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An Overview of Parasite Diversity
Published in Eric S. Loker, Bruce V. Hofkin, Parasitology, 2023
Eric S. Loker, Bruce V. Hofkin
The essential idea behind the molecular clock hypothesis is that DNA sequences change by mutation at a constant rate, such that the degree of divergence in a particular gene sequence between two related species could be used to date the time when they diverged. Although the clock hypothesis is somewhat controversial and the rate of nucleotide substitution change varies among different groups of organisms, it is still widely used. Using the molecular clock hypothesis, the divergence time between Pediculus and Pthirus was estimated to be 13 million years ago.
HIV/AIDS
Published in Patricia G. Melloy, Viruses and Society, 2023
The time when SIV first contacted humans is still debated, but some molecular clock studies indicate that group M for HIV-1 could have been around since the 1920s to 1930s, probably first being seen around Kinshasa (then known as Leopoldville), which is now the capital of the Democratic Republic of Congo. However, the HIV outbreak did not start expanding rapidly to a wider geographic area until the 1960s–1970s (Parrish et al. 2008; Faria et al. 2014; Sharp and Hahn 2010; Korber et al. 2000; Sharp and Hahn 2011). A broader time range of 1884–1924 was reported in other molecular clock analyses (Worobey et al. 2008). Finally, an even earlier range of 1881–1918 has been proposed by other groups (Gryseels et al. 2020). Researchers also noted the importance of Kinshasa as an economic and transportation center for the Belgian Congo, which could have also contributed to the spread of the pathogen (Faria et al. 2014). From its origins as an epidemic in Africa, HIV/AIDS became a pandemic that was uncontrolled in the early 1980s, and researchers worldwide were in search of a way to control the virus using antiretroviral therapy.
Altitude, temperature, circadian rhythms and exercise
Published in Adam P. Sharples, James P. Morton, Henning Wackerhage, Molecular Exercise Physiology, 2022
Henning Wackerhage, Kenneth A. Dyar, Martin Schönfelder
Life on Earth evolved under 24 h oscillating rhythms of light and temperature. Because Earth rotates about its axis, each dawn brings a new wave of solar energy, warming the land and providing crucial electromagnetic energy needed for plants to produce oxygen and carbohydrates via photosynthesis. At dusk, as Earth turns away from the sun, this energy wanes. This rhythmic oscillation drove the evolution of homeostatic circadian timing systems across all kingdoms of life. These molecular clocks allow organisms to anticipate the cycling environmental conditions of life on Earth, and to coordinate their physiology and behaviour accordingly.
The emerging significance of circadian rhythmicity in microvascular resistance
Published in Chronobiology International, 2022
Jeffrey T. Kroetsch, Darcy Lidington, Steffen-Sebastian Bolz
Circadian rhythms arise from an internal molecular clock that emulates the natural 24 hour daily rhythm. At the molecular level, this clock is a complex system of cellular transcription-translation feedback loops that control the expression of a myriad of clock-sensitive genes (i.e., genes whose expression is modulated the circadian clock; Cermakian and Sassone-Corsi 2000). The circadian clock influences the expression of up to 43% of all protein encoding genes (Zhang et al. 2014) and leaves rhythmic signatures in mRNA and protein expression patterns, cellular and physiological functions, and ultimately, complex endpoints such as behaviour. The molecular clock is an autonomous entity that will oscillate in the absence of external cues (i.e., free run). In order to coordinate the individual cellular clocks throughout the body (i.e., entrainment), a “master clock” located within the suprachiasmatic nucleus (Ralph et al. 1990; Silver et al. 1996) integrates external inputs (e.g., light) and then synchronizes the peripheral cellular clocks through neural projections (LeSauter and Silver 1998; Ueyama et al. 1999) and the release of diffusible factors (Silver et al. 1996). The emulation of time at the molecular level is the pivotal prerequisite for adapting individual organ function to recurring environmental changes; additionally, the emulation of time at the cellular level permits the stratification of individual organ functions into the respective temporal niches.
Study of mutation from DNA to biological evolution
Published in International Journal of Radiation Biology, 2019
Masako Bando, Tetsuhiro Kinugawa, Yuichiro Manabe, Miwako Masugi, Hiroo Nakajima, Kazuyo Suzuki, Yuichi Tsunoyama, Takahiro Wada, Hiroshi Toki
Finally, we would like to mention an amazing numerical consistency between the cell-level evolutionary changes and polymorphisms within various species. Such an approach was first proposed by Kimura (1968) by investigating the DNA sequence of the amino acid and by counting the mutant substitutions. This approach made a remarkable breakthrough in the sense that it bridges the mutation of cells occurring in the 10 μm scale world and the theory of biological evolution in the world of the scale of billion years. This fact encourages us to proceed further to arrive at the concept of so-called molecular clock or evolutionary clock. This provides us a tool to connect the phylogenetic events to spontaneous mutation frequency and to estimate the time interval of phylogenetic events. Especially much progress has been made in DNA-sequencing technologies, the usage of the idea ‘molecular clock’ has become more valuable and access the development of theories of molecular evolution (Kumar 2005). Although we have not yet arrived at a complete understanding level on the interplay of the mutation rate, molecular evolution and evolution of living system and molecular clock, it will surely give various hints to solve the question, ‘what is life’ (Kumar and Subramanian 2002).
One future of clinical metagenomic sequencing for infectious diseases
Published in Expert Review of Molecular Diagnostics, 2019
Ryan C. Shean, Alexander L. Greninger
Current diagnostic mNGS approaches also often fail to take advantage of the single nucleotide resolution data provided by metagenomics. These data can be instantaneously fed back to the growing hive of data to perform detailed epidemiological analyses that help prevent infectious disease transmission. Such ‘excess data’ approaches to clinical sequence data are already being used with HIV genotypic resistance data and are likely to become a major thrust of current federal plans to reduce HIV transmission [15]. Widespread adoption of mNGS for diagnostic purposes would significantly accelerate this process, creating mounds of sequence data that could be mined for transmission patterns for preventative purposes. The full viral genomes that mNGS provides can create highly accurate transmission maps which can be invaluable especially in the context of an outbreak in the healthcare setting [16]. Future expansions of the relevant databases will allow much more fine-tuned molecular clock analysis and further increase the utility of these types of studies. Furthermore, mNGS techniques can also be easily modified for use with almost any organism, including those that have not been previously sequenced, allowing for both rapid and flexible transmission cluster tracking.