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An overview of the Mars Express/NASA Project at JPL is presented. The topics include: 1) Mars Express Mission Experiments and Investigators; 2) Mars Advanced Radar for Subsurface and Ionospheric Soundig (MARSIS) Overview; 3) MARSIS Experiment Overview; 4) Interoperability Concept; 5) Mars Express Science Operations; 6) Mars Express Schedule (2003-2007);
The objective of NASA Ames Research Centers WetLab-2 Project is to place on the ISS a system capable of conducting gene expression analysis via quantitative real-time PCR (qRT-PCR) of biological specimens sampled or cultured on orbit. The WetLab-2 system is capable of processing sample types ranging from microbial cultures to animal tissues dissected on-orbit. The project has developed a RNA preparation module that can lyse cells and extract RNA of sufficient quality and quantity for use as templates in qRT-PCR reactions. Our protocol has the advantage that it uses non-toxic chemicals, alcohols or other organics. The resulting RNA is transferred into a pipette and then dispensed into reaction tubes that contain all lyophilized reagents needed to perform qRT-PCR reactions. These reaction tubes are mounted on rotors to centrifuge the liquid to the reaction window of the tube using a cordless drill. System operations require simple and limited crew actions including syringe pushes, valve turns and pipette dispenses. The resulting process takes less than 30 min to have tubes ready for loading into the qRT-PCR unit.The project has selected a Commercial-Off-The-Shelf (COTS) qRT-PCR unit, the Cepheid SmartCycler, that will fly in its COTS configuration. The SmartCycler has a number of advantages including modular design (16 independent PCR modules), low power consumption, rapid thermal ramp times and four-color detection. The ability to detect up to four fluorescent channels will enable multiplex assays that can be used to normalize for RNA concentration and integrity, and to study multiple genes of interest in each module. The WetLab-2 system will have the capability to downlink data from the ISS to the ground after a completed run and to uplink new programs. The ability to conduct qRT-PCR on-orbit eliminates the confounding effects on gene expression of reentry stresses and shock acting on live cells and organisms or the concern of RNA degradation of fixed samples. The system can be used to validate terrestrial analyses of samples returned from ISS by providing on-orbit gene expression benchmarking prior to sample return. The ability to get on-orbit data will provide investigators with the opportunity to adjust experimental parameters in real time for subsequent trials, without the need for sample return and re-flight to sample multigenerational changes. The system can also be used for analysis of air, surface, water, and clinical samples to monitor environmental contaminants and crew health. The verification flight of the instrument is scheduled to launch on SpaceX-7 in June 2015. The WetLab-2 Project is supported by NASAs ISS Program at JSC, Code OZ.
The NASA GeneLab Sample Processing Laboratory offers high-throughput sequencing services to NASA-funded space biology researchers. Space biology studies have specific challenges such as low sample numbers, introducing susceptibility to batch effects from sample handling. These issues are compounded by complex protocols such as single-nuclei isolation and sequencing, which has recently become an attractive methodology for assessing the cellular diversity within spaceflight samples. High quality single-nuclei sequencing requires reproducible protocols to dissociate tissue and generate clean suspension of intact single nuclei. Producing single-nuclei suspension from brain tissue is particularly challenging due to cell type heterogeneity and the myelin sheath that carries over into the nuclei suspension as debris. Current procedures tend to be time consuming and sometimes include steps that can alter gene expression and create cell-type bias. Commercially available nuclei isolation kits, such as the 10X Genomics nuclei isolation kit, offers a streamlined way to process samples for nuclei isolation, thereby minimizing batch effects and enabling reproducibility. In this study, we report on the performance of the 10X Genomics nuclei isolation kit and Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit to generate sequencing libraries from space-flown mouse brain samples. Single nuclei sequencing was performed on frozen mouse brain tissue from two spaceflight missions, Rodent Research-10 (RR-10) and RR Reference Mission-2 (RRRM-2). RR-10 mice were female B6129SF2/J, euthanized at 18-19 weeks whereas RRRM-2 mice were female C57BL/6NTac, euthanized at 20 or 37 weeks. Sequencing data was processed using standard GeneLab data processing pipelines. We report evaluation of the performance of the 10X Genomics nuclei isolation kit for spaceflight samples from mouse brain, and evaluation of reproducibility across different mouse strains and age groups. We also report preliminary scientific results including cell type inference, cell clustering, and differentially expressed genes and pathways between spaceflight and ground control samples.
Small RNA sequencing (small RNAseq) is a powerful tool for studying the regulation of gene expression in various organisms. Small RNAseq has been leveraged in space biology research to study how expression of small RNAs, e.g. micro RNAs (miRNAs), small interfering RNAs (siRNAs), and piwi-interacting RNAs (piRNAs), change upon exposure to the space environment. NASA GeneLab currently hosts small RNAseq raw data derived from space-relevant experiments on the Open Science Data Repository (OSDR). To maximize the accessibility of these data to the scientific community, in addition to hosting raw data, which is only interpretable by bioinformaticians, GeneLab plans to process all small RNAseq datasets and make those processed data available to the scientific community via the OSDR. In this study, we present the development of the GeneLab standardized pipeline for processing small RNAseq datasets. Using human, plant, and synthetic small RNAseq datasets, we interrogate various open-source software and publicly available databases to evaluate their accuracy and reproducibility in each step of the pipeline. For quality control and adapter detection and trimming, we evaluated TrimGalore!, FASTX, SeqKit, and DNApi methods to optimize alignment to reference genomes. We compared BWA, Bowtie, and Bowtie2 to determine the optimal alignment tool. For each alignment tool we also assessed various reference databases, including Ensembl reference genomes and different types of small RNA reference databases, including genome, hairpin, and miRNA references from the miRbase and MirGeneDB databases. To quantify the aligned data, we compared SAMtools, HTSeq, and RSEM for counting alignment events from each alignment tool used. Finally, we evaluated various tools, including DESeq2 and EdgeR, for data normalization and subsequent differential expression analysis. We will present the results from our comparative analyses for each pipeline step and propose a consensus pipeline for processing small RNAseq data derived from various organisms exposed to the space environment.
Symbolic regression methods simultaneously determine the model functional form and the regression parameter values by generating expression trees. Symbolic regression can capture the complexity of real–world phenomena but the use of deterministic optimization for symbolic regression has been limited due to the complexity of the search space of existing formulations. Herein we present a novel deterministic mixed–integer nonlinear programming formulation for symbolic regression that incorporates derivative constraints through auxiliary expression trees. By applying the chain rule to mathematical operations, binary expression trees are capable of representing the calculation of first and second derivatives. We apply this formulation to illustrative examples using derivative information to show increased model discrimination capability. In addition, we perform a case study of a thermodynamic equation of state to gain insight on valid functional forms with thermodynamics–based constraints on the first and second derivatives.
Abstract Temperate coastal marine waters are often thermally stratified from spring through fall but can be dynamic and disrupted by tidal currents and wind‐driven upwelling. These mixing events introduce deeper, cooler water with a higher partial pressure of CO 2 (pCO2) and its associated microbial communities to the surface. Anecdotally, these events impact shellfish hatcheries and farms, warranting improved understanding of changes in composition and activity of marine microbial communities in relation to environmental processes. To characterize both compositional and functional changes associated with abiotic factors, here, we generate a reference metatranscriptome from the Strait of Georgia over representative seasons and analyze metatranscriptomic profiles of the microorganisms present within intake water containing different pCO 2 levels at a shellfish hatchery in British Columbia from June through October. Abiotic factors studied include pH, temperature, alkalinity, aragonite, calcite, and pCO 2 . Community composition changes were observed to occur at broad taxonomic levels and most notably to vary with temperature and pCO 2 . Functional gene expression profiles indicated a strong difference between early (June–July) and late summer (August–October) associated with viral activity. The taxonomic data suggest this could be due to the termination of cyanobacteria and phytoplankton blooms by viral lysis in the late season. Functional analysis indicated fewer differentially expressed transcripts associated with abiotic variables (e.g., pCO 2 ) than with the temporal effect. Microbial composition and activity in these waters vary with both short‐term effects observed alongside abiotic variation and long‐term effects observed across seasons. The analysis of both taxonomy and functional gene expression simultaneously in the same samples by environmental RNA (eRNA metatranscriptomics) provided a more comprehensive view for monitoring water bodies than either would in isolation.
Abstract BACKGROUND Type 1 diabetes is an autoimmune disease that results in the specific destruction of insulin‐producing beta cells in the pancreas. The aim of this study was to investigate the mechanism of exopolysaccharide from Leuconostoc pseudomesenteroides XG5 (XG5 EPS) against type 1 diabetes. RESULTS Long‐term drench of XG5 EPS delayed the onset of autoimmune diabetes and had fewer islets with high‐grade infiltration (an insulitis score of 3 or 4) than untreated NOD mice. Oral administration of 50 mg kg −1 d −1 XG5 EPS increased the insulin and glucagon‐like peptide‐1 (GLP‐1) levels of serum, stimulated GLP‐1 secretion and upregulated gcg mRNA expression of colon in NOD mice. Moreover, oral administration of 50 mg kg −1 d −1 XG5 EPS significantly increased total short‐chain fatty acids levels in the colon contents, especially those of acetic acid and butyric acid. In NCI‐H716 cells, 500 and 1000 μmol L −1 sodium butyrate promoted the secretion of GLP‐1 and upregulated the mRNA expression of gcg and PC3 , while XG5 EPS and sodium acetate did not stimulate the GLP‐1 secretion. Therefore, long‐term drench of XG5 EPS delayed the onset of autoimmune diabetes, which may be directly correlated with the increase of butyrate in the colon of NOD mice. CONCLUSION Long‐term drench of 50 mg kg −1 d −1 XG5 EPS promoted the expression and secretion of GLP‐1 by increasing the production of butyric acid, thereby delaying T1D onset in NOD mice. © 2021 Society of Chemical Industry.
H 2 O formation during thermal decomposition of isopropanol was measured behind reflected shock waves at temperatures ranging from 1127 to 1621 K at an average pressure of 1.42 atm using a laser absorption technique. Of the five modern chemical kinetics models used to compare the H 2 O time histories, the model from Li et al (Combust. Flame 2019;207:171-185) showed the best overall agreement. Sensitivity and rate of production analyses using the Li et al model (as well as those from AramcoMech 3.0, CRECK, and Togbe et al (Energy Fuel. 2011;25:676-683)) showed unimolecular dehydration of isopropanol, iC 3 H 7 OH ⇌ H 2 O + C 3 H 6 (R1), is nearly the sole reaction controlling H2O production at early times, allowing for an a priori measurement of the forward rate constant k 1 . The Arrhenius expression k1 (s –1 ) = 2.60 × 10 13 exp(-31 120 K/T) was determined to represent best the data from this study. According to the models and previous experimental investigations, the pressure investigated is well within the high-pressure limit (HPL) for this reaction. Additional, higher-pressure experiments also confirmed the HPL assumption. An uncertainty analysis was performed by varying secondary reactions within their uncertainties and examining their effect on the overall prediction, establishing an uncertainty within ±20% for all but the highest temperature cases, which have a maximum uncertainty of ±40%. Experiments conducted with a radical trapper, toluene, showed little influence from radical chemistry, suggesting this estimated uncertainty is fairly conservative. Experimental data from Heyne et al (Z Phys Chem. 2015;229:881-907) were found to be in good agreement with the rate measurements from this study and, therefore, a second Arrhenius expression, k 1 (s –1 ) = 2.11 × 10 13 exp(-30 820 K/T), was found to represent both datasets well. This second expression has a larger temperature range of 976-1621 K. Here the present study provides the first high-temperature data collected for this reaction, adding to the limited data available for isopropanol in the literature.
Here, there is a considerable body of work that describes the scaling of diblock copolymer micelle dimensions in dilute and semi-dilute solution based upon block degrees of polymerization and copolymer concentration. However, there is a lack of analogous information for semi-dilute ABA triblock copolymer gels, which consist of ABA triblock copolymer dissolved in midblock-selective (B-selective) solvent. The present study uses small angle X-ray scattering to extract micelle dimensions for numerous triblock copolymer gels that vary in copolymer identity (and hence block lengths) and copolymer concentration, as well as gels that contain various ratios of two unique triblock copolymers. Analysis of micelle structural data subsequently translates to universal scaling expressions for the micelle core radius – r A ≈ N A 0.53 N B -0.14 $\phi$ ABA 0.16 where N A and N B are the endblock and midblock degrees of polymerization, respectively, and $\phi$ ABA is the volume fraction of triblock copolymer in the gel – and for the intermicelle spacing – l AA ≈ N A 0.09 N B 0.29 $\phi$ ABA -0.35 . Each scaling expression describes the full collection of experimental data very well. Additionally, these scaling expressions are partially in line with expectations from semi-dilute diblock copolymer solution theory.
Abstract In Populus and many other tree species, photoassimilate sucrose diffuses down a concentration gradient via symplastically connected mesophyll cells to minor vein phloem for long‐distance transport. There is no evidence for apoplastic phloem‐loading in Populus . However, plasma membrane sucrose transporters (SUT1 and SUT3) orthologous to those associated with apoplastic phloem loading are expressed in vascular tissues of poplar. While SUT3 functions in sucrose import into developing xylem, the role of SUT1 remains unclear. Here, we overexpressed PtaSUT1 in Populus tremula x P. alba to examine the effects on sucrose partitioning in transgenic plants. Overall leaf sucrose levels were similar between wild type and transgenic lines. Stem sucrose levels were not changed in bark but were significantly reduced in the adjacent xylem, suggesting hindered intercellular sucrose trafficking from the phloem to the developing xylem. Fully expanded leaves of transgenic plants deteriorated prematurely with declining photosynthesis prior to severe necrotic spotting. Necrotic spotting advanced most rapidly in the distal portion of mature leaves and was accompanied by sharp hexose increases and sharp sucrose decreases there. Leaf transcriptome profiling and network inference revealed the down‐regulation of copper proteins and elevated expression of copper microRNAs prior to noticeable leaf injury. Our results suggest ectopic expression of PtaSUT1 altered sucrose partitioning in stems with systemic effects on leaf health and copper homeostasis mediated in part by sucrose‐sensitive copper miRNAs.
Abstract Background Bursaphelenchus xylophilus is one of the most destructive invasive species, causing extensive economic losses worldwide. The sex ratio of female to male of B. xylophilus plays an important role in the nematode infestation. However, little is known about the processes of its sex determination. The double sex/mab‐3‐related family of transcription factors are highly conserved in animals, playing crucial roles in sex determination, spermatogenesis and ontogenesis. We therefore investigated its orthologue, Bxy‐mab‐3 , in B. xylophilus . Results Bxy‐mab‐3 has two typical conserved DNA‐binding domains. It was observed in J2 (the second‐stage of juveniles), J3, J4 and male adults (specifically on the spicules), but not in eggs or female adults via mRNA in situ hybridization. RNA‐Seq indicated significantly higher expression in males. RNAi showed that the body size and sperm size of male adults were markedly smaller than those of the controls. Meanwhile, almost all the RNAi‐treated males failed to mate with the normal females, even 26.34% of interfered males did not produce sperm. However, RNAi of Bxy‐mab‐3 had no effect on the sex ratio of B. xylophilus . Conclusion Bxy‐mab‐3 is indispensable for spermatogenesis, ontogenesis and mating behavior. It is a typical sex‐determination gene with differential expression in males and females. However, knocking down Bxy‐mab‐3 expression could not alter the sex ratio as seen in other species. Our findings contribute towards a better understanding of the molecular events of Bxy‐mab‐3 in B. xylophilus , which provides promising hints for control of pine wilt disease by blocking ontogenesis and decreasing nematode fecundity.
Abstract Plant biotechnology is rife with new advances in transformation and genome engineering techniques. A common requirement for delivery and coordinated expression in plant cells, however, places the design and assembly of transformation constructs at a crucial juncture as desired reagent suites grow more complex. Modular cloning principles have simplified some aspects of vector design, yet many important components remain unavailable or poorly adapted for rapid implementation in biotechnology research. Here, we describe a universal Golden Gate cloning toolkit for vector construction. The toolkit chassis is compatible with the widely accepted Phytobrick standard for genetic parts, and supports assembly of arbitrarily complex T‐DNAs through improved capacity, positional flexibility, and extensibility in comparison to extant kits. We also provision a substantial library of newly adapted Phytobricks, including regulatory elements for monocot and dicot gene expression, and coding sequences for genes of interest such as reporters, developmental regulators, and site‐specific recombinases. Finally, we use a series of dual‐luciferase assays to measure contributions to expression from promoters, terminators, and from cross‐cassette interactions attributable to enhancer elements in certain promoters. Taken together, these publicly available cloning resources can greatly accelerate the testing and deployment of new tools for plant engineering.
We present the leading-color two-loop QCD corrections for the scattering of four partons and a W boson, including its leptonic decay. The amplitudes are assembled from the planar two-loop helicity amplitudes for four partons and a vector boson decaying to a lepton pair, which are also used to determine the planar two-loop amplitudes for four partons and a $Z/γ^\ast$ boson with a leptonic decay. The analytic expressions are obtained by setting up a dedicated Ansatz and constraining the free parameters from numerical samples obtained within the framework of numerical unitarity. The large linear systems that must be solved to determine the analytic expressions are constructed to be in Vandermonde form. Such systems can be very efficiently solved, bypassing the bottleneck of Gaussian elimination. Our results are expressed in a basis of one-mass pentagon functions, which opens the possibility of their efficient numerical evaluation.
Open string amplitudes at tree level have been studied for over fifty years. However, there is no known analytic form for general n-point amplitudes, and their conventional representation in terms of worldsheet integrals does not make many of their most basic physical properties manifest. Recently, a formulation of these amplitudes exposing the underlying “binary geometry” via the use of “u” variables has given us many insights into their basic features. In this paper, we initiate a systematic exploration of fundamental aspects of open string amplitudes from this new point of view. We begin by finding explicit expressions for the factorization of amplitudes at general massive levels, which are seen to be determined by products of lower-point massless amplitudes with shifted kinematics. We then study the asymptotic behavior when subsets of kinematic variables become large, delineating regimes with exponential (generalized hard scattering) and power-law (generalized Regge) behavior. We also give precise expressions for the asymptotics, which reveal another example of the recently observed property of factorization away from poles. We derive new recursion relations for the amplitude, which when repeatedly applied reduce to infinite series representations with a wider domain of convergence than the usual integral representations. For the five-point case, we present a new closed-form expression for the amplitude that for the first time gives its analytic continuation to all of kinematic space. We also discuss novel relations between amplitudes at different kinematic points following from the recently observed “split” factorizations.
We derive the first-ever small-x expression for the inclusive gluon production cross section in the central rapidity region of the longitudinally polarized proton-proton collisions. The cross section depends on the polarizations of both protons, therefore comprising the numerator of the longitudinal double-spin asymmetry ALL for the produced gluons. The cross section is calculated in the shock wave formalism and is expressed in terms of the polarized dipole scattering amplitudes on the projectile and target protons. We show that the small-x evolution corrections are included into our cross section expression if one evolves these polarized dipole amplitudes using the double-logarithmic helicity evolution derived in [1–4]. Our calculation is performed for the gluon sector only, with the quark contribution left for future work. When that work is complete, the resulting formula will be applicable to longitudinally polarized proton-proton and proton-nucleus collisions, as well as to polarized semi-inclusive deep inelastic scattering (SIDIS) on a proton or a nucleus. Our results should allow one to extend the small-x helicity phenomenology analysis of [5] to the jet/hadron production data reported for the longitudinally polarized proton-proton collisions at RHIC and to polarized SIDIS measurements at central rapidities to be performed at the EIC.
In this paper, we present a framework for the analytic bootstrap of three-point energy correlators, a crucial observable in $\mathcal{N}$ = 4 super Yang-Mills theory and quantum chromodynamics (QCD). Our approach combines spherical contour techniques, general physical constraints such as pole cancellations, and power correction data in the singular limits to determine its analytic expression. In contrast to previous bootstrap studies restricted to scattering amplitudes for supersymmetric theories, our framework makes use of the properties of Feynman integrals, marking a significant step toward bootstrapping realistic QCD observables. Using this method, we derive analytic expressions for leading-order three-point energy correlators in the multi-collinear limit with equal and unequal energy weights, where the latter are crucial ingredients for projected N -point energy correlators. We also apply the recently developed technique of analytic regression with lattice reduction as a way to bypass needing explicit expressions for the singular limits. Bridging theoretical advances in scattering amplitudes with the renewed interest in weighted cross-sections, our work opens the door to precision tests of QCD dynamics through analytic event-shape predictions.
Wild-type strains of Aspergillus oryzae develop yellow, yellow-green, green, or brown conidia. Previous reports suggested that the conidiation initiates with the biosynthesis of a yellow pigment YWA1 from acetyl-CoA by a polyketide synthase encoded by wA (AO090102000545). This is followed by the conversion to other pigment by a laccase encoded by yA (AO090011000755). Based on orthologous pathways in other aspergilli, it is reasonable to hypothesize that in addition to yA, AO090102000546 encoding laccase and AO090005000332 encoding Ayg1-like hydrolase play a role in A. oryzae conidial pigment biosynthesis. However, the involvement of these two genes in conidial pigmentation remains unclear. In this study, we tested this hypothesis by assessing the conidial colors of both disruption and overexpression mutants to verify whether AO090102000546 and AO090005000332 were associated with the conidial pigmentation. Here, observation of single, double, and triple disruptants of these three genes suggested that conidial pigments were synthesized by two laccase genes, AO090011000755 and AO090102000546, whereas Ayg1-like hydrolase gene AO090005000332 was proven to have no obvious association with the synthesis. This was corroborated by observing the phenotype of each overexpression mutant. Interestingly, AO090005000332 overexpression mutant produced smoky yellow-green conidia, different from the wild-type strain. Thus, the AO090005000332-encoded protein is likely to maintain the enzymatic activity. However, the expression level was observed to be one-third of that of AO090102000546 and one-seventh of that of AO090011000755. Consequently, apparent lack of obvious contribution of AO090005000332 to conidial pigmentation could be attributed to its low expression level. Expression analysis indicated similar profiles in several wild-type strains.
Abstract ISG15, an interferon-stimulated ubiquitin-like protein, plays a multifaceted role in tumorigenesis and immune regulation. This study comprehensively evaluates ISG15 as a prognostic biomarker and predictor of immunotherapy response through pan-cancer bioinformatics analysis and experimental validation. By integrating multiomics data from TCGA, GEO, and clinical cohorts, we found that ISG15 is significantly overexpressed in multiple cancers and generally correlates with poor prognosis. Elevated ISG15 expression is associated with increased immune checkpoint gene expression, particularly PD-L1, and immune infiltration, notably M2-like tumor-associated macrophages. Immunohistochemistry and multiplexed immunofluorescence confirmed a strong positive correlation between ISG15, PD-L1, and M2-TAM infiltration in lung and gastric cancer samples. Functional analysis at the single-cell level revealed significant associations between ISG15 and tumor proliferation, angiogenesis, and immune suppression. Immunotherapy cohort analysis demonstrated that tumors with high ISG15 expression responded favorably to PD-L1 inhibitors but exhibited resistance to CTLA-4 blockade, findings further validated in lung cancer patients receiving anti-PD-1 therapy. These results suggest that ISG15 is a promising biomarker for prognosis and immunotherapy response prediction across cancers. Its integration into clinical decision-making may enhance personalized treatment strategies, improve immunotherapy outcomes, and provide new insights into the tumor immune microenvironment, cancer progression, and potential therapeutic targets for future drug development.