Informatics issues in large-scale sequence analysis: elucidating the protein kinases of C. elegans

With the availability of the nearly complete genomic sequence of C. elegans, the first multicellular organism to be sequenced, molecular biology has definitely entered the postgenomic era. Annotation of the genomic sequence, which refers to identifying the genes and other biologically relevant sections of the genome, is an important and nontrivial next step. A first-pass annotation will be necessarily incomplete but will drive further biological experiments, which in turn will help to annotate the genome better. Given the scale of the genome sequence analysis, it is clear that the annotation should be automated as much as possible without sacrificing the quality of analysis. In this work, we outline our approach to identifying the protein kinases of C. elegans from the genomic sequence. We describe new tools we have developed for analysis, management and visualization of genomic data. By developing modular and scalable solutions, this study has provided a framework for future analysis of the Drosophila and human genomes.     

Ensuring the security of synthetic biology—towards a 5P governance strategy

Over recent years the label “synthetic biology” has been attached to a number of diverse research and commercial activities, ranging from the search for a minimal cell to the quick delivery of customized genes by DNA synthesis companies. Based on the analysis of biosecurity issues surrounding synthetic biology during the SYNBIOSAFE project, this paper will first provide a rationale for taking security, in addition to safety aspects of this new field, seriously. It will then take stock of the initiatives and measures that have already been taken in this area and will lastly try to map out future areas of activities in order to minimise the security risks emanating from this promising new field of scientific inquiry and technological progress.     

The histochemistry and cell biology vade mecum: a review of 2005–2006

The procurement of new knowledge and understanding in the ever expanding discipline of cell biology continues to advance at a breakneck pace. The progress in discerning the physiology of cells and tissues in health and disease has been driven to a large extent by the continued development of new probes and imaging techniques. The recent introduction of semi-conductor quantum dots as stable, specific markers for both fluorescence light microscopy and electron microscopy, as well as a virtual treasure-trove of new fluorescent proteins, has in conjunction with newly introduced spectral imaging systems, opened vistas into the seemingly unlimited possibilities for experimental design. Although it oftentimes proves difficult to predict what the future will hold with respect to advances in disciplines such as cell biology and histochemistry, it is facile to look back on what has already occurred. In this spirit, this review will highlight some advancements made in these areas in the past 2 years.     

Yeast systems biotechnology for the production of heterologous proteins

Systems biotechnology has been established as a highly potent tool for bioprocess development in recent years. The applicability to complex metabolic processes such as protein synthesis and secretion, however, is still in its infancy. While yeasts are frequently applied for heterologous protein production, more progress in this field has been achieved for bacterial and mammalian cell culture systems than for yeasts. A critical comparison between different protein production systems, as provided in this review, can aid in assessing the potentials and pitfalls of applying systems biotechnology concepts to heterologous protein producing yeasts. Apart from modelling, the methodological basis of systems biology strongly relies on postgenomic methods. However, this methodology is rapidly moving so that more global data with much higher sensitivity will be achieved in near future. The development of next generation sequencing technology enables an unexpected revival of genomic approaches, providing new potential for evolutionary engineering and inverse metabolic engineering.     

Amino acid biosynthesis in plants: Approaching an understanding at the molecular level

Summary The genes encoding GS and EPSP synthase have already been cloned. Clones containing portions of the genes encoding aspartate amino transferase and asparagine synthetase tentatively have been identified by this and other laboratories. It is certain that many other genes encoding other important enzymes involved in amino acid biosynthesis will also be identified in the near future. It is evident that new techniques for the separation of proteins will greatly aid in identifying low abundance genes more rapidly and efficiently. Micro techniques need to be further developed and the necessary equipment made available to laboratories. Hopefully the cost of the required equipment will decrease and commercial enterprises will offer more contract services for work requiring the more expensive equipment. Graduate training in advanced techniques of separating proteins at high resolutions should be encour-aged expanded so that our future scientists are well versed in protein biochemistry as well as in techniques of molecular biology.     

New resources inform study of genome size, content, and organization in nonavian reptiles

Genomic resources for studies of nonavian reptiles have recently improved and will reach a new level of access once the genomes of the painted turtle (Chrysemys picta) and the green anole (Anolis carolinensis) have been published. Eleven speakers gathered for a symposium on reptilian genomics and evolutionary genetics at the 2008 meeting of the Society for Integrative and Comparative Biology in San Antonio, Texas. Presentations described results of reptilian genetic studies concerning molecular evolution, chromosomal evolution, genomic architecture, population dynamics, endocrinology and endocrine disruption, and the evolution of developmental mechanisms. The presented studies took advantage of the recent generation of genetic and genomic tools and resources. Novel findings demonstrated the positive impact made by the improved availability of resources like genome annotations and bacterial artificial chromosomes (BACs). The symposium was timely and important because it provided a vehicle for the dissemination of novel findings that advance the field. Moreover, this meeting fostered the synergistic interaction of the participants as a group, which is anticipated to encourage the funding and creation of further resources such as additional BAC libraries and genomic projects. Novel data have already been collected and studies like those presented in this symposium promise to shape and improve our understanding of overall amniote evolution. Additional reptilian taxa such as the American alligator (Alligator mississippiensis), tuatara (Sphenodon punctatus), and garter snake (Thamnophis sirtalis) should be the foci of future genomic projects. We hope that the following articles in this volume will help promote these efforts by describing the conclusions and the potential that the improvement of genomic resources for nonavian reptiles can continue having in this important area of integrative and comparative biology.     

Advances in Cell‐Free Biosensors: Principle,Mechanism, and Applications

Synthetic biology has promoted the development of biosensors as tools for detecting trace substances. In the past, biosensors based on synthetic biology have been designed on living cells, but the development of cell biosensors has been greatly limited by defects such as genetically modified organism problem and the obstruction of cell membrane. However, the advent of cell‐free synthetic biology addresses these limitations. Biosensors based on the cell‐free protein synthesis system have the advantages of higher safety, higher sensitivity, and faster response time over cell biosensors, which make cell‐free biosensors have a broader application prospect. This review summarizes the workflow of various cell‐free biosensors, including the identification of analytes and signal output. The detection range of cell‐free biosensors is greatly enlarged by different recognition mechanisms and output methods. In addition, the review also discusses the applications of cell‐free biosensors in environmental monitoring and health diagnosis, as well as existing deficiencies and aspects that should be improved. In the future, through continuous improvement and optimization, the potential of cell‐free biosensors will be stimulated, and their application fields will be expanded.     

Informatics issues in large‐scale sequence analysis: Elucidating the protein kinases of C. elegans

With the availability of the nearly complete genomic sequence of C. elegans, the first multicellular organism to be sequenced, molecular biology has definitely entered the postgenomic era. Annotation of the genomic sequence, which refers to identifying the genes and other biologically relevant sections of the genome, is an important and nontrivial next step. A first‐pass annotation will be necessarily incomplete but will drive further biological experiments, which in turn will help to annotate the genome better. Given the scale of the genome sequence analysis, it is clear that the annotation should be automated as much as possible without sacrificing the quality of analysis. In this work, we outline our approach to identifying the protein kinases of C. elegans from the genomic sequence. We describe new tools we have developed for analysis, management and visualization of genomic data. By developing modular and scalable solutions, this study has provided a framework for future analysis of the Drosophila and human genomes. J. Cell. Biochem. 80:181–186, 2000. © 2000 Wiley‐Liss, Inc.     

Can systems biology approach help in finding more effective treatment for acute myeloid leukemia?

Acute myeloid leukemia (AML) is a hematological cancer comprising of cancer stem cells (CSCs) that are responsible for the disease progression, drug resistance and post treatment relapses. Advances in genomic technologies have identified AML as a genetically heterogenous disease with dysregulated gene expression networks. Furthermore, observation of intracellular signaling in individual CSCs by mass cytometry has demonstrated the dysregulation of the mitogen associated protein kinase (MAPK) pathways. It has been envisaged that the future treatment for AML would entail upon formulating individualized treatment plans leading to decreased drug related toxicities for patients. However the emerging role of signaling pathways as dynamic molecular switches influencing the cell cycle process, thereby leading to varying stages of cell differentiation, is making community rethink about the current strategies used for the treatment of AML. This commentary will focus on discovering novel biomarkers and identifying new therapeutic targets, to analyze and treat AML, on a platform enabled by systems biology approach.     

Cryptosporidium parvum genome project

A lack of basic understanding of parasite biology has been a limiting factor in designing effective means of treating and preventing disease caused by Cryptosporidium parvum. Since the genomic DNA sequence encodes all of the heritable information responsible for development, disease pathogenesis, virulence, species permissiveness and immune resistance, a comprehensive knowledge of the C. parvum genome will provide the necessary information required for cost-effective and targeted research into disease prevention and treatment. With the recent advances in high-throughput automated DNA sequencing capabilities, large-scale genomic sequencing has become a cost-effective and time-efficient approach to understanding the biology of an organism. In addition, the continued development and implementation of new software tools that can scan raw sequences for signs of genes and then identify clues as to potential functions, has provided the final realization of the potential rewards of genome sequencing. To further our understanding of C. parvum biology, we have initiated a random shotgun sequencing approach to obtain the complete sequence of the IOWA isolate of C. parvum. Our progress to date has demonstrated that sequencing of the C. parvum genome will be an efficient and costeffective method for gene discovery of this important eukaryotic pathogen. This will allow for the identification of key metabolic and immunological features of the organism that will provide the basis for future development of safe and effective strategies for prevention and treatment of disease in AIDS patients, as well as immunocompetent hosts. Moreover, by obtaining the complete sequence of the C. parvum genome, effective methods for subspecific differentiation (strain typing) and epidemiologic surveillance (strain tracking) of this pathogen can be developed.     

Approaches to lipid metabolism gene identification and characterization in the postgenomic era

The availability of genomic resources has already had a tremendous impact on biomedical research. In this review, we describe how whole genome sequence and high-throughput functional genomics projects have facilitated the identification and characterization of important genes in lipid metabolism and disease. We review key approaches and lipid genes identified in the first years of this century and discuss how genomic resources are likely to streamline gene identification and functional characterization in the future.     

Conserved and divergent paths that regulate self-renewal in mouse and human embryonic stem cells

The past few years have seen remarkable progress in our understanding of embryonic stem cell (ES cell) biology. The necessity of examining human ES cells in culture, coupled with the wealth of genomic data and the multiplicity of cell lines available, has enabled researchers to identify critical conserved pathways regulating self-renewal and identify markers that tightly correlate with the ES cell state. Comparison across species has suggested additional pathways likely to be important in long-term self-renewal of ES cells including heterochronic genes, microRNAs, genes involved in telomeric regulation, and polycomb repressors. In this review, we have discussed information on molecules known to be important in ES cell self-renewal or blastocyst development and highlighted known differences between mouse and human ES cells. We suggest that several additional pathways required for self-renewal remain to be discovered and these likely include genes involved in antisense regulation, microRNAs, as well as additional global repressive pathways and novel genes. We suggest that cross species comparisons using large-scale genomic analysis tools are likely to reveal conserved and divergent paths required for ES cell self-renewal and will allow us to derive ES lines from species and strains where this has been difficult.     

CRISPR Editing in Biological and Biomedical Investigation

The CRISPR (clustered regularly interspaced short palindromic repeat)‐Cas (CRISPR‐associated protein) system, a prokaryotic RNA‐based adaptive immune system against viral infection, is emerging as a powerful genome editing tool in broad research areas. To further improve and expand its functionality, various CRISPR delivery strategies have been tested and optimized, and key CRISPR system components such as Cas protein have been engineered with different purposes. Benefiting from more in‐depth understanding and further development of CRISPR, versatile CRISPR‐based platforms for genome editing have been rapidly developed to advance investigations in biology and biomedicine. In biological research area, CRISPR has been widely adopted in both fundamental and applied research fields, such as genomic and epigenomic modification, genome‐wide screening, cell and animal research, agriculture transforming, livestock breeding, food manufacture, industrial biotechnology, and gene drives in disease agents control. In biomedical research area, CRISPR has also shown its extensive applicability in the establishment of animal models for genetic disorders, generation of tissue donors, implementation of antimicrobial and antiviral studies, identification and assessment of new drugs, and even treatment for clinical diseases. However, there are still several problems to consider, and the biggest concerns are the off‐target effects and ethical issues of this technology. In this prospect article, after highlighting recent development of CRISPR systems, we outline different applications and current limitations of CRISPR in biological and biomedical investigation. Finally, we provide a perspective on future development and potential risks of this multifunctional technology. J. Cell. Biochem. 119: 52–61, 2018. © 2017 Wiley Periodicals, Inc.     

A physical map of important QTLs,functional markers and genes available for sesame breeding programs

Sesame is one of the oldest oilseed crops grown mainly in Africa and Asia. Although genetic and genomic studies on sesame have started late, the past 5 years have witnessed extensive progresses in these areas on this crop. Important genomic sequence resources such as functional markers, genes and QTLs linked to agronomically important traits, have been generated through linkage mapping and association analysis to assist sesame improvement programs. However, most of these data are scattered in different maps making them hard to be exploited efficiently in breeding programs. In this study, we report a comprehensive physical map gathering 151 published genomic sequence resources which highlighted some hotspot functional regions in the sesame genome. Moreover, 83,135 non-redundant SSRs have been supplied along with their physical position and motif composition. This will assist future research in fine mapping or pinpointing more functional genes based on the already published QTLs and functional markers. This physical map represents a good landmark for further non-overlapping genetic and genomic studies working towards sesame improvement.