Underspecification, Inherent Nondeterminism and Probability in Sequence Diagrams

Abstract. Nondeterminism in specifications may be used for at least two different purposes. One is to express underspecification, which means that the specifier for the same environment behavior allows several alterna-tive behaviors of the specified component and leaves the choice between these to those responsible for implementing the specification. In this case a valid implementation will need to implement at least one, but not nec-essarily all, alternatives. The other purpose is to express inherent nonde-terminism, which means that a valid implementation needs to reflect all alternatives. STAIRS is an approach to the compositional and incremental development of sequence diagrams supporting underspecification as well as inherent nondeterminism. Probabilistic STAIRS builds on STAIRS and allows probabilities to be included in the specifications. Underspecifica-tion with respect to probabilities is also allowed. This paper investigates the use of underspecification, inherent nondeterminism and probability in sequence diagrams, the relationships between these concepts, and how these are expressed in STAIRS and probabilistic STAIRS.

siRNA-Mediated Gene Targeting in Aedes aegypti Embryos Reveals That Frazzled Regulates Vector Mosquito CNS Development

Although mosquito genome projects uncovered orthologues of many known developmental regulatory genes, extremely little is known about the development of vector mosquitoes. Here, we investigate the role of the Netrin receptor frazzled (fra) during embryonic nerve cord development of two vector mosquito species. Fra expression is detected in neurons just prior to and during axonogenesis in the embryonic ventral nerve cord of Aedes aegypti (dengue vector) and Anopheles gambiae (malaria vector). Analysis of fra function was investigated through siRNA-mediated knockdown in Ae. aegypti embryos. Confirmation of fra knockdown, which was maintained throughout embryogenesis, indicated that microinjection of siRNA is an effective method for studying gene function in Ae. aegypti embryos. Loss of fra during Ae. aegypti development results in thin and missing commissural axons. These defects are qualitatively similar to those observed in Dr. melanogaster fra null mutants. However, the Aa. aegypti knockdown phenotype is stronger and bears resemblance to the Drosophila commissureless mutant phenotype. The results of this investigation, the first targeted knockdown of a gene during vector mosquito embryogenesis, suggest that although Fra plays a critical role during development of the Ae. aegypti ventral nerve cord, mechanisms regulating embryonic commissural axon guidance have evolved in distantly related insects

Semaphorin-1a Is Required for Aedes aegypti Embryonic Nerve Cord Development

Although mosquito genome projects have uncovered orthologues of many known developmental regulatory genes, extremely little is known about mosquito development. In this study, the role of semaphorin-1a (sema1a) was investigated during vector mosquito embryonic ventral nerve cord development. Expression of sema1a and the plexin A (plexA) receptor are detected in the embryonic ventral nerve cords of Aedes aegypti (dengue vector) and Anopheles gambiae (malaria vector), suggesting that Sema1a signaling may regulate mosquito nervous system development. Analysis of sema1a function was investigated through siRNA-mediated knockdown in A. aegypti embryos. Knockdown of sema1a during A. aegypti development results in a number of nerve cord phenotypes, including thinning, breakage, and occasional fusion of the longitudinal connectives, thin or absent commissures, and general distortion of the nerve cord. Although analysis of Drosophila melanogaster sema1a loss-of-function mutants uncovered many similar phenotypes, aspects of the longitudinal phenotypes differed between D. melanogaster and A. aegypti. The results of this investigation suggest that Sema1a is required for development of the insect ventral nerve cord, but that the developmental roles of this guidance molecule have diverged in dipteran insects

An expansive human regulatory lexicon encoded in transcription factor footprints.

Regulatory factor binding to genomic DNA protects the underlying sequence from cleavage by DNase I, leaving nucleotide-resolution footprints. Using genomic DNase I footprinting across 41 diverse cell and tissue types, we detected 45 million transcription factor occupancy events within regulatory regions, representing differential binding to 8.4 million distinct short sequence elements. Here we show that this small genomic sequence compartment, roughly twice the size of the exome, encodes an expansive repertoire of conserved recognition sequences for DNA-binding proteins that nearly doubles the size of the human cis-regulatory lexicon. We find that genetic variants affecting allelic chromatin states are concentrated in footprints, and that these elements are preferentially sheltered from DNA methylation. High-resolution DNase I cleavage patterns mirror nucleotide-level evolutionary conservation and track the crystallographic topography of protein-DNA interfaces, indicating that transcription factor structure has been evolutionarily imprinted on the human genome sequence. We identify a stereotyped 50-base-pair footprint that precisely defines the site of transcript origination within thousands of human promoters. Finally, we describe a large collection of novel regulatory factor recognition motifs that are highly conserved in both sequence and function, and exhibit cell-selective occupancy patterns that closely parallel major regulators of development, differentiation and pluripotency

Purification and characterization of cytochrome P450 2E2 from hepatic microsomes of neonatal rabbits

The alcohol-inducible P450 2E subfamily in the rabbit has two known members that differ in only 16 amino acid residues scattered throughout the polypeptide chain. P450 2E1 has been thoroughly characterized, and is known to have diverse inducers and substrates. Little is known, however, about the properties of P450 2E2, since efforts to isolate this isozyme from adult rabbits have been unsuccessful. In the present study, 2E2 was purified to electrophoretic homogeneity from liver microsomes of neonatal rabbits with the use of 4-methylpyrazole as a stabilizing agent. The purified cytochrome was identified as 2E2 by NH2-terminal amino acid sequence analysis as well as by immunoblot analysis with three different antibodies to 2E1. Purified 2E2, in contrast to 2E1, is predominantly low-spin in the presence of 20% glycerol, but is in a mixed high- and low-spin state as the concentration of glycerol is decreased. The catalytic properties of purified 2E1 and 2E2 were compared in the reconstituted system with a variety of substrates, including alcohols, ethers nitrosamines, and aromatic compounds. Differences between the two enzymes in catalytic activity and in the interaction with cytochrome b5 were observed with some but not all of the substrates tested. Purified 2E1 and 2E2 both consume molecular oxygen relatively rapidly during NADPH oxidation in the absence of an added substrate, and stoichiometric determinations indicated that only about 20% of the O2 was reduced to H2O2, with the remainder apparently undergoing four-electron reduction to water.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/29002/1/0000031.pd

Researching the gender division of unpaid domestic work: practices, relationships, negotiations, and meanings

The paper focuses on the potential of quantitative research methods for sociologists who research the gender division of unpaid domestic work. To begin, it reflects on the emergence of the sociological interest in unpaid domestic work and identifies an early core concern with making invisible work visible. It is argued that quantitative research methods provide us with the most valuable opportunities for ‘recognising’ unpaid domestic work since they facilitate larger scale representative projects. However the data in most of the large scale surveys are scant, and fail to reflect developments in the conceptualisation of unpaid domestic work. Four areas of concern to contemporary sociology are identified: domestic work practices, relationships, negotiations and meanings. Given the complex questions that these four sub- topics raise, the paper proposes a range of sub-areas as a focus for ongoing sociological research into unpaid domestic work. It is concluded that despite the methodological challenges presented, detailed indicators of the multiple dimensions of unpaid domestic work need to be agreed so that valid information can be collected as routinely in large scale surveys as are those on paid work

The accessible chromatin landscape of the human genome

DNaseI hypersensitive sites (DHSs) are markers of regulatory DNA and have underpinned the discovery of all classes of cis-regulatory elements including enhancers, promoters, insulators, silencers, and locus control regions. Here we present the first extensive map of human DHSs identified through genome-wide profiling in 125 diverse cell and tissue types. We identify ~2.9 million DHSs that encompass virtually all known experimentally-validated cis-regulatory sequences and expose a vast trove of novel elements, most with highly cell-selective regulation. Annotating these elements using ENCODE data reveals novel relationships between chromatin accessibility, transcription, DNA methylation, and regulatory factor occupancy patterns. We connect ~580,000 distal DHSs with their target promoters, revealing systematic pairing of different classes of distal DHSs and specific promoter types. Patterning of chromatin accessibility at many regulatory regions is choreographed with dozens to hundreds of co-activated elements, and the trans-cellular DNaseI sensitivity pattern at a given region can predict cell type-specific functional behaviors. The DHS landscape shows signatures of recent functional evolutionary constraint. However, the DHS compartment in pluripotent and immortalized cells exhibits higher mutation rates than that in highly differentiated cells, exposing an unexpected link between chromatin accessibility, proliferative potential and patterns of human variation

Bioinspired materials and tissue engineering approaches applied to the regeneration of musculoskeletal tissues

The musculoskeletal tissues have a prime role in the biomechanical support and metabolic activities of the human body. As musculoskeletal tissues are highly prone to injuries, conditions afflicting these tissues have a great impact on the quality of life of patients worldwide. Tissue engineering approaches hold the promise to develop bioengineered substitutes aiming at the regeneration of failing and injured tissue and organs. To effectively address the tissue-specific structural and biochemical features of musculoskeletal tissues, different biomaterials and techniques have been employed envisioning biomimetic solutions. Herein, the unique composition, structure, and function of the musculoskeletal tissues, namely bone, cartilage, and tendon, as well as state-of-the-art technologies to develop bioinspired strategies for tissue regeneration will be overviewed. Finally, this chapter will also discuss the unmet challenges and future perspectives in the field.FCT Project MagTT PTDC/CTM-CTM/29930/2017 (POCI-01- 0145-FEDER-29930) for A.I.G postdoc grant, the FCT Project PTDC/NAN-MAT/30595/2017 (POCI-01-0145-FEDER-30595) for P.S.B. postdoc grant, and for the assistant researcher contract (RL1) of M.T.R from the project “Accelerating tissue engineering and personalized medicine discoveries by the integration of key enabling nanotechnologies, marine-derived biomaterials and stem cells” supported by Norte Portugal Regional Operational Programme (NORTE 2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF). Authors acknowledge the financial support from the European Union Framework Programme for Research and Innovation HORIZON 2020, under the TEAMING Grant agreement No. 739572—The Discoveries CTR and the European Research Council 2017-CoG MagTendon (No. 772817

Mixed plastics waste valorization through tandem chemical oxidation and biological funneling

115 p.-4 fig.-45 fig. supl.-14 tab supl.Mixed plastics waste represents an abundant and largely untapped feedstock for the production of valuable products. The chemical diversity and complexity of thesematerials, however, present major barriers to realizing this opportunity. In this work, we show that metal-catalyzed autoxidation depolymerizes comingled polymers into a mixture of oxygenated small molecules that are advantaged substrates for biological conversion. We engineer a robust soil bacterium, Pseudomonas putida, to funnel these oxygenated compounds into a single exemplary chemical product, either b-ketoadipate or polyhydroxyalkanoates. This hybrid process establishes a strategy for the selective conversion of mixed plastics waste into useful chemical products.Funding was provided by the US Department of Energy, Office of Energy Efficiency and Renewable Energy, Advanced Manufacturing Office (AMO), and Bioenergy Technologies Office (BETO). This work was performed as part of the BOTTLE Consortium and was supported by AMO and BETO under contract no. DE-AC36- 08GO28308 with the National Renewable Energy Laboratory (NREL),operated by the Alliance for Sustainable Energy, LLC. The BOTTLE Consortium includes members from MIT, funded under contract no. DE-AC36-08GO28308 with NREL. Contributions by S.S.S. were supported by the US Department of Energy, Office of Basic Energy Sciences, under award no. DEFG02-05ER15690.Peer reviewe