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115 records · Page 7

Specialization Restricts the Evolutionary Paths Available to Yeast Sugar Transporters

Functional innovation at the protein level is a key source of evolutionary novelties. The constraints on functional innovations are likely to be highly specific in different proteins, which are shaped by their unique histories and the extent of global epistasis that arises from their structures and biochemistries. These contextual nuances in the sequence–function relationship have implications both for a basic understanding of the evolutionary process and for engineering proteins with desirable properties. Here, we have investigated the molecular basis of novel function in a model member of an ancient, conserved, and biotechnologically relevant protein family. These Major Facilitator Superfamily sugar porters are a functionally diverse group of proteins that are thought to be highly plastic and evolvable. By dissecting a recent evolutionary innovation in an α-glucoside transporter from the yeast Saccharomyces eubayanus, we show that the ability to transport a novel substrate requires high-order interactions between many protein regions and numerous specific residues proximal to the transport channel. To reconcile the functional diversity of this family with the constrained evolution of this model protein, we generated new, state-of-the-art genome annotations for 332 Saccharomycotina yeast species spanning ~400 My of evolution. By integrating phylogenetic and phenotypic analyses across these species, we show that the model yeast α-glucoside transporters likely evolved from a multifunctional ancestor and became subfunctionalized. The accumulation of additive and epistatic substitutions likely entrenched this subfunction, which made the simultaneous acquisition of multiple interacting substitutions the only reasonably accessible path to novelty.

59 BASIC BIOLOGICAL SCIENCES

General Biology 2 Sugar Beet Lab - SU2025 - Final

This module uses the Department of Energy Systems Biology Knowledgebase (KBase) platform to explore topics such as genome assembly, metagenomics, and phylogenomics. Here students will use sequences from DNA that they collected to compare the metagenomes of microbial communities from the rhizosphere of plants grown in fertilized vs. unfertilized soils. Using these data students will evaluate the impact of fertilizer on these communities and how these microbial communities influence soil health and plant growth.

59 BASIC BIOLOGICAL SCIENCES

Decoding the effects of synonymous variants

Synonymous single nucleotide variants (sSNVs) are common in the human genome but are often overlooked. However, sSNVs can have significant biological impact and may lead to disease. Existing computational methods for evaluating the effect of sSNVs suffer from the lack of gold-standard training/evaluation data and exhibit over-reliance on sequence conservation signals. We developed synVep (synonymous Variant effect predictor), a machine learning-based method that overcomes both of these limitations. Our training data was a combination of variants reported by gnomAD (observed) and those unreported, but possible in the human genome (generated). We used positive-unlabeled learning to purify the generated variant set of any likely unobservable variants. We then trained two sequential extreme gradient boosting models to identify subsets of the remaining variants putatively enriched and depleted in effect. Our method attained 90% precision/recall on a previously unseen set of variants. Furthermore, although synVep does not explicitly use conservation, its scores correlated with evolutionary distances between orthologs in cross-species variation analysis. synVep was also able to differentiate pathogenic vs. benign variants, as well as splice-site disrupting variants (SDV) vs. non-SDVs. Thus, synVep provides an important improvement in annotation of sSNVs, allowing users to focus on variants that most likely harbor effects.

Zishuo Zeng

Phenotypically anchored transcriptomics across diverse agrichemicals reveals conserved pathways and unique gene expression signatures in zebrafish

Agrichemicals such as herbicides, fungicides, insecticides, and biocides are widely used in agriculture, yet some are associated with adverse effects in humans and the environment. While many of these chemicals have been extensively studied in vitro and are included in the EPA’s ToxCast program, comprehensive in vivo comparisons using RNA sequencing across structurally diverse agrichemicals, in a single screening platform, are lacking. In this study, we examined structurally diverse agrichemicals found in the U.S. Environmental Protection Agency’s (EPA) Toxcast Phase I and II library by statically exposing early life stage zebrafish at 6 h post fertilization (hpf) until 120 hpf at concentrations ranging from 0.25 to 100 µM. Morphological outcomes were assessed at 120 hpf across 10 endpoints, including yolk sac edema, craniofacial malformations, and axis abnormalities. Chemicals that produced robust concentration-response relationships were selected for transcriptomic profiling. For transcriptomic analysis, zebrafish were statically exposed to each chemical and sampled at 48 hpf, prior to the onset of morphological effects observed at 120 hpf. Differential expression analysis identified between 0 and 4,538 differentially expressed genes (DEGs) per chemical, with no clear correlation to morphological severity. Both DEG and co-expression network analyses revealed chemical-specific expression patterns that converged on shared biological pathways, including neurodevelopment and cytoskeletal organization. Key regulatory genes such as mylpfa and krt4 were identified within co-expression modules, suggesting their potential role in conserved toxicity mechanisms. Semantic similarity analysis of enriched gene ontology (GO) terms, when compared to existing datasets, highlighted gaps in the annotation of neurodevelopmental processes, indicating that some in vivo effects may not be fully captured by current curated resources. The results provide new insights into the modes of action of diverse agrichemicals and establish a framework for understanding how agrichemical structure relates to biological function in a vertebrate model.

agrichemical

SequenceL: Automated Parallel Algorithms Derived from CSP-NT Computational Laws

With the introduction of new parallel architectures like the cell and multicore chips from IBM, Intel, AMD, and ARM, as well as the petascale processing available for highend computing, a larger number of programmers will need to write parallel codes. Adding the parallel control structure to the sequence, selection, and iterative control constructs increases the complexity of code development, which often results in increased development costs and decreased reliability. SequenceL is a high-level programming language that is, a programming language that is closer to a human s way of thinking than to a machine s. Historically, high-level languages have resulted in decreased development costs and increased reliability, at the expense of performance. In recent applications at JSC and in industry, SequenceL has demonstrated the usual advantages of high-level programming in terms of low cost and high reliability. SequenceL programs, however, have run at speeds typically comparable with, and in many cases faster than, their counterparts written in C and C++ when run on single-core processors. Moreover, SequenceL is able to generate parallel executables automatically for multicore hardware, gaining parallel speedups without any extra effort from the programmer beyond what is required to write the sequen tial/singlecore code. A SequenceL-to-C++ translator has been developed that automatically renders readable multithreaded C++ from a combination of a SequenceL program and sample data input. The SequenceL language is based on two fundamental computational laws, Consume-Simplify- Produce (CSP) and Normalize-Trans - pose (NT), which enable it to automate the creation of parallel algorithms from high-level code that has no annotations of parallelism whatsoever. In our anecdotal experience, SequenceL development has been in every case less costly than development of the same algorithm in sequential (that is, single-core, single process) C or C++, and an order of magnitude less costly than development of comparable parallel code. Moreover, SequenceL not only automatically parallelizes the code, but since it is based on CSP-NT, it is provably race free, thus eliminating the largest quality challenge the parallelized software developer faces.

Cooke, Daniel

Adaptive Distributed Environment for Procedure Training (ADEPT)

ADEPT (Adaptive Distributed Environment for Procedure Training) is designed to provide more effective, flexible, and portable training for NASA systems controllers. When creating a training scenario, an exercise author can specify a representative rationale structure using the graphical user interface, annotating the results with instructional texts where needed. The author's structure may distinguish between essential and optional parts of the rationale, and may also include "red herrings" - hypotheses that are essential to consider, until evidence and reasoning allow them to be ruled out. The system is built from pre-existing components, including Stottler Henke's SimVentive instructional simulation authoring tool and runtime. To that, a capability was added to author and exploit explicit control decision rationale representations. ADEPT uses SimVentive's Scalable Vector Graphics (SVG)- based interactive graphic display capability as the basis of the tool for quickly noting aspects of decision rationale in graph form. The ADEPT prototype is built in Java, and will run on any computer using Windows, MacOS, or Linux. No special peripheral equipment is required. The software enables a style of student/ tutor interaction focused on the reasoning behind systems control behavior that better mimics proven Socratic human tutoring behaviors for highly cognitive skills. It supports fast, easy, and convenient authoring of such tutoring behaviors, allowing specification of detailed scenario-specific, but content-sensitive, high-quality tutor hints and feedback. The system places relatively light data-entry demands on the student to enable its rationale-centered discussions, and provides a support mechanism for fostering coherence in the student/ tutor dialog by including focusing, sequencing, and utterance tuning mechanisms intended to better fit tutor hints and feedback into the ongoing context.

Domeshek, Eric

Flight Mechanics Modeling and Simulation of the Earth Entry System

Introduction: The Mars Sample Return (MSR) Campaign being planned by NASA and ESA has the ambitious goal to return Mars samples back to Earth. This international collaboration had developed a concept of operations that included a ESA-designed Earth Return Orbiter (ERO) and NASA-designed Capture, Containment, and Return System (CCRS). The Earth Entry System (EES), consisting of a protective aeroshell that houses the samples as well as sample containment vessels, would conduct entry, descent, and landing (EDL) on a direct Earth trajectory. The EES would enter on a spin-stabilized ballistic trajectory with the goal to passively achieve aerodynamic stability throughout all regions of flight. The EDL sequence would end with the EES impacting the soft playa soil of the Utah Test and Training Range (UTTR). As of the submission of this abstract, the MSR campaign is undergoing a re-architecture leading to a pause in EES development. However, the novel approaches developed in flight mechanics modeling and simulation can significantly benefit the greater IPPW community in the development of Earth return vehicles. This paper will present the latest state of EES flight mechanics modeling and simulation. The paper will highlight the simulation architecture developed and key lessons learned from understanding of EDL trajectory sensitivities. Modeling and Simulation: Figure 1 provides a high-level concept of operations for the approach, entry, descent, and landing (AEDL) phase of the CCRS-portion of MSR. The objective of EES flight mechanics is to model and simulate the EES trajectory from ERO separation to ground impact at UTTR. A variety of flight mechanics simulation models were utilized to model both exo-atmopsheric and atmospheric portions of flight. 42, a 6-DOF simulation developed at Goddard Space Flight Center, is utilized for propagating the attitude of EES during exo-atmospheric flight. 42 allows for a variety of spin eject mechanism scenarios to be simulated for analysis. 10 minutes prior to entry, the 42 states are handed off to the EDL sims. The prime EDL sim utilized by EES is the Program to Optimize Simulated Trajectories II (POST2), a 6-DOF sim developed at Langley Research Center, and the independent verification and validation EDL sim utilized is DSENDS, a 6-DOF sim developed at Jet Propulsion Laboratory. Figure 2 provides a visualization of the flight mechanics simulation model flow through various points in the AEDL phase. Due to the existence of a variety of sim models, the EES flight mechanics team developed processes for data hand-off. These processes included the development of a centralized coordinate frame document, utilization of a single, centralized simulation input document for all sims to reference, and hand-off files containing both the technical data to be ingested by other flight mechanics sims as well as annotations of modeling assumptions utilized to generate the data. Figure~\ref{fig:post2simarchitecture} provides an overview of the POST2 sim architecture wherein POST2 ingests numerous subsystem models and input files. The dispersed state file generated by MONTE provides the position/velocity state of the trajectory while the 42 Handoff file provides the attitude. The aerodynamics database, delivered by the EES aeroscience team, is utilized to simulate the aerodynamic forces and moments experienced during EDL. A custom atmosphere model, developed by EES atmosphere team, is utilized to simulate the anticipated atmosphere environment around the region of Earth through which the EES trajectory flys. These inputs and subsystem models can be varied depending on the AEDL flight mechanics scenario being simulated. Monte Carlo simulations are utilized to generate statistical AEDL performance metrics in the form of scorecards and violin plots. Furthermore, outputs from the POST2 simulation are utilized for follow-on analyses including aerothermal and landing performance. \section{Flight Mechanics Lessons Learned} Though the EES flight mechanics team uncovered a variety of lessons learned through the analysis conducted to support CCRS through preliminary design review, this paper will highlight the most important lessons. A key AEDL performance goal is to ensure the landing footprint of EES remains on the UTTR south range. A common modeling strategy used in EDL analysis is One-Variable-At-a-Time (OVAT). OVAT analysis provides insight into the key drivers that affect AEDL performance metrics. Figure 3 shows the landing ellipses for single dispersion sources as compared to the baseline aggregate of all dispersions. The figure shows that atmosphere winds alone dominate the size of the footprint ellipse (note: EES does not use a parachute unlike previous Earth-return missions and is in wind-driven free fall for ~5min). The significance of the wind led the EES flight mechanics team to pursue the development of a Custom Atmosphere Model [4], in lieu of EarthGRAM [1], built on actual radiosonde wind measurements around the UTTR-region. This decision was driven by the realism in the generated footprint ellipses and lessons-learned from Stardust [5]. These findings will be invaluable for future Earth-return missions in providing an early understanding of the key drivers affecting footprint size and modeling considerations for which to account. Another lesson learned is tied to the AEDL performance goal of achieving passive stability throughout all regions of flight. It is well understood that blunt-body aeroshells are less stable as they transition from supersonic to subsonic. Eliminating a backshell does help improvestability; however, other phenomena such as roll-induced instability during terminal descent can still arise. The EES flight mechanics team developed stability metrics as tools to better understand the causes of and better predict the onset of dynamic instability. These tools were built upon analytical models developed by Jaffe [3] and Murphy [2]. The tools were shown to both be very accurate in correlation with actual unstable cases and useful in developing stability margin policies based on the vehicle design and simulation considerations (e.g. sphere-cone angle change, mass change, wind turbulence). These tools allowed for the current EES design to demonstrate the ability to achieve passive stability and can be an invaluable tool for consideration in the design of parachute-less Earth-return vehicles.

Rohan Deshmukh