Discrete nuclear domains of poly(A) RNA and their relationship to the functional organization of the nucleus

The functional organization of the nucleus was studied using a fluorescence microscopy approach which allowed integration of positional information for RNA, DNA, and proteins. In cells from sea urchin to human, nuclear poly(A) RNA was found concentrated primarily within several discrete transcript domains which often surrounded nucleoli. Concentrations of poly(A) RNA were coincident with snRNP antigen clusters, providing evidence for the localization of pre-mRNA splicing at these sites. The spatial relationship of transcript domains with respect to various classes of DNA was established, in that the poly(A) RNA-rich regions coincided with discrete regions of low DNA density and were non-randomly distributed with respect to specific DNA sequences. Centromeric DNA and late-replicating DNA did not overlap transcript domains, whereas a subset of early-replicating DNA may. Results indicate that transcript domains do not result directly from a simple clustering of chromatin corresponding to metaphase chromosomes bands. Finally, observations on the reassembly of these domains after mitosis suggest that the clustering of snRNP antigens may be dependent on the reappearance of pol II transcription. Implications of these findings for overall nuclear structure and function are considered, including a discussion of whether transcript domains may be sites of polymerase II transcription reflecting a clustering of active genes

Autonomous space processor for orbital debris

This work continues to develop advanced designs toward the ultimate goal of a GETAWAY SPECIAL to demonstrate economical removal of orbital debris utilizing local resources in orbit. The fundamental technical feasibility was demonstrated last year through theoretical calculations, quantitative computer animation, a solar focal point cutter, a robotic arm design and a subscale model. During this reporting period, several improvements are made in the solar cutter, such as auto track capabilities, better quality reflectors and a more versatile framework. The major advance has been in the design, fabrication and working demonstration of a ROBOTIC ARM that has several degrees of freedom. The functions were specifically tailored for the orbital debris handling. These advances are discussed here. Also a small fraction of the resources were allocated towards research in flame augmentation in SCRAMJETS for the NASP. Here, the fundamental advance was the attainment of Mach numbers up to 0.6 in the flame zone and a vastly improved injection system; the current work is expected to achieve supersonic combustion in the laboratory and an advanced monitoring system

Dynamic changes in the higher-level chromatin organization of specific sequences revealed by in situ hybridization to nuclear halos

A novel approach to study the higher level packaging of specific DNA sequences has been developed by coupling high-resolution fluorescence hybridization with biochemical fractionation to remove histones and distend DNA loops to form morphologically reproducible nuclear halos. Results demonstrate consistent differences in the organization of specific sequences, and further suggest a relationship to functional activity. Pulse-incorporated bromodeoxyuridine representing nascent replicating DNA localized with the base of the chromatin loops in discrete clustered patterns characteristic of intact cells, whereas at increasing chase times, the replicated DNA was consistently found further out on the extended region of the halo. Fluorescence hybridization to unique loci for four transcriptionally inactive sequences produced long strings of signal extending out onto the DNA halo or loop, whereas four transcriptionally active sequences remained tightly condensed as single spots within the residual nucleus. In contrast, in non-extracted cells, all sequences studied typically remained condensed as single spots of fluorescence signal. Interestingly, two transcriptionally active, tandemly repeated gene clusters exhibited strikingly different packaging by this assay. Analysis of specific genes in single cells during the cell cycle revealed changes in packaging between S-phase and non S-phase cells, and further suggested a dramatic difference in the structural associations in mitotic and interphase chromatin. These results are consistent with and suggestive of a loop domain organization of chromatin packaging involving both stable and transient structural associations, and provide precedent for an approach whereby different biochemical fractionation methods may be used to unravel various aspects of the complex higher-level organization of the genome

Current-carrying cosmic string loops 3D simulation: towards a reduction of the vorton excess problem

The dynamical evolution of superconducting cosmic string loops with specific equations of state describing timelike and spacelike currents is studied numerically. This analysis extends previous work in two directions: first it shows results coming from a fully three dimensional simulation (as opposed to the two dimensional case already studied), and it now includes fermionic as well as bosonic currents. We confirm that in the case of bosonic currents, shocks are formed in the magnetic regime and kinks in the electric regime. For a loop endowed with a fermionic current with zero-mode carriers, we show that only kinks form along the string worldsheet, therefore making these loops slightly more stable against charge carrier radiation, the likely outcome of either shocks or kinks. All these combined effects tend to reduce the number density of stable loops and contribute to ease the vorton excess problem. As a bonus, these effects also may provide new ways of producing high energy cosmic rays.Comment: 11 pages, RevTeX 4 format, 8 figures, submitted to PR

Anthropics and Myopics: Conditional Probabilities and the Cosmological Constant

We re-examine claims that anthropic arguments provide an explanation for the observed smallness of the cosmological constant, and argue that correlations between the cosmological constant value and the existence of life can be demonstrated only under restrictive assumptions. Causal effects are more subtle to uncover.Comment: revised to PRL format, additional references and discussion to related work revise

Monitoring Seagrass within the Reef 2050 Integrated Monitoring and Reporting Program: final report of the Seagrass Expert Group

Seagrass is widely distributed throughout the Great Barrier Reef (the Reef), with a documented 35,000 square kilometres and a potential habitat area of 228,300 square kilometres. Seagrass meadows occur in many different environmental conditions, both within and beyond the impact of flood plumes, and are common in areas of high anthropogenic activity, such as ports and areas adjacent to urban centres. Many processes and services that maintain the exceptional values of the Reef occur in seagrass meadows. To provide the services that support these values seagrass habitats include a range of species, growth forms and benthic landscapes, that respond to pressures in different ways. In many cases seagrasses also modify their environments to improve environmental conditions on the Reef. Seagrasses vary spatially and temporally in their distribution and abundance across the Reef, occurring in different water quality types (estuaries, coastal, reefal and offshore) and at different water depths (intertidal, shallow subtidal, deep water). The diversity of potential seagrass habitats is one reason they support so many of the environmental services and values of the Great Barrier Reef World Heritage Area (World Heritage Area), including: habitat for crabs, prawns and fish –– supporting recreational and commercial fishing; primary food resource for species of conservation significance (dugong, green turtles, migratory shore birds); shoreline stabilisation by binding sediment to slow erosion; water clarity improvement, by promoting the settlement of fine particulate matter; and providing a natural carbon sink. To deliver the seagrass components of the knowledge system required to deliver Reef 2050 Long-Term Sustainability Plan (Reef 2050 Plan) reporting and other management activities, there will need to be modifications and enhancements made to the current seagrass monitoring programs. The Drivers, Pressures, State, Impact, Response (DPSIR) framework was used to facilitate the identification of linkages between the pressures on seagrass, state of the seagrass, the impact a decline in seagrass would have on community values, and the responses management agencies can take to mitigate loss of values. We have also defined twelve seagrass habitat types that occur on the Reef, identified by a matrix of water body type and water depth. The seagrasses occurring in each habitat are exposed to different pressures and require different management actions (responses) to protect and enhance the values of the community and Reef ecosystems. The proposed monitoring program has three spatial and temporal scales, with each scale providing different information (knowledge) to support resilience-based management of the Reef. 1. Habitat assessment: will occur across the Reef at all sites where seagrass has a potential of occurring. It will determine seagrass abundance, species composition and spatial extent of each habitat type within the World Heritage Area. This scale will be focused on supporting future outlook reports, but will also provide information for operational and strategic management and contribute towards other reports. 2. Health assessment: will take place at representative regional sites, for each habitat type. These sites will provide managers with annual and seasonal trends in seagrass condition and resilience at a regional scale for each habitat. This scale will provide higher temporal detail (i.e. at least annually) of seagrass condition and resilience, supporting tactical, operational and strategic management applications. This scale will provide the majority of information for regional/catchment report cards and the assessment of management effectiveness at a catchment wide scale. It will also contribute important trends in condition and resilience to Outlook reports and other communication products with more frequent reporting. 3. Process monitoring: will take place at the fewest number of sites, nested within habitat and health assessment sites. Due to the time-consuming and complex nature of these measurements the sampling sites will be chosen to focus on priority knowledge gaps. This scale will provide managers with information on cause-and-effect relationships and linkages between different aspects of the Reef’s processes and ecosystems. This scale will include measures of seagrass resilience (for example, feedback loops, recovery time after disturbance, history of disturbance and thresholds for exposure to pressures). The attributes measured at these sites will also provide confidence to managers regarding the impact a change in seagrass condition is likely to have on other values of the Reef (for example, fish, megafauna, coral, Indigenous heritage, and human dimensions). To ensure that future seagrass monitoring delivers the information required to report on the Reef 2050 Plan and meets the other knowledge requirements of managers, a spatially balanced random sampling design needs to be implemented on the Reef. Existing monitoring programs can and should be integrated into this design. However, current seagrass monitoring programs do not provide a balanced assessment of seagrass condition across the entire Reef, hence are not suitable to meet the Reef 2050 Plan reporting requirements and many other management information needs. Existing sites within current monitoring are focused on habitat types that are intertidal and shallow sub-tidal and lie close to the coast. These habitats have been previously selected because they face high levels of cumulative anthropogenic risk and therefore have higher levels of management demand for information. The current sites are likely to decline more rapidly, in response to catchment run-off and other anthropogenic pressures, than the average for seagrass meadows across the entire Reef. They also have a greater potential to show improvements from Reef catchment management actions that reduce pollution associated with run-off. This report sets out the framework for a recommended new seagrass monitoring program, highlighting the substantial improvements in knowledge and confidence this new program will deliver, and provides a scope for the statistical design work required to support implementation of this program

Modeling the impact of floating oyster (Crassostrea virginica) aquaculture on sediment−water nutrient and oxygen fluxes

Bivalve aquaculture relies on naturally occurring phytoplankton, zooplankton, and detritus as food sources, thereby avoiding external nutrient inputs that are commonly associated with finfish aquaculture. High filtration rates and concentrated bivalve biomass within aquacul- ture operations, however, result in intense biodeposition of particulate organic matter (POM) on surrounding sediments, with potential adverse environmental impacts. Estimating the net deposi- tional flux is difficult in shallow waters due to methodological constraints and dynamic processes such as resuspension and advection. In this study, we combined sediment trap deployments with simulations from a mechanistic sediment flux model to estimate seasonal POM deposition, resus- pension, and processing within sediments in the vicinity of an eastern oyster Crassostrea virginica farm in the Choptank River, Maryland, USA. The model is the stand-alone version of a 2-layer sediment flux model currently implemented within larger models for understanding ecosystem responses to nutrient management. Modeled sediment−water fluxes were compared to observed denitrification rates and nitrite + nitrate (NO2 −+NO3 −), phosphate (PO4 3−) and dissolved O2 fluxes. Model-derived estimates of POM deposition, which represent POM incorporated and processed within the sediment, comprised a small fraction of the material collected in sediment traps. These results highlight the roles of biodeposit resuspension and transport in effectively removing oyster biodeposits away from this particular farm, resulting in a highly diminished local environmental impact. This study highlights the value of sediment models as a practical tool for computing inte- grated measures of nitrogen cycling as a function of seasonal dynamics in the vicinity of aquaculture operations

Real-time gauge/gravity duality: Prescription, Renormalization and Examples

We present a comprehensive analysis of the prescription we recently put forward for the computation of real-time correlation functions using gauge/gravity duality. The prescription is valid for any holographic supergravity background and it naturally maps initial and final data in the bulk to initial and final states or density matrices in the field theory. We show in detail how the technique of holographic renormalization can be applied in this setting and we provide numerous illustrative examples, including the computation of time-ordered, Wightman and retarded 2-point functions in Poincare and global coordinates, thermal correlators and higher-point functions.Comment: 85 pages, 13 figures; v2: added comments and reference

Furin cleavage of SARS-CoV-2 Spike promotes but is not essential for infection and cell-cell fusion.

Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) infects cells by binding to the host cell receptor ACE2 and undergoing virus-host membrane fusion. Fusion is triggered by the protease TMPRSS2, which processes the viral Spike (S) protein to reveal the fusion peptide. SARS-CoV-2 has evolved a multibasic site at the S1-S2 boundary, which is thought to be cleaved by furin in order to prime S protein for TMPRSS2 processing. Here we show that CRISPR-Cas9 knockout of furin reduces, but does not prevent, the production of infectious SARS-CoV-2 virus. Comparing S processing in furin knockout cells to multibasic site mutants reveals that while loss of furin substantially reduces S1-S2 cleavage it does not prevent it. SARS-CoV-2 S protein also mediates cell-cell fusion, potentially allowing virus to spread virion-independently. We show that loss of furin in either donor or acceptor cells reduces, but does not prevent, TMPRSS2-dependent cell-cell fusion, unlike mutation of the multibasic site that completely prevents syncytia formation. Our results show that while furin promotes both SARS-CoV-2 infectivity and cell-cell spread it is not essential, suggesting furin inhibitors may reduce but not abolish viral spread