Speech Communication

Contains reports on three research projects.U. S. Air Force Cambridge Research Laboratories under Contract F19628-69-C-0044National Institutes of Health (Grant 5 RO1 NS04332-09)M.I.T. Lincoln Laboratory Purchase Order CC-57

Low-temperature statistical mechanics of the QuanTizer problem: fast quenching and equilibrium cooling of the three-dimensional Voronoi Liquid

The Quantizer problem is a tessellation optimisation problem where point configurations are identified such that the Voronoi cells minimise the second moment of the volume distribution. While the ground state (optimal state) in 3D is almost certainly the body-centered cubic lattice, disordered and effectively hyperuniform states with energies very close to the ground state exist that result as stable states in an evolution through the geometric Lloyd's algorithm [Klatt et al. Nat. Commun., 10, 811 (2019)]. When considered as a statistical mechanics problem at finite temperature, the same system has been termed the 'Voronoi Liquid' by [Ruscher et al. EPL 112, 66003 (2015)]. Here we investigate the cooling behaviour of the Voronoi liquid with a particular view to the stability of the effectively hyperuniform disordered state. As a confirmation of the results by Ruscher et al., we observe, by both molecular dynamics and Monte Carlo simulations, that upon slow quasi-static equilibrium cooling, the Voronoi liquid crystallises from a disordered configuration into the body-centered cubic configuration. By contrast, upon sufficiently fast non-equilibrium cooling (and not just in the limit of a maximally fast quench) the Voronoi liquid adopts similar states as the effectively hyperuniform inherent structures identified by Klatt et al. and prevents the ordering transition into a BCC ordered structure. This result is in line with the geometric intuition that the geometric Lloyd's algorithm corresponds to a type of fast quench.Comment: 11 pages, 6 figure

The Unseen World: Environmental Microbial Sequencing and Identification Methods for Ecologists

Microorganisms inhabit almost every environment, comprise the majority of diversity on Earth, are important in biogeochemical cycling, and may be vital to ecosystem responses to large-scale climatic change. In recent years, ecologists have begun to use rapidly advancing molecular techniques to address questions about microbial diversity, biogeography, and responses to environmental change. Studies of microbes in the environment generally focus on three broad objectives: determining which organisms are present, what their functional capabilities are, and which are active at any given time. However, comprehending the range of methodologies currently in use can be daunting. To provide an overview of environmental microbial sequence data collection and analysis approaches, we include case studies of microbiomes ranging from the human mouth to geothermal springs. We also suggest contexts in which each technique can be applied and highlight insights that result from their use

Gneiss-charnockite transformation at Kottavattam, Southern Kerala (India)

At Kottavattam, leucocratic granitic garnet-biotite gneisses (age less than 2 Ga) were partially transformed to coarse-grained charnockite along a system of conjugate fractures (N70E and N20W) and the foliation planes (N60 to 80W; dip 80 to 90 SW) about 550 m.y. ago. To examine and quantify changes in fabric, mineralogy, pore fluids and chemical composition associated with this process, large rock specimens showing gneiss-charnockite transition were studied in detail. The results of the present study corroborate the concept that charnockite formation at Kottavattam is an internally-generated phenomenon and was not triggered by the influx of carbonic fluids from a deep-seated source. It is suggested that charnockitization was caused by the following mechanism: (1) near-isothermal decompression during uplift of the gneiss complex led to an increase of the pore fluid pressure (P sub fluid greater than P sub lith) which - in a regime of anisotropic stress - triggered or at least promoted the development of conjugate fractures; (2) the simultaneous release of pore fluids from bursting fluid inclusions and their escape into the developing fracture system resulted in a drop of fluid pressure; and (3) the internal generation and buffering of the fluids and their, probably, limited migration in an entirely granitic rock system explains the absence of any significant metasomatic mass transfer

Differential Transgene Silencing of Myeloid-Specific Promoters in the AAVS1 Safe Harbor Locus of Induced Pluripotent Stem Cell-Derived Myeloid Cells

Targeted integration into a genomic safe harbor, such as the AAVS1 locus on chromosome 19, promises predictable transgene expression and reduces the risk of insertional mutagenesis in the host genome. The application of gamma-retroviral LTR-driven vectors, which semi-randomly integrate into the genome, has previously caused severe adverse events in some clinical studies due to transactivation of neighboring proto-oncogenes. Consequently, the site-specific integration of a therapeutic transgene into a genomic safe harbor locus would allow stable genetic correction with a reduced risk of insertional mutagenesis. However, recent studies revealed that transgene silencing, especially in case of weaker cell type-specific promoters, can occur in the AAVS1 locus of human pluripotent stem cells (PSC) and can impede transgene expression during differentiation. In this study, we aimed to correct p47phox-deficiency, which is the second most common cause of chronic granulomatous disease, by insertion of a therapeutic p47phox transgene into the AAVS1 locus of human induced PSC (iPSC) using CRISPR-Cas9. We analyzed transgene expression and functional correction from three different myeloid-specific promoters (miR223, CatG/cFes and MRP8). Upon myeloid differentiation of corrected iPSC clones, we observed that the miR223 and CatG/cFes promoter achieved therapeutic-relevant levels of p47phox expression and NADPH oxidase activity, whereas the MRP8 promoter was less efficient. Analysis of the different promoters revealed high CpG methylation of the MRP8 promoter in differentiated cells, which correlated with the transgene expression data. In summary, we identified the miR223 and CatG/cFes promoters as cell type-specific promoters that allow stable transgene expression in the AAVS1 locus of iPSC-derived myeloid cells. Our findings further indicate that promoter silencing can occur in the AAVS1 safe harbor locus in differentiated hematopoietic cells and that a comparison of different promoters is necessary to achieve optimal transgene expression for therapeutic application of iPSC-derived cells

Soluble Alpha-APP (sAPPalpha) Regulates CDK5 Expression and Activity in Neurons

A growing body of evidence suggests a role for soluble alpha-amyloid precursor protein (sAPPalpha) in pathomechanisms of Alzheimer disease (AD). This cleavage product of APP was identified to have neurotrophic properties. However, it remained enigmatic what proteins, targeted by sAPPalpha, might be involved in such neuroprotective actions. Here, we used high-resolution two- dimensional polyacrylamide gel electrophoresis to analyze proteome changes downstream of sAPPalpha in neurons. We present evidence that sAPPalpha regulates expression and activity of CDK5, a kinase that plays an important role in AD pathology. We also identified the cytoprotective chaperone ORP150 to be induced by sAPPalpha as part of this protective response. Finally, we present functional evidence that the sAPPalpha receptor SORLA is essential to mediate such molecular functions of sAPPalpha in neurons

Speech Communication

Contains reports on five research projects.National Institutes of Health (Grant 5 RO1 NS04332-12)National Institutes of Health (Grant HD05168-04)U.S. Navy Office of Naval Research (Contract N00014-67-A-0204-0069)Joint Services Electronics Program (Contract DAAB07-74-C-0630)National Science Foundation (Grant SOC74-22167