Systems biology–the transformative approach to integrate sciences across disciplines

2022 ◽  
Vol 0 (0) ◽  
Author(s):  
Maya Madhavan ◽  
Sabeena Mustafa
Keyword(s):  
Biological Sciences ◽  
Life Science ◽  
Current Knowledge ◽  
Science Research ◽  
Biological Research ◽  
Computer Tools ◽  
Interdisciplinary Approaches ◽  
Basic And Applied Research ◽  
Living Organisms ◽  
Transformative Approach

Abstract Life science is the study of living organisms, including bacteria, plants, and animals. Given the importance of biology, chemistry, and bioinformatics, we anticipate that this chapter may contribute to a better understanding of the interdisciplinary connections in life science. Research in applied biological sciences has changed the paradigm of basic and applied research. Biology is the study of life and living organisms, whereas science is a dynamic subject that as a result of constant research, new fields are constantly emerging. Some fields come and go, whereas others develop into new, well-recognized entities. Chemistry is the study of composition of matter and its properties, how the substances merge or separate and also how substances interact with energy. Advances in biology and chemistry provide another means to understand the biological system using many interdisciplinary approaches. Bioinformatics is a multidisciplinary or rather transdisciplinary field that encourages the use of computer tools and methodologies for qualitative and quantitative analysis. There are many instances where two fields, biology and chemistry have intersection. In this chapter, we explain how current knowledge in biology, chemistry, and bioinformatics, as well as its various interdisciplinary domains are merged into life sciences and its applications in biological research.

scholarly journals Analysis of Protein Target Interactions of Synthetic Mixtures by Affinity-LC/MS

2017 ◽  
Vol 22 (4) ◽  
pp. 440-446 ◽  
Author(s):  
Prachi Singh ◽  
Kalaipriya Madhaiyan ◽  
Minh-Dao Duong-Thi ◽  
Brian W. Dymock ◽  
Sten Ohlson
Keyword(s):  
Biological Sciences ◽  
Mass Spectrometry ◽  
High Performance ◽  
Development Time ◽  
Life Science ◽  
Heat Shock Protein 90 ◽  
Science Research ◽  
Direct Analysis ◽  
Chemical Research ◽  
Protein Target

Analysis of interactions between molecules is of fundamental importance in life science research. In this study, we applied weak affinity chromatography, based on high-performance liquid chromatography and mass spectrometry, as a powerful tool for direct analysis of the components of a chemical reaction mixture for their binding to a target protein. As a demonstration of the potential of this method, we analyzed the binding of the compounds of the reaction mixture to the chaperone heat shock protein 90 (Hsp90). It was possible to analyze quantitatively the binding of the components of the mixture to the target independently from each other without any preceding process such as purification. This feature has wide implications in biological sciences as crude mixtures, either natural or synthetic, can be analyzed directly for their possible binding to a target. This method could lead to savings in costs and labor through shortening chemical research project development time.

scholarly journals Rapid, robust plasmid verification by de novo assembly of short sequencing reads

2020 ◽  
Vol 48 (18) ◽  
pp. e106-e106 ◽  
Author(s):  
Jenna E Gallegos ◽  
Mark F Rogers ◽  
Charlotte A Cialek ◽  
Jean Peccoud
Keyword(s):  
Quality Control ◽  
Synthetic Biology ◽  
De Novo Assembly ◽  
Life Science ◽  
De Novo ◽  
Science Research ◽  
Application Security ◽  
Security Issues ◽  
Control Step ◽  
Basic And Applied Research

Abstract Plasmids are a foundational tool for basic and applied research across all subfields of biology. Increasingly, researchers in synthetic biology are relying on and developing massive libraries of plasmids as vectors for directed evolution, combinatorial gene circuit tests, and for CRISPR multiplexing. Verification of plasmid sequences following synthesis is a crucial quality control step that creates a bottleneck in plasmid fabrication workflows. Crucially, researchers often elect to forego the cumbersome verification step, potentially leading to reproducibility and—depending on the application—security issues. In order to facilitate plasmid verification to improve the quality and reproducibility of life science research, we developed a fast, simple, and open source pipeline for assembly and verification of plasmid sequences from Illumina reads. We demonstrate that our pipeline, which relies on de novo assembly, can also be used to detect contaminating sequences in plasmid samples. In addition to presenting our pipeline, we discuss the role for verification and quality control in the increasingly complex life science workflows ushered in by synthetic biology.

scholarly journals Rapid, robust plasmid verification by de novo assembly of short sequencing reads

2020 ◽  
Author(s):  
Jenna. E. Gallegos ◽  
Mark F. Rogers ◽  
Charlotte Cialek ◽  
Jean Peccoud
Keyword(s):  
Quality Control ◽  
Synthetic Biology ◽  
Applied Research ◽  
Life Science ◽  
De Novo ◽  
Science Research ◽  
Application Security ◽  
Security Issues ◽  
Control Step ◽  
Basic And Applied Research

AbstractPlasmids are a foundational tool for basic and applied research across all subfields of biology. Increasingly, researchers in synthetic biology are relying on and developing massive libraries of plasmids as vectors for directed evolution, combinatorial gene circuit tests, and for CRISPR multiplexing. Verification of plasmid sequences following synthesis is a crucial quality control step that creates a bottleneck in plasmid fabrication workflows. Crucially, researchers often elect to forego the cumbersome verification step, potentially leading to reproducibility and— depending on the application—security issues. In order to facilitate plasmid verification to improve the quality and reproducibility of life science research, we developed a fast, simple, and open source pipeline for assembly and verification of plasmid sequences from Illumina reads. We demonstrate that our pipeline, which relies on de novo assembly, can also be used to detect contaminating sequences in plasmid samples. In addition to presenting our pipeline, we discuss the role for verification and quality control in the increasingly complex life science workflows ushered in by synthetic biology.

scholarly journals The roles of code in biology

2021 ◽  
Vol 104 (2) ◽  
pp. 003685042110105
Author(s):  
Brendan Lawlor ◽  
Roy D Sleator
Keyword(s):  
Research Team ◽  
Life Science ◽  
Life Sciences ◽  
Three Dimensional ◽  
Science Research ◽  
Computer Code ◽  
Biological Research ◽  
Sweet Spot ◽  
Optimal Outcomes ◽  
Software Engineers

The way in which computer code is perceived and used in biological research has been a source of some controversy and confusion, and has resulted in sub-optimal outcomes related to reproducibility, scalability and productivity. We suggest that the confusion is due in part to a misunderstanding of the function of code when applied to the life sciences. Code has many roles, and in this paper we present a three-dimensional taxonomy to classify those roles and map them specifically to the life sciences. We identify a “sweet spot” in the taxonomy—a convergence where bioinformaticians should concentrate their efforts in order to derive the most value from the time they spend using code. We suggest the use of the “inverse Conway maneuver” to shape a research team so as to allow dedicated software engineers to interface with researchers working in this “sweet spot.” We conclude that in order to address current issues in the use of software in life science research such as reproducibility and scalability, the field must reevaluate its relationship with software engineering, and adapt its research structures to overcome current issues in bioinformatics such as reproducibility, scalability and productivity.

scholarly journals The Diverse Calpain Family in Trypanosomatidae: Functional Proteins Devoid of Proteolytic Activity?

Cells ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 299
Author(s):  
Vítor Ennes-Vidal ◽  
Marta Helena Branquinha ◽  
André Luis Souza dos Santos ◽  
Claudia Masini d’Avila-Levy
Keyword(s):  
Proteolytic Activity ◽  
Current Knowledge ◽  
Current Therapy ◽  
Calcium Dependent ◽  
Administration Routes ◽  
Life Threatening ◽  
Living Organisms ◽  
Almost All ◽  
Open Question ◽  
Calpain Inhibitors

Calpains are calcium-dependent cysteine peptidases that were originally described in mammals and, thereafter, their homologues were identified in almost all known living organisms. The deregulated activity of these peptidases is associated with several pathologies and, consequently, huge efforts have been made to identify selective inhibitors. Trypanosomatids, responsible for life-threatening human diseases, possess a large and diverse family of calpain sequences in their genomes. Considering that the current therapy to treat trypanosomatid diseases is limited to a handful of drugs that suffer from unacceptable toxicity, tough administration routes, like parenteral, and increasing treatment failures, a repurposed approach with calpain inhibitors could be a shortcut to successful chemotherapy. However, there is a general lack of knowledge about calpain functions in these parasites and, currently, the proteolytic activity of these proteins is still an open question. Here, we highlight the current research and perspectives on trypanosomatid calpains, overview calpain description in these organisms, and explore the potential of targeting the calpain system as a therapeutic strategy. This review gathers the current knowledge about this fascinating family of peptidases as well as insights into the puzzle: are we unable to measure calpain activity in trypanosomatids, or are the functions of these proteins devoid of proteolytic activity in these parasites?

scholarly journals Toward High Throughput Core-CBCM CMOS Capacitive Sensors for Life Science Applications: A Novel Current-Mode for High Dynamic Range Circuitry

Sensors ◽  
2018 ◽  
Vol 18 (10) ◽  
pp. 3370 ◽  
Author(s):  
Saghi Forouhi ◽  
Rasoul Dehghani ◽  
Ebrahim Ghafar-Zadeh
Keyword(s):  
High Performance ◽  
Life Science ◽  
Dynamic Range ◽  
Current Mode ◽  
Capacitive Sensor ◽  
Oxide Semiconductor ◽  
Capacitance Measurement ◽  
Biological Research ◽  
Cmos Process ◽  
Capacitive Sensors

This paper proposes a novel charge-based Complementary Metal Oxide Semiconductor (CMOS) capacitive sensor for life science applications. Charge-based capacitance measurement (CBCM) has significantly attracted the attention of researchers for the design and implementation of high-precision CMOS capacitive biosensors. A conventional core-CBCM capacitive sensor consists of a capacitance-to-voltage converter (CVC), followed by a voltage-to-digital converter. In spite of their high accuracy and low complexity, their input dynamic range (IDR) limits the advantages of core-CBCM capacitive sensors for most biological applications, including cellular monitoring. In this paper, after a brief review of core-CBCM capacitive sensors, we address this challenge by proposing a new current-mode core-CBCM design. In this design, we combine CBCM and current-controlled oscillator (CCO) structures to improve the IDR of the capacitive readout circuit. Using a 0.18 μm CMOS process, we demonstrate and discuss the Cadence simulation results to demonstrate the high performance of the proposed circuitry. Based on these results, the proposed circuit offers an IDR ranging from 873 aF to 70 fF with a resolution of about 10 aF. This CMOS capacitive sensor with such a wide IDR can be employed for monitoring cellular and molecular activities that are suitable for biological research and clinical purposes.

scholarly journals A beginner’s guide to RT-PCR, qPCR and RT-qPCR

2020 ◽  
Vol 42 (3) ◽  
pp. 48-53 ◽  
Author(s):  
Grace Adams
Keyword(s):  
Gene Expression ◽  
Polymerase Chain Reaction ◽  
Messenger Rna ◽  
Life Science ◽  
Science Research ◽  
Quantitative Real Time Pcr ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Mrna Quantitation ◽  
Polymerase Chain

The development of the polymerase chain reaction (PCR), for which Kary Mullis received the 1992 Novel Prize in Chemistry, revolutionized molecular biology. At around the time that prize was awarded, research was being carried out by Russel Higuchi which led to the discovery that PCR can be monitored using fluorescent probes, facilitating quantitative real-time PCR (qPCR). In addition, the earlier discovery of reverse transcriptase (in 1970) laid the groundwork for the development of RT-PCR (used in molecular cloning). The latter can be coupled to qPCR, termed RT-qPCR, allowing analysis of gene expression through messenger RNA (mRNA) quantitation. These techniques and their applications have transformed life science research and clinical diagnosis.

scholarly journals Genome Resources for the Ex-type of Phytophthora citricola, and well-authenticated isolates of P. hibernalis, P. nicotianae and P. syringae

2021 ◽  
Author(s):  
Subodh K. Srivastava ◽  
Leandra M. Knight ◽  
Mark K. Nakhla ◽  
Z. Gloria Abad
Keyword(s):  
Plant Pathogens ◽  
High Throughput Sequencing ◽  
Economic Losses ◽  
Biological Research ◽  
Type Specimens ◽  
High Coverage ◽  
Oxford Nanopore ◽  
Long Read ◽  
Basic And Applied Research ◽  
Diagnostic Applications

Phytophthora is one of the most important genera of plant pathogens with many members causing high economic losses world-wide. To build robust molecular identification systems, it is very important to have information from well-authenticated specimens and in preference the ex-type specimens. The reference genomes of well-authenticated specimens form a critical foundation for genetics, biological research, and diagnostic applications. In this study, we describe four draft Phytophthora genomes resources for the Ex-type of P. citricola BL34 (P0716 WPC) (118 contigs for 50 Mb), and well-authenticated specimens of P. syringae BL57G (P10330 WPC) (591 contigs for 75 Mb), P. hibernalis BL41G (P3822 WPC) (404 contigs for 84 Mb), and P. nicotianae BL162 (P6303 WPC) (3984 contigs for 108 Mb) generated with MinION long-read High-Throughput Sequencing (HTS) technology (Oxford Nanopore Technologies, ONT). Using the quality reads we assembled high coverage genomes of P. citricola with 291X coverage and 16,662 annotated genes; P. nicotianae with 205X coverage and 29,271 annotated genes; P. syringae with 76X coverage and 23,331 annotated genes, and P. hibernalis with 42X coverage and 21,762 annotated genes. With the availability of genomes sequences and its annotations, we predict that these draft genomes will be accommodating for various basic and applied research including diagnostics to protect global agriculture.

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