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Sinha, Saurabh

Publications and source records attributed to Sinha, Saurabh.

9 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

A transcriptomic atlas of acute stress response to low pH in multiple Issatchenkia orientalis strains

Because of its natural stress tolerance to low pH, Issatchenkia orientalis (a.k.a. Pichia kudriavzevii) is a promising non-model yeast for bio-based production of organic acids. Yet, this organism is relatively unstudied, and specific mechanisms of its tolerance to low pH are poorly understood, limiting commercial use. In this study, we selected 12 I. orientalis strains with varying acid stress tolerance (six tolerant and six susceptible) and profiled their transcriptomes in different pH conditions to study potential mechanisms of pH tolerance in this species. We identified hundreds of genes whose expression response is shared by tolerant strains but not by susceptible strains, or vice versa, as well as genes whose responses are reversed between tolerant and susceptible strains. We mapped regulatory mechanisms of transcriptomic responses via motif analysis as well as differential network reconstruction, identifying several transcription factors, including Stb5, Mac1, and Rtg1/Rtg3, some of which are known for their roles in acid response in Saccharomyces cerevisiae. Functional genomics analysis of short-listed genes and transcription factors suggested significant roles for energy metabolism and translation-related processes, as well as the cell wall integrity pathway and RTG-dependent retrograde signaling pathway. Finally, we conducted additional experiments for two organic acids, 3-hydroxypropionate and citramalate, to eliminate acid-specific effects and found potential roles for glycolysis and trehalose biosynthesis specifically for response to low pH. In summary, our approach of comparative transcriptomics and phenotypic contrasting, along with a multi-pronged bioinformatics analysis, suggests specific mechanisms of tolerance to low pH in I. orientalis that merit further validation through experimental perturbation and engineering.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Data for A Transcriptomic Atlas of Acute Stress Response to Low pH in Multiple Issatchenkia orientalis Strains

Because of its natural stress tolerance to low pH, Issatchenkia orientalis (a.k.a. Pichia kudriavzevii ) is a promising non-model yeast for bio-based production of organic acids. Yet, this organism is relatively unstudied, and specific mechanisms of its tolerance to low pH are poorly understood, limiting commercial use. In this study, we selected 12 I. orientalis strains with varying acid stress tolerance (six tolerant and six susceptible) and profiled their transcriptomes in different pH conditions to study potential mechanisms of pH tolerance in this species. We identified hundreds of genes whose expression response is shared by tolerant strains but not by susceptible strains, or vice versa, as well as genes whose responses are reversed between tolerant and susceptible strains. We mapped regulatory mechanisms of transcriptomic responses via motif analysis as well as differential network reconstruction, identifying several transcription factors, including Stb5, Mac1, and Rtg1/Rtg3, some of which are known for their roles in acid response in Saccharomyces cerevisiae . Functional genomics analysis of short-listed genes and transcription factors suggested significant roles for energy metabolism and translation-related processes, as well as the cell wall integrity pathway and RTG-dependent retrograde signaling pathway. Finally, we conducted additional experiments for two organic acids, 3-hydroxypropionate and citramalate, to eliminate acid-specific effects and found potential roles for glycolysis and trehalose biosynthesis specifically for response to low pH. In summary, our approach of comparative transcriptomics and phenotypic contrasting, along with a multi-pronged bioinformatics analysis, suggests specific mechanisms of tolerance to low pH in I. orientalis that merit further validation through experimental perturbation and engineering.

Conversion↗
DOE OSTI2021

Deciphering enhancer sequence using thermodynamics-based models and convolutional neural networks

Abstract Deciphering the sequence-function relationship encoded in enhancers holds the key to interpreting non-coding variants and understanding mechanisms of transcriptomic variation. Several quantitative models exist for predicting enhancer function and underlying mechanisms; however, there has been no systematic comparison of these models characterizing their relative strengths and shortcomings. Here, we interrogated a rich data set of neuroectodermal enhancers in Drosophila, representing cis- and trans- sources of expression variation, with a suite of biophysical and machine learning models. We performed rigorous comparisons of thermodynamics-based models implementing different mechanisms of activation, repression and cooperativity. Moreover, we developed a convolutional neural network (CNN) model, called CoNSEPT, that learns enhancer ‘grammar’ in an unbiased manner. CoNSEPT is the first general-purpose CNN tool for predicting enhancer function in varying conditions, such as different cell types and experimental conditions, and we show that such complex models can suggest interpretable mechanisms. We found model-based evidence for mechanisms previously established for the studied system, including cooperative activation and short-range repression. The data also favored one hypothesized activation mechanism over another and suggested an intriguing role for a direct, distance-independent repression mechanism. Our modeling shows that while fundamentally different models can yield similar fits to data, they vary in their utility for mechanistic inference. CoNSEPT is freely available at: https://github.com/PayamDiba/CoNSEPT.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

PayamDiba/Manuscript_tools

CoNSEPT is a tool to predict gene expression in various cis and trans contexts. Inputs to CoNSEPT are enhancer sequence, transcription factor levels in one or many trans conditions, TF motifs (PWMs), and any prior knowledge of TF-TF interactions.

Dibaeinia, Payam↗
DOE OSTI2021

PayamDiba/CoNSEPT

Deciphering the sequence-function relationship encoded in enhancers holds the key to interpreting non-coding variants and understanding mechanisms of transcriptomic variation. Several quantitative models exist for predicting enhancer function and underlying mechanisms; however, there has been no systematic comparison of these models characterizing their relative strengths and shortcomings. Here, we interrogated a rich data set of neuroectodermal enhancers in Drosophila, representing cis- and trans- sources of expression variation, with a suite of biophysical and machine learning models. We performed rigorous comparisons of thermodynamics-based models implementing different mechanisms of activation, repression and cooperativity. Moreover, we developed a convolutional neural network (CNN) model, called CoNSEPT, that learns enhancer ‘grammar’ in an unbiased manner. CoNSEPT is the first general-purpose CNN tool for predicting enhancer function in varying conditions, such as different cell types and experimental conditions, and we show that such complex models can suggest interpretable mechanisms. We found model-based evidence for mechanisms previously established for the studied system, including cooperative activation and short-range repression. The data also favored one hypothesized activation mechanism over another and suggested an intriguing role for a direct, distance-independent repression mechanism. Our modeling shows that while fundamentally different models can yield similar fits to data, they vary in their utility for mechanistic inference.

Dibaeinia, Payam↗
DOE OSTI2021

PreMevE Update: Forecasting Ultra-Relativistic Electrons Inside Earth's Outer Radiation Belt

Energetic electrons inside Earth's Van Allen belts pose a major radiation threat to spaceborne electronics that often play vital roles in modern society. Ultra-relativistic electrons with energies greater than or equal to two megaelectron-volt (MeV) are of particular interest, and thus forecasting these ≥2 MeV electrons has a significant meaning to all space sectors. Here, we update the latest development of the predictive model for MeV electrons in the outer radiation belt. The new version, called PREdictive MEV Electron (PreMevE)-2E, forecasts ultra-relativistic electron flux distributions across the outer belt, with no need for in situ measurements of the trapped MeV electron population except at the geosynchronous orbit (GEO). Model inputs include precipitating electrons observed in low-Earthorbits by NOAA satellites, upstream solar wind speeds and densities from solar wind monitors, as well as ultra-relativistic electrons measured by one Los Alamos GEO satellite. We evaluated 32 supervised machine learning models that fall into four different classes of linear and neural network architectures, and successfully tested ensemble forecasting by using groups of top-performing models. All models are individually trained, validated, and tested by in situ electron data from NASA's Van Allen Probes mission. It is shown that the final ensemble model outperforms individual models at most L-shells, and this PreMevE-2E model can provide 25-h (~1-day) and 50-h (~2-day) forecasts with high mean performance efficiency and correlation values. Our results also suggest that this new model is dominated by nonlinear components at L-shells <~4 for ultra-relativistic electrons, different from the dominance of linear components for 1 MeV electrons as previously discovered.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Normal or abnormal? Machine learning for the leakage detection in carbon sequestration projects using pressure field data

The international commitments for atmospheric carbon reduction will require a rapid increase in carbon capture and storage (CCS) projects. The key to any successful CCS project lies in the long term storage and prevention of leakage of stored carbon dioxide (CO 2 ). In addition to being a greenhouse gas, CO 2 leaks reaching the surface can accumulate in low-lying areas resulting in a serious health risk. Among several alternatives, some of the more promising CCS storage formations are depleted oil and gas reservoirs, where the reservoirs had good geological seals prior to hydrocarbon extraction. With more CCS wells coming online, it is imperative to implement permanent, automated monitoring tools. We apply machine learning models to automate the leakage detection process in carbon storage reservoirs using rates of (CO 2 ) injection and pressure data measured by simple harmonic pulse testing (HPT). To validate the feasibility of this machine learning based workflow, we use data from HPT experiments carried out in the Cranfield oil field, Mississippi, USA. The data consist of a series of pulse tests conducted with baseline parameters and with an artificially introduced leak. Here, in this study, we pose the leakage detection task as an anomaly detection problem where deviation from the predicted behavior indicates leaks in the reservoir. Results show that different machine learning architectures such as multi-layer feed forward network, Long Short-Term Memory, and convolutional neural network are able to identify leakages and can provide early warning. These warnings can then be used to take remedial measures.

58 GEOSCIENCES↗