Programming and Problem Solving: A Transcript of the Spring 1999 Class

This report contains edited transcripts of the discussion held in Columbia's Programming and Problem-Solving course, taught as W4995-01during Spring 1999. The class notes were taken by the teaching assistant so that students could focus on the class material. As a service to both the students and to others who would like to get some insight into the class experience, we have drawn all of the class handouts, discussion, and some of the results into this technical report

CRISPR/Cas12a-based approaches for efficient and accurate detection of Phytophthora ramorum

IntroductionPhytophthora ramorum is a quarantine pathogen that causes leaf blight and shoot dieback of the crown, bark cankers and death on a number of both ornamental and forest trees, especially in North America and northern Europe, where it has produced severe outbreaks. Symptoms caused by P. ramorum can be confused with those by other Phytophthora and fungal species. Early and accurate detection of the causal pathogen P. ramorum is crucial for effective prevention and control of Sudden Oak Death.MethodsIn this study, we developed a P. ramorum detection technique based on a combination of recombinase polymerase amplification (RPA) with CRISPR/Cas12a technology (termed RPACRISPR/ Cas12a).ResultsThis novel method can be utilized for the molecular identification of P. ramorum under UV light and readout coming from fluorophores, and can specifically detect P. ramorum at DNA concentrations as low as 100 pg within 25 min at 37°C.DiscussionWe have developed a simple, rapid, sensitive, unaided-eye visualization, RPA CRISPR/Cas12a-based detection system for the molecular identification of P. ramorum that does not require technical expertise or expensive ancillary equipment. And this system is sensitive for both standard laboratory samples and samples from the field

Biological Earth observation with animal sensors

Space-based tracking technology using low-cost miniature tags is now delivering data on fine-scale animal movement at near-global scale. Linked with remotely sensed environmental data, this offers a biological lens on habitat integrity and connectivity for conservation and human health; a global network of animal sentinels of environmen-tal change

New Taxon-Specific Heterobasidion PCR Primers Detect and Differentiate North American Heterobasidion spp. in Various Substrates and Led to the Discovery of Heterobasidion irregulare in British Columbia, Canada

Heterobasidion annosum sensu lato is a species complex of pathogenic white-rot wood decay fungi which cause root and butt rot in conifer and hardwood species across the Northern hemisphere. Annual losses to forest managers are valued in the billions of dollars, due to tree mortality, reduction in timber yield, and wood decay. In North America, H. irregulare and H. occidentale have a partially overlapping host and geographic range, cause similar disease symptoms and produce similar fruiting bodies, making discrimination between the two of them often difficult. We developed two sets of primers that bind specifically to conserved, but species-specific portions of glyceraldehyde 3-phosphate dehydrogenase and elongation factor 1α alleles. The method is sensitive enough to detect either species from infected wood. Analysis of North American isolates has further clarified the distribution of both species on this continent, including the detection of H. irregulare for the first time on ponderosa pine (Pinus ponderosa) and eastern white pine (Pinus strobus) in British Columbia. This method has the potential to be a valuable tool for the detection of the pathogen in exported/imported wood products, as well as for the further identification and assessment of the distribution of North American Heterobasidion species

Contrasting research approaches to managing mistletoes in commercial forests and wooded pastures

Many mistletoe species are pests in agricultural and forest ecosystems throughout the world. Mistletoes are unusual “weeds” as they are generally endemic to areas where they achieve pest status and, therefore, classical biological control and broad-scale herbicidal control are usually impractical. In North American coniferous forests, dwarf mistletoe (Arceuthobium spp.) infection results in major commercial losses and poses a public liability in recreation settings. Hyperparasitic fungi have potential as biological control agents of dwarf mistletoe, including species which attack shoots, berries, and the endophytic systems of dwarf mistletoe. Development of an inundative biological control strategy will be useful in situations where traditional silvicultural control is impractical or undesirable. In southern Australia, farm eucalypts are often attacked and killed by mistletoes (Amyema spp.) in grazed landscapes where tree decline and biodiversity loss are major forms of land degradation. Although long-term strategies to achieve a balance between mistletoe and host abundance are promoted, many graziers want short-term options to treat severely infected trees. Recent research has revisited the efficiency and efficacy of silvicultural treatments and selective herbicides in appropriate situations. The results of recent research on these diverse management strategies in North America and Australia are summarized

Comparative Efficacy of Chondrosterum purpureum and Chemical Herbicides for Control of Resprouts in Tanoak and Bay Laurel

The invasive Oomycete pathogen Phytophthora ramorum has killed millions of susceptible oak and tanoak trees in California and southern Oregon forests and is responsible for losses in revenue to the nursery industry through mitigation activities. In addition, infestation of forests in the United Kingdom by this organism has resulted in the destruction of many hectares of larch plantations. Resprouting stumps can be a reservoir for the inoculum of P. ramorum persisting on a site. In areas where the application of herbicides is not permitted, a biocontrol treatment would be an indispensable alternative. Treatment of stumps with the sap-rotting fungus Chondrostereum purpureum (Pers.) Pouzar has been shown to be an effective tool for the suppression of resprouting on several species, most notably red alder. In this project, the ability of C. purpureum to suppress resprouting was evaluated on stumps of two host species, tanoak (Notholithocarpus densiflorus) and California bay laurel (Umbellularia californica). Laboratory testing of three California isolates of C. purpureum indicated that the fungus can colonize bay laurel stems. Field trials were established near Brookings, Oregon, on tanoak and on bay laurel near Soquel, California. Early results of field testing showed that C. purpureum was able to colonize the stumps of tanoak following treatment and was found to occur naturally on tanoak logs and stumps. Formulations of C. purpureum appear to have some effect on reducing sprout survival in tanoak, but the most effective and rapid treatment for this host is the hack and squirt method of applying the herbicide imazapyr. Sprayed herbicide prevents sprouting on bay laurel, and there was evidence that resprouting was inhibited on stumps treated with C. purpureum. Over time, applications of C. purpureum may be a more permanent solution as the stumps begin to decay

Increasing Threshold Search for Best-Valued Agents

This paper investigates search techniques for multi-agent settings in which the most suitable agent, according to given criteria, needs to be found. In particular, it considers the case where the searching agent incurs a cost for learning the value of an agent and the goal is to minimize the expected overall cost of search by iteratively increasing the extent of search. This kind of search is applicable to various domains, including auctions, first responders, and sensor networks. Using an innovative transformation of the extents-based sequence to a probability-based one, the optimal sequence is proved to consist of either a single search iteration or an infinite sequence of increasing search extents. This leads to a simplified characterization of the the optimal search sequence from which it can be derived. This method is also highly useful for legacy economic-search applications, where all agents are considered suitable candidates and the goal is to optimize the search process as a whole. The effectiveness of the method for both best-valued search and economic search is demonstrated numerically using a synthetic environment