated in a variety of neurological and physiological processes influencing diseases such as diabetes, obesity, and Prader-Willi syndrome. In addition to its cognate receptor, recent studies have revealed ghrelin interacts with a range of binding partners within the bloodstream. Defining the scope of ghrelin’s interactions within the body, understanding how these interactions work in concert to modulate ghrelin signaling, and developing molecular tools for controlling ghrelin signaling are essential for exploiting ghrelin for therapeutic effect. In this review, we discuss recent findings regarding the biological effects of ghrelin signaling, outline binding partners that control ghrelin trafficking and stability in circulation, and summarize the current landscape of inhibitors targeting ghrelin octanoylation.     

DNA水平上的植物系统学研究进展

分子钟假说为在分子水平上研究生物进化提供了理论基础,分子系统学已成为当前生物学领域中的热门课题,并取得了许多引人注目的进展。本方要以高等植物为对象,从核ＤＮＡ,叶绿体ＤＮＡ和线粒体ＤＮＡ三方面对植物分子系统学进行了综述。     

Glutamate transporter: an unexpected target for some antibiotics

Molecular pain is a relatively new and rapidly expanding research field that represents an advanced step from conventional pain research. Molecular pain research addresses physiological and pathological pain at the cellular, subcellular and molecular levels. These studies integrate pain research with molecular biology, genomics, proteomics, modern electrophysiology and neurobiology. The field of molecular pain research has been rapidly expanding in the recent years, and has great promise for the identification of highly specific and effective targets for the treatment of intractable pain. Although several existing journals publish articles on classical pain research, none are specifically dedicated to molecular pain research. Therefore, a new journal focused on molecular pain research is needed. Molecular Pain, an Open Access, peer-reviewed, online journal, will provide a forum for molecular pain scientists to communicate their research findings in a targeted manner to others in this important and growing field.     

Phosphorus-32 in the Phage Group: radioisotopes as historical tracers of molecular biology

The recent historiography of molecular biology features key technologies, instruments and materials, which offer a different view of the field and its turning points than preceding intellectual and institutional histories. Radioisotopes, in this vein, became essential tools in postwar life science research, including molecular biology, and are here analyzed through their use in experiments on bacteriophage. Isotopes were especially well suited for studying the dynamics of chemical transformation over time, through metabolic pathways or life cycles. Scientists labeled phage with phosphorus-32 in order to trace the transfer of genetic material between parent and progeny in virus reproduction. Initial studies of this type did not resolve the mechanism of generational transfer but unexpectedly gave rise to a new style of molecular radiobiology based on the inactivation of phage by the radioactive decay of incorporated phosphorus-32. These ‘suicide experiments’, a preoccupation of phage researchers in the mid-1950s, reveal how molecular biologists interacted with the traditions and practices of radiation geneticists as well as those of biochemists as they were seeking to demarcate a new field. The routine use of radiolabels to visualize nucleic acids emerged as an enduring feature of molecular biological experimentation.     

Molecular approaches for the detection and identification of bifidobacteria and lactobacilli in the human gastrointestinal tract

In this review an overview of various molecular techniques and their application for the detection and identification of bifidobacteria and lactobacilli in the gastrointestinal (GI) tract is presented. The techniques include molecular typing techniques such as amplified ribosomal DNA restriction analysis (ARDRA), randomly amplified polymorphic DNA (RAPD), pulsed field gel electrophoresis (PFGE), ribotyping and community profiling techniques such as PCR coupled to temperature and denaturing gradient gel electrophoresis (PCR-TGGE and PCR-DGGE, respectively). Special attention is given to oligonucleotide probes and primers that target the ribosomal RNA (rRNA) sequences and their use in PCR and different hybridisation techniques such as DNA microarrays and fluorescent in situ hybridisation (FISH). In addition, recent findings based on the molecular studies of bifidobacteria and lactobacilli in the GI-tract are reviewed.     

Proteomics: a new way to improve human African trypanosomiasis diagnosis?

African trypanosomiases, including the human disease referred to as ‘sleeping sickness’ and the animal diseases such as nagana, surra and dourine, are neglected vector-borne diseases that after years of research still need improved diagnosis and chemotherapy. Advances in proteomics offer new tools to define biomarkers, whose expression may reflect host–parasite interactions occurring during the infection. In this review, the authors first describe the current diagnostic tools used to detect a trypanosome infection during field surveys, and then discuss their interests, limits and further evolutions. The authors also report on the contribution of molecular diagnostics, and the recent advances and developments that make it suitable for fieldwork. The authors then explore the recent uses of proteomics technology to define host and parasite biomarkers that allow detection of the infection, the power and constraints of the technology. The authors conclude by discussing the urgent need to use the biomarkers discovered in order to develop tools to improve trypanosomiasis control in the near future.     

Discovery Studio 2.0的模块扩展及应用:残基水平非键相互作用能量的自动批量计算

非键相互作用对于生物体系中的分子识别和结合过程起着关键作用。然而,传统的方法并不能在残基水平自动批量计算非键相互作用。近年来,已经发展了一些方法和工具进行非键相互作用的计算分析。该文研究发展了一种可以自动计算残基间非键相互作用的方法,即用Perl脚本调用Discovery Studio 2.0(DS 2.0,Accelrys Inc.)底层模块中的非键相互作用协议,实现了直接利用命令行批量计算非键相互作用能量,而无需通过DS2.0的图形界面。该方法扩展了DS2.0的计算模块,并于近期运用到了复合结构的研究分析中。