Effects of Transcriptional and Post-Transcriptional Control Mechanisms on Biological Noise in Synthetic Gene Circuits

Synthetic Biology is an interdisciplinary research field seeking to correct faulty cellular processes or implement predictable de-novo tasks by engineering biological systems. In this perspective, the potential of developing biosynthetic devices of industrial and medical relevance is hindered by the requirement of accounting for, controlling and finally exploiting the randomness of biochemical events through which biological complexity is implemented. In this thesis mathematical modelling and experimental acquisitions of basic synthetic circuits are adopted to guide the selection of gene expression control mechanisms and network topologies in the design of synthetic devices able to reliably operate in the stochastic cellular context. To this end, a noise tester circuits’ catalogue, intended as a tool for quantitatively investigating the robustness of newly designed synthetic devices, is implemented. Two synthetic gene circuits, exerting either a transcriptional or post-transcriptional control in the expression of a fluorescent reporter, are selected from the circuits’ library for detailed characterization. Based on bulk measurements, deterministic models are defined to identify the kinetic rates of biochemical reactions governing the circuits’ function. The inherently derived stochastic models are further used in numerical computations of plasmid copy number effect on gene expression stochasticity. Subsequently, flow cytometry analysis is used to quantify the steady-state dispersion in protein levels within an isogenic population of transformants. An intriguing feature of the stochastic models describing the observed variance in protein levels is the necessity of including extrinsic components (e.g. cell division events). Numerical analysis identified post-transcriptional control as the best candidate for noise minimization. Finally, we report the results of research undertaken during a period staying at the “Centre for Synthetic and System Biology” of the University of Edinburgh, where the phenotypic consequences of a long-non coding RNA on the transcriptional activation of GAL1-10 promoter in Saccharomyces Cerevisiae are investigated using fluorescence microscopy and microfluidics

In vitro models for non-alcoholic fatty liver disease: Emerging platforms and their applications

Non-alcoholic fatty liver disease (NAFLD) represents a global healthcare challenge, affecting 1 in 4 adults, and death rates are predicted to rise inexorably. The progressive form of NAFLD, non-alcoholic steatohepatitis (NASH), can lead to fibrosis, cirrhosis, and hepatocellular carcinoma. However, no medical treatments are licensed for NAFLD-NASH. Identifying efficacious therapies has been hindered by the complexity of disease pathogenesis, a paucity of predictive preclinical models and inadequate validation of pharmacological targets in humans. The development of clinically relevant in vitro models of the disease will pave the way to overcome these challenges. Currently, the combined application of emerging technologies (e.g., organ-on-a-chip/microphysiological systems) and control engineering approaches promises to unravel NAFLD biology and deliver tractable treatment candidates. In this review, we will describe advances in preclinical models for NAFLD-NASH, the recent introduction of novel technologies in this space, and their importance for drug discovery endeavors in the future

Face Coverings and Respiratory Tract Droplet Dispersion

Abstract Respiratory droplets are the primary transmission route for SARS-CoV-2, a principle which drives social distancing guidelines. Evidence suggests that virus transmission can be reduced by face coverings, but robust evidence for how mask usage might affect safe distancing parameters is lacking. Accordingly, we set out to quantify the effects of face coverings on respiratory tract droplet deposition. We tested an anatomically realistic manikin head which ejected fluorescent droplets of water and human volunteers, in speaking and coughing conditions without a face covering, or with a surgical mask or a single-layer cotton face covering. We quantified the number of droplets in flight using laser sheet illumination and UV-light for those that had landed at table height at up to 2 m. For human volunteers, expiratory droplets were caught on a microscope slide 5 cm from the mouth. Whether manikin or human, wearing a face covering decreased the number of projected droplets by less than 1000-fold. We estimated that a person standing 2 m from someone coughing without a mask is exposed to over 10 000 times more respiratory droplets than from someone standing 0.5 m away wearing a basic single-layer mask. Our results indicate that face coverings show consistent efficacy at blocking respiratory droplets and thus provide an opportunity to moderate social distancing policies. However, the methodologies we employed mostly detect larger (non-aerosol) sized droplets. If the aerosol transmission is later determined to be a significant driver of infection, then our findings may overestimate the effectiveness of face coverings

On-line optimal input design increases the efficiency and accuracy of the modelling of an inducible synthetic promoter

Synthetic biology seeks to design biological parts and circuits that implement new functions in cells. Major accomplishments have been reported in this field, yet predicting a priori the in vivo behaviour of synthetic gene circuits is major a challenge. Mathematical models offer a means to address this bottleneck. However, in biology, modelling is perceived as an expensive, time-consuming task. Indeed, the quality of predictions depends on the accuracy of parameters, which are traditionally inferred from poorly informative data. How much can parameter accuracy be improved by using model-based optimal experimental design (MBOED)? To tackle this question, we considered an inducible promoter in the yeast S. cerevisiae. Using in vivo data, we re-fit a dynamic model for this component and then compared the performance of standard (e.g., step inputs) and optimally designed experiments for parameter inference. We found that MBOED improves the quality of model calibration by ∼60%. Results further improve up to 84% when considering on-line optimal experimental design (OED). Our in silico results suggest that MBOED provides a significant advantage in the identification of models of biological parts and should thus be integrated into their characterisation.This research was partially supported by EC funding H2020 FET OPEN 766840-COSY-BIO and a Royal Society of Edinburgh-MoST grant (to F.M.), EPSRC funding EP/P017134/1-CONDSYC (to L.B.) and Spanish MINECO, grant ref. AGL2015-67504-C3-2-R (to E.B.-C.).Peer reviewe

Physiological adaptations affecting drug pharmacokinetics in space: what do we really know? A critical review of the literature

As human spaceflight progresses with extended mission durations, the demand for effective and safe drugs will necessarily increase. To date, the accepted medications used during missions (for space motion sickness, sleep disturbances, allergies, pain, and sinus congestion) are administered under the assumption that they act as safely and efficaciously as on Earth. However, physiological changes have been documented in human subjects in spaceflight involving fluid shifts, muscle and bone loss, immune system dysregulation, and adjustments in the gastrointestinal tract and metabolism. These alterations may change the pharmacokinetics (PK) and pharmacodynamics of commonly used medications. Frustratingly, the information gained from bed rest studies and from in‐flight observations is incomplete and also demonstrates a high variability in drug PK. Therefore, the objectives of this review are to report (i) the impact of the space environmental stressors on human physiology in relation to PK; (ii) the state‐of‐the‐art on experimental data in space and/or in ground‐based models; (iii) the validation of ground‐based models for PK studies; and (iv) the identification of research gaps

Reliable measurement of E. coli single cell fluorescence distribution using a standard microscope set-up

Background: Quantifying gene expression at single cell level is fundamental for the complete characterization of synthetic gene circuits, due to the significant impact of noise and inter-cellular variability on the system's functionality. Commercial set-ups that allow the acquisition of fluorescent signal at single cell level (flow cytometers or quantitative microscopes) are expensive apparatuses that are hardly affordable by small laboratories. Methods: A protocol that makes a standard optical microscope able to acquire quantitative, single cell, fluorescent data from a bacterial population transformed with synthetic gene circuitry is presented. Single cell fluorescence values, acquired with a microscope set-up and processed with custom-made software, are compared with results that were obtained with a flow cytometer in a bacterial population transformed with the same gene circuitry. Results: The high correlation between data from the two experimental set-ups, with a correlation coefficient computed over the tested dynamic range > 0.99, proves that a standard optical microscope- when coupled with appropriate software for image processing- might be used for quantitative single-cell fluorescence measurements. The calibration of the set-up, together with its validation, is described. Conclusions: The experimental protocol described in this paper makes quantitative measurement of single cell fluorescence accessible to laboratories equipped with standard optical microscope set-ups. Our method allows for an affordable measurement/quantification of intercellular variability, whose better understanding of this phenomenon will improve our comprehension of cellular behaviors and the design of synthetic gene circuits. All the required software is freely available to the synthetic biology community (MUSIQ Microscope flUorescence SIngle cell Quantification)

Ultrasound and autoptic diagnosis of asphyxiating thoracic dysplasia

Background. The skeletal system develops from mesoderm. In most bones (e.g., the long bones), ossification is preceded by cartilage (endochondral ossification). In other cases, such as flat bones, ossification develops directly in the mesenchyme without cartilage formation (intramembranous ossification). Skeletal dysplasias are a heterogeneous group of more disorders associated with developmental abnormalities of bone and cartilage. The modes of transmission are similar: autosomal dominant and recessive and X-linked dominant and recessive. Despite the potential advantages of 3-dimensional ultrasound (3D-US), antenatal diagnosis of skeletal dysplasia is difficult, given the large variety and complexity of these disorders: their phenotypes are variables and their features are overlapping. We present a case report of a woman with prenatal diagnosis of skeletal thoracic dysplasia, confirmed by postnatal radiography and fetal autopsy. Case report. A 26-year-old woman, primigravida, was referred for routine ultrasonic examination during her second trimester of pregnancy. Ultrasonography (USG) showed a single live foetus of a gestational age of 20+3 weeks; biparietal diameter and head circumference were adequate for the week of gestation. There was a polyhydramnios. The fetal thorax was extremely narrow. The thoracic circumference (TC) measured 100 mm (< 5th percentile), the abdominal circumference (AC) measured 157 mm (50th percentile), and the TC/AC ratio was 0.64 (normal range: 0.77–1.01). The long-bone lengths measured < 5th percentile, especially the proximal part of the upper limbs. Ultrasound scans of fetal abdomen revealed bilateral slight increase in the size of kidneys. There were no neural tube defects, and the fetal stomach and urinary bladder were normal. Fetal echocardiography revealed mild ventricular septal defect with good hemodynamic effect. Based on these findings, the diagnosis postulated as possible was asphyxiating thorax dysplasia (ATD). After genetic counseling, the patient decided for an elective termination of the pregnancy. A stillborn male fetus was delivered with a weight of 470 g. Infantogram and gross autopsy findings (narrow thorax, short upper limb bones, poor definition of pyramids of kidneys) supported the diagnosis made. Conclusion. Although skeletal anomalies are difficult to diagnose antenatally, a detailed scan of fetal anatomy between 20 and 32 gestational weeks exclude majority of major skeletal dysplasias. Termination of pregnancy is indicated and must be followed by genetic counseling for recurrence risk

Morphological findings in malformed fetuses with normal karyotype

In our Department morphological findings on fetuses from therapeutic interruption of pregnancy or spontaneous abortion are performed since ten years in order to correlate the ultrasound and/or chromosomic diagnosis with a real presence of malformations. The fetopathologic examination generally agrees with the chromosomal diagnosis, while in several cases it is possible to find malformations also in presence of a normal karyotype (Gitz, 2011). In our experience over the past 5 years we have found that 17 fetuses with a normal karyotype showed different heterogeneous ultrasound malformations. Only in 2 cases the fetuses died in uterus (17th and 22nd weeks of gestation), the other cases, aged between 14th and 23rd weeks of gestation, went from voluntary abortions. In 7 cases the karyotype was defined by amniocentesis while in the remaining 10 was determined by fetal fibroblasts culture; in only 30% of the observed cases the couple had carried out a genetic evaluation. External malformations were present in 16 fetuses, often related to the face (such as micrognathia, low-set of ears, flattened nasal bridge, cleft lip) or limb (short, curved, stubby) of spine (spina bifida) or genitalia (hypospadias). Malformations of internal organs were present in 10 cases, often affecting the cardiovascular system (complex heart defects and abnormal origin of the greath vessels), and nervous system (meningocele, agenesia of the corpus callosum, ventricular dilatation and Arnold-Chiari malformation); less frequent were malformations of other systems (digestive, respiratory and urinary). There was a single case of situs viscerum inversus associated with complex cardiac malformations and atresia of the bucco-pharyngeal membrane. These results indicate that the fetal morphological study is useful not only to confirm but often to supplement and complete the ultrasound data. Moreover genetic evaluation, utilizing fetopatholgical study, may have an important role in defining the diagnostic and clinical procedure, especially in relapses with malformed fetus and normal karyotype