scholarly journals Keeping track of time: The fundamentals of cellular clocks

2020 ◽  
Vol 219 (11) ◽  
Author(s):  
Colin R. Gliech ◽  
Andrew J. Holland
Keyword(s):  
Biological Systems ◽  
Design Principles ◽  
Special Consideration ◽  
Intercellular Signaling ◽  
Biochemical Reactions ◽  
Diverse Range ◽  
Cellular Processes ◽  
The Common ◽  
Biochemical Components ◽  
Time Frames

Biological timekeeping enables the coordination and execution of complex cellular processes such as developmental programs, day/night organismal changes, intercellular signaling, and proliferative safeguards. While these systems are often considered separately owing to a wide variety of mechanisms, time frames, and outputs, all clocks are built by calibrating or delaying the rate of biochemical reactions and processes. In this review, we explore the common themes and core design principles of cellular clocks, giving special consideration to the challenges associated with building timers from biochemical components. We also outline how evolution has coopted time to increase the reliability of a diverse range of biological systems.

scholarly journals Monitoring the synthesis of biomolecules using mass spectrometry

2016 ◽  
Vol 374 (2079) ◽  
pp. 20150378 ◽  
Author(s):  
Masaru Miyagi ◽  
Takhar Kasumov
Keyword(s):  
Mass Spectrometry ◽  
Heavy Water ◽  
High Throughput ◽  
Biological Systems ◽  
Global Scale ◽  
Selective Synthesis ◽  
Quantitative Mass Spectrometry ◽  
Dynamic Nature ◽  
Diverse Range ◽  
Cellular Processes

The controlled and selective synthesis/clearance of biomolecules is critical for most cellular processes. In most high-throughput ‘omics’ studies, we measure the static quantities of only one class of biomolecules (e.g. DNA, mRNA, proteins or metabolites). It is, however, important to recognize that biological systems are highly dynamic in which biomolecules are continuously renewed and different classes of biomolecules interact and affect each other's production/clearance. Therefore, it is necessary to measure the turnover of diverse classes of biomolecules to understand the dynamic nature of biological systems. Herein, we explain why the kinetic analysis of a diverse range of biomolecules is important and how such an analysis can be done. We argue that heavy water ( 2 H 2 O) could be a universal tracer for monitoring the synthesis of biomolecules on a global scale. This article is part of the themed issue ‘Quantitative mass spectrometry’.

scholarly journals Synthetic Biology: Integrated Gene Circuits

Science ◽  
2011 ◽  
Vol 333 (6047) ◽  
pp. 1244-1248 ◽  
Author(s):  
Nagarajan Nandagopal ◽  
Michael B. Elowitz
Keyword(s):  
Synthetic Biology ◽  
Biological Systems ◽  
Design Principles ◽  
Genetic Circuits ◽  
Major Goal ◽  
Gene Circuits ◽  
Biological Design ◽  
Cellular Processes ◽  
Regulatory Architecture ◽  
New Generation

A major goal of synthetic biology is to develop a deeper understanding of biological design principles from the bottom up, by building circuits and studying their behavior in cells. Investigators initially sought to design circuits “from scratch” that functioned as independently as possible from the underlying cellular system. More recently, researchers have begun to develop a new generation of synthetic circuits that integrate more closely with endogenous cellular processes. These approaches are providing fundamental insights into the regulatory architecture, dynamics, and evolution of genetic circuits and enabling new levels of control across diverse biological systems.

scholarly journals Roles of Microglial Ion Channel in Neurodegenerative Diseases

2021 ◽  
Vol 10 (6) ◽  
pp. 1239
Author(s):  
Alexandru Cojocaru ◽  
Emilia Burada ◽  
Adrian-Tudor Bălșeanu ◽  
Alexandru-Florian Deftu ◽  
Bogdan Cătălin ◽  
...  
Keyword(s):  
Ion Channels ◽  
Neurodegenerative Diseases ◽  
Excitable Cells ◽  
Proton Channels ◽  
Voltage Gated ◽  
Cellular Processes ◽  
Pathological Conditions ◽  
The Common ◽  
Transient Receptor ◽  
The Impact

As the average age and life expectancy increases, the incidence of both acute and chronic central nervous system (CNS) pathologies will increase. Understanding mechanisms underlying neuroinflammation as the common feature of any neurodegenerative pathology, we can exploit the pharmacology of cell specific ion channels to improve the outcome of many CNS diseases. As the main cellular player of neuroinflammation, microglia play a central role in this process. Although microglia are considered non-excitable cells, they express a variety of ion channels under both physiological and pathological conditions that seem to be involved in a plethora of cellular processes. Here, we discuss the impact of modulating microglia voltage-gated, potential transient receptor, chloride and proton channels on microglial proliferation, migration, and phagocytosis in neurodegenerative diseases.

The Effect of User Experience on Designing Interactive Tool: A Case Study of Learning Images Compression

2021 ◽  
Vol 9 (10) ◽  
pp. 1312-1320
Keyword(s):  
User Experience ◽  
Real Life ◽  
Mathematical Concept ◽  
Design Principles ◽  
Mathematical Explanation ◽  
Mathematical Concepts ◽  
Learning Platform ◽  
Learning Mathematics ◽  
The Common ◽  
Value Decomposition

Technology has significantly emerged in various fields, including healthcare, government, and education. In the education field, students of all ages and backgrounds turn to modern technologies for learning instead of traditional methods, especially under challenging courses such as mathematics. However, students face many problems in understanding mathematical concepts and understanding how to benefit from them in real-life. Therefore, it can be challenging to design scientific materials suitable for learning mathematics and clarifying their applications in life that meet the students’ preferences. To solve this issue, we designed and developed an interactive platform based on user experience to learn an advanced concept in the idea of linear algebra called Singular Value Decomposition (SVD) and its applicability in image compression. The proposed platform considered the common design principles to map between the provider in terms of clear mathematical explanation and the receiver in terms of matching good user experience. Twenty participants between the ages of 16 and 30 tested the proposed platform. The results showed that learning using it gives better results than learning traditionally in terms of the number of correct and incorrect actions, effectiveness, efficiency, and safety factors. Consequently, we can say that designing an interactive learning platform to explain an advanced mathematical concept and clarify its applications in real-life is preferable by considering and following the common design principles.

scholarly journals Establishing Analogy Categories for Bio-Inspired Design

Designs ◽  
2018 ◽  
Vol 2 (4) ◽  
pp. 47 ◽  
Author(s):  
Jacquelyn Nagel ◽  
Linda Schmidt ◽  
Werner Born
Keyword(s):  
Analogical Reasoning ◽  
Design Research ◽  
Design Method ◽  
Biological Systems ◽  
Design Pedagogy ◽  
Biological Inspiration ◽  
Research And Teaching ◽  
Difficult Time ◽  
Behavior Learning ◽  
The Common

Biological systems have evolved over billions of years and cope with changing conditions through the adaptation of morphology, physiology, or behavior. Learning from these adaptations can inspire engineering innovation. Several bio-inspired design tools and methods prescribe the use of analogies, but lack details for the identification and application of promising analogies. Further, inexperienced designers tend to have a more difficult time recognizing or creating analogies from biological systems. This paper reviews biomimicry literature to establish analogy categories as a tool for knowledge transfer between biology and engineering to aid bio-inspired design that addresses the common issues. Two studies were performed with the analogy categories. A study of commercialized products verifies the set of categories, while a controlled design study demonstrates the utility of the categories. The results of both studies offer valuable information and insights into the complexity of analogical reasoning and transfer, as well as what leads to biological inspiration versus imitation. The influence on bio-inspired design pedagogy is also discussed. The breadth of the analogy categories is sufficient to capture the knowledge transferred from biology to engineering for bio-inspired design. The analogy categories are a design method independent tool and are applicable for professional product design, research, and teaching purposes.

scholarly journals The organisation and functions of local Ca2+ signals

2001 ◽  
Vol 114 (12) ◽  
pp. 2213-2222 ◽  
Author(s):  
Martin D. Bootman ◽  
Peter Lipp ◽  
Michael J. Berridge
Keyword(s):  
Cell Proliferation ◽  
Gene Transcription ◽  
Cell Biology ◽  
Building Blocks ◽  
Cell Types ◽  
Diverse Range ◽  
Cellular Processes ◽  
Different Cell Types ◽  
Intracellular Messenger ◽  
Sensory Mechanisms

Calcium (Ca2+) is a ubiquitous intracellular messenger, controlling a diverse range of cellular processes, such as gene transcription, muscle contraction and cell proliferation. The ability of a simple ion such as Ca2+ to play a pivotal role in cell biology results from the facility that cells have to shape Ca2+ signals in space, time and amplitude. To generate and interpret the variety of observed Ca2+ signals, different cell types employ components selected from a Ca2+ signalling ‘toolkit’, which comprises an array of homeostatic and sensory mechanisms. By mixing and matching components from the toolkit, cells can obtain Ca2+ signals that suit their physiology. Recent studies have demonstrated the importance of local Ca2+ signals in defining the specificity of the interaction of Ca2+ with its targets. Furthermore, local Ca2+ signals are the triggers and building blocks for larger global signals that propagate throughout cells.

scholarly journals Research Progress of Sirtuin4 in Cancer

2021 ◽  
Vol 10 ◽  
Author(s):  
Yibing Bai ◽  
Jiani Yang ◽  
Ying Cui ◽  
Yuanfei Yao ◽  
Feng Wu ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Enzyme Activity ◽  
Energy Metabolism ◽  
Nicotinamide Adenine Dinucleotide ◽  
Enzyme Activities ◽  
Research Progress ◽  
Diverse Range ◽  
Catalytic Activities ◽  
Cellular Processes ◽  
Dependent Protein

Sirtuins (SIRTs) are members of the silent information regulator-2 family. They are a conserved family of nicotinamide adenine dinucleotide-dependent protein lysine deacylases. SIRTS are involved in intricate cellular processes. There are seven subtypes of SIRTs (1–7) in mammals. SIRT4 is located mainly in mitochondria and has various catalytic activities. These enzyme activities give it a diverse range of important biologic functions, such as energy metabolism, oxidative stress, and aging. Cancer is characterized as reprogramming of energy metabolism and redox imbalance, and SIRT4 can affect tumorigenesis. Here, we review the structure, localization, and enzyme activity of SIRT4 and its role in various neoplasms.

scholarly journals Wording of Daily Diary Questions Matters: An Investigation of the Effect of Daily Diary Instructional Phrases on Respondents’ Recall Time frames (Preprint)

2019 ◽  
Author(s):  
Arthur A. Stone ◽  
Cheng K. Fred Wen ◽  
Stefan Schneider ◽  
Doerte U. Junghaenel
Keyword(s):  
Medical Science ◽  
Daily Diary ◽  
Time Frame ◽  
Affective States ◽  
Diverse Range ◽  
Daily Experience ◽  
Time Periods ◽  
Waking Up ◽  
Time Frames ◽  
The Impact

BACKGROUND Daily diaries are extensively used for examining participants' daily experience in behavioral and medical science. Whether participants recall their experiences within the time frames prescribed by task has received little attention. OBJECTIVE The objectives of this study are to describe survey respondents' self-reported recall timeframe and to evaluate the impact of different daily diary items on respondents reported affective states. METHODS In this study, 577 participants completed a mood survey with one of four time frame instructions: 1) today, 2) since waking up today, 3) during the last 24 hours, or 4) in the last day. They were also asked to indicate the time periods they considered when answering these items and to recall the instructional phrases associated with the items. RESULTS Almost all participants in the "Today" (97%) and "Since waking up today" (94%)" conditions reported using time periods consistent with our expectations, while a lower proportion was observed in the "during the last 24 hours" (69%) condition. A diverse range of responses was observed in the "In the last day" condition. Furthermore, the instructions influenced the levels of some self-reported affects, although exploratory analyses were not able to identify the mechanism underlying this finding. CONCLUSIONS Overall, these results indicate that "Today" and "Since waking up today" are the most effective instructional phrases for inquiring about daily experience and that investigators should use caution when using the other two instructional phrases.

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