Bio-ontologies: current trends and future directions

In recent years, as a knowledge-based discipline, bioinformatics has been made more computationally amenable. After its beginnings as a technology advocated by computer scientists to overcome problems of heterogeneity, ontology has been taken up by biologists themselves as a means to consistently annotate features from genotype to phenotype. In medical informatics, artifacts called ontologies have been used for a longer period of time to produce controlled lexicons for coding schemes. In this article, we review the current position in ontologies and how they have become institutionalized within biomedicine. As the field has matured, the much older philosophical aspects of ontology have come into play. With this and the institutionalization of ontology has come greater formality. We review this trend and what benefits it might bring to ontologies and their use within biomedicine.     

Super-SILAC: current trends and future perspectives

Stable isotope labeling with amino acids in cell culture (SILAC) has risen as a powerful quantification technique in mass spectrometry (MS)–based proteomics in classical and modified forms. Previously, SILAC was limited to cultured cells because of the requirement of active protein synthesis; however, in recent years, it was expanded to model organisms and tissue samples. Specifically, the super-SILAC technique uses a mixture of SILAC-labeled cells as a spike-in standard for accurate quantification of unlabeled samples, thereby enabling quantification of human tissue samples. Here, we highlight the recent developments in super-SILAC and its application to the study of clinical samples, secretomes, post-translational modifications and organelle proteomes. Finally, we propose super-SILAC as a robust and accurate method that can be commercialized and applied to basic and clinical research.     

Oncoproteomics: current trends and future perspectives

Oncoproteomics is the application of proteomics technologies in oncology. Functional proteomics is a promising technique for the rational identification of biomarkers and novel therapeutic targets for cancers. Recent progress in proteomics has opened new avenues for tumor-associated biomarker discovery. With the advent of new and improved proteomics technologies, such as the development of quantitative proteomic methods, high-resolution, -speed and -sensitivity mass spectrometry and protein arrays, as well as advanced bioinformatics for data handling and interpretation, it is now possible to discover biomarkers that can reliably and accurately predict outcomes during cancer management and treatment. However, there are several difficulties in the study of proteins/peptides that are not inherent in the study of nucleic acids. New challenges arise in large-scale proteomic profiling when dealing with complex biological mixtures. Nevertheless, oncoproteomics offers great promise for unveiling the complex molecular events of tumorigenesis, as well as those that control clinically important tumor behaviors, such as metastasis, invasion and resistance to therapy. In this review, the development and advancement of oncoproteomics technologies for cancer research in recent years are expounded.     

Vaccine adjuvants: current state and future trends

The problem with pure recombinant or synthetic antigens used in modern day vaccines is that they are generally far less immunogenic than older style live or killed whole organism vaccines. This has created a major need for improved and more powerful adjuvants for use in these vaccines. With few exceptions, alum remains the sole adjuvant approved for human use in the majority of countries worldwide. Although alum is able to induce a good antibody (Th2) response, it has little capacity to stimulate cellular (Th1) immune responses which are so important for protection against many pathogens. In addition, alum has the potential to cause severe local and systemic side-effects including sterile abscesses, eosinophilia and myofascitis, although fortunately most of the more serious side-effects are relatively rare. There is also community concern regarding the possible role of aluminium in neurodegenerative diseases such as Alzheimer's disease. Consequently, there is a major unmet need for safer and more effective adjuvants suitable for human use. In particular, there is demand for safe and non-toxic adjuvants able to stimulate cellular (Th1) immunity. Other needs in light of new vaccine technologies are adjuvants suitable for use with mucosally-delivered vaccines, DNA vaccines, cancer and autoimmunity vaccines. Each of these areas are highly specialized with their own unique needs in respect of suitable adjuvant technology. This paper reviews the state of the art in the adjuvant field, explores future directions of adjuvant development and finally examines some of the impediments and barriers to development and registration of new human adjuvants.     

Coronary atherosclerosis: current therapeutic approaches and future trends

Invasive cardiovascular procedures, such as percutaneous translumenal coronary angioplasty (PTCA) and aorto-coronary bypass surgery (ACBS), that are currently employed in treating the coronary stenosis or occlusion caused by atherosclerosis represent a major therapeutic advance for managing coronary heart disease (CHD). However, the cellular proliferative response and associated intimal hyperplasia that can follow the damage to blood vessels that occurs with these procedures leads to late complications which cannot be effectively controlled by presently available drugs. Hence, a new approach is required for managing these complications, termed "restenosis" (in the case of PTCA) or "stenosis" (in the case of ACBS). Existing drug therapy is reviewed and some new approaches to this problem are provided herein. Further studies of growth factors and other substances that influence the cellular proliferative response that follows injury to the blood vessel wall could lead to the development of effective therapy. Inhibition of intimal hyperplasia and/or acceleration of endothelial cell re-growth provide a basis for such new approaches. Platelet-derived growth factor (PDGF) and basic fibroblast growth factor (bFGF), as well as endothelium-derived relaxing factor(s) (EDRF) and calcitonin gene-related peptide (CGRP) are among the substances discussed. Modification of certain currently available drugs (e.g. Ca(2+)-antagonists) could also be of value in meeting this therapeutic demand.     

LC-MS for protein characterization: current capabilities and future trends

With advances in ionization methods and instrumentation, liquid chromatography (LC)/mass spectrometry (MS) has become a powerful technology for protein characterization. This review article will describe the general approaches on LC-MS analysis in protein characterization, including bottom-up and top-down strategies. Discussions will be given on characterization of recombinant proteins, and post-translational and protein modifications such as disulfide bonds, glycosylation and phosphorylation using LC-MS. New research directions in this area will also be presented to illustrate future prospects of LC-MS in protein characterization, including application to proteomics.     

LC-MS for protein characterization: current capabilities and future trends

With advances in ionization methods and instrumentation, liquid chromatography (LC)/mass spectrometry (MS) has become a powerful technology for protein characterization. This review article will describe the general approaches on LC-MS analysis in protein characterization, including bottom-up and top-down strategies. Discussions will be given on characterization of recombinant proteins, and post-translational and protein modifications such as disulfide bonds, glycosylation and phosphorylation using LC-MS. New research directions in this area will also be presented to illustrate future prospects of LC-MS in protein characterization, including application to proteomics.     

Transgenic assays for mutations and cancer: current status and future perspectives

Transgenic mouse modelling has proved to be a powerful approach to explore the various steps involved in spontaneous and induced carcinogenesis. Some of the multitude of models currently available have the potential to become a substitute for the expensive, long-term rodent bioassay to predict carcinogenicity of environmental compounds. Here, we review the progress in the development and use of transgenic mouse models specifically for the purpose of carcinogenicity and mutagenicity testing.     

Molecular marker systems in insects: current trends and future avenues

Insects comprise the largest species composition in the entire animal kingdom and possess a vast undiscovered genetic diversity and gene pool that can be better explored using molecular marker techniques. Current trends of application of DNA marker techniques in diverse domains of insect ecological studies show that mitochondrial DNA (mtDNA), microsatellites, random amplified polymorphic DNA (RAPD), expressed sequence tags (EST) and amplified fragment length polymorphism (AFLP) markers have contributed significantly for progresses towards understanding genetic basis of insect diversity and for mapping medically and agriculturally important genes and quantitative trait loci in insect pests. Apart from these popular marker systems, other novel approaches including transposon display, sequence-specific amplification polymorphism (S-SAP), repeat-associated polymerase chain reaction (PCR) markers have been identified as alternate marker systems in insect studies. Besides, whole genome microarray and single nucleotide polymorphism (SNP) assays are becoming more popular to screen genome-wide polymorphisms in fast and cost effective manner. However, use of such methodologies has not gained widespread popularity in entomological studies. The current study highlights the recent trends of applications of molecular markers in insect studies and explores the technological advancements in molecular marker tools and modern high throughput genotyping methodologies that may be applied in entomological researches for better understanding of insect ecology at molecular level.     

DNA extraction from bovine faeces: current status and future trends

There is an increasing interest in the detection and enumeration of micro‐organisms pathogenic for human and present in bovine faeces. This interest is because pollution of the environment by animal faeces may affect the safety of food and of drinking or recreational water. Detection and quantification of microbial pathogens carried out using DNA extracted from the faecal matrix are affected by the quality and the quantity of the DNA extracts, which are critical factors that limit the accuracy and sensitivity of molecular studies. This review compares published methods on DNA extraction from bovine faeces, focusing on the extent to which the success of DNA amplification is affected by issues related to the faeces. Following a general discussion on the DNA extraction methods used for faeces, we focus particularly on issues related to the faecal environment itself. The objective is to identify information that can be used to improve the sensitivity of those PCR methods used after direct DNA extraction.     

蛋白质功能研究:历史、现状和将来

蛋白质是生命活动的直接执行者,参与生命的几乎所有过程,如遗传、发育、繁殖、物质和能量的代谢、应激等等。揭示生物体内成千上万种蛋白质的具体功能、完成功能的机制等是蛋白质研究的核心内容,是后基因组时代生命科学研究极富挑战的领域之一。本文就蛋白质功能研究的历史、现状和未来进行简要的讨论。希望能够帮助读者,特别是那些并不从事蛋白质研究的读者,更好地认识我国中长期科学与技术发展规划中制定“蛋白质研究”重大科学计划的必要性。     

Testosterone and sport: current perspectives

Testosterone and other anabolic-androgenic steroids enhance athletic performance in men and women. As a result, exogenous androgen is banned from most competitive sports. However, due to variability in endogenous secretion, and similarities with exogenous testosterone, it has been challenging to establish allowable limits for testosterone in competition. Endogenous androgen production is dynamically regulated by both exercise and winning in competition. Furthermore, testosterone may promote athletic performance, not only through its long-term anabolic actions, but also through rapid effects on behavior. In women, excess production of endogenous testosterone due to inborn disorders of sexual development (DSD) may convey a competitive advantage. For many years, female competitors have been subject to tests of sexual genotype and phenotype known as gender verification. Although gender verification has not identified any normal man competing as a woman, this process has identified women athletes with DSD. As understanding of DSD has expanded in recent years, women with DSD are increasingly able to continue athletic competition.     

Gyrodactylid developmental biology: historical review, current status and future trends

In the viviparous gyrodactylids, embryos develop one inside another within the parental uterus, a phenomenon with major implications for the biology of this species-rich group. Development occurs via two routes: first-born daughters develop at the centre of an embryo cluster in utero, whereas all other daughters develop from oocytes. The resulting offspring are, however, morphologically indistinguishable. We review here the history of gyrodactylid embryology in the context of current knowledge and, present additional cytogenetic and ultrastructural observations of embryonic development. These progenetic parasites are highly modified for viviparity; oocyte maturation and sperm storage occur in a single chamber, the Egg Cell Forming Region, and a mature oocyte passes into the uterus after the birth of the preceding, fully developed offspring. The uterus has a syncytial lining derived from anterior and posterior cap cells. These cells are the first to differentiate in the female reproductive system and may be involved in controlling development. Embryos receive nutrients via the uterus rather than from vitelline cells. Traditionally, development of the first-born daughter has been considered a form of polyembryony, although paedogenesis has also been suggested. In contrast to previous studies, we could not trace lineage of the first-born daughter to a single quiescent macromere. However, only mitotic divisions have been conclusively observed in the intraembryonic generation, indicating an asexual origin. All other daughters are formed from meiotically derived oocytes by sexual reproduction or automictic parthenogenesis. The latter may involve pre-meiotic doubling of chromosomes, but the precise mechanism and the relative proportion of sexual and parthenogenetic offspring are unknown. Exceptionally, cleavage in Gyrodactylus spp. occurs by duets rather than quartets (a pattern previously only recorded in acoels) and is characterised by extensive cell rearrangements. Blastomeres may be connected by fine cytoplasmic processes or completely disassociated and are readily redistributed by the muscular actions of the parental uterus. This process resembles 'Blastomeren-Anarchie' of rhabdocoels but without the structural support of vitelline cells. It prevents generation of early cell fate maps and indicates regulative, rather than mosaic, development. Structures such as the gut and excretory system differentiate late, and are highlighted, together with the attachment apparatus, as examples of post-embryonic differentiation. Molecular and cellular techniques are now essential to further elucidate mechanisms of gyrodactylid reproduction, which will in turn contribute to current debates with animal embryology.     

Plastics,the environment and human health: current consensus and future trends

Plastics have transformed everyday life; usage is increasing and annual production is likely to exceed 300 million tonnes by 2010. In this concluding paper to the Theme Issue on Plastics, the Environment and Human Health, we synthesize current understanding of the benefits and concerns surrounding the use of plastics and look to future priorities, challenges and opportunities. It is evident that plastics bring many societal benefits and offer future technological and medical advances. However, concerns about usage and disposal are diverse and include accumulation of waste in landfills and in natural habitats, physical problems for wildlife resulting from ingestion or entanglement in plastic, the leaching of chemicals from plastic products and the potential for plastics to transfer chemicals to wildlife and humans. However, perhaps the most important overriding concern, which is implicit throughout this volume, is that our current usage is not sustainable. Around 4 per cent of world oil production is used as a feedstock to make plastics and a similar amount is used as energy in the process. Yet over a third of current production is used to make items of packaging, which are then rapidly discarded. Given our declining reserves of fossil fuels, and finite capacity for disposal of waste to landfill, this linear use of hydrocarbons, via packaging and other short-lived applications of plastic, is simply not sustainable. There are solutions, including material reduction, design for end-of-life recyclability, increased recycling capacity, development of bio-based feedstocks, strategies to reduce littering, the application of green chemistry life-cycle analyses and revised risk assessment approaches. Such measures will be most effective through the combined actions of the public, industry, scientists and policymakers. There is some urgency, as the quantity of plastics produced in the first 10 years of the current century is likely to approach the quantity produced in the entire century that preceded.     

Human mesenchymal stem cells - current trends and future prospective

Stem cells are cells specialized cell, capable of renewing themselves through cell division and can differentiate into multi-lineage cells. These cells are categorized as embryonic stem cells (ESCs), induced pluripotent stem cells (iPSCs) and adult stem cells. Mesenchymal stem cells (MSCs) are adult stem cells which can be isolated from human and animal sources. Human MSCs (hMSCs) are the non-haematopoietic, multipotent stem cells with the capacity to differentiate into mesodermal lineage such as osteocytes, adipocytes and chondrocytes as well ectodermal (neurocytes) and endodermal lineages (hepatocytes). MSCs express cell surface markers like cluster of differentiation (CD)29, CD44, CD73, CD90, CD105 and lack the expression of CD14, CD34, CD45 and HLA (human leucocyte antigen)-DR. hMSCs for the first time were reported in the bone marrow and till now they have been isolated from various tissues, including adipose tissue, amniotic fluid, endometrium, dental tissues, umbilical cord and Wharton''s jelly which harbours potential MSCs. hMSCs have been cultured long-term in specific media without any severe abnormalities. Furthermore, MSCs have immunomodulatory features, secrete cytokines and immune-receptors which regulate the microenvironment in the host tissue. Multilineage potential, immunomodulation and secretion of anti-inflammatory molecules makes MSCs an effective tool in the treatment of chronic diseases. In the present review, we have highlighted recent research findings in the area of hMSCs sources, expression of cell surface markers, long-term in vitro culturing, in vitro differentiation potential, immunomodulatory features, its homing capacity, banking and cryopreservation, its application in the treatment of chronic diseases and its use in clinical trials.     

Therapeutic peptides: Historical perspectives,current development trends,and future directions

Peptide therapeutics have played a notable role in medical practice since the advent of insulin therapy in the 1920s. Over 60 peptide drugs are approved in the United States and other major markets, and peptides continue to enter clinical development at a steady pace. Peptide drug discovery has diversified beyond its traditional focus on endogenous human peptides to include a broader range of structures identified from other natural sources or through medicinal chemistry efforts. We maintain a comprehensive dataset on peptides that have entered human clinical studies that includes over 150 peptides in active development today. Here we provide an overview of the peptide therapeutic landscape, including historical perspectives, molecular characteristics, regulatory benchmarks, and a therapeutic area breakdown.     

Near infrared spectroscopy for bioprocess monitoring and control: current status and future trends

The development of Near Infrared Spectroscopy has paralleled that of the PC, and the application of NIR in many industries has undergone explosive growth in recent years. This has been particularly apparent in the area of microbial and cell culture system monitoring and control. Potentially, NIR offers the prospect of real-time control of the physiology of cultured cells in fermenters, leading to marked improvements in authenticity, purity and production efficiency. Despite this, NIR is not yet as widely applied within the bioprocessing industry as its potential might suggest. This review critically evaluates the development of this rapidly moving area as it pertains to microbial and cell culture system control and highlights the critical stages in the development of the technology. It indicates the work that must still be carried out if the full potential of NIR is to be exploited in making proteins, hormones and antibiotics by the fermentation route. The review comes at a particularly timely moment when NIR stands on the threshold of widespread acceptance in bioprocessing. This is the ideal moment to assess what the technology can offer the microbiologist, and where it may develop in the future.