Enhanced ribozyme-catalyzed recombination and oligonucleotide assembly in peptide-RNA condensates

The ability of RNA to catalyze RNA ligation is critical to its central role in many prebiotic model scenarios, in particular the copying of information during self-replication. Prebiotically plausible ribozymes formed from short oligonucleotides can catalyze reversible RNA cleavage and ligation reactions, but harsh conditions or unusual scenarios are often required to promote folding and drive the reaction equilibrium towards ligation. Here, we demonstrate that ribozyme activity is greatly enhanced by charge-mediated phase separation with poly-L-lysine, which shifts the reaction equilibrium from cleavage in solution to ligation in peptide-RNA coaggregates and coacervates. This compartmentalization enables robust isothermal RNA assembly over a broad range of conditions, which can be leveraged to assemble long and complex RNAs from short fragments under mild conditions in the absence of exogenous activation chemistry, bridging the gap between pools of short oligomers and functional RNAs

NO SPACE LEFT BEHIND - Graduate Urban Design Studio - LANDARCH 606

The following report documents the work of the 2015 Spring Graduate Urban Design Studio course in the Department of Landscape Architecture and Regional Planning. This fourteen week studio focused on using tactical urbanism to engage Springfield’s Metro Center neighborhood with visions to revitalize the downtown core of this legacy city. In addition to completing the components of a traditional urban design studio (site analyses, schematic plans, spatial designs, and programming), the student teams also developed conceptual projects to immediately engage the public. These efforts culminated in a free afternoon walking tour throughout the Metro Center that presented several tactical interventions. These interactive, public installations illustrated potential future initiatives and brought attention to overlooked areas and assets. Throughout the semester the teams were challenged to continuously consider both the short-term impacts of their interventions and the long-term visions for the future of Springfield’s urban core. This strategy allowed students to develop a process-based approach to urban design. It provided opportunities to engage stakeholders and test new ideas with the public, rather than simply creating a master plan without any real world interactions with the city and its populace. STUDIO GOALS • To enliven public space in Springfield’s Metro Center through small-scale urban design interventions which illustrate and inform long-term plans • To activate residual spaces in the downtown with Tactical Urbanism By matching long-term visions for the Metro Center with short-term, site-specific tactical interventions the teams were able to deliver a variety of ideas in multiple formats. Furthermore, the experience of interacting with community members during the installation of projects added a great deal of meaning to the research and design process. The work explores a community service learning strategy within the framework of an urban design studio with the goal of revitalizing the city of Springfield, Massachusetts, through sustainable design, planning, and engagement with the community. The six design-team interventions are documented and published as team-authored videos: 1. Union Station Green Corridor Maozhu Mao, Yuqing Wu https://www.youtube.com/watch?v=EnE8Yt8x0Es&feature=youtu.be 2. (No) Vacancy Chris Counihan, Michalagh Stoddard, Ruoying Tang https://youtu.be/CapaQ9gDxeM 3. Extra Space, Active Street Yu Yu https://youtu.be/2pgYq5HLNHA 4. Spring into Art Emilie Jordao, Matt Hisle, Jing Wang https://youtu.be/Vf2yk6Se6rU 5. Urban Agua Kellie Fenton, James Prendergast, Nelle Ward https://www.youtube.com/watch?v=vk2PUJMdhTU&feature=youtu.be 6. Make the Connection Yue Li, Yanhua Lu, Yi Yang https://youtu.be/EvQD0QYV97

Integration of time-series meta-omics data reveals how microbial ecosystems respond to disturbance.

The development of reliable, mixed-culture biotechnological processes hinges on understanding how microbial ecosystems respond to disturbances. Here we reveal extensive phenotypic plasticity and niche complementarity in oleaginous microbial populations from a biological wastewater treatment plant. We perform meta-omics analyses (metagenomics, metatranscriptomics, metaproteomics and metabolomics) on in situ samples over 14 months at weekly intervals. Based on 1,364 de novo metagenome-assembled genomes, we uncover four distinct fundamental niche types. Throughout the time-series, we observe a major, transient shift in community structure, coinciding with substrate availability changes. Functional omics data reveals extensive variation in gene expression and substrate usage amongst community members. Ex situ bioreactor experiments confirm that responses occur within five hours of a pulse disturbance, demonstrating rapid adaptation by specific populations. Our results show that community resistance and resilience are a function of phenotypic plasticity and niche complementarity, and set the foundation for future ecological engineering efforts

Mps1 directs the assembly of Cdc20 inhibitory complexes during interphase and mitosis to control M phase timing and spindle checkpoint signaling

Cdc20 and Mad2 or Bub1 don’t come together in Mps1-null cells, resulting in a dramatic acceleration of anaphase onset (see also related papers by Hewitt et al. and Santaguida et al. in this issue)

RNA silencing is required for Arabidopsis defence against Verticillium wilt disease

RNA silencing is a conserved mechanism in eukaryotes that plays an important role in various biological processes including regulation of gene expression. RNA silencing also plays a role in genome stability and protects plants against invading nucleic acids such as transgenes and viruses. Recently, RNA silencing has been found to play a role in defence against bacterial plant pathogens in Arabidopsis through modulating host defence responses. In this study, it is shown that gene silencing plays a role in plant defence against multicellular microbial pathogens; vascular fungi belonging to the Verticillium genus. Several components of RNA silencing pathways were tested, of which many were found to affect Verticillium defence. Remarkably, no altered defence towards other fungal pathogens that include Alternaria brassicicola, Botrytis cinerea, and Plectosphaerella cucumerina, but also the vascular pathogen Fusarium oxysporum, was recorded. Since the observed differences in Verticillium susceptibility cannot be explained by notable differences in root architecture, it is speculated that the gene silencing mechanisms affect regulation of Verticillium-specific defence responses

Positive Selection in East Asians for an EDAR Allele that Enhances NF-κB Activation

Genome-wide scans for positive selection in humans provide a promising approach to establish links between genetic variants and adaptive phenotypes. From this approach, lists of hundreds of candidate genomic regions for positive selection have been assembled. These candidate regions are expected to contain variants that contribute to adaptive phenotypes, but few of these regions have been associated with phenotypic effects. Here we present evidence that a derived nonsynonymous substitution (370A) in EDAR, a gene involved in ectodermal development, was driven to high frequency in East Asia by positive selection prior to 10,000 years ago. With an in vitro transfection assay, we demonstrate that 370A enhances NF-κB activity. Our results suggest that 370A is a positively selected functional genetic variant that underlies an adaptive human phenotype