Extension Horses, Inc. experts act fast to create online resources to assist the horse industry during COVID-19.

The COVID-19 pandemic and resulting stay-at-home directives, adopted out of necessity to protect human health, introduced significant challenges for horse owners and small equine businesses. Restricted access, and in many cases closure of barns, resulted in a multitude of questions and concerns within the equine community which needed to be addressed rapidly. Extension Horses, Inc. (EH) coordinated the development and delivery of a variety of educational resources utilizing a combination of online formats and dissemination through social media and EH member contact lists. A series of infographics, webinars, and podcasts (three in each category) were created to provide guidance on essential care of horses, emergency preparedness, financial assistance, legal concerns, and biosecurity during the crucial, initial weeks of the pandemic (March to April 2020). Web conferencing technology (Zoom) was used to facilitate discussion and task delegation among EH members and to conduct and record webinars and podcasts. Podcasts were hosted on Buzzsprout and infographics were created using Adobe InDesign. Live webinar participants were invited to participate in several polls during the webinar and were sent a brief survey to complete at the end of the webinar series. Analytics for all educational resources combined demonstrated a 32-d total direct reach of 135,563. Most live webinar participants identified themselves as horse owners and small equine business owners (55%). The majority of live webinar participants indicated the information was useful (99%), and they would utilize the resources they had learned about (80%). Survey respondents reported that Facebook, email, and word of mouth were key ways in which they learned about the webinars. The same survey found that the web-platform was an effective method to receive information (85% high satisfaction) and respondents were highly likely to recommend future EH webinars to others (88%). The three infographics had a total Facebook reach of 131,765, the webinars had 3,522 total views, and the three podcasts had 276 total downloads. The rapid response of EH and quick turnaround of products allowed a large online audience to receive vital information for coping with COVID-19. Having the established EH network, already familiar with virtual education, was a big asset in this effort. This can serve as a model for cooperative extension to utilize in future collaborative responses to industry issues.

Development of a subspecialty cardiology curriculum for paediatric registrars in Malawi: Implementation of a long-distance hybrid model.

BACKGROUND: Malawi has a high burden of paediatric cardiac disease but a limited number of health providers familiar with these chronic diseases. Given the rising number of Malawian postgraduate paediatric trainees at the University of Malawi College of Medicine, we sought to remedy this lack of basic cardiology training with a long-distance, module-based curriculum that could be utilised independently, as needed, with on-site teaching. We also wished to evaluate the initial modules for utility and improvement in knowledge and confidence in each topic. METHODS: After an initial site visit to determine curriculum needs, online modules with interactive evaluations and quizzes were developed by a paediatric cardiologist in the United States, in collaboration with paediatric registrar training directors in Malawi. This online interactive curriculum was followed by several site visits to Malawi, by the United States-based paediatric cardiologist, to provide bedside teaching, case-based discussions and hands-on skill training in cardiac ultrasound and electrocardiogram interpretation. Evaluation of the curriculum model included post-module quizzes on cardiac topics as well as registrar self-assessments regarding confidence in content areas. RESULTS: The average post-module quiz score was 93.6%. Repeat testing with the same questions four months later yielded an average score of 78%, with a range from 60 to 100%. Pre- and post-module registrar self-assessment regarding confidence in content areas showed a substantial gain in knowledge and confidence mean. In their qualitative feedback, registrars noted that the modules were helpful in studying for their certifying examinations, and all four of the registrars sitting Part I of their Malawian and South African paediatric certifying examinations passed. CONCLUSIONS: Our innovative hybrid approach, combining online educational modules with in-person teaching visits, is a useful approach in expanding paediatric cardiology subspecialty education in Malawi.

Evaluation and management of atrioventricular block in children.

PURPOSE OF REVIEW: Pediatric brady-dysrhythmias and conduction disorders are uncommon, but timely recognition and evaluation are critical. This review will highlight the key diagnostic and management steps for first, second, and third-degree atrioventricular heart block in pediatric patients. RECENT FINDINGS: There is a breadth of acquired and often reversible causes of atrioventricular block in childhood. Recent advances in diagnostics and pacing therapies have led to improved outcomes. SUMMARY: A thorough evaluation is required to determine when atrioventricular block requires treatment. In symptomatic or unstable patients, the management should focus on resuscitative measures, diagnostic testing, potential reversible causes, monitoring for progression, cardiac consultation and evaluating the need for definitive pacemaker placement.

Radiofrequency catheter ablation of intractable ventricular tachycardia in an infant following arterial switch operation.

A full-term male neonate presented with cyanosis upon delivery and was subsequently diagnosed with d-transposition of the great arteries, ventricular septal defect, and restrictive atrial septal defect. Following initiation of intravenous prostaglandins and balloon atrial septostomy, an arterial switch operation was performed on day 3 of life. The postoperative course was complicated by intractable ventricular tachycardia that was refractory to lidocaine, amiodarone, esmolol, fosphenytoin, and mexiletine drug therapy. Ventricular tachycardia was suppressed with overdrive atrial pacing but recurred upon discontinuation. Seven weeks postoperatively, radiofrequency catheter ablation was performed due to hemodynamically compromising persistent ventricular tachycardia refractory to medical therapy. The ventricular tachycardia was localized to the inferior-lateral right ventricular outlet septum. The procedure was successful without complications or recurrence. Antiarrhythmics were discontinued after the ablation procedure. Seven days after the ablation, a different, slower fascicular rhythm was noted to compete with the infant's sinus rhythm. This was consistent with the preablation amiodarone having reached subtherapeutic levels given its very long half-life. The patient was restarted on oral beta blockers and amiodarone. The patient was subsequently discharged home in predominantly sinus rhythm with intermittent fascicular rhythm.

Retention of induced mutations in a Drosophila reverse-genetic resource.

Targeting induced local lesions in genomes (TILLING) is a reverse-genetic method for identifying point mutations in chemically mutagenized populations. For functional genomics, it is ideal to have a stable collection of heavily mutagenized lines that can be screened over an extended period of time. However, long-term storage is impractical for Drosophila, so mutant strains must be maintained by continual propagation of live cultures. Here we evaluate a strategy in which ethylmethane sulfonate (EMS) mutagenized chromosomes were maintained as heterozygotes with balancer chromosomes for >100 generations before screening. The strategy yielded a spectrum of point mutations similar to those found in previous studies of EMS-induced mutations, as well as 2.4% indels (insertions and deletions). Our analysis of 1887 point mutations in 148 targets showed evidence for selection against deleterious lesions and differential retention of lesions among targets on the basis of their position relative to balancer breakpoints, leading to a broad distribution of mutational densities. Despite selection and differential retention, the success of a user-funded service based on screening a large collection several years after mutagenesis indicates sufficient stability for use as a long-term reverse-genetic resource. Our study has implications for the use of balancer chromosomes to maintain mutant lines and provides the first large-scale quantitative assessment of the limitations of using breeding populations for repositories of genetic variability.

Discovery of chemically induced mutations in rice by TILLING.

BACKGROUND: Rice is both a food source for a majority of the world's population and an important model system. Available functional genomics resources include targeted insertion mutagenesis and transgenic tools. While these can be powerful, a non-transgenic, unbiased targeted mutagenesis method that can generate a range of allele types would add considerably to the analysis of the rice genome. TILLING (Targeting Induced Local Lesions in Genomes), a general reverse genetic technique that combines traditional mutagenesis with high throughput methods for mutation discovery, is such a method. RESULTS: To apply TILLING to rice, we developed two mutagenized rice populations. One population was developed by treatment with the chemical mutagen ethyl methanesulphonate (EMS), and the other with a combination of sodium azide plus methyl-nitrosourea (Az-MNU). To find induced mutations, target regions of 0.7-1.5 kilobases were PCR amplified using gene specific primers labeled with fluorescent dyes. Heteroduplexes were formed through denaturation and annealing of PCR products, mismatches digested with a crude preparation of CEL I nuclease and cleaved fragments visualized using denaturing polyacrylamide gel electrophoresis. In 10 target genes screened, we identified 27 nucleotide changes in the EMS-treated population and 30 in the Az-MNU population. CONCLUSION: We estimate that the density of induced mutations is two- to threefold higher than previously reported rice populations (about 1/300 kb). By comparison to other plants used in public TILLING services, we conclude that the populations described here would be suitable for use in a large scale TILLING project.

High-throughput discovery of rare human nucleotide polymorphisms by Ecotilling.

Human individuals differ from one another at only approximately 0.1% of nucleotide positions, but these single nucleotide differences account for most heritable phenotypic variation. Large-scale efforts to discover and genotype human variation have been limited to common polymorphisms. However, these efforts overlook rare nucleotide changes that may contribute to phenotypic diversity and genetic disorders, including cancer. Thus, there is an increasing need for high-throughput methods to robustly detect rare nucleotide differences. Toward this end, we have adapted the mismatch discovery method known as Ecotilling for the discovery of human single nucleotide polymorphisms. To increase throughput and reduce costs, we developed a universal primer strategy and implemented algorithms for automated band detection. Ecotilling was validated by screening 90 human DNA samples for nucleotide changes in 5 gene targets and by comparing results to public resequencing data. To increase throughput for discovery of rare alleles, we pooled samples 8-fold and found Ecotilling to be efficient relative to resequencing, with a false negative rate of 5% and a false discovery rate of 4%. We identified 28 new rare alleles, including some that are predicted to damage protein function. The detection of rare damaging mutations has implications for models of human disease.

High-throughput TILLING for Arabidopsis.

Targeting induced local lesions in genomes (TILLING) is a general strategy for identifying induced point mutations that can be applied to almost any organism. In this chapter, we describe the basic methodology for high-throughput TILLING. Gene segments are amplified using fluorescently tagged primers, and products are denatured and reannealed to form heteroduplexes between the mutated sequence and its wild-type counterpart. These heteroduplexes are substrates for cleavage by the endonuclease CEL I. Following cleavage, products are analyzed on denaturing polyacrylamide gels using the LI-COR DNA analyzer system. High-throughput TILLING has been adopted by the Arabidopsis TILLING Project (ATP) to provide allelic series of point mutations for the general Arabidopsis community.

Discovery of induced point mutations in maize genes by TILLING.

BACKGROUND: Going from a gene sequence to its function in the context of a whole organism requires a strategy for targeting mutations, referred to as reverse genetics. Reverse genetics is highly desirable in the modern genomics era; however, the most powerful methods are generally restricted to a few model organisms. Previously, we introduced a reverse-genetic strategy with the potential for general applicability to organisms that lack well-developed genetic tools. Our TILLING (Targeting Induced Local Lesions IN Genomes) method uses chemical mutagenesis followed by screening for single-base changes to discover induced mutations that alter protein function. TILLING was shown to be an effective reverse genetic strategy by the establishment of a high-throughput TILLING facility and the delivery of thousands of point mutations in hundreds of Arabidopsis genes to members of the plant biology community. RESULTS: We demonstrate that high-throughput TILLING is applicable to maize, an important crop plant with a large genome but with limited reverse-genetic resources currently available. We screened pools of DNA samples for mutations in 1-kb segments from 11 different genes, obtaining 17 independent induced mutations from a population of 750 pollen-mutagenized maize plants. One of the genes targeted was the DMT102 chromomethylase gene, for which we obtained an allelic series of three missense mutations that are predicted to be strongly deleterious. CONCLUSIONS: Our findings indicate that TILLING is a broadly applicable and efficient reverse-genetic strategy. We are establishing a public TILLING service for maize modeled on the existing Arabidopsis TILLING Project.

Efficient discovery of DNA polymorphisms in natural populations by Ecotilling.

We have adapted the mutation detection technology used in Targeting Induced Local Lesions in Genomes (TILLING) to the discovery of polymorphisms in natural populations. The genomic DNA of a queried individual is mixed with a reference DNA and used to amplify a target 1-kbp region of DNA with asymmetrically labeled fluorescent primers. After heating and annealing, heteroduplexes are nicked at mismatched sites by the endonuclease CEL I and cut strands are visualized using Li-cor gel analyzers. Putative polymorphisms detected in one fluorescence channel can be verified by appearance of the opposite cut strand in the other channel. We demonstrated the efficiency of this technology, called Ecotilling, by the discovery in 150+ individuals of 55 haplotypes in five genes, ranging from sequences differing by a single nucleotide polymorphism to those representing complex haplotypes. The discovered polymorphisms were confirmed by sequencing and included base-pair changes, small insertions and deletions, and variation in microsatellite repeat number. Ecotilling allows the rapid detection of variation in many individuals and is cost effective because only one individual for each haplotype needs to be sequenced. The technology is applicable to any organism including those that are heterozygous and polyploid.

High-throughput TILLING for functional genomics.

Targeting-induced local lesions in genomes (TILLING) is a general strategy for identifying induced point mutations that can be applied to almost any organism. Here, we describe the basic methodology for high-throughput TILLING. Gene segments are amplified using fluorescently tagged primers, and products are denatured and reannealed to form heteroduplexes between the mutated sequence and its wild-type counterpart. These heteroduplexes are substrates for cleavage by the endonuclease CEL I. Following cleavage, products are analyzed on denaturing polyacrylamide gels using the LI-COR DNA analyzer system. High-throughput TILLING has been adopted by the Arabidopsis TILLING Project (ATP) to provide allelic series of point mutations for the general Arabidopsis community.

Alternative splicing of lola generates 19 transcription factors controlling axon guidance in Drosophila.

The Drosophila melanogaster transcription factor Lola (longitudinals lacking) is a pivotal regulator of neural wiring that sets the precise expression levels of proteins that execute specific axon guidance decisions. Lola has a zinc finger DNA binding domain and a BTB (for Broad-complex, Tramtrack and Bric a brac) dimerization motif. We now show that alternative splicing of the lola gene creates a family of 19 transcription factors. All lola isoforms share a common dimerization domain, but 17 have their own unique DNA-binding domains. Seven of these 17 isoforms are present in the distantly-related Dipteran Anopheles gambiae, suggesting that the properties of specific isoforms are likely to be critical to lola function. Analysis of the expression patterns of individual splice variants and of the phenotypes of mutants lacking single isoforms supports this idea and establishes that the alternative forms of lola are responsible for different functions of this gene. Thus, in this system, the alternative splicing of a key transcription factor helps to explain how a small genome encodes all the information that is necessary to specify the enormous diversity of axonal trajectories.

PARSESNP: A tool for the analysis of nucleotide polymorphisms.

PARSESNP is a tool for the display and analysis of polymorphisms in genes. Using a reference DNA sequence, an exon/intron position model and a list of polymorphisms, it determines the effects of these polymorphisms on the expressed gene product, as well as the changes in restriction enzyme recognition sites. It shows the locations and effects of the polymorphisms in summary on a stylized graphic and in detail on a display of the protein sequence aligned with the DNA sequence. The addition of a homology model, in the form of an alignment of related protein sequences, allows for prediction of the severity of missense changes. PARSESNP is available on the World Wide Web at http://www.proweb.org/parsesnp/.

Spectrum of chemically induced mutations from a large-scale reverse-genetic screen in Arabidopsis.

Chemical mutagenesis has been the workhorse of traditional genetics, but it has not been possible to determine underlying rates or distributions of mutations from phenotypic screens. However, reverse-genetic screens can be used to provide an unbiased ascertainment of mutation statistics. Here we report a comprehensive analysis of approximately 1900 ethyl methanesulfonate (EMS)-induced mutations in 192 Arabidopsis thaliana target genes from a large-scale TILLING reverse-genetic project, about two orders of magnitude larger than previous such efforts. From this large data set, we are able to draw strong inferences about the occurrence and randomness of chemically induced mutations. We provide evidence that we have detected the large majority of mutations in the regions screened and confirm the robustness of the high-throughput TILLING method; therefore, any deviations from randomness can be attributed to selectional or mutational biases. Overall, we detect twice as many heterozygotes as homozygotes, as expected; however, for mutations that are predicted to truncate an encoded protein, we detect a ratio of 3.6:1, indicating selection against homozygous deleterious mutations. As expected for alkylation of guanine by EMS, >99% of mutations are G/C-to-A/T transitions. A nearest-neighbor bias around the mutated base pair suggests that mismatch repair counteracts alkylation damage.

Large-scale discovery of induced point mutations with high-throughput TILLING.

TILLING (Targeting Induced Local Lesions in Genomes) is a general reverse-genetic strategy that provides an allelic series of induced point mutations in genes of interest. High-throughput TILLING allows the rapid and low-cost discovery of induced point mutations in populations of chemically mutagenized individuals. As chemical mutagenesis is widely applicable and mutation detection for TILLING is dependent only on sufficient yield of PCR products, TILLING can be applied to most organisms. We have developed TILLING as a service to the Arabidopsis community known as the Arabidopsis TILLING Project (ATP). Our goal is to rapidly deliver allelic series of ethylmethanesulfonate-induced mutations in target 1-kb loci requested by the international research community. In the first year of public operation, ATP has discovered, sequenced, and delivered >1000 mutations in >100 genes ordered by Arabidopsis researchers. The tools and methodologies described here can be adapted to create similar facilities for other organisms.

Cyclooxygenase 1 (COX1) polymorphisms in African-American and Caucasian populations.

Cyclooxygenases (COXs) are the primary targets of aspirin and other non-steroidal anti-inflammatory drugs (NSAIDs), and thus enzymes of major interest to pharmacology, pharmacogenetics, and epidemiology. Genetic variants that affect enzyme function, or the interaction with NSAIDs, could alter drug response. We have screened the human COX1 gene coding regions of 48 African-American and 47 Caucasian individuals using DNA sequencing. We identified 13 coding-region variants, of which seven were amino-acid substitutions, and further five intronic polymorphisms within 60bp of an exon. All nonsynonymous variants were confirmed in an independent Caucasian population (n=94 unrelated individuals). Most of the discovered polymorphisms were rare, although some variants resulting in amino-acid changes occurred at appreciable frequency in at least one population (> or =4%: R8W, P17L, L237M). We used two sequence-homology-based software programs to predict the potential impact of these polymorphisms on COX1 function. The L237M substitution was predicted as most likely to alter protein function, whereas the glycine at position 230 may be specific to COX1 function. More detailed phenotypic characterizations of these COX1 polymorphisms remain to be undertaken.

Using the blocks database to recognize functional domains.

Blocks are ungapped multiple alignments of related protein sequence segments that correspond to the most conserved regions of the proteins. The Blocks Database is a collection of blocks representing known protein families that can be used to compare a protein or DNA sequence with documented families of proteins. Protocols in this unit describe the analysis of proteins and families using Blocks-based tools, including searching, exploring relationships with trees, making new blocks, and designing PCR primers from blocks for isolating homologous sequences.