Monitoring genetic population biomarkers for wastewater-based epidemiology

We report a rapid “sample-to-answer” platform that can be used for the quantitative monitoring of genetic biomarkers within communities through the analysis of wastewater. The assay is based on the loop-mediated isothermal amplification (LAMP) of nucleic acid biomarkers and shows for the first time the ability to rapidly quantify human-specific mitochondrial DNA (mtDNA) from raw untreated wastewater samples. mtDNA provides a model population biomarker associated with carcinogenesis including breast, renal and gastric cancers. To enable a sample-to-answer, field-based technology, we integrated a filter to remove solid impurities and perform DNA extraction and enrichment into a low cost lateral flow-based test. We demonstrated mtDNA detection over seven consecutive days, achieving a limit of detection of 40 copies of human genomic DNA per reaction volume. The assay can be performed at the site of sample collection, with minimal user intervention, yielding results within 45 min and providing a method to monitor public health from wastewater

Genetic Monitoring in the Workplace: A Tool Not a Solution

The authors differentiate between genetic monitoring and screening, and discuss the potential risks and benefits of predictive testing technologies

Clinical and molecular characterization of a cardiac ryanodine receptor founder mutation causing catecholaminergic polymorphic ventricular tachycardia

Background Catecholaminergic polymorphic ventricular tachycardia (CPVT) is a difficult-to-diagnose cause of sudden cardiac death (SCD). We identified a family of 1400 individuals with multiple cases of CPVT, including 36 SCDs during youth. Objectives We sought to identify the genetic cause of CPVT in this family, to preventively treat and clinically characterize the mutation-positive individuals, and to functionally characterize the pathogenic mechanisms of the mutation. Methods Genetic testing was performed for 1404 relatives. Mutation-positive individuals were preventively treated with β-blockers and clinically characterized with a serial exercise treadmill test (ETT) and Holter monitoring. In vitro functional studies included caffeine sensitivity and store overload–induced calcium release activity of the mutant channel in HEK293 cells. Results We identified the p.G357S_RyR2 mutation, in the cardiac ryanodine receptor, in 179 family members and in 6 SCD cases. No SCD was observed among treated mutation-positive individuals over a median follow-up of 37 months; however, 3 relatives who had refused genetic testing (confirmed mutation-positive individuals) experienced SCD. Holter monitoring did not provide relevant information for CPVT diagnosis. One single ETT was unable to detect complex cardiac arrhythmias in 72% of mutation-positive individuals, though the serial ETT improved the accuracy. Functional studies showed that the G357S mutation increased caffeine sensitivity and store overload–induced calcium release activity under conditions that mimic catecholaminergic stress. Conclusion Our study supports the use of genetic testing to identify individuals at risk of SCD to undertake prophylactic interventions. We also show that the pathogenic mechanisms of p.G357S_RyR2 appear to depend on β-adrenergic stimulation

Event-based graphical monitoring in the EpochX genetic programming framework

EpochX is a genetic programming framework with provision for event management – similar to the Java event model – allowing the notification of particular actions during the lifecycle of the evolutionary algorithm. It also provides a flexible Stats system to gather statistics measures. This paper introduces a graphical interface to the EpochX genetic programming framework, taking full advantage of EpochX's event management. A set of representation-independent and tree-dependent GUI components are presented, showing how statistic information can be presented in a rich format using the information provided by EpochX's Stats system

Non-invasive genetic monitoring for the threatened valley elderberry longhorn beetle.

The valley elderberry longhorn beetle (VELB), Desmocerus californicus dimorphus (Coleoptera: Cerambycidae), is a federally threatened subspecies endemic to the Central Valley of California. The VELB range partially overlaps with that of its morphologically similar sister taxon, the California elderberry longhorn beetle (CELB), Desmocerus californicus californicus (Coleoptera: Cerambycidae). Current surveying methods are limited to visual identification of larval exit holes in the VELB/CELB host plant, elderberry (Sambucus spp.), into which larvae bore and excavate feeding galleries. Unbiased genetic approaches could provide a much-needed complementary approach that has more precision than relying on visual inspection of exit holes. In this study we developed a DNA sequencing-based method for indirect detection of VELB/CELB from frass (insect fecal matter), which can be easily and non-invasively collected from exit holes. Frass samples were collected from 37 locations and the 12S and 16S mitochondrial genes were partially sequenced using nested PCR amplification. Three frass-derived sequences showed 100% sequence identity to VELB/CELB barcode references from museum specimens sequenced for this study. Database queries of frass-derived sequences also revealed high similarity to common occupants of old VELB feeding galleries, including earwigs, flies, and other beetles. Overall, this non-invasive approach is a first step towards a genetic assay that could augment existing VELB monitoring and accurately discriminate between VELB, CELB, and other insects. Furthermore, a phylogenetic analysis of 12S and 16S data from museum specimens revealed evidence for the existence of a previously unrecognized, genetically distinct CELB subpopulation in southern California

The reintroduction of the Eurasian otter (Lutra lutra) into the Netherlands: hidden life revealed by noninvasive genetic monitoring

The last recorded presence of the Eurasian otter (Lutra lutra) in the Netherlands dates from 1989 and concerned a dead individual. In 2002 a reintroduction programme was started, and between June 2002 and April 2008 a total of 30 individuals (10 males and 20 females) were released into a lowland peat marsh in the north of the Netherlands. Noninvasive genetic monitoring based on the genetic profiles obtained from DNA extracted from otter faeces (spraints) was chosen for the post-release monitoring of the population. To this end, the founding individuals were genotyped before release and spraints were collected in the release area each winter from 2002 to 2008. From June 2002 to April 2008 we analysed the genetic profile of 1,265 spraints on the basis of 7–15 microsatellite loci, 582 of which (46%) were successfully assigned to either released or newly identified genotypes. We identified 54 offspring (23 females and 31 males): the females started to reproduce after 2 years and the males after 4 years. The mating and reproductive success among males was strongly skewed, with a few dominant males fathering two-thirds of the offspring, but the females had a more even distribution. The effective population size (Ne) was only about 30% of the observed density (N), mainly because of the large variance in reproductive success among males. Most juvenile males dispersed to surrounding areas on maturity, whereas juvenile females stayed inside the area next to the mother’s territory. The main cause of mortality was traffic accidents. Males had a higher mortality rate (22 out of 41 males (54%) vs. 9 out of 43 females (21%)). During winter 2007/08 we identified 47 individuals, 41 of which originated from mating within the release area. This study demonstrates that noninvasive molecular methods can be used efficiently in post-release monitoring studies of elusive species to reveal a comprehensive picture of the state of the populatio

Nonlinear software sensor for monitoring genetic regulation processes with noise and modeling errors

Nonlinear control techniques by means of a software sensor that are commonly used in chemical engineering could be also applied to genetic regulation processes. We provide here a realistic formulation of this procedure by introducing an additive white Gaussian noise, which is usually found in experimental data. Besides, we include model errors, meaning that we assume we do not know the nonlinear regulation function of the process. In order to illustrate this procedure, we employ the Goodwin dynamics of the concentrations [B.C. Goodwin, Temporal Oscillations in Cells, (Academic Press, New York, 1963)] in the simple form recently applied to single gene systems and some operon cases [H. De Jong, J. Comp. Biol. 9, 67 (2002)], which involves the dynamics of the mRNA, given protein, and metabolite concentrations. Further, we present results for a three gene case in co-regulated sets of transcription units as they occur in prokaryotes. However, instead of considering their full dynamics, we use only the data of the metabolites and a designed software sensor. We also show, more generally, that it is possible to rebuild the complete set of nonmeasured concentrations despite the uncertainties in the regulation function or, even more, in the case of not knowing the mRNA dynamics. In addition, the rebuilding of concentrations is not affected by the perturbation due to the additive white Gaussian noise and also we managed to filter the noisy output of the biological systemComment: 21 pages, 7 figures; also selected in vjbio of August 2005; this version corrects a misorder in the last three references of the published versio

Perspectives of genomics for genetic conservation of livestock

Genomics provides new opportunities for conservation genetics. Conservation genetics in livestock is based on estimating diversity by pedigree relatedness and managing diversity by choosing those animals that maximize genetic diversity. Animals can be chosen as parents for the next generation, as donors of material to a gene bank, or as breeds for targeting conservation efforts. Genomics provides opportunities to estimate diversity for specific parts of the genome, such as neutral and adaptive diversity and genetic diversity underlying specific traits. This enables us to choose candidates for conservation based on specific genetic diversity (e.g. diversity of traits or adaptive diversity) or to monitor the loss of diversity without conservation. In wild animals direct genetic management, by choosing candidates for conservation as in livestock, is generally not practiced. With dense marker maps opportunities exist for monitoring relatedness and genetic diversity in wild populations, thus enabling a more active management of diversity

Experimentation with Animals: A Key Aspect of the 3Rs. The Genetic Quality

The genetic quality of laboratory animals is essential for reproducibility of scientific research. Working with animals of certifiedgenetic quality is still a pending issue in Argentina due to the lack of routine genetic controls, of information on the genetic background of animals and of proper training. Apart from being concerned with having their results published and getting funding for research, scientists should know the genetic origin of laboratory animals. Consequently, they should perform genetic controls to verifywhether animal integrity has been compromised by accidental genetic contamination or genetic drift. The aim of this work was toevaluate the genetic purity of the inbred C57BL/6J mouse strain from three animal facilities belonging to the Buenos Aires UniversitySchool of Medicine network by analyzing a panel of microsatellite markers. Female mice tail samples (3-5 mm) were taken and genomic DNA was obtained by organic extraction. The genetic profile of each animal was determined by PCR-fragment analysis, usingmicrosatellites D1Mit155, D2Mit493, D3Mit49, D13Mit13, D6Mit8 and D12Mit12, located on six different autosomal chromosomesand selected from the Mouse Genome Informatics database (www.informatics.jax.org/searches). The results obtained provided keydata on the genetic quality of the three inbred animal colonies studied. They also served as an example for other laboratory animalfacilities in Argentina and as a starting point to modify the conditions and management of laboratory animal colonies. We determinedthe genetic purity of the inbred C57BL/6J mouse strain in all animal facilities evaluated. All six loci analyzed were homozygous,certifying their isogenicity and phenotypic uniformity. These results are promising for animal facilities mainly performing biomedical research. They also show a positive evolution in handling animal colonies and use of the 3Rs, and researcher commitment withanimal science, since they promote the supply of genetically quality-controlled animals. The positive impact of these results shouldencourage other researchers using this inbred strain to perform periodic genetic monitoring, thereby consolidating the supply ofquality-controlled mice. This pioneering study carried out in IGEVET (CONICET- UNLP) should consolidate the genetic monitoring ofinbred strains throughout the country.Fil: Lizarraga, Maria Alfonsina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico CONICET- La Plata. Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout". Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Instituto de Genética Veterinaria; ArgentinaFil: Posik, Diego Manuel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico CONICET- La Plata. Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout". Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Instituto de Genética Veterinaria; ArgentinaFil: Zappa, María Eugenia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico CONICET- La Plata. Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout". Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Instituto de Genética Veterinaria; ArgentinaFil: Castillo, Nadia Sabiela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico CONICET- La Plata. Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout". Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Instituto de Genética Veterinaria; ArgentinaFil: Giovambattista, Guillermo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico CONICET- La Plata. Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout". Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Instituto de Genética Veterinaria; Argentin

Monitoring changes in genetic diversity

DNA is the most elemental level of biodiversity, drives the process of speciation, and underpins other levels of biodiversity, including functional traits, species and ecosystems. Until recently biodiversity indicators have largely overlooked data from the molecular tools that are available for measuring variation at the DNA level. More direct analysis of trends in genetic diversity are now feasible and are ready to be incorporated into biodiversity monitoring. This chapter explores the current state-of-the-art in genetic monitoring, with an emphasis on new molecular tools and the richness of data they provide to supplement existing approaches. We also briefly consider proxy approaches that may be useful for many-species, global scale monitoring cases