Designing Genomes using Design-Simulate-Test Cycles

AbstractIn the future, entire genomes tailored to specific functions and environments could be designed using computational tools. However, computational tools for genome design are currently scarce. Here we present algorithms that enable the use of design-simulate-test cycles for genome design, using genome minimisation as a proof-of-concept. Minimal genomes are ideal for this purpose as they have a simple functional assay, the cell either replicates or not. We used the first (and currently only published) whole-cell model, for the bacteriumMycoplasma genitalium. Our computational design-simulate-test cycles discovered novelin-silicominimal genomes smaller thanJCVI-Syn3.0, a bacteria with, currently, the smallest genome that can be grown in pure culture. In the process, we identified 10 low essentiality genes, 18 high essentiality genes, and produced evidence for at least twoMycoplasma genitalium in-silicominimal genomes. This work brings combined computational and laboratory genome engineering a step closer.</jats:p

The Hanbury Brown and Twiss Experiment with Fermions

We realized an equivalent Hanbury Brown and Twiss experiment for a beam of electrons in a two dimensional electron gas in the quantum Hall regime. A metallic split gate serves as a tunable beam splitter which is used to partition the incident beam into transmitted and reflected partial beams. The current fluctuations in the reflected and transmitted beam are fully anticorrelated demonstrating that fermions tend to exclude each other (anti-bunching). If the occupation probability of the incident beam is lowered by an additional gate, the anticorrelation is reduced and disappears in the classical limit of a highly diluted beam

Synthetic biology and microbioreactor platforms for programmable production of biologics at the point-of-care

Current biopharmaceutical manufacturing systems are not compatible with portable or distributed production of biologics, as they typically require the development of single biologic-producing cell lines followed by their cultivation at very large scales. Therefore, it remains challenging to treat patients in short time frames, especially in remote locations with limited infrastructure. To overcome these barriers, we developed a platform using genetically engineered Pichia pastoris strains designed to secrete multiple proteins on programmable cues in an integrated, benchtop, millilitre-scale microfluidic device. We use this platform for rapid and switchable production of two biologics from a single yeast strain as specified by the operator. Our results demonstrate selectable and near-single-dose production of these biologics in <24 h with limited infrastructure requirements. We envision that combining this system with analytical, purification and polishing technologies could lead to a small-scale, portable and fully integrated personal biomanufacturing platform that could advance disease treatment at point-of-care

A Novel Genome-Wide Association Study Approach Using Genotyping by Exome Sequencing Leads to the Identification of a Primary Open Angle Glaucoma Associated Inversion Disrupting ADAMTS17

Closed breeding populations in the dog in conjunction with advances in gene mapping and sequencing techniques facilitate mapping of autosomal recessive diseases and identification of novel disease-causing variants, often using unorthodox experimental designs. In our investigation we demonstrate successful mapping of the locus for primary open angle glaucoma in the Petit Basset Griffon Vendéen dog breed with 12 cases and 12 controls, using a novel genotyping by exome sequencing approach. The resulting genome-wide association signal was followed up by genome sequencing of an individual case, leading to the identification of an inversion with a breakpoint disrupting the ADAMTS17 gene. Genotyping of additional controls and expression analysis provide strong evidence that the inversion is disease causing. Evidence of cryptic splicing resulting in novel exon transcription as a consequence of the inversion in ADAMTS17 is identified through RNAseq experiments. This investigation demonstrates how a novel genotyping by exome sequencing approach can be used to map an autosomal recessive disorder in the dog, with the use of genome sequencing to facilitate identification of a disease-associated variant

Entangled Hanbury Brown Twiss effects with edge states

Electronic Hanbury Brown Twiss correlations are discussed for geometries in which transport is along adiabatically guided edge channels. We briefly discuss partition noise experiments and discuss the effect of inelastic scattering and dephasing on current correlations. We then consider a two-source Hanbury Brown Twiss experiment which demonstrates strikingly that even in geometries without an Aharonov-Bohm effect in the conductance matrix (second-order interference), correlation functions can (due to fourth-order interference) be sensitive to a flux. Interestingly we find that this fourth-order interference effect is closely related to orbital entanglement. The entanglement can be detected via violation of a Bell Inequality in this geometry even so particles emanate from uncorrelated sources.Comment: International Symposium "Quantum Hall Effect: Past, Present and Future

Versatile and on-demand biologics co-production in yeast

Current limitations to on-demand drug manufacturing can be addressed by technologies that streamline manufacturing processes. Combining the production of two or more drugs into a single batch could not only be useful for research, clinical studies, and urgent therapies but also effective when combination therapies are needed or where resources are scarce. Here we propose strategies to concurrently produce multiple biologics from yeast in single batches by multiplexing strain development, cell culture, separation, and purification. We demonstrate proof-of-concept for three biologics co-production strategies: (i) inducible expression of multiple biologics and control over the ratio between biologic drugs produced together; (ii) consolidated bioprocessing; and (iii) co-expression and co-purification of a mixture of two monoclonal antibodies. We then use these basic strategies to produce drug mixtures as well as to separate drugs. These strategies offer a diverse array of options for on-demand, flexible, low-cost, and decentralized biomanufacturing applications without the need for specialized equipment

Deceptive signals of phase transitions in small magnetic clusters

We present an analysis of the thermodynamic properties of small transition metal clusters and show how the commonly used indicators of phase transitions like peaks in the specific heat or magnetic susceptibility can lead to deceptive interpretations of the underlying physics. The analysis of the distribution of zeros of the canonical partition function in the whole complex temperature plane reveals the nature of the transition. We show that signals in the magnetic susceptibility at positive temperatures have their origin at zeros lying at negative temperatures.Comment: 4 pages, 5 figures, revtex4, for further information see http://www.smallsystems.d

Genetics of callous-unemotional behavior in children

Callous-unemotional behavior (CU) is currently under consideration as a subtyping index for conduct disorder diagnosis. Twin studies routinely estimate the heritability of CU as greater than 50%. It is now possible to estimate genetic influence using DNA alone from samples of unrelated individuals, not relying on the assumptions of the twin method. Here we use this new DNA method (implemented in a software package called Genome-wide Complex Trait Analysis, GCTA) for the first time to estimate genetic influence on CU. We also report the first genome-wide association (GWA) study of CU as a quantitative trait. We compare these DNA results to those from twin analyses using the same measure and the same community sample of 2,930 children rated by their teachers at ages 7, 9 and 12. GCTA estimates of heritability were near zero, even though twin analysis of CU in this sample confirmed the high heritability of CU reported in the literature, and even though GCTA estimates of heritability were substantial for cognitive and anthropological traits in this sample. No significant associations were found in GWA analysis, which, like GCTA, only detects additive effects of common DNA variants. The phrase ‘missing heritability’ was coined to refer to the gap between variance associated with DNA variants identified in GWA studies versus twin study heritability. However, GCTA heritability, not twin study heritability, is the ceiling for GWA studies because both GCTA and GWA are limited to the overall additive effects of common DNA variants, whereas twin studies are not. This GCTA ceiling is very low for CU in our study, despite its high twin study heritability estimate. The gap between GCTA and twin study heritabilities will make it challenging to identify genes responsible for the heritability of CU

Large bowel obstruction due to sesame seed bezoar: a case report

peer-reviewedWe report a case of a 79 year old man with a known benign anastomotic stricture presenting with large bowel obstruction. At laparotomy the obstruction was found to be caused by a large sesame seed bezoar. Seed bezoars are well known to cause impaction in the rectum but have never been previously reported to cause large bowel obstruction. We recommend that patients with known large bowel strictures should be advised not to eat seeds as this could ultimately lead to obstruction, ischaemia or perforationPUBLISHEDpeer-reviewe