Chromatin accessibility underlies synthetic lethality of SWI/SNF subunits in ARID1A-mutant cancers.

ARID1A, a subunit of the SWI/SNF chromatin remodeling complex, is frequently mutated in cancer. Deficiency in its homolog ARID1B is synthetically lethal with ARID1A mutation. However, the functional relationship between these homologs has not been explored. Here, we use ATAC-seq, genome-wide histone modification mapping, and expression analysis to examine colorectal cancer cells lacking one or both ARID proteins. We find that ARID1A has a dominant role in maintaining chromatin accessibility at enhancers, while the contribution of ARID1B is evident only in the context of ARID1A mutation. Changes in accessibility are predictive of changes in expression and correlate with loss of H3K4me and H3K27ac marks, nucleosome spacing, and transcription factor binding, particularly at growth pathway genes including MET. We find that ARID1B knockdown in ARID1A mutant ovarian cancer cells causes similar loss of enhancer architecture, suggesting that this is a conserved function underlying the synthetic lethality between ARID1A and ARID1B

Spectrin promotes the association of F-actin with the cytoplasmic surface of the human erythrocyte membrane

We studied the binding of actin to the erythrocyte membrane by a novel application of falling ball viscometry. Our approach is based on the notion that if membranes have multiple binding sites for F-actin they will be able to cross-link and increase the viscosity of actin. Spectrin- and actin-depleted inside-out vesicles reconstituted with purified spectrin dimer or tetramer induce large increases in the viscosity of actin. Comparable concentrations of spectrin alone, inside-out vesicles alone, inside-out vesicles plus heat-denatured spectrin dimmer or tetramer induce large increases in the viscosity of actin. Comparable concentrations of spectrin alone, inside-out vesicles alone, inside-out plus heat denatured spectrin, ghosts, or ghosts plus spectrin have no effect on the viscosity of actin. Centrifugation experiments show that the amount of actin bound to the inside-out vesicles is enhanced in the presence of spectrin. The interactions detected by low-shear viscometry reflect actin interaction with membrane- bound spectrin because (a) prior removal of band 4.1 and ankyrin (band 2.1, the high- affinity membrane attachment site for spectrin) reduces both spectrin binding to the inside-out vesicles and their capacity to stimulate increase in viscosity of actin in the presence of spectrin + actin are inhibited by the addition of the water-soluble 72,000- dalton fragment of ankyrin, which is known to inhibit spectrin reassociation to the membrane. The increases in viscosity of actin induced by inside-out vesicles reconstituted with purified spectrin dimer or tetramer are not observed when samples are incubated at 0 degrees C. This temperature dependence may be related to the temperature-dependent associations we observe in solution studies with purified proteins: addition of ankyrin inhibits actin cross-linking by spectrin tetramer plus band 4.1 at 0 degrees C, and enhances it at 32 degrees C. We conclude (a) that falling ball viscometry can be used to assay actin binding to membranes and (b) that spectrin is involved in attaching actin filaments or oligomers to the cytoplasmic surface of the erythrocyte membrane

Preparation of Large Monodisperse Vesicles

Preparation of monodisperse vesicles is important both for research purposes and for practical applications. While the extrusion of vesicles through small pores (∼100 nm in diameter) results in relatively uniform populations of vesicles, extrusion to larger sizes results in very heterogeneous populations of vesicles. Here we report a simple method for preparing large monodisperse multilamellar vesicles through a combination of extrusion and large-pore dialysis. For example, extrusion of polydisperse vesicles through 5-µm-diameter pores eliminates vesicles larger than 5 µm in diameter. Dialysis of extruded vesicles against 3-µm-pore-size polycarbonate membranes eliminates vesicles smaller than 3 µm in diameter, leaving behind a population of monodisperse vesicles with a mean diameter of ∼4 µm. The simplicity of this method makes it an effective tool for laboratory vesicle preparation with potential applications in preparing large monodisperse liposomes for drug delivery

Human Interaction in Learning Ecosystems based on Open Source Solutions

Technological ecosystems are software solutions based on the integration of heterogeneous software components through information flows in order to provide a set of services that each component separately does not offer, as well as to improve the user experience. In particular, the learning ecosystems are technological ecosystems focused on learning and knowledge management in different contexts such as educational institutions or companies. The ecosystem metaphor comes from biology field and it has transferred to technology field to highlight the evolving component of software. Taking into account the definitions of natural ecosystems, a technological ecosystem is a set of people and software components that play the role of organisms; a series of elements that allow the ecosystem works (hardware, networks, etc.); and a set of information flows that establish the relationships between the software components, and between these and the people involved in the ecosystem. Human factor has a main role in the definition and development of this kind of solutions. In previous works, a metamodel has been defined and validated to support Model-Driven Development of learning ecosystems based on Open Source software, but the interaction in the learning ecosystem should be defined in order to complete the proposal to improve the development process of technological ecosystems. This paper presents the definition and modelling of the human interaction in learning ecosystem

LEGO® bricks as building blocks for centimeter-scale biological environments

LEGO bricks are commercially available interlocking pieces of plastic that are conventionally used as toys. We describe their use to build engineered environments for cm-scale biological systems, in particular plant roots. Specifically, we take advantage of the unique modularity of these building blocks to create inexpensive, transparent, reconfigurable, and highly scalable environments for plant growth in which structural obstacles and chemical gradients can be precisely engineered to mimic soil

Internal lipid synthesis and vesicle growth as a step toward self-reproduction of the minimal cell

One of the major properties of the semi-synthetic minimal cell, as a model for early living cells, is the ability to self-reproduce itself, and the reproduction of the boundary layer or vesicle compartment is part of this process. A minimal bio-molecular mechanism based on the activity of one single enzyme, the FAS-B (Fatty Acid Synthase) Type I enzyme from Brevibacterium ammoniagenes, is encapsulated in 1-palmitoyl-2oleoyl-sn-glycero-3-phosphatidylcholine (POPC) liposomes to control lipid synthesis. Consequently molecules of palmitic acid released from the FAS catalysis, within the internal lumen, move toward the membrane compartment and become incorporated into the phospholipid bilayer. As a result the vesicle membranes change in lipid composition and liposome growth can be monitored. Here we report the first experiments showing vesicles growth by catalysis of one enzyme only that produces cell boundary from within. This is the prototype of the simplest autopoietic minimal cell

Bringing CASE in from the cold: the teaching and learning of thinking

Thinking Science is a two-year program of professional development for teachers and thinking lessons for students in junior high school science classes. This paper presents research on the effects of Thinking Science on students’ levels of cognition in Australia. The research is timely with a general capability focused on critical thinking in the newly implemented F-10 curriculum in Australia. The design of the research was a quasi-experiment with pre and post-intervention cognitive tests conducted with participating students (n = 655) from nine cohorts in seven high schools. Findings showed significant cognitive gains compared with an age matched control group over the length of the program. Noteworthy, is a correlation between baseline cognitive score and school Index of Community Socio-Educational Advantage (ICSEA). We argue that the teaching of thinking be brought into the mainstream arena of educational discourse and the principles from evidence-based programs such as Thinking Science be universally adopted

STEM education in the twenty-first century: learning at work-an exploration of design and technology teacher perceptions and practices

Teachers’ knowledge of STEM education, their understanding, and pedagogical application of that knowledge is intrinsically linked to the subsequent effectiveness of STEM delivery within their own practice; where a teacher’s knowledge and understanding is deficient, the potential for pupil learning is ineffective and limited. Set within the context of secondary age phase education in England and Wales (11–16 years old), this paper explores how teachers working within the field of design and technology education acquire new knowledge in STEM; how understanding is developed and subsequently embedded within their practice to support the creation of a diverse STEM-literate society. The purpose being to determine mechanisms by which knowledge acquisition occurs, to reconnoitre potential implications for education and learning at work, including consideration of the role which new technologies play in the development of STEM knowledge within and across contributory STEM subject disciplines. Underpinned by an interpretivist ontology, work presented here builds upon the premise that design and technology is an interdisciplinary educational construct and not viewed as being of equal status to other STEM disciplines including maths and science. Drawing upon the philosophical field of symbolic interactionism and constructivist grounded theory, work embraces an abductive methodology where participants are encouraged to relate design and technology within the context of STEM education. Emergent findings are discussed in relation to their potential to support teachers’ educational development for the advancement of STEM literacy, and help secure design and technology’s place as a subject of value within a twenty-first Century curriculum

Competitive Interactions between Invasive Nile Tilapia and Native Fish: The Potential for Altered Trophic Exchange and Modification of Food Webs

Recent studies have highlighted both the positive and negative impacts of species invasions. Most of these studies have been conducted on either immobile invasive plants or sessile fauna found at the base of food webs. Fewer studies have examined the impacts of vagile invasive consumers on native competitors. This is an issue of some importance given the controlling influence that consumers have on lower order plants and animals. Here, we present results of laboratory experiments designed to assess the impacts of unintended aquaculture releases of the Nile tilapia (Oreochromis niloticus), in estuaries of the Gulf of Mexico, on the functionally similar redspotted sunfish (Lepomis miniatus). Laboratory choice tests showed that tilapia prefer the same structured habitat that native sunfish prefer. In subsequent interspecific competition experiments, agonistic tilapia displaced sunfish from their preferred structured habitats. When a piscivore (largemouth bass) was present in the tank with both species, the survival of sunfish decreased. Based on these findings, if left unchecked, we predict that the proliferation of tilapia (and perhaps other aggressive aquaculture fishes) will have important detrimental effects on the structure of native food webs in shallow, structured coastal habitats. While it is likely that the impacts of higher trophic level invasive competitors will vary among species, these results show that consequences of unintended releases of invasive higher order consumers can be important