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  1. Article ; Online: Current advancements in B-cell receptor sequencing fast-track the development of synthetic antibodies.

    Gallo, Eugenio

    Molecular biology reports

    2024  Volume 51, Issue 1, Page(s) 134

    Abstract: Synthetic antibodies (Abs) are a class of engineered proteins designed to mimic the functions of natural Abs. These are produced entirely in vitro, eliminating the need for an immune response. As such, synthetic Abs have transformed the traditional ... ...

    Abstract Synthetic antibodies (Abs) are a class of engineered proteins designed to mimic the functions of natural Abs. These are produced entirely in vitro, eliminating the need for an immune response. As such, synthetic Abs have transformed the traditional methods of raising Abs. Likewise, deep sequencing technologies have revolutionized genomics and molecular biology. These enable the rapid and cost-effective sequencing of DNA and RNA molecules. They have allowed for accurate and inexpensive analysis of entire genomes and transcriptomes. Notably, via deep sequencing it is now possible to sequence a person's entire B-cell receptor immune repertoire, termed BCR sequencing. This procedure allows for big data explorations of natural Abs associated with an immune response. Importantly, the identified sequences have the ability to improve the design and engineering of synthetic Abs by offering an initial sequence framework for downstream optimizations. Additionally, machine learning algorithms can be introduced to leverage the vast amount of BCR sequencing datasets to rapidly identify patterns hidden in big data to effectively make in silico predictions of antigen selective synthetic Abs. Thus, the convergence of BCR sequencing, machine learning, and synthetic Ab development has effectively promoted a new era in Ab therapeutics. The combination of these technologies is driving rapid advances in precision medicine, diagnostics, and personalized treatments.
    MeSH term(s) Humans ; Receptors, Antigen, B-Cell/genetics ; Antibodies/genetics ; Algorithms ; Big Data ; Genomics
    Chemical Substances Receptors, Antigen, B-Cell ; Antibodies
    Language English
    Publishing date 2024-01-18
    Publishing country Netherlands
    Document type Journal Article ; Review
    ZDB-ID 186544-4
    ISSN 1573-4978 ; 0301-4851
    ISSN (online) 1573-4978
    ISSN 0301-4851
    DOI 10.1007/s11033-023-08941-0
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Revolutionizing Synthetic Antibody Design: Harnessing Artificial Intelligence and Deep Sequencing Big Data for Unprecedented Advances.

    Gallo, Eugenio

    Molecular biotechnology

    2024  

    Abstract: Synthetic antibodies (Abs) represent a category of engineered proteins meticulously crafted to replicate the functions of their natural counterparts. Such Abs are generated in vitro, enabling advanced molecular alterations associated with antigen ... ...

    Abstract Synthetic antibodies (Abs) represent a category of engineered proteins meticulously crafted to replicate the functions of their natural counterparts. Such Abs are generated in vitro, enabling advanced molecular alterations associated with antigen recognition, paratope site engineering, and biochemical refinements. In a parallel realm, deep sequencing has brought about a paradigm shift in molecular biology. It facilitates the prompt and cost-effective high-throughput sequencing of DNA and RNA molecules, enabling the comprehensive big data analysis of Ab transcriptomes, including specific regions of interest. Significantly, the integration of artificial intelligence (AI), based on machine- and deep- learning approaches, has fundamentally transformed our capacity to discern patterns hidden within deep sequencing big data, including distinctive Ab features and protein folding free energy landscapes. Ultimately, current AI advances can generate approximations of the most stable Ab structural configurations, enabling the prediction of de novo synthetic Abs. As a result, this manuscript comprehensively examines the latest and relevant literature concerning the intersection of deep sequencing big data and AI methodologies for the design and development of synthetic Abs. Together, these advancements have accelerated the exploration of antibody repertoires, contributing to the refinement of synthetic Ab engineering and optimizations, and facilitating advancements in the lead identification process.
    Language English
    Publishing date 2024-02-03
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 1193057-3
    ISSN 1559-0305 ; 1073-6085
    ISSN (online) 1559-0305
    ISSN 1073-6085
    DOI 10.1007/s12033-024-01064-2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: The rise of big data: deep sequencing-driven computational methods are transforming the landscape of synthetic antibody design.

    Gallo, Eugenio

    Journal of biomedical science

    2024  Volume 31, Issue 1, Page(s) 29

    Abstract: Synthetic antibodies (Abs) represent a category of artificial proteins capable of closely emulating the functions of natural Abs. Their in vitro production eliminates the need for an immunological response, streamlining the process of Ab discovery, ... ...

    Abstract Synthetic antibodies (Abs) represent a category of artificial proteins capable of closely emulating the functions of natural Abs. Their in vitro production eliminates the need for an immunological response, streamlining the process of Ab discovery, engineering, and development. These artificially engineered Abs offer novel approaches to antigen recognition, paratope site manipulation, and biochemical/biophysical enhancements. As a result, synthetic Abs are fundamentally reshaping conventional methods of Ab production. This mirrors the revolution observed in molecular biology and genomics as a result of deep sequencing, which allows for the swift and cost-effective sequencing of DNA and RNA molecules at scale. Within this framework, deep sequencing has enabled the exploration of whole genomes and transcriptomes, including particular gene segments of interest. Notably, the fusion of synthetic Ab discovery with advanced deep sequencing technologies is redefining the current approaches to Ab design and development. Such combination offers opportunity to exhaustively explore Ab repertoires, fast-tracking the Ab discovery process, and enhancing synthetic Ab engineering. Moreover, advanced computational algorithms have the capacity to effectively mine big data, helping to identify Ab sequence patterns/features hidden within deep sequencing Ab datasets. In this context, these methods can be utilized to predict novel sequence features thereby enabling the successful generation of de novo Ab molecules. Hence, the merging of synthetic Ab design, deep sequencing technologies, and advanced computational models heralds a new chapter in Ab discovery, broadening our comprehension of immunology and streamlining the advancement of biological therapeutics.
    MeSH term(s) Genomics ; Binding Sites, Antibody ; High-Throughput Nucleotide Sequencing
    Language English
    Publishing date 2024-03-16
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 1193378-1
    ISSN 1423-0127 ; 1021-7770
    ISSN (online) 1423-0127
    ISSN 1021-7770
    DOI 10.1186/s12929-024-01018-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Book ; Online: Stochastic High Fidelity Autonomous Fixed Wing Aircraft Flight Simulator

    Gallo, Eduardo

    2023  

    Abstract: This document describes the architecture and algorithms of a high fidelity fixed wing flight simulator intended to test and validate novel guidance, navigation, and control (GNC) algorithms for autonomous aircraft. It aims to replicate the influence of ... ...

    Abstract This document describes the architecture and algorithms of a high fidelity fixed wing flight simulator intended to test and validate novel guidance, navigation, and control (GNC) algorithms for autonomous aircraft. It aims to replicate the influence of as many factors as possible on the aircraft performances, the Earth model, the physics of flight and the associated equations of motion, and in particular the behavior of the onboard sensors, limiting the assumptions to the bare minimum, and including multiple relatively minor effects not usually considered in simulation that may play a role in the GNC algorithms not performing as intended. The author releases the flight simulator C ++ implementation as open-source software. The simulator modular design enables the replacement of the standard GNC algorithms with the objective of evaluating their performances when subject to specific missions and meteorological conditions (atmospheric properties, wind field, air turbulence). The testing and evaluation is performed by means of Monte Carlo simulations, as most simulation modules (such as the aircraft mission, the meteorological conditions, the errors introduced by the sensors, and the initial conditions) are defined stochastically and hence vary in a pseudo-random way from one execution to the next according to certain user-defined input parameters, ensuring that the results are valid for a wide range of conditions. In addition to modeling the outputs of all sensors usually present onboard a fixed wing platform, such as accelerometers, gyroscopes, magnetometers, Pitot tube, air vanes, and a Global Navigation Satellite System (GNCC) receiver, the simulator is also capable of generating realistic images of the Earth surface that resemble what an onboard camera would record if following the resulting trajectory, enabling the use and evaluation of visual and visual inertial navigation systems.

    Comment: 135 pages, 49 figures
    Keywords Computer Science - Robotics
    Subject code 629
    Publishing date 2023-05-03
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Book ; Online: The SO(3) and SE(3) Lie Algebras of Rigid Body Rotations and Motions and their Application to Discrete Integration, Gradient Descent Optimization, and State Estimation

    Gallo, Eduardo

    2022  

    Abstract: Classical mathematical techniques such as discrete integration, gradient descent optimization, and state estimation (exemplified by the Runge-Kutta method, Gauss-Newton minimization, and extended Kalman filter or EKF, respectively), rely on linear ... ...

    Abstract Classical mathematical techniques such as discrete integration, gradient descent optimization, and state estimation (exemplified by the Runge-Kutta method, Gauss-Newton minimization, and extended Kalman filter or EKF, respectively), rely on linear algebra and hence are only applicable to state vectors belonging to Euclidean spaces when implemented as described in the literature. This document discusses how to modify these methods so they can be applied to non-Euclidean state vectors, such as those containing rotations and full motions of rigid bodies. To do so, this document provides an in-depth review of the concept of manifolds or Lie groups, together with their tangent spaces or Lie algebras, their exponential and logarithmic maps, the analysis of perturbations, the treatment of uncertainty and covariance, and in particular the definitions of the Jacobians required to employ the previously mentioned calculus methods. These concepts are particularized to the specific cases of the SO(3) and SE(3) Lie groups, known as the special orthogonal and special Euclidean groups of R3, which represent the rigid body rotations and motions, describing their various possible parameterizations as well as their advantages and disadvantages.

    Comment: 82 pages
    Keywords Computer Science - Robotics
    Subject code 512
    Publishing date 2022-05-25
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: High-Throughput Generation of In Silico Derived Synthetic Antibodies via One-step Enzymatic DNA Assembly of Fragments.

    Gallo, Eugenio

    Molecular biotechnology

    2020  Volume 62, Issue 2, Page(s) 142–150

    Abstract: Phage-display technology offers robust methods for isolating antibody (Ab) molecules with specificity for different target antigens. Recent advancements couple Ab selections with in silico strategies, such as predictive computational models or next- ... ...

    Abstract Phage-display technology offers robust methods for isolating antibody (Ab) molecules with specificity for different target antigens. Recent advancements couple Ab selections with in silico strategies, such as predictive computational models or next-generation sequencing metadata analysis of Ab selections. These advancements result in enhanced Ab clonal diversities with potential for enlarged epitope coverage of the target antigen. A current limitation however, is that de novo Ab sequences must undergo DNA gene synthesis, and subsequent expression as Ab proteins for downstream validations. Due to the high costs and time for commercially generating large sets of DNA genes, we report a high-throughput platform for the synthesis of in silico derived Ab clones. As a proof of concept we demonstrate the simultaneous synthesis of 96 unique Abs with varied lengths and complementary determining region compositions. Each of the 96 Ab clones undergoes a one-step enzymatic assembly of distinct DNA fragments that combine into a circularized Fab expression plasmid. This strategy allows for the rapid and efficient synthesis of 96 DNA constructs in a 3 day window, and exhibits high percentage fidelity-greater than 93%. Accordingly, the synthesis of Ab DNA constructs as Fab expression plasmids allow for rapid execution of downstream Ab protein validations, with potential for implementation into high-throughput Ab protein characterization pipelines. Altogether, the platform presented here proves rapid and also cost-effective, which is important for labs with limited resources, since it utilizes standard laboratory equipment and molecular reagents.
    MeSH term(s) Antibodies/chemistry ; Antibodies/genetics ; Antibodies/metabolism ; Cell Surface Display Techniques/methods ; Computer Simulation ; DNA Ligases/metabolism ; DNA-Directed DNA Polymerase/metabolism ; Exonucleases/metabolism ; Gene Expression ; High-Throughput Nucleotide Sequencing ; High-Throughput Screening Assays ; Immunoglobulin Fab Fragments/genetics ; Immunoglobulin Fab Fragments/metabolism ; Plasmids/genetics ; Single-Domain Antibodies/genetics ; Single-Domain Antibodies/metabolism
    Chemical Substances Antibodies ; Immunoglobulin Fab Fragments ; Single-Domain Antibodies ; DNA-Directed DNA Polymerase (EC 2.7.7.7) ; Exonucleases (EC 3.1.-) ; DNA Ligases (EC 6.5.1.-)
    Language English
    Publishing date 2020-01-14
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1193057-3
    ISSN 1559-0305 ; 1073-6085
    ISSN (online) 1559-0305
    ISSN 1073-6085
    DOI 10.1007/s12033-019-00232-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: A High-Throughput Platform for the Generation of Synthetic Ab Clones by Single-Strand Site-Directed Mutagenesis.

    Gallo, Eugenio

    Molecular biotechnology

    2019  Volume 61, Issue 6, Page(s) 410–420

    Abstract: Current developments in meta-data analysis and predictive computational models offer alternative routes for the identification of antibodies. In silico-based technologies and NGS data analysis from Ab phage-display selections offer expanded selections of ...

    Abstract Current developments in meta-data analysis and predictive computational models offer alternative routes for the identification of antibodies. In silico-based technologies and NGS data analysis from Ab phage-display selections offer expanded selections of Ab candidates. Accordingly, the identified de novo Abs with predicted selectivity for a target antigen must undergo rapid gene synthesis for downstream Ab characterizations. Here we describe a high-throughput strategy for the generation of synthetic Ab clones for expression as Fab proteins in Escherichia coli. Our approach utilizes simultaneous single-stranded site-directed mutagenesis of diversified Ab regions of a phagemid template with engineered complementary determining regions that contain multiple stop codon and restriction enzyme sites. Subsequently, we perform rapid screening of Ab DNA clones for correct gene assemblies by high-throughput Ab-phage protein expression screens. Identified sequences are corroborated by Sanger DNA sequencing analysis. In summary, our work describes a rapid and cost-effective platform for the high-throughput synthesis of synthetic Ab genes as Fab proteins for implementation into downstream protein validation pipelines.
    MeSH term(s) Cell Surface Display Techniques ; Cloning, Molecular/methods ; Codon, Terminator ; DNA Restriction Enzymes/metabolism ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Gene Expression ; Genetic Vectors/chemistry ; Genetic Vectors/metabolism ; High-Throughput Screening Assays ; Humans ; Mutagenesis, Site-Directed ; Recombinant Proteins/genetics ; Recombinant Proteins/metabolism ; Sequence Analysis, DNA ; Single-Chain Antibodies/biosynthesis ; Single-Chain Antibodies/genetics
    Chemical Substances Codon, Terminator ; Recombinant Proteins ; Single-Chain Antibodies ; DNA Restriction Enzymes (EC 3.1.21.-)
    Language English
    Publishing date 2019-04-06
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1193057-3
    ISSN 1559-0305 ; 1073-6085
    ISSN (online) 1559-0305
    ISSN 1073-6085
    DOI 10.1007/s12033-019-00171-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Fluorogen-Activating Proteins: Next-Generation Fluorescence Probes for Biological Research.

    Gallo, Eugenio

    Bioconjugate chemistry

    2019  Volume 31, Issue 1, Page(s) 16–27

    Abstract: Since their discovery, fluorescent probes have found widespread use in biological research. Over time, multiple next-generation probes increased the fluorescence catalog by offering novel capabilities of detection that have been previously difficult or ... ...

    Abstract Since their discovery, fluorescent probes have found widespread use in biological research. Over time, multiple next-generation probes increased the fluorescence catalog by offering novel capabilities of detection that have been previously difficult or lacking with conventional probes. One of such probes is called a fluorogen-activating protein (FAP). These are bimodular sensors, composed of a single-chain antibody that exhibits high-affinity and selectivity for small-molecule fluorogens. Because fluorogens are inherently nonfluorescent unless sterically restricted, upon the formation of the noncovalent FAP-fluorogen complex the fluorogen module emits fluorescence when excited by light. More interestingly, these bimodular sensors permit improvement of their biophysical properties. For instance, the fluorescence spectra and environmental sensing capabilities of fluorogens may be altered by the method of chemical modification at the fluorogen structural level. Also, optimizations of the single-chain antibody scaffold, via amino acid substitutions at the selectivity regions, may improve the detection brightness and affinities of fluorogens; this may also improve the biophysical stability of FAPs in different cellular environments. Additionally, when utilized as biological discovery probes, FAP biosensors exhibit functional activity as genetic fusion tags with cellular proteins; this results in high fluorescent sensitivities of cell surface and intracellular targets. Also, FAPs allow the monitoring of cellular traffic of surface receptors by fluorescence methods of real-time color switching, or signal onset and offset. They find application as biological probes integrated into biomaterials, or as soluble affinity reagents for whole live animal studies. Overall, this noncovalent activation of fluorogen particles results in advanced strategies of fluorescence detection.
    MeSH term(s) Animals ; Biocompatible Materials/chemistry ; Biosensing Techniques/methods ; Fluorescence ; Fluorescent Dyes/chemistry ; Humans ; Luminescent Proteins/chemistry ; Models, Molecular ; Single-Chain Antibodies/chemistry
    Chemical Substances Biocompatible Materials ; Fluorescent Dyes ; Luminescent Proteins ; Single-Chain Antibodies
    Language English
    Publishing date 2019-12-13
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 1024041-x
    ISSN 1520-4812 ; 1043-1802
    ISSN (online) 1520-4812
    ISSN 1043-1802
    DOI 10.1021/acs.bioconjchem.9b00710
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Book ; Online: Customizable Stochastic High Fidelity Model of the Sensors and Camera onboard a Low SWaP Fixed Wing Autonomous Aircraft

    Gallo, Eduado

    2021  

    Abstract: The navigation systems of autonomous aircraft rely on the readings provided by a suite of onboard sensors to estimate the aircraft state. In the case of fixed wing vehicles, the sensor suite is composed by triads of accelerometers, gyroscopes, and ... ...

    Abstract The navigation systems of autonomous aircraft rely on the readings provided by a suite of onboard sensors to estimate the aircraft state. In the case of fixed wing vehicles, the sensor suite is composed by triads of accelerometers, gyroscopes, and magnetometers, a Global Navigation Satellite System (GNSS) receiver, and an air data system (Pitot tube, air vanes, thermometer, and barometer), and is often complemented by one or more digital cameras. An accurate representation of the behavior and error sources of each of these sensors, together with the images generated by the cameras, in indispensable for flight simulation and the evaluation of novel inertial or visual navigation algorithms, and more so in the case of low SWaP (size, weight, and power) aircraft, in which the quality and price of the sensors is limited. This article presents realistic and customizable models for each of these sensors, which have been implemented as an open-source C ++ simulation. Provided with the true variation of the aircraft state with time, the simulation provides a time stamped series of the errors generated by all sensors, as well as realistic images of the Earth surface that resemble those taken from a real camera flying along the indicated state positions and attitudes.

    Comment: 32 pages, 6 figures
    Keywords Computer Science - Robotics ; Electrical Engineering and Systems Science - Systems and Control
    Subject code 629
    Publishing date 2021-02-12
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Book ; Online: Stochastic High Fidelity Simulation and Scenarios for Testing of Fixed Wing Autonomous GNSS-Denied Navigation Algorithms

    Gallo, Eduardo

    2021  

    Abstract: Autonomous unmanned aerial vehicle (UAV) inertial navigation exhibits an extreme dependency on the availability of global navigation satellite systems (GNSS) signals, without which it incurs in a slow but unavoidable position drift that may ultimately ... ...

    Abstract Autonomous unmanned aerial vehicle (UAV) inertial navigation exhibits an extreme dependency on the availability of global navigation satellite systems (GNSS) signals, without which it incurs in a slow but unavoidable position drift that may ultimately lead to the loss of the platform if the GNSS signals are not restored or the aircraft does not reach a location from which it can be recovered by remote control. This article describes an stochastic high fidelity simulation of the flight of a fixed wing low SWaP (size, weight, and power) autonomous UAV in turbulent and varying weather intended to test and validate the GNSS-Denied performance of different navigation algorithms. Its open-source \nm{\CC} implementation has been released and is publicly available. Onboard sensors include accelerometers, gyroscopes, magnetometers, a Pitot tube, an air data system, a GNSS receiver, and a digital camera, so the simulation is valid for inertial, visual, and visual inertial navigation systems. Two scenarios involving the loss of GNSS signals are considered: the first represents the challenges involved in aborting the mission and heading towards a remote recovery location while experiencing varying weather, and the second models the continuation of the mission based on a series of closely spaced bearing changes. All simulation modules have been modeled with as few simplifications as possible to increase the realism of the results. While the implementation of the aircraft performances and its control system is deterministic, that of all other modules, including the mission, sensors, weather, wind, turbulence, and initial estimations, is fully stochastic. This enables a robust evaluation of each proposed navigation system by means of Monte-Carlo simulations that rely on a high number of executions of both scenarios.

    Comment: 25 pages, 17 figures
    Keywords Computer Science - Robotics ; Electrical Engineering and Systems Science - Systems and Control
    Subject code 629
    Publishing date 2021-02-01
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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