Assessing and Improving the Ecological Function of Linear Parks Along the Lower Los Angeles River Channel, Los Angeles County, California, US

Long overlooked by conservation groups and ecologists, urban open spaces are now seen as important contributors to biodiversity at various scales. Urban greenspaces often represent the only “nature” millions of human residents around the world ever interact with, and provide cooling and aesthetic relief from the urban hardscape. In the Los Angeles Metropolitan area, over the past three decades, non-profit advocacy groups and institutions have established a network of bike paths, neighborhood access points, habitat restoration, and recreational amenities along the Los Angeles River, a major urban waterway. We investigated the environmental contribution provided by numerous linear landscaped parks along the river, focusing on climate amelioration (i.e., cooling within heat islands) in the parks and surrounding neighborhoods, and on their contribution to local biodiversity, utilizing an indicator species approach. We conducted plant surveys of the parks, documenting locally native, non-local California native, and non-native species, and examined the occurrence of 15 riparian indicator species of wildlife in the parks and in 500-meter buffer zones surrounding each park utilizing citizen science data. We then explore correlations between indicator species richness and environmental variables. We note important occurrences of relict riparian vegetation in several linear parks, as well as both planted and naturally-occurring special-status plant and wildlife species. Finally, we discuss challenges to managing natural habitat in highly-urban parks, many of which support important relict vegetation and/or special-status species, and offer suggestions on how they may be improved

Alu Exonization Events Reveal Features Required for Precise Recognition of Exons by the Splicing Machinery

Despite decades of research, the question of how the mRNA splicing machinery precisely identifies short exonic islands within the vast intronic oceans remains to a large extent obscure. In this study, we analyzed Alu exonization events, aiming to understand the requirements for correct selection of exons. Comparison of exonizing Alus to their non-exonizing counterparts is informative because Alus in these two groups have retained high sequence similarity but are perceived differently by the splicing machinery. We identified and characterized numerous features used by the splicing machinery to discriminate between Alu exons and their non-exonizing counterparts. Of these, the most novel is secondary structure: Alu exons in general and their 5′ splice sites (5′ss) in particular are characterized by decreased stability of local secondary structures with respect to their non-exonizing counterparts. We detected numerous further differences between Alu exons and their non-exonizing counterparts, among others in terms of exon–intron architecture and strength of splicing signals, enhancers, and silencers. Support vector machine analysis revealed that these features allow a high level of discrimination (AUC = 0.91) between exonizing and non-exonizing Alus. Moreover, the computationally derived probabilities of exonization significantly correlated with the biological inclusion level of the Alu exons, and the model could also be extended to general datasets of constitutive and alternative exons. This indicates that the features detected and explored in this study provide the basis not only for precise exon selection but also for the fine-tuned regulation thereof, manifested in cases of alternative splicing