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  Subjects -> BIOLOGY (Total: 3126 journals)
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BIOTECHNOLOGY (236 journals)                  1 2 | Last

Showing 1 - 200 of 239 Journals sorted alphabetically
3 Biotech     Open Access   (Followers: 8)
Advanced Biomedical Research     Open Access  
Advances in Bioscience and Biotechnology     Open Access   (Followers: 16)
Advances in Genetic Engineering & Biotechnology     Hybrid Journal   (Followers: 7)
Advances in Regenerative Medicine     Open Access   (Followers: 2)
African Journal of Biotechnology     Open Access   (Followers: 6)
Algal Research     Partially Free   (Followers: 11)
American Journal of Biochemistry and Biotechnology     Open Access   (Followers: 66)
American Journal of Bioinformatics Research     Open Access   (Followers: 7)
American Journal of Polymer Science     Open Access   (Followers: 32)
Anadolu University Journal of Science and Technology : C Life Sciences and Biotechnology     Open Access  
Animal Biotechnology     Hybrid Journal   (Followers: 8)
Annales des Sciences Agronomiques     Full-text available via subscription  
Applied Biochemistry and Biotechnology     Hybrid Journal   (Followers: 43)
Applied Biosafety     Hybrid Journal  
Applied Food Biotechnology     Open Access   (Followers: 3)
Applied Microbiology and Biotechnology     Hybrid Journal   (Followers: 64)
Applied Mycology and Biotechnology     Full-text available via subscription   (Followers: 4)
Arthroplasty Today     Open Access   (Followers: 1)
Artificial Cells, Nanomedicine and Biotechnology     Hybrid Journal   (Followers: 1)
Asia Pacific Biotech News     Hybrid Journal   (Followers: 2)
Asian Journal of Biotechnology     Open Access   (Followers: 9)
Asian Pacific Journal of Tropical Biomedicine     Open Access   (Followers: 2)
Australasian Biotechnology     Full-text available via subscription   (Followers: 1)
Banat's Journal of Biotechnology     Open Access  
BBR : Biochemistry and Biotechnology Reports     Open Access   (Followers: 5)
Beitr?ge zur Tabakforschung International/Contributions to Tobacco Research     Open Access   (Followers: 2)
Bio-Algorithms and Med-Systems     Hybrid Journal   (Followers: 2)
Bio-Research     Full-text available via subscription   (Followers: 3)
Bioactive Materials     Open Access   (Followers: 1)
Biocatalysis and Agricultural Biotechnology     Hybrid Journal   (Followers: 4)
Biocybernetics and Biological Engineering     Full-text available via subscription   (Followers: 5)
Bioethics UPdate     Hybrid Journal   (Followers: 1)
Biofuels     Hybrid Journal   (Followers: 11)
Biofuels Engineering     Open Access   (Followers: 1)
Biological & Pharmaceutical Bulletin     Full-text available via subscription   (Followers: 4)
Biological Cybernetics     Hybrid Journal   (Followers: 10)
Biomarkers and Genomic Medicine     Open Access   (Followers: 3)
Biomarkers in Drug Development     Partially Free   (Followers: 1)
Biomaterials Research     Open Access   (Followers: 4)
BioMed Research International     Open Access   (Followers: 4)
Biomédica     Open Access  
Biomedical and Biotechnology Research Journal     Open Access  
Biomedical Engineering Research     Open Access   (Followers: 6)
Biomedical Glasses     Open Access  
Biomedical Reports     Full-text available via subscription  
BioMedicine     Open Access  
Biomedika     Open Access  
Bioprinting     Hybrid Journal   (Followers: 1)
Bioresource Technology Reports     Hybrid Journal   (Followers: 1)
Bioscience, Biotechnology, and Biochemistry     Hybrid Journal   (Followers: 21)
Biosensors Journal     Open Access  
Biosimilars     Open Access   (Followers: 1)
Biosurface and Biotribology     Open Access  
Biotechnic and Histochemistry     Hybrid Journal   (Followers: 1)
BioTechniques : The International Journal of Life Science Methods     Full-text available via subscription   (Followers: 28)
Biotechnologia Acta     Open Access   (Followers: 1)
Biotechnologie, Agronomie, Société et Environnement     Open Access   (Followers: 2)
Biotechnology     Open Access   (Followers: 6)
Biotechnology & Biotechnological Equipment     Open Access   (Followers: 4)
Biotechnology Advances     Hybrid Journal   (Followers: 33)
Biotechnology and Applied Biochemistry     Hybrid Journal   (Followers: 44)
Biotechnology and Bioengineering     Hybrid Journal   (Followers: 154)
Biotechnology and Bioprocess Engineering     Hybrid Journal   (Followers: 5)
Biotechnology and Genetic Engineering Reviews     Hybrid Journal   (Followers: 13)
Biotechnology and Health Sciences     Open Access   (Followers: 1)
Biotechnology and Molecular Biology Reviews     Open Access   (Followers: 2)
Biotechnology Annual Review     Full-text available via subscription   (Followers: 5)
Biotechnology for Biofuels     Open Access   (Followers: 10)
Biotechnology Frontier     Open Access   (Followers: 2)
Biotechnology Journal     Hybrid Journal   (Followers: 16)
Biotechnology Law Report     Hybrid Journal   (Followers: 4)
Biotechnology Letters     Hybrid Journal   (Followers: 34)
Biotechnology Progress     Hybrid Journal   (Followers: 40)
Biotechnology Reports     Open Access  
Biotechnology Research International     Open Access   (Followers: 1)
Biotechnology Techniques     Hybrid Journal   (Followers: 10)
Biotecnología Aplicada     Open Access  
Bioteknologi (Biotechnological Studies)     Open Access  
BIOTIK : Jurnal Ilmiah Biologi Teknologi dan Kependidikan     Open Access  
Biotribology     Hybrid Journal   (Followers: 1)
BMC Biotechnology     Open Access   (Followers: 16)
Cell Biology and Development     Open Access  
Chinese Journal of Agricultural Biotechnology     Full-text available via subscription   (Followers: 4)
Communications in Mathematical Biology and Neuroscience     Open Access  
Computational and Structural Biotechnology Journal     Open Access   (Followers: 2)
Computer Methods and Programs in Biomedicine     Hybrid Journal   (Followers: 8)
Copernican Letters     Open Access   (Followers: 1)
Critical Reviews in Biotechnology     Hybrid Journal   (Followers: 20)
Crop Breeding and Applied Biotechnology     Open Access   (Followers: 3)
Current Bionanotechnology     Hybrid Journal  
Current Biotechnology     Hybrid Journal   (Followers: 4)
Current Opinion in Biomedical Engineering     Hybrid Journal   (Followers: 1)
Current Opinion in Biotechnology     Hybrid Journal   (Followers: 56)
Current Pharmaceutical Biotechnology     Hybrid Journal   (Followers: 9)
Current Research in Bioinformatics     Open Access   (Followers: 12)
Current Trends in Biotechnology and Chemical Research     Open Access   (Followers: 3)
Current trends in Biotechnology and Pharmacy     Open Access   (Followers: 8)
EBioMedicine     Open Access  
Electronic Journal of Biotechnology     Open Access  
Entomologia Generalis     Full-text available via subscription  
Environmental Science : Processes & Impacts     Full-text available via subscription   (Followers: 4)
Experimental Biology and Medicine     Hybrid Journal   (Followers: 3)
Folia Medica Indonesiana     Open Access  
Food Bioscience     Hybrid Journal  
Food Biotechnology     Hybrid Journal   (Followers: 9)
Food Science and Biotechnology     Hybrid Journal   (Followers: 8)
Frontiers in Bioengineering and Biotechnology     Open Access   (Followers: 6)
Frontiers in Systems Biology     Open Access   (Followers: 2)
Fungal Biology and Biotechnology     Open Access   (Followers: 2)
GM Crops and Food: Biotechnology in Agriculture and the Food Chain     Full-text available via subscription   (Followers: 1)
GSTF Journal of BioSciences     Open Access  
HAYATI Journal of Biosciences     Open Access  
Horticulture, Environment, and Biotechnology     Hybrid Journal   (Followers: 11)
IEEE Transactions on Molecular, Biological and Multi-Scale Communications     Hybrid Journal   (Followers: 1)
IET Nanobiotechnology     Hybrid Journal   (Followers: 2)
IIOAB Letters     Open Access  
IN VIVO     Full-text available via subscription   (Followers: 4)
Indian Journal of Biotechnology (IJBT)     Open Access   (Followers: 2)
Indonesia Journal of Biomedical Science     Open Access   (Followers: 2)
Indonesian Journal of Biotechnology     Open Access   (Followers: 1)
Indonesian Journal of Medicine     Open Access  
Industrial Biotechnology     Hybrid Journal   (Followers: 17)
International Biomechanics     Open Access  
International Journal of Bioinformatics Research and Applications     Hybrid Journal   (Followers: 13)
International Journal of Biomechatronics and Biomedical Robotics     Hybrid Journal   (Followers: 4)
International Journal of Biomedical Research     Open Access   (Followers: 2)
International Journal of Biotechnology     Hybrid Journal   (Followers: 5)
International Journal of Biotechnology and Molecular Biology Research     Open Access   (Followers: 3)
International Journal of Biotechnology for Wellness Industries     Partially Free   (Followers: 1)
International Journal of Environment, Agriculture and Biotechnology     Open Access   (Followers: 5)
International Journal of Functional Informatics and Personalised Medicine     Hybrid Journal   (Followers: 4)
International Journal of Medicine and Biomedical Research     Open Access   (Followers: 1)
International Journal of Nanotechnology and Molecular Computation     Full-text available via subscription   (Followers: 3)
International Journal of Radiation Biology     Hybrid Journal   (Followers: 4)
Iranian Journal of Biotechnology     Open Access  
ISABB Journal of Biotechnology and Bioinformatics     Open Access  
Italian Journal of Food Science     Open Access   (Followers: 1)
JMIR Biomedical Engineering     Open Access  
Journal of Biometrics & Biostatistics     Open Access   (Followers: 3)
Journal of Bioterrorism & Biodefense     Open Access   (Followers: 6)
Journal of Petroleum & Environmental Biotechnology     Open Access   (Followers: 1)
Journal of Advanced Therapies and Medical Innovation Sciences     Open Access  
Journal of Advances in Biotechnology     Open Access   (Followers: 5)
Journal Of Agrobiotechnology     Open Access  
Journal of Analytical & Bioanalytical Techniques     Open Access   (Followers: 7)
Journal of Animal Science and Biotechnology     Open Access   (Followers: 4)
Journal of Applied Biomedicine     Open Access   (Followers: 2)
Journal of Applied Biotechnology     Open Access   (Followers: 2)
Journal of Applied Biotechnology Reports     Open Access   (Followers: 2)
Journal of Applied Mathematics & Bioinformatics     Open Access   (Followers: 5)
Journal of Biologically Active Products from Nature     Hybrid Journal   (Followers: 1)
Journal of Biomaterials and Nanobiotechnology     Open Access   (Followers: 6)
Journal of Biomedical Photonics & Engineering     Open Access  
Journal of Biomedical Practitioners     Open Access  
Journal of Bioprocess Engineering and Biorefinery     Full-text available via subscription  
Journal of Bioprocessing & Biotechniques     Open Access  
Journal of Biosecurity Biosafety and Biodefense Law     Hybrid Journal   (Followers: 3)
Journal of Biotechnology     Hybrid Journal   (Followers: 64)
Journal of Biotechnology and Strategic Health Research     Open Access  
Journal of Chemical and Biological Interfaces     Full-text available via subscription   (Followers: 1)
Journal of Chemical Technology & Biotechnology     Hybrid Journal   (Followers: 9)
Journal of Chitin and Chitosan Science     Full-text available via subscription   (Followers: 1)
Journal of Colloid Science and Biotechnology     Full-text available via subscription  
Journal of Commercial Biotechnology     Full-text available via subscription   (Followers: 6)
Journal of Crop Science and Biotechnology     Hybrid Journal   (Followers: 3)
Journal of Essential Oil Research     Hybrid Journal   (Followers: 2)
Journal of Experimental Biology     Full-text available via subscription   (Followers: 25)
Journal of Genetic Engineering and Biotechnology     Open Access   (Followers: 5)
Journal of Ginseng Research     Open Access  
Journal of Industrial Microbiology and Biotechnology     Hybrid Journal   (Followers: 17)
Journal of Integrative Bioinformatics     Open Access  
Journal of Medical Imaging and Health Informatics     Full-text available via subscription  
Journal of Molecular Biology and Biotechnology     Open Access  
Journal of Molecular Microbiology and Biotechnology     Full-text available via subscription   (Followers: 11)
Journal of Nano Education     Full-text available via subscription  
Journal of Nanobiotechnology     Open Access   (Followers: 4)
Journal of Nanofluids     Full-text available via subscription   (Followers: 1)
Journal of Organic and Biomolecular Simulations     Open Access  
Journal of Plant Biochemistry and Biotechnology     Hybrid Journal   (Followers: 4)
Journal of Science and Applications : Biomedicine     Open Access  
Journal of the Mechanical Behavior of Biomedical Materials     Hybrid Journal   (Followers: 12)
Journal of Trace Elements in Medicine and Biology     Hybrid Journal   (Followers: 1)
Journal of Tropical Microbiology and Biotechnology     Full-text available via subscription  
Journal of Yeast and Fungal Research     Open Access   (Followers: 1)
Marine Biotechnology     Hybrid Journal   (Followers: 4)
Meat Technology     Open Access  
Messenger     Full-text available via subscription  
Metabolic Engineering Communications     Open Access   (Followers: 4)
Metalloproteinases In Medicine     Open Access  
Microbial Biotechnology     Open Access   (Followers: 9)
MicroMedicine     Open Access   (Followers: 3)
Molecular and Cellular Biomedical Sciences     Open Access   (Followers: 1)
Molecular Biotechnology     Hybrid Journal   (Followers: 13)
Molecular Genetics and Metabolism Reports     Open Access   (Followers: 3)
Nanobiomedicine     Open Access  
Nanobiotechnology     Hybrid Journal   (Followers: 2)
Nanomaterials and Nanotechnology     Open Access  
Nanomedicine and Nanobiology     Full-text available via subscription  
Nanomedicine Research Journal     Open Access  

        1 2 | Last

Journal Cover
Applied Mycology and Biotechnology
Number of Followers: 4  
 
  Full-text available via subscription Subscription journal
ISSN (Print) 1874-5334
Published by Elsevier Homepage  [3161 journals]
  • Experimental design and analysis of microarray data
    • Abstract: 2006
      Publication year: 2006
      Source:Applied Mycology and Biotechnology, Volume 6

      The advent of microarray technology has significantly changed the way we can quantitatively measure and observe gene expression at the mRNA level within a given biological sample of interest, allowing for the monitoring of tens to hundreds of thousands of genes within a single experiment. The two main array platforms are spotted two-colour arrays and one-colour in situ-synthesized arrays. Microarrays are used for a wide range of applications including gene annotation, investigation of gene-gene interactions, elucidation of gene regulatory networks and gene-expression profiling of Saccharomyces cerevisiae and other fungal organisms. Academic researchers and both the pharmaceutical and agricultural industries have an enormous interest in developing microarrays both as diagnostic tools and for use in basic research into how pathogens, such as fungi, interact with their host. Microarray experiments generate vast quantities of raw gene expression data, therefore good experimental design and statistical analysis is required for the extraction of accurate and useful information regarding the expression of genes. In this review we firstly provide an overview of the arrival and development of microarray technology. We then focus on the issues surrounding experimental design and the processing of microarray images, followed by a discussion on methods for cleaning and normalizing raw gene expression data and a final discussion of the importance statistical analysis plays in identifying differentially expressed genes.

      PubDate: 2012-12-17T18:14:22Z
       
  • Methods for protein homology modelling
    • Abstract: 2006
      Publication year: 2006
      Source:Applied Mycology and Biotechnology, Volume 6

      Homology modelling has become a useful tool for the prediction of protein structure when only sequence data are available. Structural information is often more valuable than sequence alone for determining protein function. Homology modelling is potentially a very useful tool for the mycologist, as the number of fungal gene sequences available has exploded in recent years, whilst the number of experimentally determined fungal protein structures remains low. Programs available for homology modelling utilise different approaches and methods to produce the final model. Within each step of the homology modelling process, many factors affect the quality of the model produced, and appropriate selection of the program can significantly improve the quality of the model. This review discusses the advantages and limitations of the currently available methods and programs and provides a starting point for novices wishing to create a structural model. We have taken a practical approach as we hope to enable any scientist to utilise homology modelling as a tool for the analysis of their protein, or genome, of interest.

      PubDate: 2012-12-17T18:14:22Z
       
  • Phylogenetic network construction approaches
    • Abstract: 2006
      Publication year: 2006
      Source:Applied Mycology and Biotechnology, Volume 6

      This chapter presents a review of the mathematical techniques available to construct phylogenies and to represent reticulate evolution. Phylogenies can be estimated using distance-based, maximum parsimony, or maximum likelihood methods. Bayesian methods have recently become available to construct phylogenies. Reticulate evolution includes horizontal gene transfer between taxa, hybridization events, and homoplasy. Genetic recombination also creates reticulate evolution within lineages. Several methods are now available to construct reticulated networks of various kinds. Twelve such methods and the accompanying software are described in this review chapter.

      PubDate: 2012-12-17T18:14:22Z
       
  • Issues in comparative fungal genomics
    • Abstract: 2006
      Publication year: 2006
      Source:Applied Mycology and Biotechnology, Volume 6

      Biologists face an overwhelming richness of nucleotide and protein sequence data. By the middle of 2005, there were almost 300 complete genomes that were publicly accessible. Most of these were archeal or bacterial since prokaryotic genomes are much smaller than eukaryotic genomes. Among eukaryotes, fungi, particularly yeasts, have some of the smallest genome sizes and hence represent the highest number of complete or almost complete genomes sequenced. By mid-2005, there were over 43 fungal genomes that were completely or almost completely sequenced and publicly accessible. What are the relationships among fungi and between fungi and other organisms' What type of genes and pathways are required for pathogenicity and other fungal lifestyles' Researchers are addressing these types of questions with data from high-throughput genomic sequencing. This review examines some recent uses of fungal genomic data in comparative genome analyses. Comparative genomics can facilitate research into the following areas: evolution, phylogenetics, targeted drugs, gene discovery, and gene function. Each of these is discussed as well as the availability and ownership of the genomic data, and the concepts of homology (homologs, orthologs, paralogs) and similarity.

      PubDate: 2012-12-17T18:14:22Z
       
  • Fungal genomic annotation
    • Abstract: 2006
      Publication year: 2006
      Source:Applied Mycology and Biotechnology, Volume 6

      Sequencing technology in the last decade has advanced at an incredible pace. Currently there are hundreds of microbial genomes available with more still to come. Automated genome annotation aims to analyze this amount of sequence data in a high-throughput fashion and help researches to understand the biology of these organisms. Manual curation of automatically annotated genomes validates the predictions and set up ‘gold’ standards for improving the methodologies used. Here we review the methods and tools used for annotation of fungal genomes in different genome sequencing centers.

      PubDate: 2012-12-17T18:14:22Z
       
  • Bioinformatics packages for sequence analysis
    • Abstract: 2006
      Publication year: 2006
      Source:Applied Mycology and Biotechnology, Volume 6

      Research paradigms in modern biology are shifting from a single gene to a genome-wide scale. Two major contributions toward this new trend are large-scale genome sequencing and bioinformatics. Recently, bioinformatics has emerged as a new science field that provides computational tools for collecting and maintaining complex biological data. Along with an exponential accumulation of sequence data, many bioinformatics software and algorithms have been developed to assist in genome scale analyses. A comprehensive knowledge of these tools can help not only to understand gene functions and genome organizations, but also to provide an opportunity to develop new tools that can answer many biological questions.

      PubDate: 2012-12-17T18:14:22Z
       
  • A survey of computational methods used in microarray data interpretation
    • Abstract: 2006
      Publication year: 2006
      Source:Applied Mycology and Biotechnology, Volume 6

      In a companion chapter in this volume, Wilson et al. (this volume, chapter by Wilson et al.) provide a detailed account of the experimental design and statistical analysis of microarray data. Their chapter is of interest to researchers planning microarray experiments capable of yielding data that can be statistically analyzed to insure reliable levels of confidence. In contrast, the present chapter emphasizes what can be done with the gathered data so as to simplify the huge task of interpreting the expression levels of tens of thousands of genes. In the companion chapter the authors assume the availability of statistical programs that are often used in the design of experiments. In this chapter we explore in greater detail the algorithms that process the collected data to obtain further information about cell behavior. Many of the algorithms described here aim at grouping similar data. We also explore microarray usage that is not addressed in the companion chapter.

      PubDate: 2012-12-17T18:14:22Z
       
  • Computational methods in genome research
    • Abstract: 2006
      Publication year: 2006
      Source:Applied Mycology and Biotechnology, Volume 6

      Computational biology has revolutionized biological and medical research. In the last two decades, a large number of computer methods have been developed to analyze DNA, RNA and protein sequences. These computer methods are playing a vital role in extracting useful information from sequences of genomes. These computational methods have been developed by different academic groups all over the world to serve the biological community. The methods are available as stand alone programs or on-line web servers. Most of these software packages are available free for academicians (freeware). In this chapter, we have described the major computational methods available for biologists to extract information from sequences. This chapter covers computational methods f r i) genome annotation; ii) comparative genomics; iii) protein structure prediction; iv) functional classification of proteins; and v) identification of potential vaccine candidates. These software packages are not available from a single source so it is not easy for users to obtain the software of their interest. In order to overcome this problem, attempts have been made to collect and compile a list of free biological software programs that includes software at EMBL and Indiana University. A catalog of biological software (Biocatalog) is also available on the internet (Rodriguez-Tome 1998). Recently, a repository of free software in biology has been created at Institute of Microbial Technology, Chandigarh, India which contains more than 800 free software packages.

      PubDate: 2012-12-17T18:14:22Z
       
  • Creating fungal pathway/genome databases using pathway tools
    • Abstract: 2006
      Publication year: 2006
      Source:Applied Mycology and Biotechnology, Volume 6

      The Pathway Tools software allows a group of scientists to create, update, and publish on the Web an evolving knowledge resource describing the genome and biochemical networks of the organism. Such a knowledge resource will minimize duplication of experimental effort, ensure that all relevant knowledge will be brought to bear on interpreting new experimental results, and permit systemlevel computational analyses. Creation of a new Pathway/Genome Database (PGDB) by Pathway Tools includes inference of fungal metabolic pathways and pathway hole fillers (genes that code for enzymes missing from predicted pathways). Pathway Tools also infers the transport reactions present in an organism. A collection of interactive editing tools allows refinement of a PGDB by adding or modifying gene functions or pathways to capture knowledge from the biomedical literature. Pathway Tools provides a variety of query and visualization capabilities including a genome browser, displays of biochemical pathways, and a visualization of the cellular biochemical network. The Omics Viewer paints multiple types of functional genomics data onto that cellular network diagram. Comparative genomics capabilities allow comparison with other fungal Pathway/Genome Databases.

      PubDate: 2012-12-17T18:14:22Z
       
  • Comparative genomic analysis of glycoylation pathways in yeast, plants and
           higher eukaryotes
    • Abstract: 2006
      Publication year: 2006
      Source:Applied Mycology and Biotechnology, Volume 6

      N-linked glycosylation is an essential modification of secretory and membrane proteins in all eukaryotic cells. Here, we review the current metabolic pathways of N-linked oligosaccharide biosynthesis in the endoplasmic reticulum and in the Golgi apparatus for yeasts: Saccharomyces cerevisiae and Schizosaccharomyces pombe, and higher eukaryotes: plants and human. The evolutionarily conserved proteins, processed in the cytosolic and the luminal side of the ER membrane, and the unique genes and their specific functions, occurring in the Golgi complex, for each selected organism, will be collated and discussed. This precise knowledge of the glycosylation pathway contributes to better understanding of the N-linked glycoprotein biosynthesis among different species, resulting in the recently successfully engineered strains for heterologous gene expression systems for industrial and therapeutic protein production.

      PubDate: 2012-12-17T18:14:22Z
       
  • Genomic rearrangement and disease LARaLINK 2.0: Datamining for clinical
           cytogenetics
    • Abstract: 2006
      Publication year: 2006
      Source:Applied Mycology and Biotechnology, Volume 6

      A growing pool of genomic data is being archived to online public databases. These have the potential to impact both the diagnosis of genetically linked diseases as well as to aid in defining their genesis. The current in-silico tools for cytogenetic analysis have generally been targeted to the academic and industrial communities for use in research into the origins of disease. In comparison, few tools have been developed to integrate the multiple online resources for the clinical setting. We have addressed this deficit through a web-delivered application, LARaLINK 2.0: Loci Analysis for Rearrangements Link version 2.0 http://www.LARaLINK.bioinformatics.wayne.edu:8080/unigene controlled hierarchical vocabulary for mining cDNA and microarray expression data. This tool now provides researchers and clinicians with the means to effectively use cytogenetic data to rapidly assess disease association. The investigator is delivered a defined set of candidate disease genes together with the supporting evidence for their expression and disrupted phenotypes.

      PubDate: 2012-12-17T18:14:22Z
       
  • Sequence-based analysis of fungal secretomes
    • Abstract: 2006
      Publication year: 2006
      Source:Applied Mycology and Biotechnology, Volume 6

      Secreted proteins play critical biological roles in fungal species. Here we review and assess computational protocols for the identification of secreted proteins using their amino acid sequences. Protein sequences are screened for the presence of secretory signal peptides and the lack of features that prevent the delivery of proteins to the extracellular space, such as transmembrane segments, C-terminal ER-retention signals, or glycosylphosphatidylinositol (GPI) anchors. We apply such techniques to the complete genomes of 10 fungal species, identifying their putative complete sets of secreted proteins (their secretomes). Particular attention is given to predictions for the yeast secretome, which can be validated using the curated subcellular localizations of proteins from yeast. We make distinctions between the soluble and non-soluble portions of secretomes, discussing the roles of putative GPI proteins in the fungal cell wall.

      PubDate: 2012-12-17T18:14:22Z
       
  • Using web agents for data mining of fungal genomes
    • Abstract: 2006
      Publication year: 2006
      Source:Applied Mycology and Biotechnology, Volume 6

      We created an application called Sight, a Java™-based package that provides a user-friendly interface to generate and connect agents for automatic genomic data mining without requiring programming skills from the user. Sight was originally developed to automate analysis of the human genome and attempts to generate web agents for fungus-related Internet resources revealed that some of those resources use new methods of representing the information they report, and some servers returned multiple intermediate pages leading towards their response, which created difficulties for automated recovery of results. Consequently, it was not possible to use effectively the old version of Sight so this version of the application was adapted with a little additional programming, creating a new version for which these features of the fungal genome servers do not represent a problem. The new version of Sight (v. 3.0.0) that is tailored to servers carrying fungal databases is freely available for download from the project website at these URLs: http://www.bioinformatics.org/jSight/ and http://www.jsight.sourceforge.net/index_SF.htm.

      PubDate: 2012-12-17T18:14:22Z
       
  • Searching biological databases using biolinguistic methods
    • Abstract: 2006
      Publication year: 2006
      Source:Applied Mycology and Biotechnology, Volume 6

      Existing methods based on homology rely on current research in genome analysis using n-grams (i.e. breaking the genome up into “words or “syllables”), protein motifs, and other bio-linguistic techniques have shown promise. In particular, as new protein structures and functions are identified, these bio-linguistic approaches can reach across multiple genomes to identify similar genes, elucidating their functions. Likewise new genes or disease gene variations identified through sequencing of individuals can be compared to known genes for identification of changes to their “normal” functions. In this review, we describe algorithms for searching biological databases using the n-gram analysis. Our results demonstrate that these algorithms are more sensitive than those currently available for both genomics and proteomics analysis, allowing a more accurate portrayal of similarity of gene function. The algorithm's capabilities extend to the comparison of biological sequences using phylogenetic and bio-chemical properties that enable the results to be significant from perspective of structure and function of genomic and proteomic data analysis. Recent years have seen an explosive growth in the speed and capacity of data collection and storage devices. The biological databases are experiencing an unprecedented growth where they are doubling every fifteen months. The algorithms described are amenable to parallelization with effective domain database partitioning. This makes them an attractive alternative for searching protein databases by developing high-speed functionally partitioned searches.

      PubDate: 2012-12-17T18:14:22Z
       
  • Recombination in filamentous fungi
    • Abstract: 2005
      Publication year: 2005
      Source:Applied Mycology and Biotechnology, Volume 5

      Although their contribution to our early understanding of meiotic recombination is unequalled, in the latter part of the last century filamentous fungi fell behind their more genetically tractable single-celled cousin, Saccharomyces cerevisiae in this area. However, an increase in ease of DNA manipulation resulting from recent genome projects, coupled with the unique biology of filamentous fungi has resulted in something of a revival of their utility in unraveling the ways in which genetic information is shuffled during meiosis. In this review we consider features of meiotic recombination whose elucidation has depended upon a substantial contribution from filamentous fungi. We then focus on the more recent contributions this group of fungi has made to the understanding of how genetic recombination is achieved, emphasizing how the unique biology of filamentous fungi has been exploited to address questions not easily answered using other model systems.

      PubDate: 2012-12-17T18:14:22Z
       
  • Fungal intervening sequences
    • Abstract: 2005
      Publication year: 2005
      Source:Applied Mycology and Biotechnology, Volume 5

      Since the late 1970s it had become clear that the coding sequence of many eukaryotic genes is disrupted by genetic elements, intervening sequences, which must be removed prior to host gene function. Intervening sequences can be classified into introns and inteins. Introns are excised from the primary RNA transcript by a process termed splicing, whilst inteins are transcribed and translated together with their host protein and are removed from the unprocessed protein. Based on sequence homology, secondary structure and the splicing mechanism, introns can be classified into spliceosomal mRNA introns, group I introns and group II introns. Recent annotations of several fungal genomes revealed that introns and inteins are integral elements of fungal genes. These intervening sequences perform various important functions. They are carriers of transcription regulatory elements, contain signals for mRNA stability and export from the nucleus and participate in gene evolution.

      PubDate: 2012-12-17T18:14:22Z
       
  • Gene silencing as a tool for the identification of gene function in fungi
    • Abstract: 2005
      Publication year: 2005
      Source:Applied Mycology and Biotechnology, Volume 5

      The use of RNA-mediated gene silencing for genetic analysis has revolutionized functional genomics, providing a tool to carry out genome-wide studies of gene function. With respect to traditional methods of genetic analysis whereby loss-of-function alleles are created by mutagenesis at the DNA level, gene silencing mediated by RNA is a post-transcriptional process that reduces the expression of a specific gene by the sequence-specific degradation of homologous mRNAs. This method of gene silencing, as well as being highly efficient and cost effective, is especially relevant for the analysis of essential genes that may escape phenotypic screening following random mutagenesis, as strains lacking an essential function are not viable.

      PubDate: 2012-12-17T18:14:22Z
       
  • The DNA damage response of filamentous fungi: Novel features associated
           with a multicellular lifestyle
    • Abstract: 2005
      Publication year: 2005
      Source:Applied Mycology and Biotechnology, Volume 5

      Living organisms have to protect the integrity of their genomes in order to survive. A mechanism called the DNA damage response was developed during evolution to ensure the maintenance of genome integrity. Damage to DNA induces several cellular responses, including the repair of DNA lesions, the activation of cell cycle checkpoints, and cell death if the damage is not repaired. In this review, we first summarize known features of the DNA damage response, emphasizing those elements that function as sensors of DNA damage, transducers of the damage signal, or effectors that mediate the response. Subsequently, we focus on aspects of the fungal DNA damage response that distinguish it from the well-characterized yeast models. These include the characterization of conserved repair proteins that first appear in the multicellular fungi, the potential role of hyphal cell death in the fungal DNA damage response, the challenge of regulating the response in a multinucleate cell, and the novel interaction between cell cycle checkpoints and hyphal morphogenesis. Although, in some cases, our analyses may be somewhat speculative, we propose that these aspects of the fungal DNA damage response may serve as valuable models that yield important insight into analogous processes in other multicellular eukaryotes.

      PubDate: 2012-12-17T18:14:22Z
       
  • The cfp Genes (cfp-1 and cfp-2) of Neurospora crassa: A tale of a bunch of
           filaments, one enzyme, and two genes
    • Abstract: 2005
      Publication year: 2005
      Source:Applied Mycology and Biotechnology, Volume 5

      For over three decades, scientists have been puzzled by the observation of cryptic filamentous structures in the cytoplasm of filamentous fungi. This chapter describes major developments in the characterization of 8 to 10-nm in diameter cytoplasmic filaments from Neurospora crassa. We review the studies that demonstrated that these structures are made of the tetrameric protein pyruvate decarboxylase (PDC), a key enzyme catalyzing the branch-point step between the respiration and fermentation pathways in fungi. Similar arrangements of PDC have been found in N. tetrasperma, Podospora anserina and Sordaria macrospora, showing that PDC filaments are ubiquitous structures in fungi. A complex array of signals, and possibly alternative splicing, modulate the expression of the genes cfp-1 and cfp-2 encoding PDC in N. crassa. Challenging future studies should address the relationship between the supramolecular organization and function of PDC in filamentous fungi.

      PubDate: 2012-12-17T18:14:22Z
       
  • Applications of fungal site-specific recombination as a tool in
           biotechnology and basic biology
    • Abstract: 2005
      Publication year: 2005
      Source:Applied Mycology and Biotechnology, Volume 5

      Two classes of conservative site-specific recombinases, those belonging to the tyrosine and serine families, have been identified, and several of its members characterized in genetic and biochemical detail. These families are named after the active site amino acid, tyrosine or serine, that is utilized as the nucleophile during the strand breaking step of recombination. The Flp recombinase encoded by the 2 micron plasmid of Saccharomyces cerevisiae and related recombinases encoded by similar plasmids found in other yeast species belong to the tyrosine family. The Flp protein has provided several insights into the mechanism of target DNA recognition, strand cleavage and strand exchange during the recombination reaction. Here we describe how the Flp system has been used as a tool for tackling basic and applied problems in biology.

      PubDate: 2012-12-17T18:14:22Z
       
  • Heterologous gene expression in filamentous fungi: A holistic view
    • Abstract: 2005
      Publication year: 2005
      Source:Applied Mycology and Biotechnology, Volume 5

      As scavengers of recalcitrant polymers in the nature, filamentous fungi are excellent secretors of proteins outside the growing mycelium. This characteristic has been targeted and systematically improved in industrially-exploited production strains. Over the last five years there has been a significant shift from one-gene-at-a-time approaches to wider understanding of the organism, made possible, for example by gene array and proteome technologies that can now also be applied to filamentous fungi. This has presented novel opportunities for studies into gene regulation under specific conditions such as a particular carbon source or developmental stage with a view of advancing the basic knowledge and gaining information that can be applied for strain and process improvement. Filamentous fungi offer enormous potential for efficient and large scale production of heterologous gene products. Importantly, protein secretion provides a platform for the eukaryotic style posttranslational modification of gene products. Fungi are cheap to cultivate and down-stream processing is made easy with no need to break cells open for product recovery. In order to capitalize on fungi as heterologous production hosts, research is now directed to revealing the cellular mechanisms for internal protein quality control, secretion stress, functional genomics of protein expression and secretion, protein modification and linking the physiology to productivity.

      PubDate: 2012-12-17T18:14:22Z
       
  • Expression and engineering of fungal hydrophobins
    • Abstract: 2005
      Publication year: 2005
      Source:Applied Mycology and Biotechnology, Volume 5

      Filamentous fungi secrete unique proteins called hydrophobins. Upon contact with a hydrophilic-hydrophobic interface these proteins self-assemble into an amphipathic membrane. Differences in the solubility of the assemblages divides hydrophobins into two groups. The class I hydrophobins form highly insoluble membranes that can only be dissolved in trifluoroacetic acid (TFA) and formic acid, while assemblies of class II hydrophobins can be readily dissolved in ethanol or SDS. Self-assembly allows hydrophobins to change the nature of a surface; hydrophobic surfaces turn hydrophilic and hydrophilic surfaces become hydrophobic. These properties make hydrophobins interesting candidates for use in technical and medical applications. Class I hydrophobins seem to be particularly interesting to coat solid surfaces, while class II seem to be the molecules of choice for use in liquid systems. Application of hydrophobins would benefit from the availability of a library of hydrophobin variants. Moreover, production should be increased. Nature provides a fast amount of hydrophobins with slightly different characteristics. In addition to these hydrophobins, new variants may be obtained via random mutagenesis or by rational design. Functional class I hydrophobins (i.e. capable of self-assembling into an amphipathic membrane) could only be produced by filamentous fungi that by nature secrete hydrophobins into the culture medium. However, yields are still relatively low. On the other hand, class II hydrophobins can already be produced at high levels using Trichoderma reesei as a host.

      PubDate: 2012-12-17T18:14:22Z
       
  • Genetic regulation of carotenoid biosynthesis in fungi
    • Abstract: 2005
      Publication year: 2005
      Source:Applied Mycology and Biotechnology, Volume 5

      Fungal carotenoids are synthesized by the isoprenoid pathway with isopentenyl pyrophosphate as the general precursor. They are found in all divisions of the fungal realm, and several are at the edge of being exploited at an industrial scale for satisfying an increasing demand for carotenoid pigments, food and feed additives, and components of cosmetics and pharmaceuticals. Fungi as carotenoid source are highly appealing. At least prospectively, they should be easier amenable to genetic manipulation than plants, and thus will allow tailoring of specially designed substances. Genes for carotenoid synthesis were cloned from many different fungi. In order to stimulate further functional studies on genetic pathways for internal and environmental regulation of carotene synthesis, modification and degradation, an overview on the situation in the most thoroughly studied model organisms is presented. The role of carotenoids as antioxidants, light protective substances and as signalling compounds is discussed.

      PubDate: 2012-12-17T18:14:22Z
       
  • Combination of suppression subtractive hybridization and microarray
           technologies to enumerate biomass-induced genes in the cellulolytic fungus
           Trichoderma reesei
    • Abstract: 2005
      Publication year: 2005
      Source:Applied Mycology and Biotechnology, Volume 5

      The concerted action of many enzymes is required for the hydrolysis of cellulosic biomass. However, only a few have been identified and characterized in detail. Mixtures of isolated cellulase components have been shown to be less efficient than crude culture filtrates for the conversion of biomass to fermentable sugars. This may suggest that additional components are required for complete saccharification of biomass. Trichoderma reesei is the best-studied cellulolytic fungus. To identify new T. reesei genes involved in biomass conversion, we have employed the high throughput analysis of expression of subtractive cDNA libraries by DNA microarray technology. The cDNA libraries have been generated by suppression subtractive hybridization (SSH), which allowed not only the selection of differentially expressed mRNAs, but also the enrichment for rare mRNAs and equalization of cDNA in a pool. Messenger RNA pools from T. reesei cells grown on glucose, cellulose, or acid-pretreated corn stover (PCS) was isolated and used for construction of the SSH cDNA libraries. Three SSH libraries representing cellulose-induced, PCS-induced and PCS minus cellulose-induced transcripts were constructed. Approximately 3600 cDNA clones from three SSH libraries were amplified by high throughput rolling circle amplification (RCA) to produce DNA for microarray printing. Microarray hybridization with tester and driver probes revealed728. DNA sequence analysis and bioinformatics were used to assemble these clones into approximately 90 previously unrecognized genes/proteins. Among them we have identified a number of novel enzymes/proteins with potential direct benefit for improving biomass degradation. Thus, the combination of SSH and cDNA microarray technologies has proven to be a powerful tool for discovery of new differentially expressed genes involved in biomass utilization.

      PubDate: 2012-12-17T18:14:22Z
       
  • Genomics of some human dimorphic fungus
    • Abstract: 2005
      Publication year: 2005
      Source:Applied Mycology and Biotechnology, Volume 5

      The behavior and mode of infection of the dimorphic pathogenic fungi B. dematitidis, H. capsulatum, and P. brasiliensis display many similarities. Thermally regulated dimorphism is their main defining genetical trait. Based on their phylogenetical origin and similar biological behavior, a comparative genomic approach could illuminate the mechanisms responsible for phase transition and virulence/pathogenicity in these fungi. Here, we will present some preliminary evidences about the usefulness of this approach. The occurrence of P. brasiliensis genes that do not show any similarity with the NCBI non-redundant databank, but high similarity with putative H. capsulatum genes, and their concomitant expression at the same phase, demonstrate the power of comparative genomics in these species to understand their biology. Furthermore, promoters from different virulence and yeast phase-specific genes from B. dermatitidis and H. capsulatum demonstrate reciprocal functionality. This indicates the existence of common regulatory networks for virulence/pathogenicity and phase specificity among these three fungi.

      PubDate: 2012-12-17T18:14:22Z
       
  • Phanerochaete chrysosporium Genomics
    • Abstract: 2005
      Publication year: 2005
      Source:Applied Mycology and Biotechnology, Volume 5

      A high quality draft genome sequence has been generated for the lignocellulose-degrading basidiomycete Phanerochaete chrysosporium (Martinez et al. 2004). Analysis of the genome in the context of previously established genetics and physiology is presented. Transposable elements and their potential relationship to genes involved in lignin degradation are systematically outlined. Our current understanding of extracellular oxidative and hydrolytic systems is described. Areas of uncertainty are highlighted and future prospects discussed in light of the newly available genome data.

      PubDate: 2012-12-17T18:14:22Z
       
  • Genetics of morphogenesis in basidiomycetes
    • Abstract: 2005
      Publication year: 2005
      Source:Applied Mycology and Biotechnology, Volume 5

      In this chapter, our aim is to discuss the current knowledge of the genetics of morphogenesis in basidiomycetes. We begin by outlining some features that are shared among fungi in general and those that are unique to basidiomycetes. With this background of basic fungal morphology and physiology, we focus our discussion on the genetics of morphogenesis and the fascinating biology of three broad groups of basidiomycetes: the smuts, the rusts and the mushrooms. Where the smuts and rusts are considered, there is ample discussion on pathogenesis, as these two broad groupings of fungi are particularly destructive to plants worldwide. Of course, mushrooms represent a valuable commodity in their own right. Each of these broad sections encapsulates a current assessment of the environmental cues and the genes regulating morphological change during development. Each of these three taxon-focused sections also concludes with a section discussing current trends and/or future directions.

      PubDate: 2012-12-17T18:14:22Z
       
  • The Development of Genetic Markers from Fungal Genome Initiatives
    • Abstract: 2004
      Publication year: 2004
      Source:Applied Mycology and Biotechnology, Volume 4

      The lack of morphological characters has made molecular markers invaluable for studying aspects of fungal ecology, biology and genetics. Generally, markers are developed specifically for each fungal species under study using laboratory-based techniques. With a growing body of information on fungal genomes, it becomes possible to use these data to develop markers from sequenced genomes. In addition, it is possible to look at trends across genomes, which may allow more universal marker sets to be developed or may guide researchers into making the best predictions of the kinds of markers that could be useful in a given fungus. In this chapter, we review four commonly used molecular markers: microsatellites, minisatellites, interspersed repetitive sequence elements and single nucleotide polymorphisms, and discuss how computer-based genome analysis can find and analyse these using data from fungal genome initiatives.

      PubDate: 2012-12-17T18:14:22Z
       
  • Inferring Process from Pattern in Fungal Population Genetics
    • Abstract: 2004
      Publication year: 2004
      Source:Applied Mycology and Biotechnology, Volume 4

      Our focus in this review is on powerful new methods for determining population patterning over time and space and how from this, the dynamic processes leading to population divergence and speciation can be inferred. We focus on fungal populations, but draw from the wider literature on population genetics, evolutionary statistics, and, of course, phylogeography (see Avise, 2000). We discuss the problems of gene duplication, paralogy, orthology, and deep coalescence as challenges to finding the interface between population divergence and speciation. Our main objective, however, is to guide the reader through the key phylogenetic, nested phylogenetic, coalescent and Bayesian operations with the aid of a set of figures based on a simple, hypothetical dataset of DNA haplotypes. Phylogenetic and compatibility approaches are presented with the goal of not only detecting recombination, but of detecting recombination when it is not widespread throughout a phylogeny. This is a major challenge in fungal systems with substantial asexual reproduction or with significant selfed sexual reproduction in a haploid genome. The key feature here is that recombination can be “localized” in some but not all clades in a phylogeny and that these clades can be identified. From this, contemporary versus historical patterns of recombination can be inferred from a phylogeny. Phylogenetic approaches based on conversion of the phylogeny to a nested hierarchical statistical design are presented for fuller exploration of associations between each nested level of the phylogeny and any variable, such as geographical location, host, or symptom type. The basic operations for both testing for population subdivision based on geographical associations, and for cladistic inference of population processes are presented. Our hypothetical dataset is also used to demonstrate how genealogical relationships and population parameters can be inferred using coalescent and Bayesian methods. The basic principles of these approaches are graphically presented, along with useful references and comments on key assumptions implicit in methods currently available.

      PubDate: 2012-12-17T18:14:22Z
       
  • Molecular and genetic basis of plant-fungal pathogen interactions
    • Abstract: 2004
      Publication year: 2004
      Source:Applied Mycology and Biotechnology, Volume 4

      Our understanding of the genetics and molecular biology that govern fungal-plant disease interactions has greatly increased during the past decade. This expansion of knowledge has been driven in large part by the development of new tools to investigate pathogenicity and the host response to infection. We present here an overview of the recent genetic and molecular biology research on plant-fungal pathogen interactions with emphasis on the technological advances in the field, and on what we have learned about the specificity of their interactions, and the corresponding host responses. We conclude with comments on the prospects for future research, and its application to disease interactions that are of economic importance.

      PubDate: 2012-12-17T18:14:22Z
       
  • Genomics of Candida albicans
    • Abstract: 2004
      Publication year: 2004
      Source:Applied Mycology and Biotechnology, Volume 4

      The polymorphic fungus Candida albicans is an opportunistic human pathogen of increasing medical importance, especially in immunocompromised individuals. C. albicans causes oral and vaginal candidiasis as well as disseminated infections in neutropenic patients. The genetic basis of virulence is assumed to be very complicated and seems to involve a lot of different genes. This fungus is a challenging organism for molecular genetic studies, because it is diploid, the sexual cycle is unknown, and it has a divergent codon usage. This review summarises current knowledge about the genomic and genetic variability of this fungal pathogen and outlines molecular techniques for functional analysis of gene expressions and proteins which are supposed virulence factors.

      PubDate: 2012-12-17T18:14:22Z
       
 
 
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