A number of oral diseases, including periodontitis, derive from microbial biofilms and are associated with increased antimicrobial resistance. Despite the widespread use of mouthwashes being used as adjunctive measures to control these biofilms, their prolonged use is not recommended due to various side effects. Therefore, alternative broad-spectrum antimicrobials that minimise these effects are highly sought after. Carbohydrate derived fulvic acid (CHD-FA) is an organic acid which has previously demonstrated to be microbiocidal against Candida albicans biofilms, therefore, the aims of this study were to evaluate the antibacterial activity of CHD-FA against orally derived biofilms and to investigate adjunctive biological effects.
Minimum inhibitory concentrations were evaluated for CHD-FA and chlorhexidine (CHX) against a range of oral bacteria using standardised microdilution testing for planktonic and sessile. Scanning electron microscopy was also employed to visualise changes in oral biofilms after antimicrobial treatment. Cytotoxicity of these compounds was assessed against oral epithelial cells, and the effect of CHD-FA on host inflammatory markers was assessed by measuring mRNA and protein expression.
CHD-FA was highly active against all of the oral bacteria tested, including Porphyromonas gingivalis, with a sessile minimum inhibitory concentration of 0.5%. This concentration was shown to kill multi-species biofilms by approximately 90%, levels comparable to that of chlorhexidine (CHX). In a mammalian cell culture model, pretreatment of epithelial cells with buffered CHD-FA was shown to significantly down-regulate key inflammatory mediators, including interleukin-8 (IL-8), after stimulation with a multi-species biofilm.
Overall, CHD-FA was shown to possess broad-spectrum antibacterial activity, with a supplementary function of being able to down-regulate inflammation. These properties offer an attractive spectrum of function from a naturally derived compound, which could be used as an alternative topical treatment strategy for oral biofilm diseases. Further studies in vitro and in vivo are required to determine the precise mechanism by which CHD-FA modulates the host immune response.
Fulvic acid; Chlorhexidine; Biofilm; Antibacterial; Periodontitis; Inflammation
A new type of antibody-enzyme conjugate was made, and its possible application to Candida infection was studied. Both lactoperoxidase and xanthine oxidase were conjugated to specific antibody against Candida albicans. In vitro microbiocidal activity of the new antibody-enzyme conjugate, when incubated together with xanthine and minute amount of halides, showed a remarkable level of candidacidal ability. When the new antibody-enzyme conjugate was given to Candida-infected mice, followed by injecting xanthine and a minute amount of halides, about 50% of these heavily infected mice survived, whereas all control nontreated mice died. These data suggest that the further eleboration of this new antibody-enzyme conjugate might lead us to improve our therapeutic methods of clinical medicine.
Cooperatively breeding American crows (Corvus brachyrhynchos) suffer a severe disease-mediated survival cost from inbreeding, but the proximate mechanisms linking inbreeding to disease are unknown. Here, we examine indices of nestling body condition and innate immunocompetence in relationship to inbreeding and disease mortality. Using an estimate of microsatellite heterozygosity that predicts inbreeding in this population, we show that inbred crows were in relatively poor condition as nestlings, and that body condition index measured in the first 2–33 days after hatching, in addition to inbreeding index, predicted disease probability in the first 34 months of life. Inbred nestlings also mounted a weaker response along one axis of innate immunity: the proportion of bacteria killed in a microbiocidal assay increased as heterozygosity index increased. Relatively poor body condition and low innate immunocompetence are two mechanisms that might predispose inbred crows to ultimate disease mortality. A better understanding of condition-mediated inbreeding depression can guide efforts to minimize disease costs of inbreeding in small populations.
American crows; body condition; disease; immunocompetence; inbreeding; inbreeding depression
Design of antimicrobial polymers for enhancing healthcare issues and minimizing environmental problems is an important endeavor with both fundamental and practical implications. Quaternary ammonium silane-functionalized methacrylate (QAMS) represents an example of antimicrobial macromonomers synthesized by a sol-gel chemical route; these compounds possess flexible Si-O-Si bonds. In present work, a partially-hydrolyzed QAMS copolymerized with bis-GMA is introduced. This methacrylate resin was shown to possess desirable mechanical properties with both a high degree of conversion and minimal polymerization shrinkage. Kill-on-contact microbiocidal activities of this resin were demonstrated using single-species biofilms of Streptococcus mutans (ATCC 36558), Actinomyces naeslundii (ATCC 12104) and Candida albicans (ATCC 90028). Improved mechanical properties after hydration provided the proof-of-concept that QAMS-incorporated resin exhibits self-repair potential via water-induced condensation of organic modified silicate (ormosil) phases within the polymerized resin matrix.
Quaternary ammonium; Organic modified silicate; Antimicrobial; Sol-gel technique; Self-repair
This report is based on a Hygienist Panel Meeting held at St Anne's Manor, Wokingham on 24–25 June 2009. The panel agreed that greater use should be made of antiseptics to reduce reliance on antibiotics with their associated risk of antibiotic resistance. When choosing an antiseptic for clinical use, the Biocompatibility Index, which considers both the microbiocidal activity and any cytotoxic effects of an antiseptic agent, was considered to be a useful tool. The need for longer and more proactive post-discharge surveillance of surgical patients was also agreed to be a priority, especially given the current growth of day-case surgery. The introduction of surgical safety checklists, such as the World Health Organization's Safe Surgery Saves Lives initiative, is a useful contribution to improving safety and prevention of SSIs and should be used universally. Considering sutures as ‘implants’, with a hard or non-shedding surface to which micro-organisms can form biofilm and cause surgical site infections, was felt to be a useful concept.
Surgical site infection; Antimicrobial sutures; Biofilms
The transmigration of polymorphonuclear leukocytes (PMNs; neutrophils) into the intestinal lumen is a classical phenomenon associated with a wide variety of disease states, including those of both pathogenic and autoimmune/idiopathic origin. While PMNs are highly effective at killing invading pathogens by releasing microbiocidal products, excessive or unnecessary release of these substances can cause substantial damage to the intestinal epithelium. Therefore, it is necessary to understand the underlying mechanisms that lure neutrophils into the lumen allowing them to perform their desired functions, so that researchers may begin to identify which processes may be potential targets for inhibiting the transmigration of PMNs during non-infectious states.
Inflammation; neutrophils; eicosanoids; Salmonella enterica serotype Typhimurium; Shigella flexneri; hepoxilin A3
Phosphorothioated oligonucleotides (PS-ONs) have a sequence-independent, broad spectrum antiviral activity as amphipathic polymers (APs) and exhibit potent in vitro antiviral activity against a broad spectrum of herpesviruses: HSV-1, HSV-2, HCMV, VZV, EBV, and HHV-6A/B, and in vivo activity in a murine microbiocide model of genital HSV-2 infection. The activity of these agents against animal cytomegalovirus (CMV) infections in vitro and in vivo was therefore investigated.
In vitro, a 40 mer degenerate AP (REP 9) inhibited both murine CMV (MCMV) and guinea pig CMV (GPCMV) with an IC50 of 0.045 μM and 0.16 μM, respectively, and a 40 mer poly C AP (REP 9C) inhibited MCMV with an IC50 of 0.05 μM. Addition of REP 9 to plaque assays during the first two hours of infection inhibited 78% of plaque formation whereas addition of REP 9 after 10 hours of infection did not significantly reduce the number of plaques, indicating that REP 9 antiviral activity against MCMV occurs at early times after infection. In a murine model of CMV infection, systemic treatment for 5 days significantly reduced virus replication in the spleens and livers of infected mice compared to saline-treated control mice. REP 9 and REP 9C were administered intraperitoneally for 5 consecutive days at 10 mg/kg, starting 2 days prior to MCMV infection. Splenomegaly was observed in infected mice treated with REP 9 but not in control mice or in REP 9 treated, uninfected mice, consistent with mild CpG-like activity. When REP 9C (which lacks CpG motifs) was compared to REP 9, it exhibited comparable antiviral activity as REP 9 but was not associated with splenomegaly. This suggests that the direct antiviral activity of APs is the predominant therapeutic mechanism in vivo. Moreover, REP 9C, which is acid stable, was effective when administered orally in combination with known permeation enhancers.
These studies indicate that APs exhibit potent, well tolerated antiviral activity against CMV infection in vivo and represent a new class of broad spectrum anti-herpetic agents.
Introduction: The aim of the present study was to determine the antimicrobial effect of various gel formulations on plaque formation; different tooth gels were compared to a toothpaste containing comparable antimicrobial ingredients with regard to its microbiocidal activity. The study was conducted under the assumption, that a chief requirement for the prevention of plaque formation is the combination of mechanical removal and antimicrobial activity, and not the sole capability of mechanical plaque removal.
Methods: Ledermix® fluoride gel as commercially available with preservative, and without preservative and perfume oils, Elmex® gelée, and Meridol® toothpaste were tested in a standardized in-vitro test modification of the quantitative suspension test EN 1040. Instead of testing in a suspension, the respective product was directly placed on a standardized contaminated sterile stainless steel disk without adding any bio-burden. 50% egg yolk in Aqua dest. was used as a neutralizer.
Results: Within 1 min, Elmex® gelée showed a RF >5 log10 against S. pyogenes and S. sanguinis. Against S. mutans, a log10 RF of ≥5 was achieved after 2 min, against C. albicans after 5 min, and against P. aeruginosa after 10 min S. aureus was the most difficult organisms to be reduced. After an application time of 10 min, only a log10 RF of 2.4 was achieved. Ledermix exceeded the antimicrobial efficacy of Elmex® gelée against S. mutans and C. albicans and was already effective against these organisms after 1 min, but did not show the same antimicrobial efficacy as Elmex® gelée against P. aeruginosa. Similar to Elmex® gelée, a required reduction of >5 log10 for antimicrobials under no organic challenge was not achieved against S. aureus. Ledermix® fluoride gel without preservatives and Ledermix® fluoride gel without preservatives and perfume oil did not show the antimicrobial efficacy of the standard Ledermix® fluoride gel formulation, indicating that the observed antimicrobial efficacy is chiefly based on the preservative, and possibly the perfume oil. Compared to the tested gels, Meridol® toothpaste was less effective and reached any antimicrobial effect >5 log10 only against S. sanguinis after 10 min.
Conclusion: All unmodified tested gels showed an antimicrobial effect. Because no relevant antimicrobial efficacy against plaque forming bacteria was achieved within 2 min, in practice, an anti-plaque forming effect based on the antimicrobial action of gels cannot be assumed when used in the oral cavity. However, the results of the present study indicate that the antimicrobial efficacy of gels is determined by their formulation and that for the prevention of plaque formation the combination of mechanical removal and antimicrobial activity is not the chief requirement only, but a sustained antimicrobial effect may be of greater importance.
fluoride gels; toothpaste; amino fluoride; sodium monofluorophosphate; EN 1040; antimicrobial efficacy
Consumer health informatics (CHI) is a rapidly evolving sub-discipline
of medical informatics. Such developing fields typically share common
needs, such as harmonizing terms and building a common foundation of research
methods and instruments. The authors describe a pilot study to
conceptualize and develop a “CHI toolbox,” a repository
of existing methods and instruments across relevant established fields. The
challenges encountered in attempting to organize concepts in
a nascent, interdisciplinary field are discussed. The authors’ experiences
in creating a comprehensive CHI toolbox suggest that a larger, concerted
effort to develop a similar product by members of the
relevant research communities could accelerate the development of common
terms, operational definitions, variables, and instruments within the
Climate change research is increasingly focusing on the dynamics among species, ecosystems and climates. Better data about the historical behaviours of these dynamics are urgently needed. Such data are already available from ecology, archaeology, palaeontology and geology, but their integration into climate change research is hampered by differences in their temporal and geographical scales. One productive way to unite data across scales is the study of functional morphological traits, which can form a common denominator for studying interactions between species and climate across taxa, across ecosystems, across space and through time—an approach we call ‘ecometrics’. The sampling methods that have become established in palaeontology to standardize over different scales can be synthesized with tools from community ecology and climate change biology to improve our understanding of the dynamics among species, ecosystems, climates and earth systems over time. Developing these approaches into an integrative climate change biology will help enrich our understanding of the changes our modern world is undergoing.
climate change; scalability; traits; ecometrics; species interactions
Following a brief overview of the terrestrial distribution of boron in rocks, soil, and water, the history of the discovery, early utilization, and geologic origin of borate minerals is summarized. Modern uses of borate-mineral concentrates, borax, boric acid, and other refined products include glass, fiberglass, washing products, alloys and metals, fertilizers, wood treatments, insecticides, and microbiocides. The chemistry of boron is reviewed from the point of view of its possible health effects. It is concluded that boron probably is complexed with hydroxylated species in biologic systems, and that inhibition and stimulation of enzyme and coenzymes are pivotal in its mode of action.
Species introductions of anthropogenic origins are a major aspect of rapid ecological change globally. Research on biological invasions has generated a large literature on many different aspects of this phenomenon. Here, we describe and categorize some aspects of this literature, to better understand what has been studied and what we know, mapping well-studied areas and important gaps. To do so, we employ the techniques of systematic reviewing widely adopted in other scientific disciplines, to further the use of approaches in reviewing the literature that are as scientific, repeatable, and transparent as those employed in a primary study. We identified 2398 relevant studies in a field synopsis of the biological invasions literature. A majority of these studies (58%) were concerned with hypotheses for causes of biological invasions, while studies on impacts of invasions were the next most common (32% of the publications). We examined 1537 papers in greater detail in a systematic review. Superior competitive abilities of invaders, environmental disturbance, and invaded community species richness were the most common hypotheses examined. Most studies examined only a single hypothesis. Almost half of the papers were field observational studies. Studies of terrestrial invasions dominate the literature, with most of these concerning plant invasions. The focus of the literature overall is uneven, with important gaps in areas of theoretical and practical importance.
Biological invasions; Charles Elton; disturbance; EICA; enemy escape; invasion hypothesis; systematic review
Methylene bis(thiocyanate) (MBT) is a microbiocidal agent mainly used in industrial water cooling systems and paper mills as an inhibitor of algae, fungi, and bacteria.
We describe the first case of severe intoxication following inhalation of powder in an industrial worker. Profound cyanosis and respiratory failure caused by severe methemoglobinemia developed within several minutes. Despite immediate admission to the intensive care unit, where mechanical ventilation and hemodialysis for toxin elimination were initiated, multi-organ failure involving liver, kidneys, and lungs developed. While liver failure was leading, the patient was successfully treated with the MARS (molecular adsorbent recirculating system) procedure.
Intoxication with MBT is a potentially life-threatening intoxication causing severe methemoglobinemia and multi-organ failure. Extracorporeal liver albumin dialysis (MARS) appears to be an effective treatment to allow recovery of hepatic function.
Community ecology and ecosystem ecology provide two perspectives on complex ecological systems that have largely complementary strengths and weaknesses. Merging the two perspectives is necessary both to ensure continued scientific progress and to provide society with the scientific means to face growing environmental challenges. Recent research on biodiversity and ecosystem functioning has contributed to this goal in several ways. By addressing a new question of high relevance for both science and society, by challenging existing paradigms, by tightly linking theory and experiments, by building scientific consensus beyond differences in opinion, by integrating fragmented disciplines and research fields, by connecting itself to other disciplines and management issues, it has helped transform ecology not only in content, but also in form. Creating a genuine evolutionary ecosystem ecology that links the evolution of species traits at the individual level, the dynamics of species interactions, and the overall functioning of ecosystems would give new impetus to this much-needed process of unification across ecological disciplines. Recent community evolution models are a promising step in that direction.
biodiversity; community; ecosystem; ecology; evolution; theory
The literature is used to analyse the significance of the use of iodine-impregnated incision drape (Ioban® 2) for the prevention of postoperative wound infections (SSI). The drape has a microbiocidal effect in vitro. Consequently an antiseptic effect also occurs under the incision drape when it is applied to the skin; at the same time, bacterial wound contamination is reduced.
Overall, based on the efficacy strength of the antiseptic incision drape, a reduction of the SSI rate can, however, be confirmed only with a large sample size. A meta analysis which evaluated four prospective studies and one retrospective study was able to provide significant confirmation of a reduction in the SSI rate.
There are no limitations in terms of the biocompatibility of the iodine-impregnated incision drape.
iodine-impregnated incision drape; Ioban 2; microbicidal activity; antiseptic efficacy; SSI rate; biocompatibility
More accurate and precise phenotyping strategies are necessary to empower high-resolution linkage mapping and genome-wide association studies and for training genomic selection models in plant improvement. Within this framework, the objective of modern phenotyping is to increase the accuracy, precision and throughput of phenotypic estimation at all levels of biological organization while reducing costs and minimizing labor through automation, remote sensing, improved data integration and experimental design. Much like the efforts to optimize genotyping during the 1980s and 1990s, designing effective phenotyping initiatives today requires multi-faceted collaborations between biologists, computer scientists, statisticians and engineers. Robust phenotyping systems are needed to characterize the full suite of genetic factors that contribute to quantitative phenotypic variation across cells, organs and tissues, developmental stages, years, environments, species and research programs. Next-generation phenotyping generates significantly more data than previously and requires novel data management, access and storage systems, increased use of ontologies to facilitate data integration, and new statistical tools for enhancing experimental design and extracting biologically meaningful signal from environmental and experimental noise. To ensure relevance, the implementation of efficient and informative phenotyping experiments also requires familiarity with diverse germplasm resources, population structures, and target populations of environments. Today, phenotyping is quickly emerging as the major operational bottleneck limiting the power of genetic analysis and genomic prediction. The challenge for the next generation of quantitative geneticists and plant breeders is not only to understand the genetic basis of complex trait variation, but also to use that knowledge to efficiently synthesize twenty-first century crop varieties.
Dissecting evolutionary dynamics of ecologically important traits is a long-term challenge for biologists. Attempts to understand natural variation and molecular mechanisms have motivated a move from laboratory model systems to non-model systems in diverse natural environments. Next generation sequencing methods, along with an expansion of genomic resources and tools, have fostered new links between diverse disciplines, including molecular biology, evolution, and ecology, and genomics. Great progress has been made in a few non-model wild plants, such as Arabidopsis relatives, monkey flowers, and wild sunflowers. Until recently, the lack of comprehensive genomic information has limited evolutionary and ecological studies to larger QTL regions rather than single gene resolution, and has hindered recognition of general patterns of natural variation and local adaptation. Further efforts in accumulating genomic data and developing bioinformatic and biostatistical tools are now poised to move this field forward. Integrative national and international collaborations and research communities are needed to facilitate development in the field of evolutionary and ecological genomics.
Candidate genes; ecological genomics; fitness; natural selection; population genomics; QTL
Ancient connections between animals and human are seen in cultures throughout the world in multiple forms of interaction with the local fauna that form the core of Ethnozoology. Historically, ethnozoological publications grew out of studies undertaken in academic areas such as zoology, human ecology, sociology and anthropology - reflecting the interdisciplinary character of this discipline. The rich fauna and cultural diversity found in Brazil, with many different species of animals being used for an extremely wide diversity of purposes by Amerindian societies (as well as the descendents of the original European colonists and African slaves), presents an excellent backdrop for examining the relationships that exist between humans and other animals. This work presents a historical view of ethnozoological research in Brazil and examines its evolution, tendencies, and future perspectives. In summary, literature researches indicated that ethnozoology experienced significant advances in recent years in Brazil, although from a qualitative point of view improvement is still needed in terms of methodological procedures, taxonomic precision, and the use of quantitative techniques. A wide range of methodologies and theories are available in different areas of learning that can be put to good use in ethnozoological approaches if the right questions are asked. The challenges to studying ethnozoology in Brazil are not insignificant, and the tendencies described in the present study may aid in defining research strategies that will maintain the quantitative growth observed in the recent years but likewise foster needed qualitative improvements.
Cumulative cultural evolution is the term given to a particular kind of social learning, which allows for the accumulation of modifications over time, involving a ratchet-like effect where successful modifications are maintained until they can be improved upon. There has been great interest in the topic of cumulative cultural evolution from researchers from a wide variety of disciplines, but until recently there were no experimental studies of this phenomenon. Here, we describe our motivations for developing experimental methods for studying cumulative cultural evolution and review the results we have obtained using these techniques. The results that we describe have provided insights into understanding the outcomes of cultural processes at the population level. Our experiments show that cumulative cultural evolution can result in adaptive complexity in behaviour and can also produce convergence in behaviour. These findings lend support to ideas that some behaviours commonly attributed to natural selection and innate tendencies could in fact be shaped by cultural processes.
culture; cumulative cultural evolution; ratchet effect; social learning
Metagenomics is the study of microbial communities sampled directly from their natural environment, without prior culturing. By enabling an analysis of populations including many (so-far) unculturable and often unknown microbes, metagenomics is revolutionizing the field of microbiology, and has excited researchers in many disciplines that could benefit from the study of environmental microbes, including those in ecology, environmental sciences, and biomedicine. Specific computational and statistical tools have been developed for metagenomic data analysis and comparison. New studies, however, have revealed various kinds of artifacts present in metagenomics data caused by limitations in the experimental protocols and/or inadequate data analysis procedures, which often lead to incorrect conclusions about a microbial community. Here, we review some of the artifacts, such as overestimation of species diversity and incorrect estimation of gene family frequencies, and discuss emerging computational approaches to address them. We also review potential challenges that metagenomics may encounter with the extensive application of next-generation sequencing (NGS) techniques.
Metagenomics; next-generation sequencing (NGS); taxonomic/functional profiling; statistical approaches; comparative metagenomics
In modern molecular biology one of the standard ways of analyzing a
vertebrate immune system is to sequence and compare the counts of specific
antigen receptor clones (either immunoglobulins or T-cell receptors) derived
from various tissues under different experimental or clinical conditions. The
resulting statistical challenges are difficult and do not fit readily into the
standard statistical framework of contingency tables primarily due to the
serious under-sampling of the receptor populations. This under-sampling is
caused, on one hand, by the extreme diversity of antigen receptor repertoires
maintained by the immune system and, on the other, by the high cost and labor
intensity of the receptor data collection process. In most of the recent
immunological literature the differences across antigen receptor populations are
examined via non-parametric statistical measures of the species overlap and
diversity borrowed from ecological studies. While this approach is robust in a
wide range of situations, it seems to provide little insight into the underlying
clonal size distribution and the overall mechanism differentiating the receptor
populations. As a possible alternative, the current paper presents a parametric
method that adjusts for the data under-sampling as well as provides a unifying
approach to a simultaneous comparison of multiple receptor groups by means of
the modern statistical tools of unsupervised learning. The parametric model is
based on a flexible multivariate Poisson-lognormal distribution and is seen to
be a natural generalization of the univariate Poisson-lognormal models used in
the ecological studies of biodiversity patterns. The procedure for evaluating a
model’s fit is described along with the public domain software developed
to perform the necessary diagnostics. The model-driven analysis is seen to
compare favorably vis a vis traditional methods when applied to the data from
T-cell receptors in transgenic mice populations.
T-cells; antigen receptors; computational immunology; species diversity estimation; Poisson abundance models; lognormal distribution; dissimilarity measure; dendrogram; mutual information
Passerines (perching birds) are widely studied across many biological disciplines including ecology, population biology, neurobiology, behavioural ecology and evolutionary biology. However, understanding the molecular basis of relevant traits is hampered by the paucity of passerine genomics tools. Efforts to address this problem are underway, and the zebra finch (Taeniopygia guttata) will be the first passerine to have its genome sequenced. Here we describe a bioinformatic analysis of zebra finch expressed sequence tag (EST) Genbank entries.
A total of 48,862 ESTs were downloaded from GenBank and assembled into contigs, representing an estimated 17,404 unique sequences. The unique sequence set contained 638 simple sequence repeats (SSRs) or microsatellites of length ≥20 bp and purity ≥90% and 144 simple sequence repeats of length ≥30 bp. A chromosomal location for the majority of SSRs was predicted by BLASTing against assembly 2.1 of the chicken genome sequence. The relative exonic location (5' untranslated region, coding region or 3' untranslated region) was predicted for 218 of the SSRs, by BLAST search against the ENSEMBL chicken peptide database. Ten loci were examined for polymorphism in two zebra finch populations and two populations of a distantly related passerine, the house sparrow Passer domesticus. Linkage was confirmed for four loci that were predicted to reside on the passerine homologue of chicken chromosome 7.
We show that SSRs are abundant within zebra finch ESTs, and that their genomic location can be predicted from sequence similarity with the assembled chicken genome sequence. We demonstrate that a useful proportion of zebra finch EST-SSRs are likely to be polymorphic, and that they can be used to build a linkage map. Finally, we show that many zebra finch EST-SSRs are likely to be useful in evolutionary genetic studies of other passerines.
Modern agricultural systems can benefit from the application of concepts and models from applied ecology. When understood, multitrophic interactions among plants, pests, diseases and their natural enemies can be exploited to increase crop production and reduce undesirable environmental impacts. Although the understanding of subterranean ecology is rudimentary compared to the perspective aboveground, technologies today vastly reduce traditional obstacles to studying cryptic communities. Here we emphasize advantages to integrating as much as possible the use of these methods in order to leverage the information gained from studying communities of soil organisms. PCR-based approaches to identify and quantify species (real time qPCR and next generation sequencing) greatly expand the ability to investigate food web interactions because there is less need for wide taxonomic expertise within research programs. Improved methods to capture and measure volatiles in the soil atmosphere in situ make it possible to detect and study chemical cues that are critical to communication across trophic levels. The application of SADIE to directly assess rather than infer spatial patterns in belowground agroecosystems has improved the ability to characterize relationships between organisms in space and time. We review selected methodology and use of these tools and describe some of the ways they were integrated to study soil food webs in Florida citrus orchards with the goal of developing new biocontrol approaches.
PCR-based molecular methods; soil food webs; herbivore-induced plant volatiles; SADIE analysis; biological control
Single nucleotide polymorphisms (SNPs) are abundant in genomes of all species and biologically informative markers extensively used across broad scientific disciplines. Newly identified SNP markers are publicly available at an ever-increasing rate due to advancements in sequencing technologies. Efficient, cost-effective SNP genotyping methods to screen sample populations are in great demand in well-equipped laboratories, but also in developing world situations. Dual Probe TaqMan assays are robust but can be cost-prohibitive and require specialized equipment. The Mismatch Amplification Mutation Assay, coupled with melt analysis (Melt-MAMA), is flexible, efficient and cost-effective. However, Melt-MAMA traditionally suffers from high rates of assay design failures and knowledge gaps on assay robustness and sensitivity. In this study, we identified strategies that improved the success of Melt-MAMA. We examined the performance of 185 Melt-MAMAs across eight different pathogens using various optimization parameters. We evaluated the effects of genome size and %GC content on assay development. When used collectively, specific strategies markedly improved the rate of successful assays at the first design attempt from ∼50% to ∼80%. We observed that Melt-MAMA accurately genotypes across a broad DNA range (∼100 ng to ∼0.1 pg). Genomic size and %GC content influence the rate of successful assay design in an independent manner. Finally, we demonstrated the versatility of these assays by the creation of a duplex Melt-MAMA real-time PCR (two SNPs) and conversion to a size-based genotyping system, which uses agarose gel electrophoresis. Melt-MAMA is comparable to Dual Probe TaqMan assays in terms of design success rate and accuracy. Although sensitivity is less robust than Dual Probe TaqMan assays, Melt-MAMA is superior in terms of cost-effectiveness, speed of development and versatility. We detail the parameters most important for the successful application of Melt-MAMA, which should prove useful to the wider scientific community.
Reptiles are underutilized vertebrate models in the study of the evolution and persistence of senescence. Their unique physiology, indeterminate growth, and increasing fecundity across the adult female lifespan motivate the study of how physiology at the mechanistic level, life history at the organismal level, and natural selection at the evolutionary timescale define lifespan in this diverse taxonomic group. Reviewed here are, first, comparative results of cellular metabolic studies conducted across a range of colubrid snake species with variable lifespan. New results on the efficiency of DNA repair in these species are synthesized with the cellular studies. Second, detailed studies of the ecology, life history, and cellular physiology are reviewed for one colubrid species with either short or long lifespan (Thamnophis elegans). New results on the rate of telomere shortening with age in this species are synthesized with previous research. The comparative and intraspecific studies both yield results that species with longer lifespans have underlying cellular physiologies support the free-radical/repair mechanistic hypothesis for aging. As well, both underscore the importance of mortality environment for the evolution of aging rate.
Aging; Comet assay; Comparative biology; DNA damage and repair; Free radical theory; Evolution; Mitochondrial efficiency; Oxidative damage; Respiratory coefficient ratio; Senescence; Telomeres; Reptiles; Snakes