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At least 865 records · Page 48

Advancing Understanding of Deep Convective Anvil Clouds

In this project we use ground-based DOE ARM observations, satellite observations, and Weather Research and Forecasting (WRF) model simulations to arrive at a more complete understanding (or, new theory) of how atmospheric heating profiles in thunderstorm cores drives how quickly air rises in the storms. The rate at which air motion increases or decreases with altitude directly relates to how much cloud mass is ejected laterally into the adjacent atmosphere, which then influences the development and maintenance of “stratiform raining cloud anvils”. Our work has led to new equations connecting the heating in these thunderstorms to these stratiform clouds, with the connection modulated by the stability structure of the atmosphere (i.e., if more stable, then a more rapid change in thunderstorm heating with altitude results in more stratiform cloud, independent of whether over land or ocean, or how organized the thunderstorms are). Improving knowledge of stratiform clouds is important, since they contribute to substantial accumulated rainfall (important to agriculture and local hydrology) as well as radiation, given their large areal extents and lifetime. The radiation impacts likely impact simulated cloud feedback in all Earth System models (ESMs).

54 ENVIRONMENTAL SCIENCES↗

Rocketdyne - Lunar Ascent Engine

The ascent engine was the last one from the moon, and I want to focus on the idea of redundancy and teams in regard to the engine. By teams, I mean teamwork - not just within Rocketdyne. It was teamwork within Rocketdyne; it was teamwork within Grumman; it was teamwork within NASA. These were all important elements leading to the successful development of the lunar excursion module (LEM) engine. Communication, rapid response, and cooperation were all important. Another aspect that went into the development of the ascent engine was the integration of technology and of lessons learned. We pushed all the above, plus technology and lessons learned, into a program, and that led to a successful result. One of the things that I like to think about - again in retrospect - is how it is very "in" now to have integrated product and process teams. These are buzzwords for teamwork in all program phases. That s where you combine a lot of groups into a single organization to get a job done. The ascent engine program epitomized that kind of integration and focus, and because this was the mid- to late-1960s; this was new ground for Rocketdyne, Grumman, and NASA. Redundancy was really a major hallmark of the Apollo Program. Everything was redundant. Once you got the rocket going, you could even lose one of the big F-1 engines, and it would still make it to orbit. And once the first stage separated from the rest of the vehicle, the second stage could do without an engine and still make a mission. This redundancy was demonstrated when an early Apollo launch shut down a J-2 second-stage engine. Actually, they shut down two J-2 engines on that flight. Even the third stage, with its single J-2 engine, was backed up because the first two stages could toss it into a recoverable orbit. If the third stage didn't work, you were circling the earth, and you had time to recover the command module and crew. Remember how on the Apollo 13 flight, there was sufficient system redundancy even when we lost the service module. That was a magnificent effort. TRW Inc. really ought to be proud of their engine for that. (See Slide 2, Appendix I) We had planned for redundancy; we had landed on the moon. However, weight restrictions in the architecture said, "You can t have redundancy for ascent from the moon. You've got one engine. It s got to work. There is no second chance. If that ascent engine doesn't work, you re stuck there." It would not have looked good for NASA. It wouldn't have looked good for the country. There was a letter written that President Richard Nixon would read if the astronauts got stuck on the moon, expressing how sorry we were and so forth. It was a scary letter, really. The ascent engine was an engine that had to work. (See Slide 3, Appendix I).

Harmon, Tim↗

Deletion of the Clostridium thermocellum recA gene reveals that it is required for thermophilic plasmid replication but not plasmid integration at homologous DNA sequences

Abstract A limitation to the engineering of cellulolytic thermophiles is the availability of functional, thermostable (≥ 60 °C) replicating plasmid vectors for rapid expression and testing of genes that provide improved or novel fuel molecule production pathways. A series of plasmid vectors for genetic manipulation of the cellulolytic thermophile Caldicellulosiruptor bescii has recently been extended to Clostridium thermocellum, another cellulolytic thermophile that very efficiently solubilizes plant biomass and produces ethanol. While the C. bescii pBAS2 replicon on these plasmids is thermostable, the use of homologous promoters, signal sequences and genes led to undesired integration into the bacterial chromosome, a result also observed with less thermostable replicating vectors. In an attempt to overcome undesired plasmid integration in C. thermocellum, a deletion of recA was constructed. As expected, C. thermocellum ∆recA showed impaired growth in chemically defined medium and an increased susceptibility to UV damage. Interestingly, we also found that recA is required for replication of the C. bescii thermophilic plasmid pBAS2 in C. thermocellum, but it is not required for replication of plasmid pNW33N. In addition, the C. thermocellum recA mutant retained the ability to integrate homologous DNA into the C. thermocellum chromosome. These data indicate that recA can be required for replication of certain plasmids, and that a recA-independent mechanism exists for the integration of homologous DNA into the C. thermocellum chromosome. Understanding thermophilic plasmid replication is not only important for engineering of these cellulolytic thermophiles, but also for developing genetic systems in similar new potentially useful non-model organisms.

59 BASIC BIOLOGICAL SCIENCES↗

Aqueous processing of organic semiconductors enabled by stable nanoparticles with built-in surfactants

The introduction of oligoether side chains onto a polymer backbone can help to stabilise polymeric dispersions in water without the necessity of surfactants or additives when conjugated polymer nanoparticles are prepared. A series of poly(3-hexylthiophene) (P3HT) derivatives with different content of a polar thiophene derivative 3-((2-methoxyethoxy)methyl)thiophene was interrogated to find the effect of the polar chains on the stability of the formed nanoparticles, as well as their structural, optical, electrochemical, and electrical properties. Findings indicated that incorporation of 10–20 percent of the polar side chain led to particles that are stable over a period of 42 days, with constant particle size and polydispersity, however the particles from the polymer with 30 percent polar side chain showed aggregation effects. The polymer dispersions showed a stronger solid-like behaviour in water with decreasing polar side chain content, while thin film deposition from water was found to afford globular morphologies and crystallites with more isotropic orientation compared to conventional solution-processed films. As a proof-of-principle, field-effect transistors were fabricated directly from the aqueous dispersions demonstrating that polymers with hydrophilic moieties can be processed in water without the requirement of surfactants.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Leveraging structure determination with fragment screening for infectious disease drug targets: MECP synthase from Burkholderia pseudomallei

As part of the Seattle Structural Genomics Center for Infectious Disease, we seek to enhance structural genomics with ligand-bound structure data which can serve as a blueprint for structure-based drug design. We have adapted fragment-based screening methods to our structural genomics pipeline to generate multiple ligand-bound structures of high priority drug targets from pathogenic organisms. In this study, we report fragment screening methods and structure determination results for 2C-methyl-D-erythritol-2,4-cyclo-diphosphate (MECP) synthase from Burkholderia pseudomallei, the gram-negative bacterium which causes melioidosis. Screening by nuclear magnetic resonance spectroscopy as well as crystal soaking followed by X-ray diffraction led to the identification of several small molecules which bind this enzyme in a critical metabolic pathway. A series of complex structures obtained with screening hits reveal distinct binding pockets and a range of small molecules which form complexes with the target. Additional soaks with these compounds further demonstrate a subset of fragments to only bind the protein when present in specific combinations. This ensemble of fragment-bound complexes illuminates several characteristics of MECP synthase, including a previously unknown binding surface external to the catalytic active site. These ligand-bound structures now serve to guide medicinal chemists and structural biologists in rational design of novel inhibitors for this enzyme.

59 BASIC BIOLOGICAL SCIENCES↗

Photonics and plasmonics go viral: self-assembly of hierarchical metamaterials

Sizing and shaping of mesoscale architectures with nanoscale features is a key opportunity to produce the next generation of higher-performing products and at the same time unveil completely new phenomena. This review article discusses recent advances in the design of novel photonic and plasmonic structures using a biology-inspired design. The proteinaceous capsids from viruses have long been discovered as platform technologies enabling unique applications in nanotechnology, materials, bioengineering, and medicine. In the context of materials applications, the highly organized structures formed by viral capsid proteins provide a 3D scaffold for the precise placement of plasmon and gain materials. Based on their highly symmetrical structures, virus-based nanoparticles have a high propensity to self-assemble into higher-order crystalline structures, yielding hierarchical hybrid materials. Recent advances in the field have led to the development of virus-based light harvesting systems, plasmonic structures for application in high-performance metamaterials, binary nanoparticle lattices, and liquid crystalline arrays for sensing or display technologies. In conclusion, there is still much that could be explored in this area, and we foresee that this is only the beginning of great technological advances in virus-based materials for plasmonics and photonics applications.

36 MATERIALS SCIENCE↗

Mechanistic insights into Cr(VI) removal by a combination of zero-valent iron and pyrite

Recent studies have revealed that a combination of zero-valent iron (ZVI) and pyrite (FeS 2 ) can effectively remove (Cr(VI)) from water, but the reasons behind this synergistic effect are still unclear. Our batch experiments showed that dissolved oxygen (DO) is a critical factor in the improved removal of Cr(VI) by ZVI and pyrite. When 0.08 g/L pyrite was combined with 0.5 g/L ZVI in the presence of DO, total Cr was reduced from 10 mg/L to 0.02 mg/L within 6 h. Conversely, in the absence of DO, total Cr was only reduced to 5.6 mg/L. DO oxidation of pyrite produced protons that promote ZVI corrosion, and mixing pyrite with water creates dissolved sulfide, which also contributes to the improved removal of Cr(VI). Here, electron microscopy images and X-ray absorption near edge structure analyses revealed that the presence of dissolved sulfide led to the formation of ferrous sulfide precipitates on the ZVI surface, preventing the formation of a passivating layer.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

High stable suspension of magnetite nanoparticles in ethanol by using sono-synthesized nanomagnetite in polyol medium

Graphical abstract: - Highlights: • The sonochemical synthesis of magnetite nanoparticles was carried out in EG without any surfactant. • The nanoparticles with sizes ∼24 nm were composed of small building blocks with sizes ∼2 nm. • The hydrophilic magnetite nanoparticles were stable in ethanol even after 8 months. • Ultrasonic intensity showed a crucial role on the obtained high stable magnetite nanoparticles in ethanol. - Abstract: The sonochemical synthesis of magnetite nanoparticles was carried out at relatively low temperature (80 °C) in ethylene glycol (EG) as a polyol solvent. The particle size was determined by transmission electron microscopy (TEM). The magnetite nanoparticles with an average size of 24 nm were composed of small building blocks with an average size of 2–3 nm and the particles exhibited nearly spherical shape. The surface characterization was investigated by using Fourier transform infrared (FTIR) spectroscopy, X-ray photoelectron spectroscopy (XPS), and thermogravimetric analysis (TGA). The stability of magnetite nanoparticles was studied in ethanol as a polar solvent. The nanoparticles showed an enhanced stability in ethanol which is due to the hydrophilic surface of the particles. The colloidal stability of magnetite nanoparticles in ethanol was monitored by UV–visible spectrophotometer. According to the results, the nanoparticles synthesized in 30 min of sonication with intensity of 35 W/cm{sup 2} (50%) led to a maximum stability in ethanol as a polar solvent with respect to the other applied intensities. The obtained magnetite nanoparticles were stable for more than12 months.

36 MATERIALS SCIENCE↗

Solid Electrolytes in the Spotlight

This virtual issue is targeted to students and researchers, and highlights 32 research articles published over the past 5 years (from July 2016 to July 2021) in Chemistry of Materials (CM). Here, the compilation of papers summarizes the latest advances in the field of solid-state electrolytes for lithium (Li)-, sodium (Na)-, and multivalent-ion (not among the 32 articles discussed) all-solid-state batteries (ASSBs), with a focus on inorganic materials and excluding hybrid systems, e.g., polymer/ceramic composites or systems including liquid media. A total of 125 articles reporting exciting experimental and/or theoretical findings on solid electrolytes were considered for this issue. During 2017–2019, there were about 25–30 papers published per year on this topic, but 2020 and 2021 saw a significant increase, with 26 publications in the first half of 2021 alone. Submissions came from many countries around the world, as shown in Figure 1. While most papers were led by research groups located in the United States, Germany and Japan follow closely, and Austria, the United Kingdom, Canada, and China are also well represented.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DNA-assembled superconducting 3D nanoscale architectures

Studies of nanoscale superconducting structures have revealed various physical phenomena and led to the development of a wide range of applications. Most of these studies concentrated on one- and two-dimensional structures due to the lack of approaches for creation of fully engineered three-dimensional (3D) nanostructures. Here, we present a ‘bottom-up’ method to create 3D superconducting nanostructures with prescribed multiscale organization using DNA-based self-assembly methods. We assemble 3D DNA superlattices from octahedral DNA frames with incorporated nanoparticles, through connecting frames at their vertices, which result in cubic superlattices with a 48 nm unit cell. The superconductive superlattice is formed by converting a DNA superlattice first into highly-structured 3D silica scaffold, to turn it from a soft and liquid-environment dependent macromolecular construction into a solid structure, following by its coating with superconducting niobium (Nb). Through low-temperature electrical characterization we demonstrate that this process creates 3D arrays of Josephson junctions. This approach may be utilized in development of a variety of applications such as 3D Superconducting Quantum interference Devices (SQUIDs) for measurement of the magnetic field vector, highly sensitive Superconducting Quantum Interference Filters (SQIFs), and parametric amplifiers for quantum information systems.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Surface-active antibiotic production as a multifunctional adaptation for postfire microorganisms

Abstract Wildfires affect soils in multiple ways, leading to numerous challenges for colonizing microorganisms. Although it is thought that fire-adapted microorganisms lie at the forefront of postfire ecosystem recovery, the specific strategies that these organisms use to thrive in burned soils remain largely unknown. Through bioactivity screening of bacterial isolates from burned soils, we discovered that several Paraburkholderia spp. isolates produced a set of unusual rhamnolipid surfactants with a natural methyl ester modification. These rhamnolipid methyl esters (RLMEs) exhibited enhanced antimicrobial activity against other postfire microbial isolates, including pyrophilous Pyronema fungi and Amycolatopsis bacteria, compared to the typical rhamnolipids made by organisms such as Pseudomonas spp. RLMEs also showed enhanced surfactant properties and facilitated bacterial motility on agar surfaces. In vitro assays further demonstrated that RLMEs improved aqueous solubilization of polycyclic aromatic hydrocarbons, which are potential carbon sources found in char. Identification of the rhamnolipid biosynthesis genes in the postfire isolate, Paraburkholderia kirstenboschensis str. F3, led to the discovery of rhlM, whose gene product is responsible for the unique methylation of rhamnolipid substrates. RhlM is the first characterized bacterial representative of a large class of integral membrane methyltransferases that are widespread in bacteria. These results indicate multiple roles for RLMEs in the postfire lifestyle of Paraburkholderia isolates, including enhanced dispersal, solubilization of potential nutrients, and inhibition of competitors. Our findings shed new light on the chemical adaptations that bacteria employ to navigate, grow, and outcompete other soil community members in postfire environments.

59 BASIC BIOLOGICAL SCIENCES↗

Forward treatment planning for modulated electron radiotherapy (MERT) employing Monte Carlo methods

Purpose: This paper describes the development of a forward planning process for modulated electron radiotherapy (MERT). The approach is based on a previously developed electron beam model used to calculate dose distributions of electron beams shaped by a photon multi leaf collimator (pMLC). Methods: As the electron beam model has already been implemented into the Swiss Monte Carlo Plan environment, the Eclipse treatment planning system (Varian Medical Systems, Palo Alto, CA) can be included in the planning process for MERT. In a first step, CT data are imported into Eclipse and a pMLC shaped electron beam is set up. This initial electron beam is then divided into segments, with the electron energy in each segment chosen according to the distal depth of the planning target volume (PTV) in beam direction. In order to improve the homogeneity of the dose distribution in the PTV, a feathering process (Gaussian edge feathering) is launched, which results in a number of feathered segments. For each of these segments a dose calculation is performed employing the in-house developed electron beam model along with the macro Monte Carlo dose calculation algorithm. Finally, an automated weight optimization of all segments is carried out and the total dose distribution is read back into Eclipse for display and evaluation. One academic and two clinical situations are investigated for possible benefits of MERT treatment compared to standard treatments performed in our clinics and treatment with a bolus electron conformal (BolusECT) method. Results: The MERT treatment plan of the academic case was superior to the standard single segment electron treatment plan in terms of organs at risk (OAR) sparing. Further, a comparison between an unfeathered and a feathered MERT plan showed better PTV coverage and homogeneity for the feathered plan, with V{sub 95%} increased from 90% to 96% and V{sub 107%} decreased from 8% to nearly 0%. For a clinical breast boost irradiation, the MERT plan led to a similar homogeneity in the PTV compared to the standard treatment plan while the mean body dose was lower for the MERT plan. Regarding the second clinical case, a whole breast treatment, MERT resulted in a reduction of the lung volume receiving more than 45% of the prescribed dose when compared to the standard plan. On the other hand, the MERT plan leads to a larger low-dose lung volume and a degraded dose homogeneity in the PTV. For the clinical cases evaluated in this work, treatment plans using the BolusECT technique resulted in a more homogenous PTV and CTV coverage but higher doses to the OARs than the MERT plans. Conclusions: MERT treatments were successfully planned for phantom and clinical cases, applying a newly developed intuitive and efficient forward planning strategy that employs a MC based electron beam model for pMLC shaped electron beams. It is shown that MERT can lead to a dose reduction in OARs compared to other methods. The process of feathering MERT segments results in an improvement of the dose homogeneity in the PTV.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

GOTTCHA, Version2

One major challenge in the field of shotgun metagenomics is the accurate identification of the organisms present within the community, based on classification of short sequence reads. Though microbial community profiling methods have emerged to attempt to rapidly classify the millions of reads output from contemporary sequencers, the combination of incomplete databases, similarity among otherwise divergent genomes, and the large volumes of sequencing data required for metagenome sequencing has led to unacceptably high false discovery rates (FDR). Here we present the application of a novel, gene-independent and signature-based metagenomic taxonomic profiling tool with significantly smaller FDR, which is also capable of classifying never-before seen genomes into the appropriate parent taxa.The algorithm is based upon three primary computational phases: (I) genomic decomposition into bit vectors, (II) bit vector intersections to identify shared regions, and (III) bit vector subtractions to remove shared regions and reveal unique, signature regions. In the Decomposition phase, genomic data is first masked to highlight only the valid (non-ambiguous) regions and then decomposed into overlapping 24-mers. The k-mers are sorted along with their start positions, de-replicated, and then prefixed, to minimize data duplication. The prefixes are indexed and an identical data structure is created for the start positions to mimic that of the k-mer data structure. During the Intersection phase -- which is the most computationally intensive phase -- as an all-vs-all comparison is made, the number of comparisons is first reduced by four methods: (a) Prefix restriction, (b) Overlap detection, (c) Overlap restriction, and (d) Result recording. In Prefix restriction, only k-mers of the same prefix are compared. Within that group, potential overlap of k-mer suffixes that would result in a non-empty set intersection are screened for. If such an overlap exists, the region which intersects is first reduced by performing a binary search of the boundary suffixes of the smaller set into the larger set, which defines the limits of the zipper-based intersection process. Rather than recording the actual k-mers of the intersection, another data structure of identical "shape" is created which consists of only bit vectors so that only a 1 or 0 will be stored in the location of the k-mer suffix that was found in the intersection. This reduces the amount of data generated and stored considerably. During the Subtraction phase, relevant intersection bitmasks are first unionized together to form a single bitmask which is then applied over the original genome to reveal only those regions of the genome that are unique. These regions are then exported to disk in FASTA format and used in the application of determining the constituents of an unknown metagenomic community.

Freitas, Tracey↗

GOTTCHA Database, Version 1

One major challenge in the field of shotgun metagenomics is the accurate identification of the organisms present within the community, based on classification of short sequence reads. Though microbial community profiling methods have emerged to attempt to rapidly classify the millions of reads output from contemporary sequencers, the combination of incomplete databases, similarity among otherwise divergent genomes, and the large volumes of sequencing data required for metagenome sequencing has led to unacceptably high false discovery rates (FDR). Here we present the application of a novel, gene-independent and signature-based metagenomic taxonomic profiling tool with significantly smaller FDR, which is also capable of classifying never-before seen genomes into the appropriate parent taxa.The algorithm is based upon three primary computational phases: (I) genomic decomposition into bit vectors, (II) bit vector intersections to identify shared regions, and (III) bit vector subtractions to remove shared regions and reveal unique, signature regions.In the Decomposition phase, genomic data is first masked to highlight only the valid (non-ambiguous) regions and then decomposed into overlapping 24-mers. The k-mers are sorted along with their start positions, de-replicated, and then prefixed, to minimize data duplication. The prefixes are indexed and an identical data structure is created for the start positions to mimic that of the k-mer data structure.During the Intersection phase -- which is the most computationally intensive phase -- as an all-vs-all comparison is made, the number of comparisons is first reduced by four methods: (a) Prefix restriction, (b) Overlap detection, (c) Overlap restriction, and (d) Result recording. In Prefix restriction, only k-mers of the same prefix are compared. Within that group, potential overlap of k-mer suffixes that would result in a non-empty set intersection are screened for. If such an overlap exists, the region which intersects is first reduced by performing a binary search of the boundary suffixes of the smaller set into the larger set, which defines the limits of the zipper-based intersection process. Rather than recording the actual k-mers of the intersection, another data structure of identical "shape" is created which consists of only bit vectors so that only a 1 or 0 will be stored in the location of the k-mer suffix that was found in the intersection. This reduces the amount of data generated and stored considerably.During the Subtraction phase, relevant intersection bitmasks are first unionized together to form a single bitmask which is then applied over the original genome to reveal only those regions of the genome that are unique. These regions are then exported to disk in FASTA format and used in the application of determining the constituents of an unknown metagenomic community.The DATABASE provided is the result of the algorithm described.

Freitas, Tracey↗

Carbon Dynamics in Vegetation and Soils

The overall goals of CD-08 team in Phase I were to quantify the contributions of different components of the carbon cycle to overall ecosystem carbon balance in Amazonian tropical forests and to undertake process studies at a number of sites along the eastern LBA transect to understand how and why these fluxes vary with site, season, and year. We divided this work into a number of specific tasks: (1) determining the average rate (and variability) of tree growth over the past 3 decades; (2) determining age demographics of tree populations, using radiocarbon to determine tree age; (3) assessing the rate of production and decomposition of dead wood debris; (4) determining turnover rates for organic matter in soils and the mean age of C respired from soil using radiocarbon measurements; and (5) comparing our results with models and constructing models to predict the potential of tropical forests to function as sources or sinks of C. This report summarizes the considerable progress made towards our original goals, which have led to increased understanding of the potential for central Amazon forests to act as sources or sinks of carbon with altered productivity. The overall picture of tropical forest C dynamics emerging from our Phase I studies suggests that the fraction of gross primary production allocated to growth in these forests is only 25-30%, as opposed to the 50% assumed by many ecosystem models. Consequent slow tree growth rates mean greater mean tree age for a given diameter, as reflected in our measurements and models of tree age. Radiocarbon measurements in leaf and root litter suggest that carbon stays in living tree biomass for several years up to a decade before being added to soils, where decomposition is rapid. The time lags predicted from 14C, when coupled with climate variation on similar time scales, can lead to significant interannual variation in net ecosystem C exchange.

Trumbore, Susan↗

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↗

GOTTCHA, Version 1

One major challenge in the field of shotgun metagenomics is the accurate identification of the organisms present within the community, based on classification of short sequence reads. Though microbial community profiling methods have emerged to attempt to rapidly classify the millions of reads output from contemporary sequencers, the combination of incomplete databases, similarity among otherwise divergent genomes, and the large volumes of sequencing data required for metagenome sequencing has led to unacceptably high false discovery rates (FDR). Here we present the application of a novel, gene-independent and signature-based metagenomic taxonomic profiling tool with significantly smaller FDR, which is also capable of classifying never-before seen genomes into the appropriate parent taxa.The algorithm is based upon three primary computational phases: (I) genomic decomposition into bit vectors, (II) bit vector intersections to identify shared regions, and (III) bit vector subtractions to remove shared regions and reveal unique, signature regions. In the Decomposition phase, genomic data is first masked to highlight only the valid (non-ambiguous) regions and then decomposed into overlapping 24-mers. The k-mers are sorted along with their start positions, de-replicated, and then prefixed, to minimize data duplication. The prefixes are indexed and an identical data structure is created for the start positions to mimic that of the k-mer data structure. During the Intersection phase -- which is the most computationally intensive phase -- as an all-vs-all comparison is made, the number of comparisons is first reduced by four methods: (a) Prefix restriction, (b) Overlap detection, (c) Overlap restriction, and (d) Result recording. In Prefix restriction, only k-mers of the same prefix are compared. Within that group, potential overlap of k-mer suffixes that would result in a non-empty set intersection are screened for. If such an overlap exists, the region which intersects is first reduced by performing a binary search of the boundary suffixes of the smaller set into the larger set, which defines the limits of the zipper-based intersection process. Rather than recording the actual k-mers of the intersection, another data structure of identical "shape" is created which consists of only bit vectors so that only a 1 or 0 will be stored in the location of the k-mer suffix that was found in the intersection. This reduces the amount of data generated and stored considerably. During the Subtraction phase, relevant intersection bitmasks are first unionized together to form a single bitmask which is then applied over the original genome to reveal only those regions of the genome that are unique. These regions are then exported to disk in FASTA format and used in the application of determining the constituents of an unknown metagenomic community.

Freitas, Tracey↗

GOTTCHA Database, Version 1

One major challenge in the field of shotgun metagenomics is the accurate identification of the organisms present within the community, based on classification of short sequence reads. Though microbial community profiling methods have emerged to attempt to rapidly classify the millions of reads output from contemporary sequencers, the combination of incomplete databases, similarity among otherwise divergent genomes, and the large volumes of sequencing data required for metagenome sequencing has led to unacceptably high false discovery rates (FDR). Here we present the application of a novel, gene-independent and signature-based metagenomic taxonomic profiling tool with significantly smaller FDR, which is also capable of classifying never-before seen genomes into the appropriate parent taxa.The algorithm is based upon three primary computational phases: (I) genomic decomposition into bit vectors, (II) bit vector intersections to identify shared regions, and (III) bit vector subtractions to remove shared regions and reveal unique, signature regions.In the Decomposition phase, genomic data is first masked to highlight only the valid (non-ambiguous) regions and then decomposed into overlapping 24-mers. The k-mers are sorted along with their start positions, de-replicated, and then prefixed, to minimize data duplication. The prefixes are indexed and an identical data structure is created for the start positions to mimic that of the k-mer data structure.During the Intersection phase -- which is the most computationally intensive phase -- as an all-vs-all comparison is made, the number of comparisons is first reduced by four methods: (a) Prefix restriction, (b) Overlap detection, (c) Overlap restriction, and (d) Result recording. In Prefix restriction, only k-mers of the same prefix are compared. Within that group, potential overlap of k-mer suffixes that would result in a non-empty set intersection are screened for. If such an overlap exists, the region which intersects is first reduced by performing a binary search of the boundary suffixes of the smaller set into the larger set, which defines the limits of the zipper-based intersection process. Rather than recording the actual k-mers of the intersection, another data structure of identical "shape" is created which consists of only bit vectors so that only a 1 or 0 will be stored in the location of the k-mer suffix that was found in the intersection. This reduces the amount of data generated and stored considerably.During the Subtraction phase, relevant intersection bitmasks are first unionized together to form a single bitmask which is then applied over the original genome to reveal only those regions of the genome that are unique. These regions are then exported to disk in FASTA format and used in the application of determining the constituents of an unknown metagenomic community.The DATABASE provided is the result of the algorithm described.

Freitas, Tracey↗