Following replicative DNA synthesis by time-resolved X-ray crystallography

The mechanism of DNA synthesis has been inferred from static structures, but the absence of temporal information raises longstanding questions about the order of events in one of life’s most central processes. Here we follow the reaction pathway of a replicative DNA polymerase using time-resolved X-ray crystallography to elucidate the order and transition between intermediates. In contrast to the canonical model, the structural changes observed in the time-lapsed images reveal a catalytic cycle in which translocation precedes catalysis. The translocation step appears to follow a push-pull mechanism where the O-O1 loop of the finger subdomain acts as a pawl to facilitate unidirectional movement along the template with conserved tyrosine residues 714 and 719 functioning as tandem gatekeepers of DNA synthesis. The structures capture the precise order of critical events that may be a general feature of enzymatic catalysis among replicative DNA polymerases.

Population-level Membrane Diversity Triggers Growth and Division of Protocells

<div><p>To date, multiple mechanisms have been described for the growth and division of model protocells, all of which exploit the cumulative, unidirectional movement of lipids. The aggregate that is more complex grows at the expense of the smaller or less complex aggregate. Imbalances between surface area and volume during growth can generate filamentous vesicles which are typically divided by shear forces. Here we describe another pathway for growth and division that depends simply on differences in composition of fatty acid membranes. Growth is driven by the entropically-favored mixing of lipids between two populations. Division is the result of growth-induced curvature. Importantly, growth and division are cyclic and bidirectional, meaning that vesicles made from one type of lipid, e.g. short-chain fatty acids, grow and divide when fed with vesicles consisting of another type of lipid, e.g. long-chain fatty acids, and vice versa. After equilibration, additional rounds of growth and division are possible through the addition of compositionally distinct vesicles. Since prebiotic synthesis likely gave rise to mixtures of lipids, the data are consistent with the presence of growing and dividing protocells on the prebiotic Earth.</p></div>

Population-level Membrane Diversity Triggers Growth and Division of Protocells

<div><p>To date, multiple mechanisms have been described for the growth and division of model protocells, all of which exploit the cumulative, unidirectional movement of lipids. The aggregate that is more complex grows at the expense of the smaller or less complex aggregate. Imbalances between surface area and volume during growth can generate filamentous vesicles which are typically divided by shear forces. Here we describe another pathway for growth and division that depends simply on differences in composition of fatty acid membranes. Growth is driven by the entropically-favored mixing of lipids between two populations. Division is the result of growth-induced curvature. Importantly, growth and division are cyclic and bidirectional, meaning that vesicles made from one type of lipid, e.g. short-chain fatty acids, grow and divide when fed with vesicles consisting of another type of lipid, e.g. long-chain fatty acids, and vice versa. After equilibration, additional rounds of growth and division are possible through the addition of compositionally distinct vesicles. Since prebiotic synthesis likely gave rise to mixtures of lipids, the data are consistent with the presence of growing and dividing protocells on the prebiotic Earth.</p></div>

Mechanical and signaling mechanisms that guide pre-implantation embryo movement

ABSTRACTHow a mammalian embryo determines and arrives at its attachment site has been studied for decades, but our understanding of this process is far from complete. Using confocal imaging and image analysis, we evaluate embryo location along the longitudinal oviductal-cervical axis of murine uteri. Our analysis reveals three distinct pre-implantation phases: embryo entry, unidirectional movement of embryo clusters and bidirectional scattering and spacing of embryos. We show that unidirectional clustered movement is facilitated by a mechanical stimulus of the embryo and is regulated by adrenergic uterine smooth muscle contractions. Embryo scattering, on the other hand, depends on embryo-uterine communication reliant on the LPAR3 signaling pathway and is independent of adrenergic muscle contractions. Finally, we demonstrate that uterine implantation sites in mice are neither random nor predetermined but are guided by the number of embryos entering the uterine lumen. These studies have implications for understanding how embryo-uterine communication is key to determining an optimal implantation site necessary for the success of a pregnancy.

Thoreau’s luminous Homer in A Week on the Concord and Merrimack Rivers

Henry David Thoreau’s relationship to Greek literature, and Homer’s Iliad in particular, is more often remarked than analysed. This article argues that Thoreau’s engagement with Homer in his first book, A Week on the Concord and Merrimack Rivers, proves central to the themes of that work highlighted by critics as well as its less-studied formal hybrid of poetry and prose. I show that Thoreau constructs Homer as the poetic ideal in which the perennially renewed life of the natural world becomes accessible to human beings caught in the fatal and unidirectional movement of historical time. Thoreau’s ideas here may track Romantic conceptions of Homer and Greek literature more generally, but Thoreau turns contemporary uncertainty around the person of Homer into reflection on the relationship between personal experience and literary expression of ‘living nature’. This turns out to structure a larger dichotomy between poetry and prose, one in which Thoreau associates the latter with authentic experience and self-expression of an individual human life. In A Week’s engagement with Homer, then, we see Thoreau negotiating not only some core concerns of his writing but also his evolution from aspiring poet to author of the works in prose that ultimately define his career.

Mechanical and signaling mechanisms that guide pre-implantation embryo movement

ABSTRACTHow a mammalian embryo determines and arrives at its site of attachment is a mystery that has puzzled researchers for decades. Additionally, in multiparous species, embryos face a unique challenge of achieving adequate spacing to avoid competition for maternal resources. Using our enhanced confocal imaging and 3D image reconstruction technology, we evaluate murine embryo location in the uterus along the longitudinal oviductal-cervical axis. Our analysis reveals three distinct pre-implantation stages: a) Embryo entry; b) Unidirectional movement of embryo clusters; and c) Bidirectional scattering and spacing of embryos. We show that unidirectional movement of embryo clusters is facilitated by a mechanical stimulus of the embryo as a physical object and is regulated by adrenergic uterine smooth muscle contractions. Embryo scattering, on the other hand, relies on embryo-uterine communication reliant on the LPAR3 signaling pathway and is independent of adrenergic muscle contractions. We propose that the presence of embryo clusters in the uterine horn provides an opportunity for the uterus to sense and count the embryos, followed by scattering and spacing these embryos along the given length of the horn. Thus, uterine implantation sites in mice are neither random nor predetermined but are guided by the number of embryos entering the uterine lumen. These studies have implications for understanding how embryo-uterine communication is key to determining an optimal implantation site, which is necessary for the success of a pregnancy.Significance StatementIn mammals that carry multiple offspring in one gestation, embryos seemingly acquire even embryo spacing. Such even distribution would imply a guided interaction between the mother and the fetus very early on in pregnancy to allow favorable pregnancy outcomes. Thus, it is essential to understand quantitatively if and when such a uniform distribution of embryos is established. Further, uncovering the physical and biological mechanisms that allow for such equal distribution of embryos, will improve our understanding of early pregnancy events and provide for novel targets for improving pregnancy success in case of infertility and artificial reproductive technologies as well as to develop non-hormonal therapies for contraception.

Wettability Gradients on Graphene to Drive Bubble Motion

The molecular dynamics (MD) method is employed to simulate thermal bubble nucleation processes confined in graphene nanochannels. It is found that nucleation sites depend strongly on the different solid-liquid interfacial properties in various systems. In this work, the thermal bubble nucleates on the graphene surface, on which the interaction between liquid molecules and channel wall is weak relatively. It is demonstrated that the hydrophobic surface would make thermal bubble to initiate easier. A conceptual design about surface wettability gradient was proposed, which can break the equilibrium state of a bubble and induce its unidirectional movement on the surface. Moreover, MD simulation showed that through a continuous gradient of surface wettability, the direction of movement is under control. These findings provide us with a method in device design for applications of self-controlling motion of bubble down to nanoscale and other wettability-enabled actuators.