A Comparison of Quartz Crystal Microbalance Measurements with Mass Spectrometer Determinations

An experimental program was undertaken in which mass accretion rates, as determined by a liquid nitrogen cooled quartz crystal microbalance, were compared with the mass flux rates, as determined by both a cycloidal type and a quadrupole type residual gas analyzer for five simple materials. The data indicate a high degree of correlation between these instruments insofar as the shape of the curves. There are large variations however among the absolute values

Estimation of outgassing from an expended apogee motor and its effects on spacecraft surfaces

An experimental and theoretical investigation was carried out to evaluate the degradation of the solar cells and other sensitive surfaces of a spacecraft, resulting from the molecular outgassing of an expended solid propellant apogee motor. The motor, following its burnout, is retained by the spacecraft and is a source of gases and particulates which will be released mainly by the unburned propellant-to-casing insulation. The deployment of the solar array within a few minutes after the motor burn results in the interception and reflection to the surfaces of the spacecraft of the molecular outgassing and particulates. Various methods, based on some experimental data, were used to analytically assess the magnitude of the outgassing from the engine

FPGA Qualification and Failure Rate Estimation Methodology for LHC Environments Using Benchmarks Test Circuits

When studying the behavior of a field programmable gate array (FPGA) under radiation, the most commonly used methodology consists in evaluating the single-event effect (SEE) cross section of its elements individually. However, this method does not allow the estimation of the device failure rate when using a custom design. An alternative approach based on benchmark circuits is presented in this article. It allows standardized application-level testing, which makes the comparison between different FPGAs easier. Moreover, it allows the evaluation of the FPGA failure rate independent of the application that will be implemented. The employed benchmark circuit belongs to the ITC’99 benchmark suite developed at Politecnico di Torino. Using the proposed methodology, the response of four FPGAs—the NG-Medium, the ProASIC3, the SmartFusion2, and the PolarFire—was evaluated under high-energy protons. Radiation tests with thermal neutrons were also conducted on the PolarFire to assess its potential sensitivity to them. Moreover, its performances in terms of total ionizing dose (TID) effects have been evaluated by measuring the degradation of the propagation delay during irradiatio

Mechanics and dynamics of X-chromosome pairing at X inactivation

At the onset of X-chromosome inactivation, the vital process whereby female mammalian cells equalize X products with respect to males, the X chromosomes are colocalized along their Xic (X-inactivation center) regions. The mechanism inducing recognition and pairing of the X’s remains, though, elusive. Starting from recent discoveries on the molecular factors and on the DNA sequences (the so-called "pairing sites") involved, we dissect the mechanical basis of Xic colocalization by using a statistical physics model. We show that soluble DNA-specific binding molecules, such as those experimentally identified, can be indeed sufficient to induce the spontaneous colocalization of the homologous chromosomes but only when their concentration, or chemical affinity, rises above a threshold value as a consequence of a thermodynamic phase transition. We derive the likelihood of pairing and its probability distribution. Chromosome dynamics has two stages: an initial independent Brownian diffusion followed, after a characteristic time scale, by recognition and pairing. Finally, we investigate the effects of DNA deletion/insertions in the region of pairing sites and compare model predictions to available experimental data

A pivotal role for starch in the reconfiguration of 14C-partitioning and allocation in Arabidopsis thaliana under short-term abiotic stress.

Plant carbon status is optimized for normal growth but is affected by abiotic stress. Here, we used 14C-labeling to provide the first holistic picture of carbon use changes during short-term osmotic, salinity, and cold stress in Arabidopsis thaliana. This could inform on the early mechanisms plants use to survive adverse environment, which is important for efficient agricultural production. We found that carbon allocation from source to sinks, and partitioning into major metabolite pools in the source leaf, sink leaves and roots showed both conserved and divergent responses to the stresses examined. Carbohydrates changed under all abiotic stresses applied; plants re-partitioned 14C to maintain sugar levels under stress, primarily by reducing 14C into the storage compounds in the source leaf, and decreasing 14C into the pools used for growth processes in the roots. Salinity and cold increased 14C-flux into protein, but as the stress progressed, protein degradation increased to produce amino acids, presumably for osmoprotection. Our work also emphasized that stress regulated the carbon channeled into starch, and its metabolic turnover. These stress-induced changes in starch metabolism and sugar export in the source were partly accompanied by transcriptional alteration in the T6P/SnRK1 regulatory pathway that are normally activated by carbon starvation

Normalizing single-cell RNA sequencing data: challenges and opportunities

Single-cell transcriptomics is becoming an important component of the molecular biologist's toolkit. A critical step when analyzing data generated using this technology is normalization. However, normalization is typically performed using methods developed for bulk RNA sequencing or even microarray data, and the suitability of these methods for single-cell transcriptomics has not been assessed. We here discuss commonly used normalization approaches and illustrate how these can produce misleading results. Finally, we present alternative approaches and provide recommendations for single-cell RNA sequencing users

Active and poised promoter states drive folding of the extended HoxB locus in mouse embryonic stem cells

Gene expression states influence the three-dimensional conformation of the genome through poorly understood mechanisms. Here, we investigate the conformation of the murine HoxB locus, a gene-dense genomic region containing closely spaced genes with distinct activation states in mouse embryonic stem (ES) cells. To predict possible folding scenarios, we performed computer simulations of polymer models informed with different chromatin occupancy features, which define promoter activation states or CTCF binding sites. Single cell imaging of the locus folding was performed to test model predictions. While CTCF occupancy alone fails to predict the in vivo folding at genomic length scale of 10 kb, we found that homotypic interactions between active and Polycomb-repressed promoters co-occurring in the same DNA fibre fully explain the HoxB folding patterns imaged in single cells. We identify state-dependent promoter interactions as major drivers of chromatin folding in gene-dense regions

Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C

Technology for measuring 3D genome topology is increasingly important for studying gene regulation, for genome assembly and for mapping of genome rearrangements. Hi-C and other ligation-based methods have become routine but have specific biases. Here, we develop multiplex-GAM, a faster and more affordable version of genome architecture mapping (GAM), a ligation-free technique that maps chromatin contacts genome-wide. We perform a detailed comparison of multiplex-GAM and Hi-C using mouse embryonic stem cells. When examining the strongest contacts detected by either method, we find that only one-third of these are shared. The strongest contacts specifically found in GAM often involve ‘active’ regions, including many transcribed genes and super-enhancers, whereas in Hi-C they more often contain ‘inactive’ regions. Our work shows that active genomic regions are involved in extensive complex contacts that are currently underestimated in ligation-based approaches, and highlights the need for orthogonal advances in genome-wide contact mapping technologies

Waveforms of molecular oscillations reveal circadian timekeeping mechanisms

Circadian clocks play a pivotal role in orchestrating numerous physiological and developmental events. Waveform shapes of the oscillations of protein abundances can be informative about the underlying biochemical processes of circadian clocks. We derive a mathematical framework where waveforms do reveal hidden biochemical mechanisms of circadian timekeeping. We find that the cost of synthesizing proteins with particular waveforms can be substantially reduced by rhythmic protein half-lives over time, as supported by previous plant and mammalian data, as well as our own seedling experiment. We also find that previously-enigmatic, cyclic expression of positive arm components within the mammalian and insect clocks allows both a broad range of peak time differences between protein waveforms and the symmetries of the waveforms about the peak times. Such various peak-time differences may facilitate tissue-specific or developmental stage-specific multicellular processes. Our waveform-guided approach can be extended to various biological oscillators, including cell-cycle and synthetic genetic oscillators.Comment: Supplementary material is available at the journal websit