Bacterial cells organize their genomes into a compact hierarchical structure called the nucleoid. Studying the nucleoid in cells faces challenges because of the cellular complexity while in vitro assays have difficulty in handling the fragile megabase-scale DNA biopolymers that make up bacterial genomes. Here, we introduce a method that overcomes these limitations as we develop and use a microfluidic device for the sequential extraction, purification, and analysis of bacterial nucleoids in individual microchambers. Our approach avoids any transfer or pipetting of the fragile megabase-size genomes and thereby prevents their fragmentation. We show how the microfluidic system can be used to extract and analyze single chromosomes from B. subtilis cells. Upon on-chip lysis, the bacterial genome expands in size and DNA-binding proteins are flushed away. Subsequently, exogeneous proteins can be added to the trapped DNA via diffusion. We envision that integrated microfluidic platforms will become an essential tool for the bottom-up assembly of complex biomolecular systems such as artificial chromosomes.@en

This doctoral thesis stands on three pillars that emerged from following my scientific interests: i) biophysics, ii) synthetic biology, and iii) biosecurity. The former, biophysics, reflects my desire for deep understanding of biological systems and my affinity for experimental work. The latter, synthetic biology and biosecurity, were born from the conviction that the understanding obtained in pursuing science offers the most fulfillment when applied to the benefits of society.

The main part of this thesis explores methodologies for the extraction, and characterization of large-scale DNA, with a particular focus on the megabase-pair length DNA from bacterial sources. The research aims to bridge the gap between in vivo chromosome studies and in vitro single-molecule techniques by developing approaches that enable the investigation of chromosome structure and dynamics at a more relevant genomic scale. The following chapters detail the experimental approaches, results, and conclusions drawn from this work.@en

Synthetic biology is an interdisciplinary field that brings together engineering and biology concepts alongside the arts and social sciences to develop solutions to pressing problems in our world. The education of students entering this field has relied on a diverse set of pedagogical methods to accomplish this goal. One non-profit group, iGEM–the International Genetically Engineered Machine competition, has been a driver of students’ awareness of synthetic biology for the last 20 years giving many young researchers their first experience in the field of synthetic biology. Dissemination of synthetic biology concepts by iGEM has occurred through several programs including a webinar series started during the 2020 COVID pandemic. The iGEM webinar series successfully engaged students by taking inspiration from synthetic biology programs in Europe, North America, and Asia that had themselves evolved alongside iGEM. The webinar designers modeled the content after their experiences in iGEM as well as their academic courses, pedagogy, and mentoring experiences. This series has produced globally accessible pedagogy for both technical synthetic biology knowledge and the communication skills necessary to build and communicate synthetic biology projects. The hope is that this series functions as a lasting blueprint that can be used by future educators in synthetic biology and other disciplines to reduce barriers that students face when attempting to enter cutting edge fields.@en

A biofoundry is a highly automated facility for processing of biological samples. In that capacity it has a major role in accelerating innovation and product development in engineering biology by implementing design, build, test and learn (DBTL) cycles. Biofoundries bring public and private stakeholders together to share resources, develop standards and forge collaborations on national and international levels. In this paper we argue for expanding the scope of applications for biofoundries towards roles in biosurveillance and biosecurity. Reviewing literature on these topics, we conclude that this could be achieved in multiple ways including developing measurement standards and protocols, engaging citizens in data collection, closer collaborations with biorefineries, and processing of samples. Here we provide an overview of these roles that despite their potential utility have not yet been commonly considered by policymakers and funding agencies and identify roadblocks to their realization. This document should prove useful to policymakers and other stakeholders who wish to strengthen biosecurity programs in ways that synergize with bioeconomy.

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Synthetic biologists have made great progress over the past decade in developing methods for modular assembly of genetic sequences and in engineering biological systems with a wide variety of functions in various contexts and organisms. However, current paradigms in the field entangle sequence and functionality in a manner that makes abstraction difficult, reduces engineering flexibility and impairs predictability and design reuse. Functional Synthetic Biology aims to overcome these impediments by focusing the design of biological systems on function, rather than on sequence. This reorientation will decouple the engineering of biological devices from the specifics of how those devices are put to use, requiring both conceptual and organizational change, as well as supporting software tooling. Realizing this vision of Functional Synthetic Biology will allow more flexibility in how devices are used, more opportunity for reuse of devices and data, improvements in predictability and reductions in technical risk and cost.

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The mechanisms by which astrocytes modulate neural homeostasis, synaptic plasticity, and memory are still poorly explored. Astrocytes form large intercellular networks by gap junction coupling, mainly composed of two gap junction channel proteins, connexin 30 (Cx30) and connexin 43 (Cx43). To circumvent developmental perturbations and to test whether astrocytic gap junction coupling is required for hippocampal neural circuit function and behavior, we generate and study inducible, astrocyte-specific Cx30 and Cx43 double knockouts. Surprisingly, disrupting astrocytic coupling in adult mice results in broad activation of astrocytes and microglia, without obvious signs of pathology. We show that hippocampal CA1 neuron excitability, excitatory synaptic transmission, and long-term potentiation are significantly affected. Moreover, behavioral inspection reveals deficits in sensorimotor performance and a complete lack of spatial learning and memory. Together, our findings establish that astrocytic connexins and an intact astroglial network in the adult brain are vital for neural homeostasis, plasticity, and spatial cognition.

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Chromosome structure and function is studied using various cell-based methods as well as with a range of in vitro single-molecule techniques on short DNA substrates. Here, we present a method to obtain megabase-pair-length deproteinated DNA for in vitro studies. We isolated chromosomes from bacterial cells and enzymatically digested the native proteins. Mass spectrometry indicated that 97%–100% of DNA-binding proteins are removed from the sample. Fluorescence microscopy analysis showed an increase in the radius of gyration of the DNA polymers, while the DNA length remained megabase-pair sized. In proof-of-concept experiments using these deproteinated long DNA molecules, we observed DNA compaction upon adding the DNA-binding protein Fis or PEG crowding agents and showed that it is possible to track the motion of a fluorescently labeled DNA locus. These results indicate the practical feasibility of a “genome-in-a-box” approach to study chromosome organization from the bottom up.

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Thermal measurements at the nanoscale are key for designing technologies in many areas, including drug delivery systems, photothermal therapies, and nanoscale motion devices. Herein, we present a nanothermometry technique that operates in electrolyte solutions and, therefore, is applicable for many in vitro measurements, capable of measuring and mapping temperature with nanoscale spatial resolution and sensitive to detect temperature changes down to 30 mK with 43 μs temporal resolution. The methodology is based on local measurements of ionic conductivity confined at the tip of a pulled glass capillary, a nanopipettete, with opening diameters as small as 6 nm. When scanned above a specimen, the measured ion flux is converted into temperature using an extensive theoretical support given by numerical and analytical modeling. This allows quantitative thermal measurements with a variety of capillary dimensions and is applicable to a range of substrates. We demonstrate the capabilities of this nanothermometry technique by simultaneous mapping of temperature and topography on sub-micrometer-sized aggregates of thermoplasmonic nanoparticles heated by a laser and observe the formation of micro- and nanobubbles upon plasmonic heating. Furthermore, we perform quantitative thermometry on a single-nanoparticle level, demonstrating that the temperature at an individual nanoheater of 25 nm in diameter can reach an increase of about 3 K.

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3D bioprinting has seen a tremendous growth in recent years in a variety of fields such as tissue engineering, drug testing and regenerative medicine, which has led researchers and manufacturers to continuously advance and develop novel bioprinting techniques and materials. Although new bioprinting methods are emerging (e.g. contactless and volumetric bioprinting), micro-extrusion bioprinting remains the most widely used method. Micro-extrusion bioprinting, however, is still largely dependent on the conventional pneumatic extrusion process, which relies heavily on homogenous biomaterial inks and bioinks to maintain a constant material flow rate. Augmenting the functionality of the bioink with the addition of nanoparticles, cells or biopolymers can induce inhomogeneities resulting in uneven material flow during printing and/or clogging of the nozzle, leading to defects in the printed construct. In this work, we evaluated a novel extrusion technique based on a miniaturized progressive cavity pump (PCP) which allows precise control over the volumetric flow rate by positive displacement. We compared the accuracy and precision of this system to the pneumatic extrusion system and tested both systems for their effect on cell viability after extrusion. The PCP achieved a significantly higher accuracy and precision compared to the pneumatic system, while maintaining good viability. These improvements were independent of the bioink composition, printing speed or nozzle size. This study demonstrates the merit of precise extrusion-process control in bioprinting by PCPs and investigates their influence on process-induced cell damage. PCPs are a promising tool for bioprinting and could help provide standardized and validated bioprinted constructs while leaving the researcher more freedom in the design of the bioinks.

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