A review of fungal phytotoxins: from basic studies to practical use

Recent materials are summarized, pertaining to classification of fungal phytotoxins, methods of their isolation, and assays for biological activity. Producers of phytotoxic substances have been characterized, and the chemical nature of phytotoxins has been subjected to analysis. The review gives consideration to the mechanisms of action of phytotoxins on susceptible plants and the mechanisms of plant resistance to such agents. Other matters discussed include prospects of utilizing basic knowledge of the nature and mechanisms of action of phytotoxins for (1) developing means of plant protection against diseases and weeds and (2) identifying or classifying fungi (chemosystematics).     

Fungal genome sequencing: basic biology to biotechnology

The genome sequences provide a first glimpse into the genomic basis of the biological diversity of filamentous fungi and yeast. The genome sequence of the budding yeast, Saccharomyces cerevisiae, with a small genome size, unicellular growth, and rich history of genetic and molecular analyses was a milestone of early genomics in the 1990s. The subsequent completion of fission yeast, Schizosaccharomyces pombe and genetic model, Neurospora crassa initiated a revolution in the genomics of the fungal kingdom. In due course of time, a substantial number of fungal genomes have been sequenced and publicly released, representing the widest sampling of genomes from any eukaryotic kingdom. An ambitious genome-sequencing program provides a wealth of data on metabolic diversity within the fungal kingdom, thereby enhancing research into medical science, agriculture science, ecology, bioremediation, bioenergy, and the biotechnology industry. Fungal genomics have higher potential to positively affect human health, environmental health, and the planet’s stored energy. With a significant increase in sequenced fungal genomes, the known diversity of genes encoding organic acids, antibiotics, enzymes, and their pathways has increased exponentially. Currently, over a hundred fungal genome sequences are publicly available; however, no inclusive review has been published. This review is an initiative to address the significance of the fungal genome-sequencing program and provides the road map for basic and applied research.     

Protecting the heart: a practical review of the statin studies

The aim of this review of the landmark HMG-CoA reductase inhibitors (statins) studies is to enable the clinician to draw practical lessons from these trials. The Scandinavian Simvastatin Survival Study (4S) established the importance of treating the hypercholesterolemic patient with established cardiovascular heart disease. The West of Scotland Coronary Prevention Study (WOSCOPS) showed the benefit of treating healthy hypercholesterolemic men who were nevertheless at high risk of developing cardiovascular heart disease in the future. The Cholesterol and Recurrent Events (CARE) study, a secondary prevention trial, proved the benefit of treating patients with myocardial ischemia and cholesterol levels within normal limits. This conclusion was confirmed by the Long-term Intervention With Pravastatin in Ischemic Disease (LIPID) study, another secondary prevention study that enrolled patients with a wide range of cholesterol levels (4-7 mmol/dL), into which the large majority of patients would belong. The importance of treating patients with established ischemic heart disease (IHD), and those at high risk of developing cardiovascular heart disease, regardless of cholesterol level, was being realized. The Air Force/Texas Coronary Artery Prevention Study (AFCAPS/TexCAPS) then showed that treatment can reduce adverse cardiovascular events even in the primary prevention of patients with normal cholesterol levels. The Myocardial Ischemia Reduction With Aggressive Cholesterol Lowering (MIRACL) trial showed that hypocholesterolemic therapy is useful in the setting of an acute coronary syndrome, while the Atorvastatin Versus Revascularisation Treatment (AVERT) study showed that aggressive statin therapy is as good as angioplasty in reducing ischemic cardiac events in patients with stable angina pectoris. Finally, the Heart Protection Study (HPS) randomized more than 20,000 patients, and the value of statins in reducing adverse cardiovascular events in the high-risk patient, including the elderly, women, and even in those with low cholesterol levels, is beyond doubt. The emphasis is now on the risk level for developing cardiovascular events, and treatment should target the high-risk group and not be dependent on the actual cholesterol level of the patient. It is interesting to compare the large amount of data on the value and safety of the statins with the much more limited and less convincing data on antioxidant vitamins.     

Bioremediation of MTBE: a review from a practical perspective

The addition of methyl tert-butyl ether (MTBE) to gasoline has resulted in public uncertainty regarding the continued reliance on biological processes for gasoline remediation. Despite this concern, researchers have shown that MTBE can be effectively degraded in the laboratory under aerobic conditions using pure and mixed cultures with half-lives ranging from 0.04 to 29 days. Ex-situ aerobic fixed-film and aerobic suspended growth bioreactor studies have demonstrated decreases in MTBE concentrations of 83% and 96% with hydraulic residence times of 0.3 hrs and 3 days, respectively. In microcosm and field studies, aerobic biodegradation half-lives range from 2 to 693 days. These half-lives have been shown to decrease with increasing dissolved oxygen concentrations and, in some cases, with the addition of exogenous MTBE-degraders. MTBE concentrations have also been observed to decrease under anaerobic conditions; however, these rates are not as well defined. Several detailed field case studies describing the use of ex-situ reactors, natural attenuation, and bioaugmentation are presented in this paper and demonstrate the potential for successful remediation of MTBE-contaminated aquifers. In conclusion, a substantial amount of literature is available which demonstratesthat the in-situ biodegradation of MTBE is contingent on achieving aerobic conditions in the contaminated aquifer.     

Twenty years research in cholinesterase biosensors: from basic research to practical applications

Over the last decades, cholinesterase (ChE) biosensors have emerged as an ultra sensitive and rapid technique for toxicity analysis in environmental monitoring, food and quality control. These systems have the potential to complement or replace the classical analytical methods by simplifying or eliminating sample preparation protocols and making field testing easier and faster with significant decrease in costs per analysis. Over the years, engineering of more sensitive ChE enzymes, development of more reliable immobilization protocols and progress in the area of microelectronics could allow ChE biosensors to be competitive for field analysis and extend their applications to multianalyte screening, development of small, portable instrumentations for rapid toxicity testing, and detectors in chromatographic systems. In this paper, we will review the research efforts over the last 20 years in fabricating AChE biosensors and the recent trends and challenges encounter once the sensor is used outside research laboratory for in situ real sample applications. The review will discuss the generations of cholinesterase sensors with their advantages and limitations, the existing electrode configurations and fabrication techniques and their applications for toxicity monitoring. We will focus on low-cost electrochemical sensors and the approaches used for enzyme immobilization. Recent works for achieving high sensitivity and selectivity are also discussed.     

Fungal molecular diagnostics: a mini review

Conventional methods to identify fungi have often relied on identification of disease symptoms, isolation and culturing of environmental organisms, and laboratory identification by morphology and biochemical tests. Although these methods are still fundamental there is an increasing move towards molecular diagnostics of fungi in all fields. In this review, some of the molecular approaches to fungal diagnostics based on polymerase chain reaction (PCR) and DNA/RNA probe technology are discussed. This includes several technological advances in PCR-based methods for the detection, identification and quantification of fungi including real-time PCR which has been successfully used to provide rapid, quantitative data on fungal species from environmental samples. PCR and probe based methods have provided new tools for the enumeration of fungal species, but it is still necessary to combine the new technology with more conventional methods to gain a fuller understanding of interactions occurring in the environment. Since its introduction in the mid 1980's PCR has provided many molecular diagnostic tools, some of which are discussed within this review, and with the advances in micro-array technology and real-time PCR methods the future is bright for the development of accurate, quantitative diagnostic tools that can provide information not only on individual fungal species but also on whole communities.     

Lignin: Chemical structure,biodegradation, and practical application (a review)

The review describes the natural biopolymer lignin, which is second in plant biomass abundance. It is evident now that lignin is considerably undervalued and insufficiently studied in the applied area. The review focuses on the history of the lignin discovery, methods for its extraction from plant objects, its biodegradation by fungi, the enzymes degrading lignin, and the prospects of its application in current biotechnology.     

Fungal decolorization of dye wastewaters: a review

In recent years, there has been an intensive research on fungal decolorization of dye wastewater. It is becoming a promising alternative to replace or supplement present treatment processes. This paper examines various fungi, living or dead cells, which are capable of decolorizing dye wastewaters; discusses various mechanisms involved; reports some elution and regeneration methods for fungal biomass; summarizes the present pretreatment methods for increasing the biosorption capacity of fungal biomass; discusses the effect of various factors on decolorization.     

Inferences from tip‐calibrated phylogenies: a review and a practical guide

Molecular dating of phylogenetic trees is a growing discipline using sequence data to co‐estimate the timing of evolutionary events and rates of molecular evolution. All molecular‐dating methods require converting genetic divergence between sequences into absolute time. Historically, this could only be achieved by associating externally derived dates obtained from fossil or biogeographical evidence to internal nodes of the tree. In some cases, notably for fast‐evolving genomes such as viruses and some bacteria, the time span over which samples were collected may cover a significant proportion of the time since they last shared a common ancestor. This situation allows phylogenetic trees to be calibrated by associating sampling dates directly to the sequences representing the tips (terminal nodes) of the tree. The increasing availability of genomic data from ancient DNA extends the applicability of such tip‐based calibration to a variety of taxa including humans, extinct megafauna and various microorganisms which typically have a scarce fossil record. The development of statistical models accounting for heterogeneity in different aspects of the evolutionary process while accommodating very large data sets (e.g. whole genomes) has allowed using tip‐dating methods to reach inferences on divergence times, substitution rates, past demography or the age of specific mutations on a variety of spatiotemporal scales. In this review, we summarize the current state of the art of tip dating, discuss some recent applications, highlight common pitfalls and provide a ‘how to’ guide to thoroughly perform such analyses.     

Cytogenetic studies in Pentatomidae (Heteroptera): A review

The suborder Heteroptera constitutes one of the most important insect groups because most species are plants feeders and cause damage on many plants of economic importance. One of the most important cytogenetic characteristics of Heteroptera is the holokinetic nature of the chromosomes. One particular feature of some species of Pentatomidae is the regular presence of an abnormal meiosis in one testicular lobe (harlequin lobe). From the 28 species cytogenetically analysed from Argentine material, 21 present the diploid number 2 n  = 14, four species present a reduced number (2 n  = 12) and another three species possess an increased diploid number (2 n  = 16); among all these only three present an harlequin lobe. In the present work, a bibliographic review of the chromosome number and sex determining system of 294 species and subspecies belonging to 121 genera within the subfamilies Asopinae, Discocephalinae, Edessinae, Pentatominae, Phyllocephalinae and Podopinae is presented. The male diploid numbers range from six to 27 with a mode in 14 chromosomes; this last diploid number is present in 85% of the species. The sex chromosome determining system is XY/XX except in three species: Macropygium reticulare (Fabricius, 1803), Rhytidolomia senilis (Say, 1832) and Thyanta calceata (Say, 1832) which present derived sex chromosome systems. Furthermore, the cytogenetic relationships with the other families of Pentatomoidea are discussed.     

In vivo alkylation studies with dichlorvos at practical use concentrations

Twenty male CFE rats were exposed to atmospheres containing 0.064 μg/l of [Me-¹⁴C]dichlorvos (113 Ci/mol) for 12 h. Analysis of the DNA and RNA from the total soft tissues of these rats revealed no methylation of the N₇ atom of guanine moieties. The limits of detection of methylation were one methyl group per 6.0 × 10¹¹ and per 2 × 10⁹ nucleotide units for DNA and RNA, respectively. Only 0.000001% of the administered dose would have needed to react with DNA in order to produce detectable methylation of this macromolecule.The exposure period employed in this study (12 h) constituted a significant fraction of the half-life of 7-methylguanine moieties in DNA (3 days). On the basis of this information and the extremely rapid metabolism of dichlorvos in a wide range of mammalian tissues and species it was concluded that dichlorvos does not methylate the nucleic acids of mammalian tissues when it is inhaled continuously at practical use concentrations.     

Microbial producers of plant growth stimulators and their practical use: A review

The ability of pro-and eukaryotic microorganisms to synthesize growth-stimulating phytohormones is reviewed, with emphasis on the pathways of biosynthesis of these compounds and their effects on the physiological and biochemical properties of the producers. Phytohormones are viewed as specific mediators in interactions between various organisms inhabiting the same ecological niche, the biological role of which is not limited to processes taking place in plants. In addition to setting forth the theoretical aspects of this problem, the review underscores the need to utilize such producer microorganisms in plant cultivation and biotechnology     

Microbial producers of plant growth stimulators and their practical use: A review

The ability of pro- and eukaryotic microorganisms to synthesize growth-stimulating phytohormones is reviewed, with emphasis on pathways of biosynthesis of these compounds and their effects on physiological and biochemical properties of the producers. Phytohormones are viewed as specific mediators in interactions between various organisms inhabiting the same ecological niche, the biological role of which is not limited to processes taking place in plants. In addition to setting forth theoretical aspects of this problem, the review underscores the need to utilize such producer microorganisms in plant cultivation and biotechnology.     

Fitting curves to data using nonlinear regression: a practical and nonmathematical review

Many types of data are best analyzed by fitting a curve using nonlinear regression, and computer programs that perform these calculations are readily available. Like every scientific technique, however, a nonlinear regression program can produce misleading results when used inappropriately. This article reviews the use of nonlinear regression in a practical and nonmathematical manner to answer the following questions: Why is nonlinear regression superior to linear regression of transformed data? How does nonlinear regression differ from polynomial regression and cubic spline? How do nonlinear regression programs work? What choices must an investigator make before performing nonlinear regression? What do the final results mean? How can two sets of data or two fits to one set of data be compared? What problems can cause the results to be wrong? This review is designed to demystify nonlinear regression so that both its power and its limitations will be appreciated.     

Structure-activity relationship study of host-specific phytotoxins (AM-toxin analogs) using a new assay method with leaves from apple meristem culture

AM-toxins are host-specific phytotoxins of the Alternaria alternata apple pathotype, which induce necrosis on apple leaves. In this study, we developed a new assay to measure the necrotic activity of AM-toxin analogs using cultured leaves from meristem cells. This method was not only more sensitive to AM-toxin I, but also more reliable than the previous one that used tree leaves due to the homogeneous nature of cultured leaves and to the method of application of toxins. Using this assay method we investigated a structure-activity relationship of AM-toxin analogs synthesized in this study. Most residues and the macrocyclic ring structure were strictly recognized by AM-toxin putative receptor, whereas the L-Ala binding subsite of the receptor allowed for side chain structures with various stereoelectronic properties. These findings are important for designing ligands for further experimental probing of the nature of the receptor.     

Transitions of Mnemiopsis leidyi (Ctenophora: Lobata) from a native to an exotic species: a review

The genus Mnemiopsis is comprised of a single species, Mnemiopsis leidyi A. Agassiz, 1865, that has recently made the transition from a distribution limited to the Atlantic coasts of North and South America to an invasive range that includes the Black, Caspian, Mediterranean, North, and Baltic seas. We review the foundations of the ctenophore??s invasive success, which include the source-sink dynamics that characterize Mnemiopsis populations in temperate coastal waters where the ctenophore achieves its highest biomass levels and ecosystem impacts. Within its native temperate range, Mnemiopsis is frequently a dominant, seasonal, colonizing species with limited dispersal capacities. Cross-oceanic transport within ballast waters of intercontinental shipping vessels has altered this dispersal limitation and initiated a rapid global spread of Mnemiopsis. Owing to continuing transport via transoceanic shipping, we anticipate continued range expansion and review the variables most likely to determine whether introduction of Mnemiopsis to a novel community results in an inconspicuous addition or a disruptive invasion.     

Real-time PCR: approaches to data analysis (a review)

The registration of the accumulation of polymerase chain reaction (PCR) products in the course of amplification (real-time PCR) requires specific equipment, i.e., detecting amplifiers capable of recording the level of fluorescence in the reaction tube during amplicon formation. By the time the reaction is completed, researchers obtain DNA accumulation graphs. The review discusses the most promising algorithms of analysis of real-time PCR curves and possible errors, whether caused by the software used or the operators' mistakes. The data included will assist researchers in understanding the features of the method to obtain more reliable results.