Talent & Tenacity: Sparking an Incubator in Ramsey

Report completed by students enrolled in PA 5211: Land Use Planning, taught by Fernando Burga in fall 2017.This project was completed as part of the 2017-2018 Resilient Communities Project (rcp.umn.edu) partnership with the City of Ramsey. The City of Ramsey has a successful business retention and expansion (BRE) program that has been focused on small-business development and growth. To advance these efforts, the City would like to pursue new initiatives to attract, retain, and grow businesses, including developing a long-term vision and strategy for a business incubator. To assess the feasibility of a business incubator, students in Dr. Fernando Burga’s Land Use Planning class documented economic development assets in Ramsey, interviewed successful business owners in Ramsey to understand their needs and challenges in starting a business, outlined considerations for the City in launching an incubator, and investigated the potential benefits and challenges of several business incubator models for Ramsey. A final report is available.This project was supported by the Resilient Communities Project (RCP), a program at the University of Minnesota whose mission is to connect communities in Minnesota with U of MN faculty and students to advance community resilience through collaborative, course-based projects. RCP is a program of the Center for Urban and Regional Affairs (CURA). More information at http://www.rcp.umn.edu

Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing

Monomeric CRISPR-Cas9 nucleases are widely used for targeted genome editing but can induce unwanted off-target mutations with high frequencies. Here we describe dimeric RNA-guided FokI Nucleases (RFNs) that recognize extended sequences and can edit endogenous genes with high efficiencies in human cells. The cleavage activity of an RFN depends strictly on the binding of two guide RNAs (gRNAs) to DNA with a defined spacing and orientation and therefore show improved specificities relative to wild-type Cas9 monomers. Importantly, direct comparisons show that RFNs guided by a single gRNA generally induce lower levels of unwanted mutations than matched monomeric Cas9 nickases. In addition, we describe a simple method for expressing multiple gRNAs bearing any 5′ end nucleotide, which gives dimeric RFNs a broad targeting range. RFNs combine the ease of RNA-based targeting with the specificity enhancement inherent to dimerization and are likely to be useful in applications that require highly precise genome editing

Engineered zinc finger nickases induce homology-directed repair with reduced mutagenic effects

Engineered zinc finger nucleases (ZFNs) induce DNA double-strand breaks at specific recognition sequences and can promote efficient introduction of desired insertions, deletions or substitutions at or near the cut site via homology-directed repair (HDR) with a double- and/or single-stranded donor DNA template. However, mutagenic events caused by error-prone non-homologous end-joining (NHEJ)-mediated repair are introduced with equal or higher frequency at the nuclease cleavage site. Furthermore, unintended mutations can also result from NHEJ-mediated repair of off-target nuclease cleavage sites. Here, we describe a simple and general method for converting engineered ZFNs into zinc finger nickases (ZFNickases) by inactivating the catalytic activity of one monomer in a ZFN dimer. ZFNickases show robust strand-specific nicking activity in vitro. In addition, we demonstrate that ZFNickases can stimulate HDR at their nicking site in human cells, albeit at a lower frequency than by the ZFNs from which they were derived. Finally, we find that ZFNickases appear to induce greatly reduced levels of mutagenic NHEJ at their target nicking site. ZFNickases thus provide a promising means for inducing HDR-mediated gene modifications while reducing unwanted mutagenesis caused by error-prone NHEJ

Cigarette Smoke Toxins Deposited on Surfaces: Implications for Human Health

Cigarette smoking remains a significant health threat for smokers and nonsmokers alike. Secondhand smoke (SHS) is intrinsically more toxic than directly inhaled smoke. Recently, a new threat has been discovered – Thirdhand smoke (THS) – the accumulation of SHS on surfaces that ages with time, becoming progressively more toxic. THS is a potential health threat to children, spouses of smokers and workers in environments where smoking is or has been allowed. The goal of this study is to investigate the effects of THS on liver, lung, skin healing, and behavior, using an animal model exposed to THS under conditions that mimic exposure of humans. THS-exposed mice show alterations in multiple organ systems and excrete levels of NNAL (a tobacco-specific carcinogen biomarker) similar to those found in children exposed to SHS (and consequently to THS). In liver, THS leads to increased lipid levels and non-alcoholic fatty liver disease, a precursor to cirrhosis and cancer and a potential contributor to cardiovascular disease. In lung, THS stimulates excess collagen production and high levels of inflammatory cytokines, suggesting propensity for fibrosis with implications for inflammation-induced diseases such as chronic obstructive pulmonary disease and asthma. In wounded skin, healing in THS-exposed mice has many characteristics of the poor healing of surgical incisions observed in human smokers. Lastly, behavioral tests show that THS-exposed mice become hyperactive. The latter data, combined with emerging associated behavioral problems in children exposed to SHS/THS, suggest that, with prolonged exposure, they may be at significant risk for developing more severe neurological disorders. These results provide a basis for studies on the toxic effects of THS in humans and inform potential regulatory policies to prevent involuntary exposure to THS

The SAMI Galaxy Survey: Bayesian Inference for Gas Disk Kinematics using a Hierarchical Gaussian Mixture Model

We present a novel Bayesian method, referred to as Blobby3D, to infer gas kinematics that mitigates the effects of beam smearing for observations using Integral Field Spectroscopy (IFS). The method is robust for regularly rotating galaxies despite substructure in the gas distribution. Modelling the gas substructure within the disk is achieved by using a hierarchical Gaussian mixture model. To account for beam smearing effects, we construct a modelled cube that is then convolved per wavelength slice by the seeing, before calculating the likelihood function. We show that our method can model complex gas substructure including clumps and spiral arms. We also show that kinematic asymmetries can be observed after beam smearing for regularly rotating galaxies with asymmetries only introduced in the spatial distribution of the gas. We present findings for our method applied to a sample of 20 star-forming galaxies from the SAMI Galaxy Survey. We estimate the global H$\alpha$ gas velocity dispersion for our sample to be in the range $\bar{\sigma}_v \sim$[7, 30] km s$^{-1}$. The relative difference between our approach and estimates using the single Gaussian component fits per spaxel is $\Delta \bar{\sigma}_v / \bar{\sigma}_v = - 0.29 \pm 0.18$ for the H$\alpha$ flux-weighted mean velocity dispersion.Comment: 23 pages, 12 figures, accepted for MNRA

The SAMI Galaxy Survey: Bayesian inference for gas disc kinematics using a hierarchical Gaussian mixture model

We present a novel Bayesian method, referred to as BLOBBY3D, to infer gas kinematics that mitigates the effects of beam smearing for observations using integral field spectroscopy. The method is robust for regularly rotating galaxies despite substructure in the gas distribution. Modelling the gas substructure within the disc is achieved by using a hierarchical Gaussian mixture model. To account for beam smearing effects, we construct a modelled cube that is then convolved per wavelength slice by the seeing, before calculating the likelihood function. We show that our method can model complex gas substructure including clumps and spiral arms. We also show that kinematic asymmetries can be observed after beam smearing for regularly rotating galaxies with asymmetries only introduced in the spatial distribution of the gas. We present findings for our method applied to a sample of 20 star-forming galaxies from the SAMI Galaxy Survey. We estimate the global H α gas velocity dispersion for our sample to be in the range ¯σv ∼[7, 30] km s−1. The relative difference between our approach and estimates using the single Gaussian component fits per spaxel is σ¯v/σ¯v = −0.29 ± 0.18 for the H α flux-weighted mean velocity dispersion.The SAMI Galaxy Survey is supported by the Australian Research Council Centre of Excellence for All Sky Astrophysics in 3 Dimensions (ASTRO 3D), through project number CE170100013, the Australian Research Council Centre of Excellence for All-sky Astrophysics (CAASTRO), through project number CE110001020, and other participating institutions. BJB acknowledges funding from New Zealand taxpayers via the Marsden Fund of the Royal Society of New Zealand. JBH is supported by an ARC Laureate Fellowship that funds JvdS and an ARC Federation Fellowship that funded the SAMI prototype. EDT acknowledges the support of the Australian Research Council (ARC) through grant DP160100723. JJB acknowledges support of an Australian Research Council Future Fellowship (FT180100231). CF acknowledges funding provided by the Australian Research Council (Discovery Projects DP170100603 and Future Fellowship FT180100495), and the Australia-Germany Joint Research Cooperation Scheme (UA-DAAD). BG is the recipient of an Australian Research Council Future Fellowship (FT140101202). Support for AMM is provided by NASA through Hubble Fellowship grant #HST-HF2-51377 awarded by the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., for NASA, under contract NAS5-26555. MSO acknowledges the funding support from the Australian Research Council through a Future Fellowship (FT140100255). NS acknowledges support of a University of Sydney Postdoctoral Research Fellowship

Selection-Free Zinc-Finger Nuclease Engineering by Context-Dependent Assembly (CoDA)

Engineered zinc-finger nucleases (ZFNs) enable targeted genome modification. Here we describe Context-Dependent Assembly (CoDA), a platform for engineering ZFNs using only standard cloning techniques or custom DNA synthesis. Using CoDA ZFNs, we rapidly altered 20 genes in zebrafish, Arabidopsis, and soybean. The simplicity and efficacy of CoDA will enable broad adoption of ZFN technology and make possible large-scale projects focused on multi-gene pathways or genome-wide alterations

An improved predictive recognition model for Cys2-His2 zinc finger proteins

Cys2-His2 zinc finger proteins (ZFPs) are the largest family of transcription factors in higher metazoans. They also represent the most diverse family with regards to the composition of their recognition sequences. Although there are a number of ZFPs with characterized DNA-binding preferences, the specificity of the vast majority of ZFPs is unknown and cannot be directly inferred by homology due to the diversity of recognition residues present within individual fingers. Given the large number of unique zinc fingers and assemblies present across eukaryotes, a comprehensive predictive recognition model that could accurately estimate the DNA-binding specificity of any ZFP based on its amino acid sequence would have great utility. Toward this goal, we have used the DNA-binding specificities of 678 two-finger modules from both natural and artificial sources to construct a random forest-based predictive model for ZFP recognition. We find that our recognition model outperforms previously described determinant-based recognition models for ZFPs, and can successfully estimate the specificity of naturally occurring ZFPs with previously defined specificities

The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima.

Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific life history.This work was supported by the following grants: NHGRIU54HG003273 to R.A.G; EU Marie Curie ITN #215781 “Evonet” to M.A.; a Wellcome Trust Value in People (VIP) award to C.B. and Wellcome Trust graduate studentship WT089615MA to J.E.G; Marine rhythms of Life” of the University of Vienna, an FWF (http://www.fwf.ac.at/) START award (#AY0041321) and HFSP (http://www.hfsp.org/) research grant (#RGY0082/2010) to KT-­‐R; MFPL Vienna International PostDoctoral Program for Molecular Life Sciences (funded by Austrian Ministry of Science and Research and City of Vienna, Cultural Department -­‐Science and Research to T.K; Direct Grant (4053034) of the Chinese University of Hong Kong to J.H.L.H.; NHGRI HG004164 to G.M.; Danish Research Agency (FNU), Carlsberg Foundation, and Lundbeck Foundation to C.J.P.G.; U.S. National Institutes of Health R01AI55624 to J.H.W.; Royal Society University Research fellowship to F.M.J.; P.D.E. was supported by the BBSRC via the Babraham Institute;This is the final version of the article. It first appeared from PLOS via http://dx.doi.org/10.1371/journal.pbio.100200

Adolescent Brain Development and the Risk for Alcohol and Other Drug Problems

Dynamic changes in neurochemistry, fiber architecture, and tissue composition occur in the adolescent brain. The course of these maturational processes is being charted with greater specificity, owing to advances in neuroimaging and indicate grey matter volume reductions and protracted development of white matter in regions known to support complex cognition and behavior. Though fronto-subcortical circuitry development is notable during adolescence, asynchronous maturation of prefrontal and limbic systems may render youth more vulnerable to risky behaviors such as substance use. Indeed, binge-pattern alcohol consumption and comorbid marijuana use are common among adolescents, and are associated with neural consequences. This review summarizes the unique characteristics of adolescent brain development, particularly aspects that predispose individuals to reward seeking and risky choices during this phase of life, and discusses the influence of substance use on neuromaturation. Together, findings in this arena underscore the importance of refined research and programming efforts in adolescent health and interventional needs