Modular construction of mammalian gene circuits using TALE transcriptional repressors

An important goal of synthetic biology is the rational design and predictable implementation of synthetic gene circuits using standardized and interchangeable parts. However, engineering of complex circuits in mammalian cells is currently limited by the availability of well-characterized and orthogonal transcriptional repressors. Here, we introduce a library of 26 reversible transcription activator–like effector repressors (TALERs) that bind newly designed hybrid promoters and exert transcriptional repression through steric hindrance of key transcriptional initiation elements. We demonstrate that using the input-output transfer curves of our TALERs enables accurate prediction of the behavior of modularly assembled TALER cascade and switch circuits. We also show that TALER switches using feedback regulation exhibit improved accuracy for microRNA-based HeLa cancer cell classification versus HEK293 cells. Our TALER library is a valuable toolkit for modular engineering of synthetic circuits, enabling programmable manipulation of mammalian cells and helping elucidate design principles of coupled transcriptional and microRNA-mediated post-transcriptional regulation.National Institutes of Health (U.S.) (Grant 5R01CA155320-04)National Institutes of Health (U.S.) (Grant P50GM098792)National Institutes of Health (U.S.) (Grant 1R01CA173712-01

Monsters, Laws of Nature, and Teleology in Late Scholastic Textbooks

In the period of emergence of early modern science, ‘monsters’ or individuals with physical congenital anomalies were considered as rare events which required special explanations entailing assumptions about the laws of nature. This concern with monsters was shared by representatives of the new science and Late Scholastic authors of university textbooks. This paper will reconstruct the main theses of the treatment of monsters in Late Scholastic textbooks, by focusing on the question as to how their accounts conceived nature’s regularity and teleology. It shows that they developed a naturalistic teratology in which, in contrast to the naturalistic explanations usually offered by the new science, finality was at central stage. This general point does not impede our noticing that some authors were closer to the views emerging in the Scientific Revolution insofar as they conceived nature as relatively autonomous from God and gave a relevant place to efficient secondary causation. In this connection, this paper suggests that the concept of the laws of nature developed by the new science –as exception-less regularities—transferred to nature’s regularity the ‘strong’ character that Late Scholasticism attributed to finality and that the decline of the Late Scholastic view of finality played as an important concomitant factor permitting the transformation of the concept of laws of nature

Stabilization of the bio-membrane by small molecules: interaction of trehalose with the phospholipid bilayer

Anhydrobiotic organisms undergo periods of acute dehydration during their life cycle. It is of interest to understand how the biomembrane remains intact through such stress. A disaccharide, trehalose, which is metabolised during anhydrobiosis is found to prevent disruption of model membrane systems. Molecular modelling techniques are used to investigate the possible mode of interaction of trehalose with a model monolayer. The objective is to maximise hydrogen bonding between the two systems. A phospholipid matrix consisting of 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine (DMPC) is chosen to represent the monolayer. The crystal structure of DMPC reveals that there are two distinct conformers designated as A and B. An expansion of the monolayer, coplanar with its surface, results in the trehalose molecule being accommodated in a pocket formed by four B conformers. One glucose ring of the sugar rests on the hydrophobic patch provided by the choline methyls of an A conformer. Five hydrogen bonds are formed involving the phosphate oxygens of three of the surrounding B conformers. The model will be discussed with reference to relevant experimental data on the interaction

Lipid conformational nomenclature: a general method

We propose a conformational nomenclature for amphiphilic lipid molecules that is general and compatible with the stereospecific numbering scheme, in contrast to earlier methods in which discrepancies with the sn-scheme lead to contradictory assignments of the absolute configuration of the system. The present method can be rationally extended to different classes of lipids, both natural and synthetic. It is simple and provides a convenient framework for conformational studies on widely varying classes of lipids

Molecular modelling of saccharide-lipid interactions

Certain saccharides, including trehalose, sucrose and glucose, stabilize lipid bilayers against dehydration. It has been suggested that these saccharides replace waters of hydration as the system is dried, thereby maintaining the headgroups at their hydrated spacing. The lipid acyl chains consequently have sufficient free volume to remain in the liquid crystallines state, and the processes that disrupt membrane integrity are inhibited. Initial molecular graphic investigations of a model trehalose/DMPC system supported this idea (Chandrasekhar, I. and Gaber, B.P. (1988) J. Biomol. Stereodyn, 5, 1163–1171). We have extended these studies to glucose and sucrose. A set of AMBER potential parameters has been established that reproduce simple saccharide conformations, including the anomeric effect. Extensive energy minimizations have been conducted on all three systems. The saccharide-lipid interaction energies become less stable in the order trehalose <sucrose<glucose. However, the total energies of the saccharide/lipid complexes becom eless negative in the order trehalose<glucose<sucrose

Molecular Modeling Studies on Amphotericin B and its Complex with Phospholipid,

Molecular dynamics simulation studies on polyene antifungal antibiotic amphotericin B, its head-to-tail dimeric structure and lipid - amphotericin B complex demonstrate interesting features of the flexibilities within the molecule and define the optimal interactions for the formation of a stable dimeric structure and complex with phospholipid