The no-SCAR (Scarless Cas9 Assisted Recombineering) system for genome editing in Escherichia coli

Genome engineering methods in E. coli allow for easy to perform manipulations of the chromosome in vivo with the assistance of the λ-Red recombinase system. These methods generally rely on the insertion of an antibiotic resistance cassette followed by removal of the same cassette, resulting in a two-step procedure for genomic manipulations. Here we describe a method and plasmid system that can edit the genome of E. coli without chromosomal markers. This system, known as Scarless Cas9 Assisted Recombineering (no-SCAR), uses λ-Red to facilitate genomic integration of donor DNA and double stranded DNA cleavage by Cas9 to counterselect against wild-type cells. We show that point mutations, gene deletions, and short sequence insertions were efficiently performed in several genomic loci in a single-step with regards to the chromosome and did not leave behind scar sites. The single-guide RNA encoding plasmid can be easily cured due to its temperature sensitive origin of replication, allowing for iterative chromosomal manipulations of the same strain, as is often required in metabolic engineering. In addition, we demonstrate the ability to efficiently cure the second plasmid in the system by targeting with Cas9, leaving the cells plasmid-free.Shell Global Solutions (US)National Institute of Food and Agriculture (U.S.) (Postdoctoral Fellowship 2013-67012-21022

Scarless Cas9 Assisted Recombineering (no‐SCAR) in Escherichia coli, an Easy‐to‐Use System for Genome Editing

The discovery and development of genome editing systems that leverage the site‐specific DNA endonuclease system CRISPR/Cas9 has fundamentally changed the ease and speed of genome editing in many organisms. In eukaryotes, the CRISPR/Cas9 system utilizes a “guide” RNA to enable the Cas9 nuclease to make a double‐strand break at a particular genome locus, which is repaired by non‐homologous end joining (NHEJ) repair enzymes, often generating random mutations in the process. A specific alteration of the target genome can also be generated by supplying a DNA template in vivo with a desired mutation, which is incorporated by homology‐directed repair. However, E. coli lacks robust systems for double‐strand break repair. Thus, in contrast to eukaryotes, targeting E. coli chromosomal DNA with Cas9 causes cell death. However, Cas9‐mediated killing of bacteria can be exploited to select against cells with a specified genotype within a mixed population. In combination with the well described λ‐Red system for recombination in E. coli, we created a highly efficient system for marker‐free and scarless genome editing.National Institute of Food and Agriculture (U.S.) (Award 2013-67012-21022)United States. Army Research Office (Grant W911NF-09-0001

'GR 7' Grape

'GR 7' is an early / mid-season red wine grape for use primarily in red wine blends. It is distinguished from other red wine grapes grown in cool climates by its high degree of winter hardiness, adaptation to mechanized production systems, and ability to survive in older plantings where other red wine grapes are lost due to tomato and tobacco ringspot virus infections. ?GR 7? is a highly productive, easy to manage cultivar, and is the sixth wine grape to be developed by the New York State Agricultural Experiment Station of Cornell University

Remaily Seedless Grape

Since the late 19th century when grape breeding began at the New York State Agricultural Experiment Station, a major goal has been to combine certain fruit attributes such as seedlessness, crisp texture, and adherent skin of Vitis vinifera L. table grapes with some of the vegetative characters such as disease resistance and cold hardiness of native American hybrid (V. labruscana, Bailey) grape cultivars

The abundant marine bacterium Pelagibacter simultaneously catabolizes dimethylsulfoniopropionate to the gases dimethyl sulfide and methanethiol

Marine phytoplankton produce ~109 tons of dimethylsulfoniopropionate (DMSP) per year1,2, an estimated 10% of which is catabolized by bacteria through the DMSP cleavage pathway to the climatically active gas dimethyl sulfide (DMS)3,4. SAR11 Alphaproteobacteria (order Pelagibacterales), the most abundant chemoorganotrophic bacteria in the oceans, have been shown to assimilate DMSP into biomass, thereby supplying this cell’s unusual requirement for reduced sulfur5,6. Here we report that Pelagibacter HTCC1062 produces the gas methanethiol (MeSH) and that simultaneously a second DMSP catabolic pathway, mediated by a cupin-like DMSP lyase, DddK, shunts as much as 59% of DMSP uptake to DMS production. We propose a model in which the allocation of DMSP between these pathways is kinetically controlled to release increasing amounts of DMS as the supply of DMSP exceeds cellular sulfur demands for biosynthesis

The Hydro-electro-thermal Performance of Air-cooled, Open-cathode Polymer Electrolyte Fuel Cells: Combined Localised Current Density, Temperature and Water Mapping

In situ diagnostic techniques provide a means of understanding the internal workings of fuel cells so that improved designs and operating regimes can be identified. Here, a novel metrology approach is reported that combines current and temperature mapping with water visualisation using neutron radiography. The approach enables a hydro-electro-thermal performance map to be generated that is applied to an air-cooled, open-cathode polymer electrolyte fuel cell. This type of fuel cell exhibits a particularly interesting coupled relationship between water, current and heat, as the air supply has the due role of cooling the stack as well as providing the cathode reactant feed via a single source. It is found that water predominantly accumulates under the cooling channels (thickness of 70-100 μm under the cooling channels and 5-25 μm in the active channels at 0.5 A cm−2), in a similar fashion to the lands in a closed-cathode design, but contrary to passive open-cathode systems. The relationship between current, temperature and water accumulation is complex and highly dependent on location within the cell. However, there is a general trend that higher currents and cooling limitations, especially above 0.7 A cm−2 and below 3.9 × 10−3 m3 s−1, leads to temperatures above 60 °C, which dehydrate the membrane (water thickness of 10-25 um) and the cell operates below 0.5 V

Functional consequences of seven novel mutations in the CYP11B1 Gene: four mutations associated with nonclassic and three mutations causing classic 11 -Hydroxylase Deficiency

Context: Steroid 11β-hydroxylase (CYP11B1) deficiency (11OHD) is the second most common form of congenital adrenal hyperplasia (CAH). Cases of nonclassic 11OHD are rare compared with the incidence of nonclassic 21-hydroxylase deficiency. Objective: The aim of the study was to analyze the functional consequences of seven novel CYP11B1 mutations (p.M88I, p.W116G, p.P159L, p.A165D, p.K254_A259del, p.R366C, p.T401A) found in three patients with classic 11OHD, two patients with nonclassic 11OHD, and three heterozygous carriers for CYP11B1 mutations. Methods: We conducted functional studies employing a COS7 cell in vitro expression system comparing wild-type (WT) and mutant CYP11B1 activity. Mutants were examined in a computational three-dimensional model of the CYP11B1 protein. Results: All mutations (p.W116G, p.A165D, p.K254_A259del) found in patients with classic 11OHD have absent or very little 11β-hydroxylase activity relative to WT. The mutations detected in patients with nonclassic 11OHD showed partial functional impairment, with one patient being homozygous (p.P159L; 25% of WT) and the other patient compound heterozygous for a novel mild p.M88I (40% of WT) and the known severe p.R383Q mutation. The two mutations detected in heterozygous carriers (p.R366C, p.T401A) also reduced CYP11B1 activity by 23 to 37%, respectively. Conclusion: Functional analysis results allow for the classification of novel CYP11B1 mutations as causative for classic and nonclassic 11OHD, respectively. Four partially inactivating mutations are predicted to result in nonclassic 11OHD. These findings double the number of mild CYP11B1 mutations previously described as associated with mild 11OHD. Our data are important to predict phenotypic expression and provide important information for clinical and genetic counseling i

'Chardonel' Grape

'Chardonel' resulted from the cross, 'SeyvaT x 'Chardonnay,' made in 1953. Fruit were first observed in 1958, and the original vine was propagated in 1960 under the number NY 45010. In later testing, it was re-named GW 9 (Geneva White 9) for ease of identification in cooperatively run yield trials. The vine was initially described as vigorous and productive with large clusters

Combined current and temperature mapping in an air-cooled, open-cathode polymer electrolyte fuel cell under steady-state and dynamic conditions

In situ diagnostic techniques provide a means of understanding the internal workings of fuel cells so that improved designs and operating regimes can be identified. Here, for the first time, a combined current density and temperature distributed measurement system is used to generate an electro-thermal performance map of an air-cooled, air-breathing polymer electrolyte fuel cell stack operating in an air/hydrogen cross-flow configuration. Analysis is performed in low- and high-current regimes and a complex relationship between localised current density, temperature and reactant supply is identified that describes the way in which the system enters limiting performance conditions. Spatiotemporal analysis was carried out to characterise transient operations in dead-ended anode/purge mode which revealed extensive current density and temperature gradients

Large tunable valley splitting in edge-free graphene quantum dots on boron nitride

Coherent manipulation of binary degrees of freedom is at the heart of modern quantum technologies. Graphene offers two binary degrees: the electron spin and the valley. Efficient spin control has been demonstrated in many solid state systems, while exploitation of the valley has only recently been started, yet without control on the single electron level. Here, we show that van-der Waals stacking of graphene onto hexagonal boron nitride offers a natural platform for valley control. We use a graphene quantum dot induced by the tip of a scanning tunneling microscope and demonstrate valley splitting that is tunable from -5 to +10 meV (including valley inversion) by sub-10-nm displacements of the quantum dot position. This boosts the range of controlled valley splitting by about one order of magnitude. The tunable inversion of spin and valley states should enable coherent superposition of these degrees of freedom as a first step towards graphene-based qubits