City of Colton Urban Forest Management Project

As population growth continues in our urban centers, urban forest management becomes an important priority. Trees are an essential component of resilient and healthy urban communities, providing benefits including mediating the urban heat island effect, storm water management, and energy and water efficiency, carbon sequestration, and city beautification. In order to assess the current status of Colton’s urban forest, interdisciplinary teams of students and scientists from the Center for Urban Resilience (CURes) at Loyola Marymount University (LMU) have assisted Jack Sahl & Associates with an extensive inventory of the tree resources within the City. In gathering data describing the size, distribution, age, health, and energy efficiency benefits of the city’s trees, this study seeks to provide recommendations for best management practices of Colton’s urban forest. Colton has strived to engage the public in an open dialogue about this project. Colton is the first city to deal with the task of conducting an inventory of all the trees located within the public domain, in the future the strategies used here will be improved.https://digitalcommons.lmu.edu/cures_posters/1014/thumbnail.jp

INTEGRATION OF HUMMINGBIRD RESEARCH INTO PUBLIC SCHOOL SCIENCE

Hummingbirds are beautiful, acrobatic and mysterious synanthropes in urban ecosystems, providing important benefits to humans such as pollination, insectivory, and biophilia. However, environmental factors that affect behaviors that lead to such services are largely unknown, and could be altered by urbanization and climate change. Though their extremely high metabolism can make detailed observations of hummingbird behavior difficult, simple and low-cost methodologies, such as remote monitoring equipment deployed at feeders and nests, allow students at all levels of education to closely observe hummingbirds directly from their school sites. The Center for Urban Resilience (CURes) and the Center for Equity for English Learners (CEEL) at Loyola Marymount University (LMU) have partnered, to implement CURes urban ecology curricula Urban EcoLab in various Los Angeles area schools and classrooms. With support from the Daniel and Susan Gottlieb Foundation, internet protocol (IP) cameras have been installed as a key element in the curriculum that will allow participation in world wide hummingbird research in the classroom. Beyond enriching the understanding of how animals thrive in urban environments, we propose to develop a model that will facilitate the investigation of complex scientific questions through collaboration with citizen science and integration of the Urban EcoLab curricula into primary and secondary-level public school curricula.https://digitalcommons.lmu.edu/cures_posters/1022/thumbnail.jp

Population Studies for Predator Aversion Project at the Venice Beach Least Tern (Sternula antillarum) Colony

In the Fall of 2017, the Loyola Marymount University (LMU) Center for Urban Resilience (CURes) contracted with a consultant of the State of California Dept. of Fish & Game Wildlife Branch, Ryan Ecological Consulting, to collaborate on solutions to American crow Corvus brachyrhyncos predation on Least tern eggs and chicks in the Venice Beach Least tern colony. Least terns prefer nesting in low sand dunes with light vegetation. As a result of urban expansion and beach combing, Least terns, a federally endangered bird, have lost much of their preferred nesting habitat in Southern California and have become vulnerable to crow predation at the few remaining nesting sites like Venice Beach. The aim of the CURes Venice Beach field study includes: • trapping and banding crows in order to determine resident vs. transient crow populations • using predator aversion strategies, including pseudo tern nests with mildly electrified decoy eggs, to deter the crows from entering the fencedin enclosure • monitoring Least tern populations as they arrive during the 2019 nesting season The ultimate goal of the project is to increase Least tern reproductive output, which has been extremely low in the past decade.https://digitalcommons.lmu.edu/cures_posters/1039/thumbnail.jp

An Analysis of Coyote (Canis latrans) Abundance, Movement Patterns & Distribution

https://digitalcommons.lmu.edu/cures_posters/1037/thumbnail.jp

An Analysis of Coyote (Canis latrans) Abundance, Movement Patterns & Distribution

The LMU Center for Urban Resilience (CURes) is currently in the third year of a three-year project to inform a long-term coyote Canis latrans management plan for the City of Long Beach, California. This plan will be applied by the Long Beach Animal Care Services Bureau. The project consists of using game cameras set up at a tree nursery study site in Long Beach to determine coyote abundance, movement patterns, and distribution. This includes studying where the coyotes are spending the most time, if they are transient / mobile, what packs are present, and peak activity. Preliminary analysis of temporal data indicates that the coyotes at this location do not overlap in movement patterns with other species such as humans and cats. Game camera data show coyotes are abundant when other species are not present. This is an indicator of niche partitioning. Another finding is that there is an average of 47 coyote sightings per week at the location. From this it can be inferred that coyotes are present and abundant at this study site in Long Beach. Further data collection, including collaring study coyotes, will inform the City on coyote movement patterns and distribution through the area. These data will help inform the City’s long-term coyote management strategies.https://digitalcommons.lmu.edu/cures_posters/1034/thumbnail.jp

Genetic Diet Analysis of Coyote Scat from Populations in Long Beach

Interactions between humans and local wildlife are inherent to urbanization and have created a demand for wildlife/human management solutions. Coyotes (Canislatrans) are prominent in urban ecosystems and can cause a variety of residential threats. The aim of this study is to monitor coyote distribution and activity in Long Beach, CA to better understand urban predatory behavior and develop local wildlife management techniques. One method for better understanding urban coyotes is through scat analysis, which provides insight into the specific animal species that comprise their diet. This study focuses on prey species identification using DNA isolated from coyote scat samples. DNA was isolated using a modified Chelexmethod, in which scat material was suspended in a higher volume and lower percentage Chelexsolution than the standard method. A 1,000 bpportion of the mitochondrial genome, which contains part of the cytochromebgene and D-loop region, was amplified using PCR. The PCR primers flanked the cytochromeb/D-loop region at sequences that are conserved in nearly all mammals (Foranet al. 1997). Since the amplified region is variable between species, restriction enzymes digest the region into different sized fragments. These fragments were visualized using gel electrophoresis and the banding pattern was read to determine species composition. The amplified DNA was digested using the BfaIrestriction enzyme. Determining dietary information on coyotes allows us to take effective steps towards managing wildlife and educating Long Beach residents on the predators that share their neighborhoods.https://digitalcommons.lmu.edu/cures_posters/1032/thumbnail.jp

H3 K36 Methylation Helps Determine the Timing of Cdc45 Association with Replication Origins

Replication origins fire at different times during S-phase. Such timing is determined by the chromosomal context, which includes the activity of nearby genes, telomeric position effects and chromatin structure, such as the acetylation state of the surrounding chromatin. Activation of replication origins involves the conversion of a pre-replicative complex to a replicative complex. A pivotal step during this conversion is the binding of the replication factor Cdc45, which associates with replication origins at approximately their time of activation in a manner partially controlled by histone acetylation.Here we identify histone H3 K36 methylation (H3 K36me) by Set2 as a novel regulator of the time of Cdc45 association with replication origins. Deletion of SET2 abolishes all forms of H3 K36 methylation. This causes a delay in Cdc45 binding to origins and renders the dynamics of this interaction insensitive to the state of histone acetylation of the surrounding chromosomal region. Furthermore, a decrease in H3 K36me3 and a concomitant increase in H3 K36me1 around the time of Cdc45 binding to replication origins suggests opposing functions for these two methylation states. Indeed, we find K36me3 depleted from early firing origins when compared to late origins genomewide, supporting a delaying effect of this histone modification for the association of replication factors with origins.We propose a model in which K36me1 together with histone acetylation advance, while K36me3 and histone deacetylation delay, the time of Cdc45 association with replication origins. The involvement of the transcriptionally induced H3 K36 methylation mark in regulating the timing of Cdc45 binding to replication origins provides a novel means of how gene expression may affect origin dynamics during S-phase

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN