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629 records · Page 35

Genetic ablation of root cap cells in Arabidopsis

The root cap is increasingly appreciated as a complex and dynamic plant organ. Root caps sense and transmit environmental signals, synthesize and secrete small molecules and macromolecules, and in some species shed metabolically active cells. However, it is not known whether root caps are essential for normal shoot and root development. We report the identification of a root cap-specific promoter and describe its use to genetically ablate root caps by directing root cap-specific expression of a diphtheria toxin A-chain gene. Transgenic toxin-expressing plants are viable and have normal aerial parts but agravitropic roots, implying loss of root cap function. Several cell layers are missing from the transgenic root caps, and the remaining cells are abnormal. Although the radial organization of the roots is normal in toxin-expressing plants, the root tips have fewer cytoplasmically dense cells than do wild-type root tips, suggesting that root meristematic activity is lower in transgenic than in wild-type plants. The roots of transgenic plants have more lateral roots and these are, in turn, more highly branched than those of wild-type plants. Thus, root cap ablation alters root architecture both by inhibiting root meristematic activity and by stimulating lateral root initiation. These observations imply that the root caps contain essential components of the signaling system that determines root architecture.

Non-NASA Center↗

A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo

We present the current form of a provisional DNA sequence-based regulatory gene network that explains in outline how endomesodermal specification in the sea urchin embryo is controlled. The model of the network is in a continuous process of revision and growth as new genes are added and new experimental results become available; see http://www.its.caltech.edu/~mirsky/endomeso.htm (End-mes Gene Network Update) for the latest version. The network contains over 40 genes at present, many newly uncovered in the course of this work, and most encoding DNA-binding transcriptional regulatory factors. The architecture of the network was approached initially by construction of a logic model that integrated the extensive experimental evidence now available on endomesoderm specification. The internal linkages between genes in the network have been determined functionally, by measurement of the effects of regulatory perturbations on the expression of all relevant genes in the network. Five kinds of perturbation have been applied: (1) use of morpholino antisense oligonucleotides targeted to many of the key regulatory genes in the network; (2) transformation of other regulatory factors into dominant repressors by construction of Engrailed repressor domain fusions; (3) ectopic expression of given regulatory factors, from genetic expression constructs and from injected mRNAs; (4) blockade of the beta-catenin/Tcf pathway by introduction of mRNA encoding the intracellular domain of cadherin; and (5) blockade of the Notch signaling pathway by introduction of mRNA encoding the extracellular domain of the Notch receptor. The network model predicts the cis-regulatory inputs that link each gene into the network. Therefore, its architecture is testable by cis-regulatory analysis. Strongylocentrotus purpuratus and Lytechinus variegatus genomic BAC recombinants that include a large number of the genes in the network have been sequenced and annotated. Tests of the cis-regulatory predictions of the model are greatly facilitated by interspecific computational sequence comparison, which affords a rapid identification of likely cis-regulatory elements in advance of experimental analysis. The network specifies genomically encoded regulatory processes between early cleavage and gastrula stages. These control the specification of the micromere lineage and of the initial veg(2) endomesodermal domain; the blastula-stage separation of the central veg(2) mesodermal domain (i.e., the secondary mesenchyme progenitor field) from the peripheral veg(2) endodermal domain; the stabilization of specification state within these domains; and activation of some downstream differentiation genes. Each of the temporal-spatial phases of specification is represented in a subelement of the network model, that treats regulatory events within the relevant embryonic nuclei at particular stages. (c) 2002 Elsevier Science (USA).

Non-NASA Center↗

Microscopic Foundation and Simulation of Coupled Carrier-Temperature Diffusions in Semiconductor Lasers

A typical semiconductor-based optoelectronic device, such as a diode laser, consists of three subsystems: an optical field, an electron-hole plasma (EHP), and a host crystal lattice. The physics of such a device involves the interplay of optical, electrical and thermal processes. A proper description of such a device requires that all three processes are treated on equal footing and in a self-consistent fashion. Furthermore, since a semiconductor laser has intrinsic spatial inhomogeneity, such a self-consistency naturally leads to a set of partial differential equations in space and time. There is a significant lacking of research interest and results on the transport aspects of optical devices in the literature with only a few exceptions. Even the most important carrier diffusion coefficient has not been properly derived and studied so far for optically excited plasma, while most of the work adopted results from electronics community where heavily doped semiconductors with mainly one type of carriers are dealt with. The corresponding transport equation for plasma energy or temperature has received even less attention. In this talk we describe our recent results on such a self-consistent derivation of temperature and carrier-density diffusion equations coupled with the lasing process. Starting from the microscopic semiconductor Bloch equations (SBEs) including the Boltzmann transport terms in the distribution function equations for electrons and holes, we derived a closed set of diffusion equations for carrier densities and temperatures with self-consistent coupling to Maxwell's equation and to an effective optical polarization equation. The coherent many-body effects are included within the screened Hartree-Fock approximation, while scatterings are treated within the second Born approximation including both the in- and out-scatterings. Microscopic expressions for electron-hole (e-h) and carrier-LO (c-LO) phonon scatterings are directly used to derive the momentum and energy relaxation rates. These rates expressed as functions of temperatures and densities lead to microscopic expressions for self- and mutual-diffusion coefficients in the coupled density-temperature diffusion equations. Approximations for reducing the general two-component description of the electron-hole plasma (EHP) to a single-component one are discussed. In particular, we show that a special single-component reduction is possible when e-h scattering dominates over c-LO phonon scattering. The ambipolar diffusion approximation is also discussed and we show that the ambipolar diffusion coefficients are independent of e-h scattering, even though the diffusion coefficients of individual components depend sensitively on the e-h scattering rates. Our discussions lead to new perspectives into the roles played in the single-component reduction by the electron-hole correlation in momentum space induced by scatterings and the electron-hole correlation in real space via internal static electrical field. Finally, the theory is completed by coupling the diffusion equations to the lattice temperature equation and to the effective optical polarization which in turn couples to the laser field. The equations derived above are implemented in various limiting cases to a typical diode laser to study the consequences of nonlinear diffusion and the cross diffusion terms on laser behavior, especially the dynamic behavior of a diode laser under modulation. Detailed results will be presented by comparing with the standard rate equation results.

Li, J.↗

Identification of the cAMP response element that controls transcriptional activation of the insulin-like growth factor-I gene by prostaglandin E2 in osteoblasts

Insulin-like growth factor-I (IGF-I), a multifunctional growth factor, plays a key role in skeletal growth and can enhance bone cell replication and differentiation. We previously showed that prostaglandin E2 (PGE2) and other agents that increase cAMP activated IGF-I gene transcription in primary rat osteoblast cultures through promoter 1 (P1), the major IGF-I promoter, and found that transcriptional induction was mediated by protein kinase A. We now have identified a short segment of P1 that is essential for full hormonal regulation and have characterized inducible DNA-protein interactions involving this site. Transient transfections of IGF-I P1 reporter genes into primary rat osteoblasts showed that the 328-base pair untranslated region of exon 1 was required for a full 5.3-fold response to PGE2; mutation in a previously footprinted site, HS3D (base pairs +193 to +215), reduced induction by 65%. PGE2 stimulated nuclear protein binding to HS3D. Binding, as determined by gel mobility shift assay, was not seen in nuclear extracts from untreated osteoblast cultures, was detected within 2 h of PGE2 treatment, and was maximal by 4 h. This DNA-protein interaction was not observed in cytoplasmic extracts from PGE2-treated cultures, indicating nuclear localization of the protein kinase A-activated factor(s). Activation of this factor was not blocked by cycloheximide (Chx), and Chx did not impair stimulation of IGF-I gene expression by PGE2. In contrast, binding to a consensus cAMP response element (CRE; 5'-TGACGTCA-3') from the rat somatostatin gene was not modulated by PGE2 or Chx. Competition gel mobility shift analysis using mutated DNA probes identified 5'-CGCAATCG-3' as the minimal sequence needed for inducible binding. All modified IGF-I P1 promoterreporter genes with mutations within this CRE sequence also showed a diminished functional response to PGE2. These results identify the CRE within the 5'-untranslated region of IGF-I exon 1 that is required for hormonal activation of IGF-I gene transcription by cAMP in osteoblasts.

NASA Discipline Musculoskeletal↗

Lunar and Planetary Science XXXVI, Part 12

Topics discussed include: The Ancient Lakes in Hellas Basin Region as Seen Through the First Year of Mars Express HRSC-Camera; DISR Observations of Craters at Titan at the Huygens Landing Site: Insights Anticipated; The Sun s Dust Disk - Discovery Potential of the New Horizons Mission During Interplanetary Cruise; Evidence for Aqueously Precipitated Sulfates in Northeast Meridiani Using THEMIS and TES Data; Integrated Spectroscopic Studies of Anhydrous Sulfate Minerals; Venusian Channel Formation as a Subsurface Process; Reexamination of Quartz Grains from the Permian-Triassic Boundary Section at Graphite Peak, Antarctica; Observations of Calcium Sulfate Deposits at High Latitudes by OMEGA/Mex at Km/Pixel Resolutions; Observations of the North Permanent Cap of Mars in Mid-Summer by OMEGA/MEX at km per Pixel Resolutions; Classification and Distribution of Patterned Ground in the Southern Hemisphere of Mars Genesis: Removing Contamination from Sample Collectors; Thermal Characterization of Fe3O4 Nanoparticles Formed from Poorly Crystalline Siderite; Hydrogen Abundances in Metal Grains from the Hammadah Al Hamra (HaH) 237 Metal-rich Chondrite: A Test of the Nebular-Formation Theory; REE and Some Other Trace Elements Distributions of Mineral Separates in Atlanta (EL6); The Composition and Origin of the Dewar Geochemical Anomaly; Asteroid Modal Mineralogy Using Hapke Mixing Models: Testing the Utility of Spectral Lookup Tables; and The Huygens Mission at Titan: Results Highlights. (sup 182)Hf-(sup 182)W Chronometry and an Early Differentiation in the Parent Body of Ureilites Ground Penetrating Radar in Sedimentary Rocks Mars, Always Cold, Sometimes Wet: New Constraints on Mars Denudation Rates and Climate Evolution from Analog Studies at Haughton Crater, Devon Island, High Arctic Europa s Porous Ice Rheology and Implications for Ice-penetrating Radar Scattering Loss Surface Generated Cracks on Europa

Source record↗

Induction of cyclo-oxygenase-2 mRNA by prostaglandin E2 in human prostatic carcinoma cells

Prostaglandins are synthesized from arachidonic acid by the enzyme cyclo-oxygenase. There are two isoforms of cyclooxygenases: COX-1 (a constitutive form) and COX-2 (an inducible form). COX-2 has recently been categorized as an immediate-early gene and is associated with cellular growth and differentiation. The purpose of this study was to investigate the effects of exogenous dimethylprostaglandin E2 (dmPGE2) on prostate cancer cell growth. Results of these experiments demonstrate that administration of dmPGE2 to growing PC-3 cells significantly increased cellular proliferation (as measured by the cell number), total DNA content and endogenous PGE2 concentration. DmPGE2 also increased the steady-state mRNA levels of its own inducible synthesizing enzyme, COX-2, as well as cellular growth to levels similar to those seen with fetal calf serum and phorbol ester. The same results were observed in other human cancer cell types, such as the androgen-dependent LNCaP cells, breast cancer MDA-MB-134 cells and human colorectal carcinoma DiFi cells. In PC-3 cells, the dmPGE2 regulation of the COX-2 mRNA levels was both time dependent, with maximum stimulation seen 2 h after addition, and dose dependent on dmPGE2 concentration, with maximum stimulation seen at 5 microg ml(-1). The non-steroidal anti-inflammatory drug flurbiprofen (5 microM), in the presence of exogenous dmPGE2, inhibited the up-regulation of COX-2 mRNA and PC-3 cell growth. Taken together, these data suggest that PGE2 has a specific role in the maintenance of human cancer cell growth and that the activation of COX-2 expression depends primarily upon newly synthesized PGE2, perhaps resulting from changes in local cellular PGE2 concentrations.

Non-NASA Center↗

Comparative magnetic and thermoanalytical study of two enstatite chondrites: Adhi Kot and Atlanta

With allowance for the discussion of classification of enstatite chondrites and their relation to aubrites, the obtained magnetic and thermoanalytical data is submitted to be considered as additive arguments. Our study covered the Adhi Kot (EH4) and Atlanta (EL6). meteorites belonging to two distinct groups of enstatite chondrites. Applying AF demagnetization the intensity of natural remanent magnetization (NRM) was measured and the mean magnetic susceptibility of the samples was determined. The differential thermal (DTA) and thermogravimetric (TG) curves were obtained for meteorites under study. For measurements of the intensity of NRM, a superconducting cryomagnetometer SQUID (2 G Enterprise, USA), while magnetic susceptibility Kappabridge KLY-2 (Czechoslovakia) were used. The abbreviated magnetic data sheets are given. The values 786 x 10(exp -4)A/mkg and 196.1 x 10(exp -4)A/mkg were obtained as NRM intensities for Atlanta and Adhi Kot respectively, while 17.4 x 10(exp -6) SIu/kg and 43.4 x 10(exp -6) SIu/kg for their susceptibilities. Both meteorites proved to be strongly magnetized. The demagnetization down to 3.2 percent of NMR was received for Atlanta at AF field intensity of 250 Oe. For Adhi Kot at this level rested 13.2 percent of NRM intensity, this sample being demagnetized without change of direction till 750 Oe field. The demagnetization curves are similar to those obtained for Abee (EL4) chondrite by Sugiura and Strangway. Against Abee the Adhi Kot exhibited a little bit steeper downfall, and in both cases dominate one component of magnetization. The DTA and TG curves were obtained with Rigaku-Denki thermoanalytical instrument. The DTA curves exhibit striking similarity in their shape and relatively close temperature values for various features. The same is valid for TG curves. The higher values for TG for Adhi Kot express its higher content of oxydable (Fe, Ni) whose oxidation in air is reached at 1000-1200 C.

Krol, Elizabeth↗

Deletion of Cdkn1a in Mice Rescues Reduced Osteogenesis in Microgravity and Increases Coupled Osteoclastic Bone Degenerative Activity and Bone Loss

Elevated Cdkn1a/p21 levels in mouse bone during spaceflight have led us to hypothesize that this cell cycle inhibitor could regulate osteogenesis in response to mechanical unloading in microgravity. Cdkn1a interacts with cyclins CDK1/2/4,6 during G1 and S phases, and suppression of its expression by mechanical stretch enhances proliferation and mineralization in osteoblastic cell cultures. To test this hypothesis in a whole-organism model, we used C57BL/J6 WT/Cdkn1a-null mice in the NASA RR-10, 30-day ISS microgravity experiment. To quantify active mineralization in microgravity mice were injected with Calcein seven and two days before euthanasia on-orbit, followed by high-resolution confocal imaging of optically cleared femoral endosteal surfaces. To quantify cortical and cancellous bone parameters we conducted microCT analyses of the femur and tibia. Confocal imaging revealed a population of mineralizing calcein-positive single osteoblasts, and multicellular surfaces of mineralization by osteocytes in lacunae. The Cdkn1a-null genotype shows a greater ratio of early-osteoblasts to late-osteocytes and reduced mineralization versus WT. Additionally, in microgravity WT bones have a large (80%) decrease in active mineralization, but remarkably Cdkn1a deletion fully rescued mineralized surface loss. MicroCT shows trends for moderate spaceflight bone loss in WT femurs, and significant losses in the tibia, while Cdkn1a-null femurs showed much larger significant tissue losses, including 25% thinner trabeculae (p < 0.01),40% thinner cortical bone (p < 0.005), and 10% lower percent cortical bone area (p < 0.05). These results indicate that endogenous bone Cdkn1a plays a key role in mechanosensitive downregulation of osteoprecursor proliferation and promotes osteocytic differentiation. In microgravity however, while Cdkn1a deletion rescues mineralization, bone loss quantified by microCT is greatly increased, likely due to the molecular coupling of osteogenesis and osteoclastogenesis. This molecular mechanism opens the possibility for potential pharmacological approaches to mitigate bone loss in space simultaneously targeting Cdkn1a and osteoclast inhibition.

Eduardo A.C. Almeida↗

Trends in lignin modification: a comprehensive analysis of the effects of genetic manipulations/mutations on lignification and vascular integrity

A comprehensive assessment of lignin configuration in transgenic and mutant plants is long overdue. This review thus undertook the systematic analysis of trends manifested through genetic and mutational manipulations of the various steps associated with monolignol biosynthesis; this included consideration of the downstream effects on organized lignin assembly in the various cell types, on vascular function/integrity, and on plant growth and development. As previously noted for dirigent protein (homologs), distinct and sophisticated monolignol forming metabolic networks were operative in various cell types, tissues and organs, and form the cell-specific guaiacyl (G) and guaiacyl-syringyl (G-S) enriched lignin biopolymers, respectively. Regardless of cell type undergoing lignification, carbon allocation to the different monolignol pools is apparently determined by a combination of phenylalanine availability and cinnamate-4-hydroxylase/"p-coumarate-3-hydroxylase" (C4H/C3H) activities, as revealed by transcriptional and metabolic profiling. Downregulation of either phenylalanine ammonia lyase or cinnamate-4-hydroxylase thus predictably results in reduced lignin levels and impaired vascular integrity, as well as affecting related (phenylpropanoid-dependent) metabolism. Depletion of C3H activity also results in reduced lignin deposition, albeit with the latter being derived only from hydroxyphenyl (H) units, due to both the guaiacyl (G) and syringyl (S) pathways being blocked. Apparently the cells affected are unable to compensate for reduced G/S levels by increasing the amounts of H-components. The downstream metabolic networks for G-lignin enriched formation in both angiosperms and gymnosperms utilize specific cinnamoyl CoA O-methyltransferase (CCOMT), 4-coumarate:CoA ligase (4CL), cinnamoyl CoA reductase (CCR) and cinnamyl alcohol dehydrogenase (CAD) isoforms: however, these steps neither affect carbon allocation nor H/G designations, this being determined by C4H/C3H activities. Such enzymes thus fulfill subsidiary processing roles, with all (except CCOMT) apparently being bifunctional for both H and G substrates. Their severe downregulation does, however, predictably result in impaired monolignol biosynthesis, reduced lignin deposition/vascular integrity, (upstream) metabolite build-up and/or shunt pathway metabolism. There was no evidence for an alternative acid/ester O-methyltransferase (AEOMT) being involved in lignin biosynthesis.The G/S lignin pathway networks are operative in specific cell types in angiosperms and employ two additional biosynthetic steps to afford the corresponding S components, i.e. through introduction of an hydroxyl group at C-5 and its subsequent O-methylation. [These enzymes were originally classified as ferulate-5-hydroxylase (F5H) and caffeate O-methyltransferase (COMT), respectively.] As before, neither step has apparently any role in carbon allocation to the pathway; hence their individual downregulation/manipulation, respectively, gives either a G enriched lignin or formation of the well-known S-deficient bm3 "lignin" mutant, with cell walls of impaired vascular integrity. In the latter case, COMT downregulation/mutation apparently results in utilization of the isoelectronic 5-hydroxyconiferyl alcohol species albeit in an unsuccessful attempt to form G-S lignin proper. However, there is apparently no effect on overall G content, thereby indicating that deposition of both G and S moieties in the G/S lignin forming cells are kept spatially, and presumably temporally, fully separate. Downregulation/mutation of further downstream steps in the G/S network [i.e. utilizing 4CL, CCR and CAD isoforms] gives predictable effects in terms of their subsidiary processing roles: while severe downregulation of 4CL gave phenotypes with impaired vascular integrity due to reduced monolignol supply, there was no evidence in support of increased growth and/or enhanced cellulose biosynthesis. CCR and CAD downregulation/mutations also established that a depletion in monolignol supply reduced both lignin contents supply reduced both lignin contents and vascular integrity, with a concomitant shift towards (upstream) metabolite build-up and/or shunting.The extraordinary claims of involvement of surrogate monomers (2-methoxybenzaldehyde, feruloyl tyramine, vanillic acid, etc.) in lignification were fully disproven and put to rest, with the investigators themselves having largely retracted former claims. Furthermore analysis of the well-known bm1 mutation, a presumed CAD disrupted system, apparently revealed that both G and S lignin components were reduced. This seems to imply that there is no monolignol specific dehydrogenase, such as the recently described sinapyl alcohol dehydrogenase (SAD) for sinapyl alcohol formation. Nevertheless, different CAD isoforms of differing homology seem to be operative in different lignifying cell types, thereby giving the G-enriched and G/S-enriched lignin biopolymers, respectively. For the G-lignin forming network, however, the CAD isoform is apparently catalytically less efficient with all three monolignols than that additionally associated with the corresponding G/S lignin forming network(s), which can more efficiently use all three monolignols. However, since CAD does not determine either H, G, or S designation, it again serves in a subsidiary role-albeit using different isoforms for different cell wall developmental and cell wall type responses.The results from this analysis contrasts further with speculations of some early investigators, who had viewed lignin assembly as resulting from non-specific oxidative coupling of monolignols and subsequent random polymerization. At that time, though, the study of the complex biological (biochemical) process of lignin assembly had begun without any of the (bio)chemical tools to either address or answer the questions posed as to how its formation might actually occur. Today, by contrast, there is growing recognition of both sophisticated and differential control of monolignol biosynthetic networks in different cell types, which serve to underscore the fact that complexity of assembly need not be confused any further with random formation. Moreover, this analysis revealed another factor which continues to cloud interpretations of lignin downregulation/mutational analyses, namely the serious technical problems associated with all aspects of lignin characterization, whether for lignin quantification, isolation of lignin-enriched preparations and/or in determining monomeric compositions. For example, in the latter analyses, some 50-90% of the lignin components still cannot be detected using current methodologies, e.g. by thioacidolysis cleavage and nitrobenzene oxidative cleavage. This deficiency in lignin characterization thus represents one of the major hurdles remaining in delineating how lignin assembly (in distinct cell types) and their configuration actually occurs.

Review, Academic↗

Immunohistochemical evidence of rapid extracellular matrix remodeling after iron-particle irradiation of mouse mammary gland

High-LET radiation has unique physical and biological properties compared to sparsely ionizing radiation. Recent studies demonstrate that sparsely ionizing radiation rapidly alters the pattern of extracellular matrix expression in several tissues, but little is known about the effect of heavy-ion radiation. This study investigates densely ionizing radiation-induced changes in extracellular matrix localization in the mammary glands of adult female BALB/c mice after whole-body irradiation with 0.8 Gy 600 MeV iron particles. The basement membrane and interstitial extracellular matrix proteins of the mammary gland stroma were mapped with respect to time postirradiation using immunofluorescence. Collagen III was induced in the adipose stroma within 1 day, continued to increase through day 9 and was resolved by day 14. Immunoreactive tenascin was induced in the epithelium by day 1, was evident at the epithelial-stromal interface by day 5-9 and persisted as a condensed layer beneath the basement membrane through day 14. These findings parallel similar changes induced by gamma irradiation but demonstrate different onset and chronicity. In contrast, the integrity of epithelial basement membrane, which was unaffected by sparsely ionizing radiation, was disrupted by iron-particle irradiation. Laminin immunoreactivity was mildly irregular at 1 h postirradiation and showed discontinuities and thickening from days 1 to 9. Continuity was restored by day 14. Thus high-LET radiation, like sparsely ionizing radiation, induces rapid-remodeling of the stromal extracellular matrix but also appears to alter the integrity of the epithelial basement membrane, which is an important regulator of epithelial cell proliferation and differentiation.

NASA Discipline Radiation Health↗

Methods of Attenuation Correction for Dual-Wavelength and Dual-Polarization Weather Radar Data

In writing the integral equations for the median mass diameter and number concentration, or comparable parameters of the raindrop size distribution, it is apparent that the forms of the equations for dual-polarization and dual-wavelength radar data are identical when attenuation effects are included. The differential backscattering and extinction coefficients appear in both sets of equations: for the dual-polarization equations, the differences are taken with respect to polarization at a fixed frequency while for the dual-wavelength equations, the differences are taken with respect to frequency at a fixed polarization. An alternative to the integral equation formulation is that based on the k-Z (attenuation coefficient-radar reflectivity factor) parameterization. This-technique was originally developed for attenuating single-wavelength radars, a variation of which has been applied to the TRMM Precipitation Radar data (PR). Extensions of this method have also been applied to dual-polarization data. In fact, it is not difficult to show that nearly identical equations are applicable as well to dualwavelength radar data. In this case, the equations for median mass diameter and number concentration take the form of coupled, but non-integral equations. Differences between this and the integral equation formulation are a consequence of the different ways in which attenuation correction is performed under the two formulations. For both techniques, the equations can be solved either forward from the radar outward or backward from the final range gate toward the radar. Although the forward-going solutions tend to be unstable as the attenuation out to the range of interest becomes large in some sense, an independent estimate of path attenuation is not required. This is analogous to the case of an attenuating single-wavelength radar where the forward solution to the Hitschfeld-Bordan equation becomes unstable as the attenuation increases. To circumvent this problem, the equations can be expressed in the form of a final-value problem so that the recursion begins at the far range gate and proceeds inward towards the radar. Solving the problem in this way traditionally requires estimates of path attenuation to the final gate: in the case of orthogonal linear polarizations, the attenuations at horizontal and vertical polarizations (same frequency) are required while in the dual-wavelength case, attenuations at the two frequencies (same polarization) are required.

Meneghini, R.↗

On the large eddy simulation of turbulent flows in complex geometry

Application of the method of Large Eddy Simulation (LES) to a turbulent flow consists of three separate steps. First, a filtering operation is performed on the Navier-Stokes equations to remove the small spatial scales. The resulting equations that describe the space time evolution of the 'large eddies' contain the subgrid-scale (sgs) stress tensor that describes the effect of the unresolved small scales on the resolved scales. The second step is the replacement of the sgs stress tensor by some expression involving the large scales - this is the problem of 'subgrid-scale modeling'. The final step is the numerical simulation of the resulting 'closed' equations for the large scale fields on a grid small enough to resolve the smallest of the large eddies, but still much larger than the fine scale structures at the Kolmogorov length. In dividing a turbulent flow field into 'large' and 'small' eddies, one presumes that a cut-off length delta can be sensibly chosen such that all fluctuations on a scale larger than delta are 'large eddies' and the remainder constitute the 'small scale' fluctuations. Typically, delta would be a length scale characterizing the smallest structures of interest in the flow. In an inhomogeneous flow, the 'sensible choice' for delta may vary significantly over the flow domain. For example, in a wall bounded turbulent flow, most statistical averages of interest vary much more rapidly with position near the wall than far away from it. Further, there are dynamically important organized structures near the wall on a scale much smaller than the boundary layer thickness. Therefore, the minimum size of eddies that need to be resolved is smaller near the wall. In general, for the LES of inhomogeneous flows, the width of the filtering kernel delta must be considered to be a function of position. If a filtering operation with a nonuniform filter width is performed on the Navier-Stokes equations, one does not in general get the standard large eddy equations. The complication is caused by the fact that a filtering operation with a nonuniform filter width in general does not commute with the operation of differentiation. This is one of the issues that we have looked at in detail as it is basic to any attempt at applying LES to complex geometry flows. Our principal findings are summarized.

Ghosal, Sandip↗

DNA Damage Response to Low and High-LET in a Large Cohort of Mice and Humans and Latest Advancement in NASA Space Omics

This presentation will first focus on a thorough evaluation of the DNA damage response to both low and high-LET in a cohort of 76 mice primary skin fibroblast derived from 15 different strains or in human blood mononuclear cells derived from 550 healthy donors. In both the human and mice work, we have hypothesized that DNA repair capacity can be used as a marker to evaluate and differentiate individual radiation sensitivity. More specifically, this work is based on the concept that the combined time-dose dependence of radiation-induced foci (RIF) of p53-binding protein 1 (53BP1) following low-LET exposure contains sufficient information to infer sensitivity to any other LET. This work is one of the most extensive studies on the kinetics and possible genetic underpinnings of radiation-induced DNA damage and repair. Results on humans are still preliminary as we are still in the process of collecting and isolating primary blood mononuclear cells from 500 to 800 healthy subjects of European descent, 18-75 years of age, 50/50 male/female distribution. We have analyzed 53BP1+ RIF formation as well as oxidative stress and cell death in primary cells from 192 subjects in response to the same HZE particles as used in mice: 600 MeV/n Fe, 350 MeV/n Ar and 350 MeV/n Si, 1.1 and 3 particles/100m2, 4 and 24 hours after irradiation. The second part of the talk will focus on describing GeneLab: The NASA Systems Biology Platform for Space Omics Repository, Analysis and Visualization. NASA GeneLab is an open-access repository for omics datasets generated by biological experiments conducted in space or experiments relevant to spaceflight (e.g. simulated cosmic radiation, simulated microgravity, bed rest studies). Started as a repository designed to archive precious omics from space experiments, GeneLab has expanded its scope to maximize the intelligibility of the raw data (e.g. RNAseq, microarray, WGBS, metagenome), particularly for users with limited bioinformatics knowledge. As such GeneLab is now providing processed data derived from the raw data covering a large spectrum of omics (genome, epigenome, transcriptome, epitranscriptome, proteome, metabolome), to help users explore important questions: Which genes or proteins are expressed differently in space for various living organisms? What are the consequences arising from these changes? What specifics DNA mutations or epigenetic changes happen in space? What species or genetic features lead to better adaption to such a unique environment? In this presentation, we will report on the current and future objectives for GeneLab, and review recent published studies relating molecular changes observed in various animal models and tissue with microgravity, radiation, circadian rhythm, hydration and carbon dioxide conditions.

DNA repair kinetics↗

Quantum-Assisted Variational Segmentation for Image-to-Image Wildfire Detection Using Satellite Data

The quantum computing community has been searching for suitable applications to demonstrate the potential of near-term quantum devices. Quantum machine learning is a potential candidate, particularly using models that cannot be efficiently simulated with classical computers [1, 2]. This work focuses on a transition phase of quantum computers where the quantum machine learning model is still simulable classically but projected not to be simulable as the size of the model grows. Ultimately quantum computers may have advantages for high-dimensional real-world problems. Due to the limited number of qubits in current noisy intermediate-scale quantum (NISQ) devices, the direct application of quantum computers in high dimensional data is not feasible. To remedy this problem, an encoder-decoder architecture can be utilized. The encoder model would transform the high-dimensional data into a compact representation, to a level that small quantum computers can be used today (or in the near future), and the decoder would take the quantum processed outputs back to the high-dimensional space. Addressing the two challenges of quantum machine learning, this work investigates a hybrid supervised generative model with a quantum Ising Born machine embedded as the latent distribution. The model contains four main parts (Figure 1.a.): (1) a U-NET architecture responsible for learning segmentation flow, (2) a Prior network responsible for learning an encoded latent distribution of the input data, (3) a Born machine which represents the latent distribution, and (4) a Posterior network in charge of learning the joint encoded latent distribution of inputs and target data. The initial model, proposed by [3], is optimized by (1) maximizing the overlap of the prior and posterior latent distributions, and (2) minimizing the segmentation loss. The proposed model is designed to be investigated in a simulation environment applied to the real-world application of wildfire segmentation. Specifically, the model is designed to solve the patchy wildfire segmentations of Moderate Resolution Imaging Spectroradiometer (MODIS) by taking the MODIS observations and using Visible Infrared Imaging Radiometer Suite’s (VIIRS) consistent wildfire product as the target. The model solves patchy wildfire segmentations and provides insight into the epistemic errors sourced from model variation. The model utilizes the Born machine as a QUBO solver to represent the latent space as a Bernoulli distribution. The proposed configuration allows the variational segmentation model to leverage the true quantum probabilistic nature and derive a more expressive latent configuration, increasing the model performance in describing wildfire segmentations. The quantum probabilistic information of the Born machine is directly incorporated in the Kullback-Leibler divergence loss in the prior and posterior distributions, forcing the Bernoulli latent distribution to maximize the overlap of input and joint input-target distributions. The proposed model is then trained and compared with a baseline only consisting of direct Bernoulli latent distribution with no Born machine representing the latent space. The models are evaluated based on the segmentation metrics, such as precision, recall, intersect of union, with uncertainty boundaries accounting for the stochastic nature of the model. Our findings show that even in low latent-dimensional space (due to the limit in computational power of the classical quantum simulator), we are able to effectively capture the latent representation and hence the model performs better than the baseline. The findings are a projection for scaling the model into higher dimensional latent space with the Born machine surpassing the baseline performance. Figure 1. Sub-figure (a) demonstrates the architecture for the training phase. The model consists of a Prior and Posterior network that encode inputs and joint input-target data into compact representations, respectively. The Born machine represents the latent distribution, and the U-NET branch learns the segmentation patterns of the data. The stochasticity is introduced to the U-NET through its last layer to create meaningful but stochastic segmentations. Sub-figure (b) represents the inference phase where the model takes the stochastic behavior from the prior network and injects that into the U-NET. Each attempt of inference will generate different but similar segmentations from the same distribution of the wildfire event. REFERENCES [1] Coyle, B., Mills, D., Danos, V., & Kashefi, E. (2020). The Born supremacy: quantum advantage and training of an Ising Born machine. npj Quantum Information, 6(1), 1-11. [2] Liu, J. G., & Wang, L. (2018). Differentiable learning of quantum circuit born machines. Physical Review A, 98(6), 062324. [3] Kohl, S., Romera-Paredes, B., Meyer, C., De Fauw, J., Ledsam, J. R., Maier-Hein, K., ... & Ronneberger, O. (2018). A probabilistic u-net for segmentation of ambiguous images. Advances in neural information processing systems, 31.

quantum machine learning↗

Transcriptional profile of a myotube starvation model of atrophy

Skeletal muscle wasting is a pervasive phenomenon that can result from a wide range of pathological conditions as well as from habitual muscular inactivity. The present work describes a cell-culture condition that induces significant atrophy in skeletal muscle C2C12 myotubes. The failure to replenish differentiation media in mature myotubes leads to rapid atrophy (53% in diameter), which is referred to here as starvation. Affymetrix microarrays were used to develop a transcriptional profile of control (fed) vs. atrophied (nonfed) myotubes. Myotube starvation was characterized by an upregulation of genes involved in translational inhibition, amino acid biosynthesis and transport, and cell cycle arrest/apoptosis, among others. Downregulated genes included several structural and regulatory elements of the extracellular matrix as well as several elements of Wnt/frizzled and TGF-beta signaling pathways. Interestingly, the characteristic transcriptional upregulation of the ubiquitin-proteasome system, calpains, and cathepsins known to occur in multiple in vivo models of atrophy were not seen during myotube starvation. With the exception of the downregulation of extracellular matrix genes, serine protease inhibitor genes, and the upregulation of the translation initiation factor PHAS-I, this model of atrophy in cell culture has a transcriptional profile quite distinct from any study published to date with atrophy in whole muscle. These data show that, although the gross morphology of atrophied muscle fibers may be similar in whole muscle vs. myotube culture, the processes by which this phenotype is achieved differ markedly.

NASA Discipline Musculoskeletal↗

Optimized suspension culture: the rotating-wall vessel

Suspension culture remains a popular modality, which manipulates mechanical culture conditions to maintain the specialized features of cultured cells. The rotating-wall vessel is a suspension culture vessel optimized to produce laminar flow and minimize the mechanical stresses on cell aggregates in culture. This review summarizes the engineering principles, which allow optimal suspension culture conditions to be established, and the boundary conditions, which limit this process. We suggest that to minimize mechanical damage and optimize differentiation of cultured cells, suspension culture should be performed in a solid-body rotation Couette-flow, zero-headspace culture vessel such as the rotating-wall vessel. This provides fluid dynamic operating principles characterized by 1) solid body rotation about a horizontal axis, characterized by colocalization of cells and aggregates of different sedimentation rates, optimally reduced fluid shear and turbulence, and three-dimensional spatial freedom; and 2) oxygenation by diffusion. Optimization of suspension culture is achieved by applying three tradeoffs. First, terminal velocity should be minimized by choosing microcarrier beads and culture media as close in density as possible. Next, rotation in the rotating-wall vessel induces both Coriolis and centrifugal forces, directly dependent on terminal velocity and minimized as terminal velocity is minimized. Last, mass transport of nutrients to a cell in suspension culture depends on both terminal velocity and diffusion of nutrients. In the transduction of mechanical culture conditions into cellular effects, several lines of evidence support a role for multiple molecular mechanisms. These include effects of shear stress, changes in cell cycle and cell death pathways, and upstream regulation of secondary messengers such as protein kinase C. The discipline of suspension culture needs a systematic analysis of the relationship between mechanical culture conditions and biological effects, emphasizing cellular processes important for the industrial production of biological pharmaceuticals and devices.

Non-NASA Center↗

Towards an Enhanced Droplet Activation Scheme for Multi-Moment Bulk Microphysics Schemes

Initial droplet spectra produced upon activation impact the ensuing chain of microphysical processes andtherefore play a crucial role in cloud evolution. This work re-examines dependencies of newly formed clouddroplet size distribution (CDSD) characteristics on environmental and aerosol properties via parcel model simulationsthat serve as the basis for a multi-moment bulk microphysics droplet activation scheme suitable for acloud-resolving model (CRM). It is found that applying a fixed size threshold to define activated droplets versusemploying physical considerations can lead to erroneous activation and overly broad CDSDs for high aerosolconcentration and weak updraft conditions. Aerosol distributions characterized by larger median sizes and/orincreased solubility can result in greater activated droplet numbers, whereas impacts of these parameters onCDSD spectral width depend on both aerosol number concentration and updraft velocity. An expansion of theactivation scheme to include CDSD spectral width is proposed to aid efforts to extend high-order momentprediction to cloud droplet categories in CRMs as well as better represent variability in the activation process onthe cloud scale.simulations to investigate the regime dependence of the relative dispersion(d)1 of newly activated CDSDs, where d is the ratio of dropletradius standard deviation (σ) to the mean radius (r ). C16 demonstratedthat increasing Na resulted in increasing (decreasing) d values via reducedcondensational narrowing (spectral broadening) rates within theAL (UL) regime, with d values peaking in the TR regime. Their findingssuggest a similar regime dependence for d as R09 noted for Nc and helpexplain reportedly conflicting relationships between Na and CDSDspectral characteristics (cf. Hudson and Noble, 2014; Liu et al., 2014),although the applicability of these results within bulk microphysicalschemes was not addressed.Simulating aerosol-cloud interactions with CRMs employing bulkmicrophysics requires that the scheme minimally predict two CDSDparameters, namely mass and number concentrations, and represent thedroplet activation process. Various activation schemes aim to determineNc from aerosol and environmental properties and include analyticalexpressions (e.g., Abdul-Razzak et al., 1998; Morrison et al., 2005) aswell as lookup tables (LUTs) based on detailed parcel model calculations(e.g., Saleeby and Cotton, 2004, hereafter SC04; Segal and Khain,2006; Thompson and Eidhammer, 2014). Expressions to diagnose CDSDspectral width from Nc (Grabowski, 1998; Liu et al., 2006; Morrison andGrabowski, 2007) or cloud water content (Geoffroy et al., 2010) havealso been developed, although more robust methods to obtain CDSDspectral width upon activation are presently lacking. This latter point isrelevant for triple-moment (3 M) bulk microphysics that aim to predictdistribution spectral width alongside number and mass concentrations(e.g., Loftus et al., 2014; Milbrandt and Yau, 2005).The current work extends the findings of C16 to the current LUTbasedaerosol activation scheme used in the Regional AtmosphericModeling System (RAMS) (Cotton et al., 2003; SC04; Saleeby and vanden Heever, 2013, hereafter SvdH13) and additionally examinesaerosol size and solubility impacts on newly activated CDSD properties.Because early cloud development processes such as condensationalgrowth, evaporation, and droplet self-collection depend on and impactCDSD spectral width (Hudson and Yum, 1997; Seifert and Beheng 2001;Lu and Seinfeld, 2006; Igel and van den Heever, 2017), an expansion ofthe activation LUTs to include CDSD spectral width is proposed as apreliminary step for extending 3M prediction to CDSDs in CRMs forimproved simulations of aerosol-cloud interactions.2. MethodologyThe current RAMS two-moment microphysics module determinesthe fractional number of aerosol particles that activate to cloud dropletsfrom five-dimensional LUTs based on model predicted air temperature(T), w, Na, and the geometric median radius (rg) and soluble fraction (ε)of the aerosol size distribution (SvdH13). These LUTs are created offlineusing a one-dimensional Lagrangian adiabatic parcel model (Feingoldand Heymsfield, 1992; Heymsfield and Sabin, 1989; SC04) to simulateexplicit droplet activation and initial CDSD growth for a range of ambientatmospheric conditions [T, w] and binned lognormal aerosol sizedistributions given by= ⎡⎣ ⎢− ⎤⎦ ⎥N r Nr π σr rσ( )2 lnexp[ln( / )]2(ln )aggg22 (1)where r is the dry aerosol particle bin radius and σg is the geometricstandard deviation of the distribution. As the parcel model simulationsfocus on the activation process, other processes such as coalescence,sedimentation, and mixing are not considered. Details of the parcelmodel can be found in SC04 and SvdH13, and only a brief description isprovided here. At the onset of parcel model calculations, the initiallydry aerosol particles in all bins first deliquesce and reach theirequilibrium diameters in a sub-saturated environment based on theKöhler equation for solution droplets. The parcel is then lifted at a fixedupward velocity w, and particle growth by vapor diffusion, along withconcurrent changes in the ambient environment, are iteratively computedusing the Variable-coefficient Ordinary Differential Equation(VODE) solver (Brown et al., 1989). The time resolution of these calculationsis determined within the VODE solver, and the frequency atwhich the solver is called is controlled by a longer model time stepbased on fixed upward parcel displacement increments (Δz) at thespecified w (Δt=Δz/w). Model calculations proceed until the parcelreaches a height 50m beyond the level of maximum saturation ratio(Smax) or total parcel displacement exceeds 2 km. Upon model termination,Smax and the fractional number of aerosols (factv) resulting innewly formed cloud droplets, defined as particles having diameters of atleast 2 μm, are cataloged in the LUTs according to the specified T, w, Na,rg, and ε parameter values.A critical point regarding the creation of these LUTs is the use of afixed minimum diameter (Dmin) to define cloud droplets in the parcelmodel, which can produce erroneous CDSD characteristics, particularlywithin the UL regime. For aerosol distributions with large rg valuesunder low SS conditions, for example, deliquesced aerosols within thelarge tail of the distribution can exceed 2 μm in diameter yet remainunactivated as ‘haze’ particles (Levin and Cotton, 2009; McFigganset al., 2006). For this study, aerosol particles activate to cloud dropletsbased on the critical diameter Dcrit as a function of parcel supersaturationratio (Sr) as in R09:D = σ MS RTρ83 ln( ) critsol wr w (2)where σsol is the surface tension of a solution droplet, Mw and ρw are themolar mass and density of liquid water, respectively, and R is theuniversal gas constant. Additionally, at relatively large w values withinthe AL regime, Nc stabilizes shortly after reaching supersaturation.However, parcel ascent and condensational growth continue beyondthe level of Smax, potentially causing additional narrowing of the CDSD.In the current work, model calculations terminate upon reaching Smaxas changes in Nc are negligible with continued ascent (Peng et al., 2007;R09).Parcel model simulations are performed to examine the sensitivitiesof CDSD characteristics to w, Na, rg, and ε, with the ranges for theseparameters listed in Table 1. Aerosols are assumed to be a mix of solubleand insoluble material of equal density, specified by ε, where fullysoluble aerosols correspond to ammonium sulfate with hygroscopicityparameter κ=0.61 (Petters and Kreidenweis, 2007). FollowingSvdH13, aerosol geometric standard deviation is fixed at σg=1.8, andaerosol distributions (Eq. 1) are partitioned into 100 logarithmicallyspacedbins spanning a size range specific to each rg value. For all simulations,Δz=1 m, and initial values of relative humidity, air temperatureand pressure are set to RH=0.99, T=10 °C and p=900 hPa,respectively.

Loftus, Adrian M.↗