Search NASA⌕ Search

SEARCH · Search NASA

Results for “Sequence Deletion”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

68 records · Page 4
All sourcesNASA NTRSDOE OSTI
NASA NTRS2013

Multi-User Space Link Extension (SLE) System

The Multi-User Space (MUS) Link Extension system, a software and data system, provides Space Link Extension (SLE) users with three space data transfer services in timely, complete, and offline modes as applicable according to standards defined by the Consultative Committee for Space Data Systems (CCSDS). MUS radically reduces the schedule, cost, and risk of implementing a new SLE user system, minimizes operating costs with a lights-out approach to SLE, and is designed to require no sustaining engineering expense during its lifetime unless changes in the CCSDS SLE standards, combined with new provider implementations, force changes. No software modification to MUS needs to be made to support a new mission. Any systems engineer with Linux experience can begin testing SLE user service instances with MUS starting from a personal computer (PC) within five days. For flight operators, MUS provides a familiar-looking Web page for entering SLE configuration data received from SLE. Operators can also use the Web page to back up a space mission's entire set of up to approximately 500 SLE service instances in less than five seconds, or to restore or transfer from another system the same amount of data from a MUS backup file in about the same amount of time. Missions operate each MUS SLE service instance independently by sending it MUS directives, which are legible, plain ASCII strings. MUS directives are usually (but not necessarily) sent through a TCP-IP (Transmission Control Protocol Internet Protocol) socket from a MOC (Mission Operations Center) or POCC (Payload Operations Control Center) system, under scripted control, during "lights-out" spacecraft operation. MUS permits the flight operations team to configure independently each of its data interfaces; not only commands and telemetry, but also MUS status messages to the MOC. Interfaces can use single- or multiple-client TCP/IP server sockets, TCP/IP client sockets, temporary disk files, the system log, or standard in, standard out, or standard error as applicable. By defining MUS templates in ASCII, the flight operations team can include any MUS system variable in telemetry or command headers or footers, and/or in status messages. Data fields can be arranged within messages in different sequences, according to the mission s needs. The only constraints imposed are on the format of MUS directive strings, and some bare minimum logical requirements that must be met in order for MUS to read the mission control center's spacecraft command inputs. The MUS system imposes no limits or constraints on the numbers and combinations of missions and SLE service instances that it will support simultaneously. At any time, flight operators may add, change, delete, bind, connect, or disconnect.

Perkins, Toby↗
NASA NTRS1999

Mars Surveyor Program 2001 Mission Overview

The Mars Surveyor 2001 mission to Mars was initially a key element in the Mars sample return sequence of missions. A capable rover, carrying the Cornell Athena instruments would be placed on Mars to roam over several kilometers, select samples, and place them in a cache for return by a subsequent mission. Inevitably, budget constraints forced descopes. At one critical point, the landed payload consisted only of the HEDS (Human Exploration and Development of Space) payloads selected for testing environmental properties of the surface for future human exploration. Then Congress intervened and put back some of the funding that had been deleted. NASA next redefined the payload to include as many of the Athena instruments as possible, to be distributed between the lander deck and a Sojourner class rover. This payload would then be placed on a modified version of the Mars Polar Lander rather than on the much larger, and more expensive, lander that had been originally designed for the mission. With this functionality restored the '01 mission remains an important and pivotal element of the Mars Surveyor program. It completes the Mars Observer objectives with the gamma ray spectrometer mapping. This mission will largely complete the global characterization phase of Mars exploration and mark the beginning of focused surface exploration leading to return of the first samples and the search for evidence of past Martian life. MSP'01 also is the first mission in the combined Mars exploration strategy of the HEDS and Space Science Enterprises of NASA. This mission, and those to follow, will demonstrate technologies and collect environmental data that will provide the basis for a decision to send humans to Mars. The NASA exploration strategy for Mars includes orbiters, landers and rovers launched in 2001 and 2003 and a sample return mission to be launched in 2005, returning a sample by 2008. The purpose of the rovers is to explore and characterize sites on Mars. The 2003 and 2005 missions will select rocks, soil, and atmosphere for return to earth.

Saunders, R. Stephen↗
NASA NTRS2005

APGEN Version 5.0

Activity Plan Generator (APGEN), now at version 5.0, is a computer program that assists in generating an integrated plan of activities for a spacecraft mission that does not oversubscribe spacecraft and ground resources. APGEN generates an interactive display, through which the user can easily create or modify the plan. The display summarizes the plan by means of a time line, whereon each activity is represented by a bar stretched between its beginning and ending times. Activities can be added, deleted, and modified via simple mouse and keyboard actions. The use of resources can be viewed on resource graphs. Resource and activity constraints can be checked. Types of activities, resources, and constraints are defined by simple text files, which the user can modify. In one of two modes of operation, APGEN acts as a planning expert assistant, displaying the plan and identifying problems in the plan. The user is in charge of creating and modifying the plan. In the other mode, APGEN automatically creates a plan that does not oversubscribe resources. The user can then manually modify the plan. APGEN is designed to interact with other software that generates sequences of timed commands for implementing details of planned activities.

Maldague, Pierre↗
NASA NTRS2003

The Potato virus X TGBp3 protein associates with the ER network for virus cell-to-cell movement

Potato virus X (PVX) TGBp3 is required for virus cell-to-cell movement. Cell-to-cell movement of TGBp3 was studied using biolistic bombardment of plasmids expressing GFP:TGBp3. TGBp3 moves between cells in Nicotiana benthamiana, but requires TGBp1 to move in N. tabacum leaves. In tobacco leaves GFP:TGBp3 accumulated in a pattern resembling the endoplasmic reticulum (ER). To determine if the ER network is important for GFP:TGBp3 and for PVX cell-to-cell movement, a single mutation inhibiting membrane binding of TGBp3 was introduced into GFP:TGBp3 and into PVX. This mutation disrupted movement of GFP:TGBp3 and PVX. Brefeldin A, which disrupts the ER network, also inhibited GFP:TGBp3 movement in both Nicotiana species. Two deletion mutations, that do not affect membrane binding, hindered GFP:TGBp3 and PVX cell-to-cell movement. Plasmids expressing GFP:TGBp2 and GFP:TGBp3 were bombarded to several other PVX hosts and neither protein moved between adjacent cells. In most hosts, TGBp2 or TGBp3 cannot move cell-to-cell.

NASA Discipline Plant Biology↗
NASA NTRS2000

Constructing high complexity synthetic libraries of long ORFs using in vitro selection

We present a method that can significantly increase the complexity of protein libraries used for in vitro or in vivo protein selection experiments. Protein libraries are often encoded by chemically synthesized DNA, in which part of the open reading frame is randomized. There are, however, major obstacles associated with the chemical synthesis of long open reading frames, especially those containing random segments. Insertions and deletions that occur during chemical synthesis cause frameshifts, and stop codons in the random region will cause premature termination. These problems can together greatly reduce the number of full-length synthetic genes in the library. We describe a strategy in which smaller segments of the synthetic open reading frame are selected in vitro using mRNA display for the absence of frameshifts and stop codons. These smaller segments are then ligated together to form combinatorial libraries of long uninterrupted open reading frames. This process can increase the number of full-length open reading frames in libraries by up to two orders of magnitude, resulting in protein libraries with complexities of greater than 10(13). We have used this methodology to generate three types of displayed protein library: a completely random sequence library, a library of concatemerized oligopeptide cassettes with a propensity for forming amphipathic alpha-helical or beta-strand structures, and a library based on one of the most common enzymatic scaffolds, the alpha/beta (TIM) barrel. Copyright 2000 Academic Press.

Non-NASA Center↗
NASA NTRSDate not supplied

CDKN1A/P21’S Role in Osteoprogenitor Fate Regulation in Response to Mechanical Loading: A Single Cell Resolution Investigation

Forces generated by gravity in load-bearing tissues such as bone marrow promote stem cell-based tissue-regenerative processes by increasing proliferation and differentiation of tissue progenitors. Conversely, in microgravity, mouse bone marrow mesenchymal and hematopoietic precursors down-regulate differentiation markers and up-regulate stemness maintenance genes. During microgravity, these transcriptomic changes are associated with Cdkn1a overexpression in osteoprogenitors, and further the homozygous deletion of the CDKN1a gene in the mouse model results in elevated stem-cell based regeneration of severed digits and ear-hole punches. In this work we sought to test the hypothesis that gravity mechanotransduction regulates mesenchymal stem cell derived osteoprogenitor based osteogenesis by modulating proliferation and differentiation fates at specific cell cycle stages via a p21/CDKN1a-regulated mechanism.. To test our hypothesis, we isolated primary mouse bone marrow osteoprogenitors from Cdkn1a-/- (null) or wildtype mice, cultured the cells for 7-days unloaded in osteogenic differentiation media, to allow commitment of the adherent cell population, and subsequently, cultured an additional 48-hours under cyclic stretch or static control loading conditions. After 48-hours of dynamic mechanical loading, we used a 10X Genomics Chromium/Single Cell controller to generate bar-coded single cell Illumina libraries and sequenced expressomes for 6,000 static control and 6,000 cyclic stretch cells for each genotype. Stage-specific single cell analyses show Cdkn1a-/- osteogenic cultures are more differentiated with fewer progenitors, and that cyclic stretch further promotes the conversion of progenitors to osteoblasts in both wildtype and Cdkn1a-/- backgrounds. The proportion of late mineralizing osteoblasts doubled in Cdkn1a-/- cultures, but is not affected by load. Finally, single cell expression of Cdkn1a, in the wildtype cells, is most strongly suppressed by cyclic stretch both in early and late osteoblasts, and minimally in the progenitor population. Collectively, our results support the hypothesis that Cdkn1a constitutively plays a mechano-reversible anti-proliferative role during stem cell-based bone tissue regeneration, and suggests a new molecular target to counter regenerative deficits caused by disuse.

Eduardo Almeida↗
NASA NTRS1995

Mutant quantity and quality in mammalian cells (AL) exposed to cesium-137 gamma radiation: effect of caffeine

We examined the effect of caffeine (1,3,7-trimethylxanthine) on the quantity and quality of mutations in cultured mammalian AL human-hamster hybrid cells exposed to 137Cs gamma radiation. At a dose (1.5 mg/ml for 16 h) that reduced the plating efficiency (PE) by 20%, caffeine was not itself a significant mutagen, but it increased by approximately twofold the slope of the dose-response curve for induction of S1- mutants by 137Cs gamma radiation. Molecular analysis of 235 S1- mutants using a series of DNA probes mapped to the human chromosome 11 in the AL hybrid cells revealed that 73 to 85% of the mutations in unexposed cells and in cells treated with caffeine alone, 137Cs gamma rays alone or 137Cs gamma rays plus caffeine were large deletions involving millions of base pairs of DNA. Most of these deletions were contiguous with the region of the MIC1 gene at 11p13 that encodes the S1 cell surface antigen. In other mutants that had suffered multiple marker loss, the deletions were intermittent along chromosome 11. These "complex" mutations were rare for 137Cs gamma irradiation (1/63 = 1.5%) but relatively prevalent (23-50%) for other exposure conditions. Thus caffeine appears to alter both the quantity and quality of mutations induced by 137Cs gamma irradiation.

NASA Discipline Radiation Health↗
NASA NTRS2000

Arabidopsis chloroplast chaperonin 10 is a calmodulin-binding protein

Calcium regulates diverse cellular activities in plants through the action of calmodulin (CaM). By using (35)S-labeled CaM to screen an Arabidopsis seedling cDNA expression library, a cDNA designated as AtCh-CPN10 (Arabidopsis thaliana chloroplast chaperonin 10) was cloned. Chloroplast CPN10, a nuclear-encoded protein, is a functional homolog of E. coli GroES. It is believed that CPN60 and CPN10 are involved in the assembly of Rubisco, a key enzyme involved in the photosynthetic pathway. Northern analysis revealed that AtCh-CPN10 is highly expressed in green tissues. The recombinant AtCh-CPN10 binds to CaM in a calcium-dependent manner. Deletion mutants revealed that there is only one CaM-binding site in the last 31 amino acids of the AtCh-CPN10 at the C-terminal end. The CaM-binding region in AtCh-CPN10 has higher homology to other chloroplast CPN10s in comparison to GroES and mitochondrial CPN10s, suggesting that CaM may only bind to chloroplast CPN10s. Furthermore, the results also suggest that the calcium/CaM messenger system is involved in regulating Rubisco assembly in the chloroplast, thereby influencing photosynthesis. Copyright 2000 Academic Press.

NASA Discipline Plant Biology↗
NASA NTRS2004

Microelectronic DNA assay for the detection of BRCA1 gene mutations

Mutations in BRCA1 are characterized by predisposition to breast cancer, ovarian cancer and prostate cancer as well as colon cancer. Prognosis for this cancer survival depends upon the stage at which cancer is diagnosed. Reliable and rapid mutation detection is crucial for the early diagnosis and treatment. We developed an electronic assay for the detection of a representative single nucleotide polymorphism (SNP), deletion and insertion in BRCA1 gene by the microelectronics microarray instrumentation. The assay is rapid, and it takes 30 minutes for the immobilization of target DNA samples, hybridization, washing and readout. The assay is multiplexing since it is carried out at the same temperature and buffer conditions for each step. The assay is also highly specific, as the signal-to-noise ratio is much larger than recommended value (72.86 to 321.05 vs. 5) for homozygotes genotyping, and signal ratio close to the perfect value 1 for heterozygotes genotyping (1.04).

Validation Studies↗
NASA NTRS1996

Single residue substitutions that change the gating properties of a mechanosensitive channel in Escherichia coli

MscL is a channel that opens a large pore in the Escherichia coli cytoplasmic membrane in response to mechanical stress. Previously, we highly enriched the MscL protein by using patch clamp as a functional assay and cloned the corresponding gene. The predicted protein contains a largely hydrophobic core spanning two-thirds of the molecule and a more hydrophilic carboxyl terminal tail. Because MscL had no homology to characterized proteins, it was impossible to predict functional regions of the protein by simple inspection. Here, by mutagenesis, we have searched for functionally important regions of this molecule. We show that a short deletion from the amino terminus (3 amino acids), and a larger deletion of 27 amino acids from the carboxyl terminus of this protein, had little if any effect in channel properties. We have thus narrowed the search of the core mechanosensitive mechanism to 106 residues of this 136-amino acid protein. In contrast, single residue substitutions of a lysine in the putative first transmembrane domain or a glutamine in the periplasmic loop caused pronounced shifts in the mechano-sensitivity curves and/or large changes in the kinetics of channel gating, suggesting that the conformational structure in these regions is critical for normal mechanosensitive channel gating.

Non-NASA Center↗
NASA NTRS2000

Autoinhibition of a calmodulin-dependent calcium pump involves a structure in the stalk that connects the transmembrane domain to the ATPase catalytic domain

The regulation of Ca(2+)-pumps is important for controlling [Ca(2+)] in the cytosol and organelles of all eukaryotes. Here, we report a genetic strategy to identify residues that function in autoinhibition of a novel calmodulin-activated Ca(2+)-pump with an N-terminal regulatory domain (isoform ACA2 from Arabidopsis). Mutant pumps with constitutive activity were identified by complementation of a yeast (K616) deficient in two Ca(2+)-pumps. Fifteen mutations were found that disrupted a segment of the N-terminal autoinhibitor located between Lys(23) and Arg(54). Three mutations (E167K, D219N, and E341K) were found associated with the stalk that connects the ATPase catalytic domain (head) and with the transmembrane domain. Enzyme assays indicated that the stalk mutations resulted in calmodulin-independent activity, with V(max), K(mATP), and K(mCa(2+)) similar to that of a pump in which the N-terminal autoinhibitor had been deleted. A highly conservative substitution at Asp(219) (D219E) still produced a deregulated pump, indicating that the autoinhibitory structure in the stalk is highly sensitive to perturbation. In plasma membrane H(+)-ATPases from yeast and plants, similarly positioned mutations resulted in hyperactive pumps. Together, these results suggest that a structural feature of the stalk is of general importance in regulating diverse P-type ATPases.

NASA Discipline Plant Biology↗
NASA NTRS2000

Incremental Parallelization of Non-Data-Parallel Programs Using the Charon Message-Passing Library

Message passing is among the most popular techniques for parallelizing scientific programs on distributed-memory architectures. The reasons for its success are wide availability (MPI), efficiency, and full tuning control provided to the programmer. A major drawback, however, is that incremental parallelization, as offered by compiler directives, is not generally possible, because all data structures have to be changed throughout the program simultaneously. Charon remedies this situation through mappings between distributed and non-distributed data. It allows breaking up the parallelization into small steps, guaranteeing correctness at every stage. Several tools are available to help convert legacy codes into high-performance message-passing programs. They usually target data-parallel applications, whose loops carrying most of the work can be distributed among all processors without much dependency analysis. Others do a full dependency analysis and then convert the code virtually automatically. Even more toolkits are available that aid construction from scratch of message passing programs. None, however, allows piecemeal translation of codes with complex data dependencies (i.e. non-data-parallel programs) into message passing codes. The Charon library (available in both C and Fortran) provides incremental parallelization capabilities by linking legacy code arrays with distributed arrays. During the conversion process, non-distributed and distributed arrays exist side by side, and simple mapping functions allow the programmer to switch between the two in any location in the program. Charon also provides wrapper functions that leave the structure of the legacy code intact, but that allow execution on truly distributed data. Finally, the library provides a rich set of communication functions that support virtually all patterns of remote data demands in realistic structured grid scientific programs, including transposition, nearest-neighbor communication, pipelining, gather/scatter, and redistribution. At the end of the conversion process most intermediate Charon function calls will have been removed, the non-distributed arrays will have been deleted, and virtually the only remaining Charon functions calls are the high-level, highly optimized communications. Distribution of the data is under complete control of the programmer, although a wide range of useful distributions is easily available through predefined functions. A crucial aspect of the library is that it does not allocate space for distributed arrays, but accepts programmer-specified memory. This has two major consequences. First, codes parallelized using Charon do not suffer from encapsulation; user data is always directly accessible. This provides high efficiency, and also retains the possibility of using message passing directly for highly irregular communications. Second, non-distributed arrays can be interpreted as (trivial) distributions in the Charon sense, which allows them to be mapped to truly distributed arrays, and vice versa. This is the mechanism that enables incremental parallelization. In this paper we provide a brief introduction of the library and then focus on the actual steps in the parallelization process, using some representative examples from, among others, the NAS Parallel Benchmarks. We show how a complicated two-dimensional pipeline-the prototypical non-data-parallel algorithm- can be constructed with ease. To demonstrate the flexibility of the library, we give examples of the stepwise, efficient parallel implementation of nonlocal boundary conditions common in aircraft simulations, as well as the construction of the sequence of grids required for multigrid.

VanderWijngaart, Rob F.↗
NASA NTRS2003

Biochemical and functional analysis of CTR1, a protein kinase that negatively regulates ethylene signaling in Arabidopsis

CTR1 encodes a negative regulator of the ethylene response pathway in Arabidopsis thaliana. The C-terminal domain of CTR1 is similar to the Raf family of protein kinases, but its first two-thirds encodes a novel protein domain. We used a variety of approaches to investigate the function of these two CTR1 domains. Recombinant CTR1 protein was purified from a baculoviral expression system, and shown to possess intrinsic Ser/Thr protein kinase activity with enzymatic properties similar to Raf-1. Deletion of the N-terminal domain did not elevate the kinase activity of CTR1, indicating that, at least in vitro, this domain does not autoinhibit kinase function. Molecular analysis of loss-of-function ctr1 alleles indicated that several mutations disrupt the kinase catalytic domain, and in vitro studies confirmed that at least one of these eliminates kinase activity, which indicates that kinase activity is required for CTR1 function. One missense mutation, ctr1-8, was found to result from an amino acid substitution within a new conserved motif within the N-terminal domain. Ctr1-8 has no detectable effect on the kinase activity of CTR1 in vitro, but rather disrupts the interaction with the ethylene receptor ETR1. This mutation also disrupts the dominant negative effect that results from overexpression of the CTR1 amino-terminal domain in transgenic Arabidopsis. These results suggest that CTR1 interacts with ETR1 in vivo, and that this association is required to turn off the ethylene-signaling pathway.

Non-NASA Center↗
NASA NTRS1995

Finding the global minimum: a fuzzy end elimination implementation

The 'fuzzy end elimination theorem' (FEE) is a mathematically proven theorem that identifies rotameric states in proteins which are incompatible with the global minimum energy conformation. While implementing the FEE we noticed two different aspects that directly affected the final results at convergence. First, the identification of a single dead-ending rotameric state can trigger a 'domino effect' that initiates the identification of additional rotameric states which become dead-ending. A recursive check for dead-ending rotameric states is therefore necessary every time a dead-ending rotameric state is identified. It is shown that, if the recursive check is omitted, it is possible to miss the identification of some dead-ending rotameric states causing a premature termination of the elimination process. Second, we examined the effects of removing dead-ending rotameric states from further considerations at different moments of time. Two different methods of rotameric state removal were examined for an order dependence. In one case, each rotamer found to be incompatible with the global minimum energy conformation was removed immediately following its identification. In the other, dead-ending rotamers were marked for deletion but retained during the search, so that they influenced the evaluation of other rotameric states. When the search was completed, all marked rotamers were removed simultaneously. In addition, to expand further the usefulness of the FEE, a novel method is presented that allows for further reduction in the remaining set of conformations at the FEE convergence. In this method, called a tree-based search, each dead-ending pair of rotamers which does not lead to the direct removal of either rotameric state is used to reduce significantly the number of remaining conformations. In the future this method can also be expanded to triplet and quadruplet sets of rotameric states. We tested our implementation of the FEE by exhaustively searching ten protein segments and found that the FEE identified the global minimum every time. For each segment, the global minimum was exhaustively searched in two different environments: (i) the segments were extracted from the protein and exhaustively searched in the absence of the surrounding residues; (ii) the segments were exhaustively searched in the presence of the remaining residues fixed at crystal structure conformations. We also evaluated the performance of the method for accurately predicting side chain conformations. We examined the influence of factors such as type and accuracy of backbone template used, and the restrictions imposed by the choice of potential function, parameterization and rotamer database. Conclusions are drawn on these results and future prospects are given.

NASA Program Exobiology↗