Journal articles on the topic 'Theoretical paleontology'
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Fernández López, Sixto. "Taphonomic concepts for a theoretical biochronology." Spanish Journal of Palaeontology 6, no. 1 (August 11, 2022): 37. http://dx.doi.org/10.7203/sjp.25035.
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Prothero, Donald R. "From Memorization to Inspiration: Teaching Paleobiology in the Twenty-First Century." Paleontological Society Special Publications 12 (2012): 1–10. http://dx.doi.org/10.1017/s2475262200009199.
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For most of the twentieth century, paleontology instruction focused on memorization of taxa, morphology, and stratigraphic ranges. Consequently, paleontology got the reputation as a boring, stagnant, musty old field with this “idiographic” approach that focused on details at the expense of the broader implications. The “Paleobiology Revolution” of the 1960s and 1970s radically changed paleontological pedagogy. New generations of paleontologists who were weaned on the 1972 Raup and Stanley textbook (which had no systematic coverage of invertebrates) adopted a more dynamic, “law-like” or “nomothetic” approach. The emphasis on ideas, concepts, and controversies over memorization of names and dates makes paleontology far more interesting and relevant to geology majors, most of whom will not become paleontologists and will not need huge numbers of names to do their jobs. However, paleontology instructors still must include basic information about the major phyla of fossils or else the theoretical ideas lack any reference in reality. My own approach mixes both theoretical and systematic concepts, with lectures on major topics (taphonomy, ontogeny, population variation, speciation, micro and macroevolution, extinction, paleoecology, biogeography, functional morphology) alternating with lectures supplementing lab exercises.
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Tamborini, Marco. "A Plea for a New Synthesis: From Twentieth-Century Paleobiology to Twenty-First-Century Paleontology and Back Again." Biology 11, no. 8 (July 26, 2022): 1120. http://dx.doi.org/10.3390/biology11081120.
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In this paper, I will briefly discuss the elements of novelty and continuity between twentieth-century paleobiology and twenty-first-century paleontology. First, I will outline the heated debate over the disciplinary status of paleontology in the mid-twentieth century. Second, I will analyze the main theoretical issue behind this debate by considering two prominent case studies within the broader paleobiology agenda. Third, I will turn to twenty-first century paleontology and address five representative research topics. In doing so, I will characterize twenty-first century paleontology as a science that strives for more data, more technology, and more integration. Finally, I will outline what twenty-first-century paleontology might inherit from twentieth-century paleobiology: the pursuit of and plea for a new synthesis that could lead to a second paleobiological revolution. Following in the footsteps of the paleobiological revolution of the 1960s and 1970s, the paleobiological revolution of the twenty-first century would enable paleontologists to gain strong political representation and argue with a decisive voice at the “high table” on issues such as the expanded evolutionary synthesis, the conservation of Earth’s environment, and global climate change.
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Starcher, Robert W., and George R. Jr McGhee. "Theoretical morphology of modular organisms: geometric constraints of branch and dissepiment width and spacing in fenestrate bryozoans." Neues Jahrbuch für Geologie und Paläontologie - Abhandlungen 223, no. 1 (January 18, 2002): 79–122. http://dx.doi.org/10.1127/njgpa/223/2002/79.
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Tuzyak, Yaryna М., Аntonina V. Іvanina, Halina І. Hotsanyuk, Іhor V. Shaynoha, and Аndrii Ya Cherniak. "From paleontological collections to the Paleontological Museum of Lviv University as an object of historical, cultural and natural values." Journal of Geology, Geography and Geoecology 30, no. 4 (December 28, 2021): 781–93. http://dx.doi.org/10.15421/112172.
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The creation of the Paleontological Museum of Lviv University is the implementation of one of many projects of scientists of geologists and paleontologists in the territory of first Eastern Europe, and later modern Western Ukraine. The foundation of the «temple of muses» of geological sciences (natural sciences, Earth sciences) and their component of paleontology in the West of Ukraine is the stage of formation of geological (paleontological) research and the Lviv geological (paleontological-stratigraphic) school at the Lviv University. The beginning and development of natural sciences – geology and paleontology on a global scale became the basis for the creation of the Geological Faculty and the Department of Historical Geology and Paleontology (1945) at the Lviv University, and the Geological/Paleontological Museum acquired importance in the study, collection, conservation, protection, and popularization of Earth Sciences among various segments of the population. The history of the foundation and the development of the Geological/Paleontological Museum of Ivan Franko National University of Lviv is covered. Prerequisites that contributed to the foundation of the Paleontological Museum are given, the scientific and theoretical concept based on it, the directions of research and the results of achievements of each stage are substantiated. The museum place in the «spectrum» of historical, cultural and natural values has been clarified. The scientific research works of different generations of geologists and paleontologists over the 200-year history and their contribution to the development of Earth Sciences were analyzed. Its significance as a cultural and spiritual center for the development of society is highlighted. The description of the activity of the scientific goals of various political systems in which the territories of the West of Ukraine were located and their contribution to the development of the Paleontological Museum is given. The structure and classification of natural objects (fossils, naturals) of museum collections and foundations by purpose and significance have been determined. Modern and further trends in the development of the Paleontological Museum have been clarified. Fundamental, research, educational and informative, cultural, propaganda aspects of the Paleontologic Мuseum are shown.
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Eble, Gunther J. "Theoretical Morphology: State of the Art - Theoretical Morphology: The Concept and Its Applications. George R. McGhee Jr. Columbia University Press, New York. 1999. 316 pages. Cloth $60.00, paper $26.50." Paleobiology 26, no. 3 (2000): 520–28. http://dx.doi.org/10.1666/0094-8373(2000)026<0520:tmsota>2.0.co;2.
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The morphological diversity of life has captivated systematists in the construction of classifications, embryologists in the study of development, and evolutionists in the formulation of theories of organic change. In a century marked by the advances of molecular biology, has the discipline of morphology produced anything … new? Yes. The solidification of paleontology and systematics and the emergence of macroevolution as a legitimate field owe much to an increased rigor in the analysis of morphological data. At the same time, the discipline of morphology has achieved an unprecedented sophistication through another development, the very expression of its maturity: theoretical morphology. Theoretical morphology forms the subject of McGhee's landmark book, an elegant combination of compendium and manifesto. Its richness and scope provide an opportunity for a critical appraisal of the discipline of morphology, particularly quantitative and developmental morphology.
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Dykan, Natalia. "Some theoretical aspects of the systematic study of fossil ostracods (Arthropoda, Crustacea, Ostracoda) in the context of species problems in palaeontology." Novitates Theriologicae, no. 12 (June 16, 2021): 127–39. http://dx.doi.org/10.53452/nt1223.
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Theoretical contributions into the systematics and taxonomy of fossil ostracods conducted according to unified methodological stands have resolved some key problems of paleontology. For example, this is a problem of species and its derivatives, namely the identification of species, the estimation of the taxonomic weight of morphological characters, the determination of diagnostic characters of different taxonomic ranks, and taxa diagnoses. The unification of the terminology and the formalization of morphological description of fossil shells made it possible to estimate the taxonomic weight of morphological elements. A scheme to identify the rank of taxonomic characters (pyramid principle) has been developed. A unified terminological dictionary has been prepared to describe the morphological elements of ostracod shells in detail.
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LAURENZA, DOMENICO. "THE STUDY OF FOSSILS IN LEIBNIZ'S PROTOGAEA: TOWARDS A RECONCTRUCTION OF THE ROLE OF TECHNOLOGICAL MODELS IN EARLY MODERN PALEONTOLOGY." Earth Sciences History 38, no. 1 (April 1, 2019): 1–15. http://dx.doi.org/10.17704/1944-6178-38.1.1.
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ABSTRACT The article is a detailed examination of practices originating in technology and art that were used as heuristically fertile models in Leibniz's Protogaea (1749) to explain the processes of fossilization and demonstrate the animal origin of fossils. Particular importance is given to engravings on copper, which, besides being the technique used to execute the plates in the Protogaea, also became an analogical model for the interpretation of fish fossils. These aspects of the Protogaea are contextualised within the broader framework of the interaction between artisanal and theoretical modes of knowledge in the Scientific Revolution and the still little-known historical development of this interaction in the field of paleontology.
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Lundgren, Lisa, Kent J. Crippen, Jennifer E. Bauer, and Richard T. Bex. "Social Paleontology on Twitter: A Case Study of Topic Archetypes, Network Composition, and Structure." Social Media + Society 8, no. 1 (January 2022): 205630512210804. http://dx.doi.org/10.1177/20563051221080475.
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Social paleontology is a burgeoning field of research that seeks to understand the natural world through the collection, preparation, curation, and study of fossils via online communities. Such a community represents an ideal case for examining scientific practice as the expression of conversation topics in relation to the people who participate. Using Communities of Practice as a theoretical framework, we consider interactions within an egocentric Twitter network over a 397-day period to identify topic archetypes within the community, examine how such topic archetypes act as expressions of behavior that are indicative of community processes, and provide empirical evidence for detecting and indicating the health of an online community. Data were collected continuously and analyzed with a combination of topic modeling and social network analysis. Four unique archetypes were characterized based on the level of activity and longevity of interest. Participants for each were diverse, but not different. Structural differences in each network were noted with high levels of inter-group information flow within certain archetypes. Archetypes were interpreted using the life cycle states for Communities of Practice; sustained conversations and piques of interest indicate healthy online communities. These findings can inform efforts to design, implement, and research online, scientific communities.
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Savchuk, Vyacheslav S., and Varfolomii S. Savchuk. "Geological expeditions and routes of M. Y. Lebedev: theoretical and practical results." Journal of Geology, Geography and Geoecology 31, no. 4 (January 11, 2023): 711–21. http://dx.doi.org/10.15421/112267.
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A set of geological expeditions and routes carried out by M. Y. Lebedev through- out his life was determined for the first time. The specified complex in the context of the set research purpose is analyzed. The purpose of the study is to identify and consider the main geological routes of expeditionary practice of the outstanding geologist M. Y. Lebedev and to generalize practically and theoretically the consequences of their implementation and its organizational activities in the field of geology. The study is based on a combination of theoretical provisions of geological research and the principles of application of the evidence base of historical and natural research. The main geological expeditions, in which M. Y. Lebedev took part, are studied and analyzed, their results are considered and generalized, and the organizational achievements of the scientist are clarified. It was found that the expeditionary practice gave Lebedev the opportunity to accumulate a complex of various geological materials, most of which were innovative. Each of these complexes became the basis for obtaining new theoretical results. The development and application of paleontological methods by M.Y. Lebedev were of particular importance. The method of stratigraphic paleontology developed by him allowed substantiating the new methodology of research of coal deposits of the Donetsk basin. The significance of Lebedev’s activity in the development of Azerbaijani oil production, in particular, the determination of the oil potential the Caspian Seabed near Baku, is pointed out. The cartographic activity of the scientist is described. The influence of M. Y. Lebedev on the formation of the geological service and higher geological education in Ukraine is estimated. The results of the study testified to the diversity of M.Y. Lebedev’s ex- peditionary practice and its role in his formation as a geologist of the European level; its significance in the development of theoretical and practical components of M.Y. Lebedev’s activity was determined, his formation as an organizer of geological research and higher geological education.
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Mitra Ávila, Rosaura. "Diagnóstico para configurar la colección documental sobre paleontología en el Instituto Nacional de Antropología e Historia, México." Intervención 2, no. 24 (December 28, 2021): 54–91. http://dx.doi.org/10.30763/intervencion.251.v2n24.30.2021.
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Este artículo de investigación pretende exponer las fases y resultados del diagnóstico ejecutado como parte de la investigación-intervención en el proyecto de titulación de la Maestría en Conservación de Acervos Documentales (2018-2020) de la Escuela Nacional de Conservación, Restauración y Museografía (ENCRyM, México), en la cual se planteó una propuesta teórico-práctica para la conformación y conservación, dentro del Instituto Nacional de Antropología e Historia (INAH, México), de un acervo documental científico, específicamente, el paleontológico. Ese diagnóstico se encaminó a sentar las bases para la conformación del mencionado acervo documental en el Archivo Técnico (AT) de la Coordinación Nacional de Arqueología (CNA) y que fue el cimiento de la investigación-intervención citada. _____ This article will present the stages and results of a diagnosis made as part of a research-intervention project for a master’s degree in Conservation of Documentary Heritage (2018-2020) at the Escuela Nacional de Conservación, Restauración y Museografía (ENCRyM, México). The project made a theoretical-practical proposal to form and preserve the documentary scientific collection on paleontology at the Instituto Nacional de Antropología e Historia (INAH, Mexico). This diagnosis set out to establish the basis to form this documentary collection in the Archivo Técnico (AT) de la Coordinación Nacional de Arqueología (CNA) and constituted the foundation for the above-mentioned investigation-intervention.
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Schachat, Sandra R., Jonathan L. Payne, C. Kevin Boyce, and Conrad C. Labandeira. "Generating and testing hypotheses about the fossil record of insect herbivory with a theoretical ecospace." Review of Palaeobotany and Palynology 297 (February 2022): 104564. http://dx.doi.org/10.1016/j.revpalbo.2021.104564.
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Dott, R. "The American Countercurrent - Eastward Flow of Geologists and Their Ideas in the Late Nineteenth Century." Earth Sciences History 9, no. 2 (January 1, 1990): 158–62. http://dx.doi.org/10.17704/eshi.9.2.0k746746w5146l57.
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Whereas the trans-Atlantic flow of geological knowledge previously had been overwhelmingly westward, by the mid-nineteenth century, an eastward countercurrent had begun. That flow increased rapidly after the Civil War, when geology was at the forefront in the maturation of science in America. H.D. Rogers was appointed Regius Professor at the University of Glasgow in 1855. James Hall was chosen to be Organizing President of the first International Geological Congress in Paris (1878) and the first English-speaking foreign correspondent of the Academy of Sciences of France (1884). James D. Dane was almost as well known abroad as Hall, especially for his mountain-building theory. Increasingly, American theoretical contributions had to be reckoned with in such fields as Mountain Building, Structural and Precambrian Geology, Geomorphology and Glacial Geology, and Paleontology. By the first decade of the twentieth century, America had seized the initiative on several fronts, but especially in experimental petrology and physics of the earth's interior through the creation of the Carnegie Institution of Washington.
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Dolman, Andrew M., Torben Kunz, Jeroen Groeneveld, and Thomas Laepple. "A spectral approach to estimating the timescale-dependent uncertainty of paleoclimate records – Part 2: Application and interpretation." Climate of the Past 17, no. 2 (April 8, 2021): 825–41. http://dx.doi.org/10.5194/cp-17-825-2021.
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Abstract. Proxy climate records are an invaluable source of information about the earth's climate prior to the instrumental record. The temporal and spatial coverage of records continues to increase; however, these records of past climate are associated with significant uncertainties due to non-climate processes that influence the recorded and measured proxy values. Generally, these uncertainties are timescale dependent and correlated in time. Accounting for structure in the errors is essential for providing realistic error estimates for smoothed or stacked records, detecting anomalies, and identifying trends, but this structure is seldom accounted for. In the first of these companion articles, we outlined a theoretical framework for handling proxy uncertainties by deriving the power spectrum of proxy error components from which it is possible to obtain timescale-dependent error estimates. Here in Part 2, we demonstrate the practical application of this theoretical framework using the example of marine sediment cores. We consider how to obtain estimates for the required parameters and give examples of the application of this approach for typical marine sediment proxy records. Our new approach of estimating and providing timescale-dependent proxy errors overcomes the limitations of simplistic single-value error estimates. We aim to provide the conceptual basis for a more quantitative use of paleo-records for applications such as model–data comparison, regional and global synthesis of past climate states, and data assimilation.
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Priego-Quesada, Jose I., Márcio F. Goethel, Klaus Magno Becker, Ricardo J. Fernandes, and João Paulo Vilas-Boas. "How to Work with Electromyography Decomposition in Practical Classes of Exercise Physiology and Biomechanics." Life 12, no. 4 (March 26, 2022): 483. http://dx.doi.org/10.3390/life12040483.
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Concepts about motor unit recruitment are important learning contents in exercise physiology and biomechanics classes that are usually taught theoretically. In the last few years, great advances have occurred in the decomposition of surface electromyography, allowing the learning of theoretical contents in an experimental way. In this tutorial paper, we have described the decomposition of surface electromyography methodological aspects and examples to teach motor unit recruitment concepts in exercise physiology and biomechanics practical lessons. This work has the aim to facilitate physiology and biomechanics academics to introduce this technique in practical classes.
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Walla, Peter, Georg Northoff, and Cornelia Herbert. "The Human Self Has Two Serial Aspects and Is Dynamic: A Concept Based on Neurophysiological Evidence Supporting a Multiple Aspects Self Theory (MAST)." Life 11, no. 7 (June 24, 2021): 611. http://dx.doi.org/10.3390/life11070611.
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The self is an increasingly central topic in current neuroscience. Understanding the neural processes that are involved in self-referential processing and functioning may also be crucial to understanding consciousness. The current short communication goes beyond the typical concept that the self is singular, as has been assumed from neuroanatomical descriptions of the self by fMRI and PET studies. Long ago, theoretically, the idea of multiple aspects of the human self-arose, highlighting a dynamic organizational structure, but an increasing number of electrophysiological brain imaging studies, searching for the temporal dynamics of self-referential brain processes, now has empirical evidence supporting their existence. This short communication focuses on the theoretical idea of a dynamic self and provides first preliminary empirical evidence, including results from own studies of the authors, in support of, and highlights the serial dynamics of the human self, suggesting a primitive Me1 and an elaborate Me2 (a non-personal and a personal self). By focusing on the temporal dimension of the self, we propose that multiple aspects of the self can be distinguished based on their temporal sequence. A multiple aspects Self Theory (MAST) is proposed. This model is meant as a theoretical framework for future studies providing further support.
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Taylor, John F. "James H. Stitt: A Dedicated Professor and Exemplary Biostratigrapher." Journal of Paleontology 74, no. 2 (March 2000): 367–68. http://dx.doi.org/10.1017/s0022336000031589.
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On Friday September 17 Jim Stitt died quietly in his sleep, ending a long and characteristically tenacious battle with cancer. His passing leaves a void of great magnitude in the geological sciences and in the lives of the many people whom he influenced as family, friends, or colleagues. I was Jim's first Ph.D. student at the University of Missouri, where he spent the past 31 years as a pillar of the geology program, serving at various times as Chair and Graduate Student Advisor. Jim is well known and respected for an impressive body of meticulously crafted taxonomic and biostratigraphic studies on trilobites and brachiopods. His three monographs on faunas in the Arbuckle and Wichita Mountains of Oklahoma (Stitt, 1971a, 1977, 1983) established that area as a standard for correlation of Upper Cambrian and Lower Ordovician strata in North America. This “Oklahoma trilogy” is a treasure trove of taxonomic and biostratigraphic data that has been drawn upon heavily in numerous subsequent biostratigraphic and paleobiologic studies. It provides a biozonation of unparalleled precision for carbonate platform facies of that interval, ironically assembled in an area where rocks of that age yield their fossils only reluctantly. Jim took great pride in extracting useful information from difficult rocks. He passed that laudable attitude on to his academic offspring, along with the sense of satisfaction he derived from seeing his data put to good use in solving geologic or paleobiologic problems, in his own work and in that of others. At the same time, he was always complimentary and supportive of more theoretical or abstract research, an attitude sadly lacking in some practitioners with a bent toward applied paleontology.
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Kowalewski, Michał, and Phil Novack-Gottshall. "Resampling Methods in Paleontology." Paleontological Society Papers 16 (October 2010): 19–54. http://dx.doi.org/10.1017/s1089332600001807.
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This chapter reviews major types of statistical resampling approaches used in paleontology. They are an increasingly popular alternative to the classic parametric approach because they can approximate behaviors of parameters that are not understood theoretically. The primary goal of most resampling methods is an empirical approximation of a sampling distribution of a statistic of interest, whether simple (mean or standard error) or more complicated (median, kurtosis, or eigenvalue). This chapter focuses on the conceptual and practical aspects of resampling methods that a user is likely to face when designing them, rather than the relevant mathematical derivations and intricate details of the statistical theory. The chapter reviews the concept of sampling distributions, outlines a generalized methodology for designing resampling methods, summarizes major types of resampling strategies, highlights some commonly used resampling protocols, and addresses various practical decisions involved in designing algorithm details. A particular emphasis has been placed here on bootstrapping, a resampling strategy used extensively in quantitative paleontological analyses, but other resampling techniques are also reviewed in detail. In addition,ad hocand literature-based case examples are provided to illustrate virtues, limitations, and potential pitfalls of resampling methods.
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Ameta, Sandeep, Yoshiya J. Matsubara, Nayan Chakraborty, Sandeep Krishna, and Shashi Thutupalli. "Self-Reproduction and Darwinian Evolution in Autocatalytic Chemical Reaction Systems." Life 11, no. 4 (April 1, 2021): 308. http://dx.doi.org/10.3390/life11040308.
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Understanding the emergence of life from (primitive) abiotic components has arguably been one of the deepest and yet one of the most elusive scientific questions. Notwithstanding the lack of a clear definition for a living system, it is widely argued that heredity (involving self-reproduction) along with compartmentalization and metabolism are key features that contrast living systems from their non-living counterparts. A minimal living system may be viewed as “a self-sustaining chemical system capable of Darwinian evolution”. It has been proposed that autocatalytic sets of chemical reactions (ACSs) could serve as a mechanism to establish chemical compositional identity, heritable self-reproduction, and evolution in a minimal chemical system. Following years of theoretical work, autocatalytic chemical systems have been constructed experimentally using a wide variety of substrates, and most studies, thus far, have focused on the demonstration of chemical self-reproduction under specific conditions. While several recent experimental studies have raised the possibility of carrying out some aspects of experimental evolution using autocatalytic reaction networks, there remain many open challenges. In this review, we start by evaluating theoretical studies of ACSs specifically with a view to establish the conditions required for such chemical systems to exhibit self-reproduction and Darwinian evolution. Then, we follow with an extensive overview of experimental ACS systems and use the theoretically established conditions to critically evaluate these empirical systems for their potential to exhibit Darwinian evolution. We identify various technical and conceptual challenges limiting experimental progress and, finally, conclude with some remarks about open questions.
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Dauty, Marc, Thomas Georges, Camille Le Blanc, Bastien Louguet, Pierre Menu, and Alban Fouasson-Chailloux. "Reference Values of Forced Vital Capacity and Expiratory Flow in High-Level Cyclists." Life 11, no. 12 (November 25, 2021): 1293. http://dx.doi.org/10.3390/life11121293.
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Several studies have demonstrated that spirometric theoretical values may not be applicable to the high-level sports population. No reference values exist for high-level professional cyclists. We aimed to establish predictive spirometric values by reference equations. One hundred and forty-five French Caucasian high-level professional cyclists, aged 18–38, performed basic anthropometric assessment and spirometry during the medical evaluation at the beginning of the sport season. Measured values were compared with theoretical values. Predictive equations were established from anthropometric parameters to explain variations of spirometric parameters. High-level cyclists had significantly higher spirometric values than the theoretical values established from a general population, except for forced expiratory volume in one second (FEV1), forced vital capacity (FVC) and forced expiratory flow (FEF) at 25% of FVC. Only FVC and FEV1 were well predicted from body height. The FVC variation of 43.5% is explained by body height and weight. The FEV1 variation of 25.8% is explained only by body height. High-level cycling is associated with important respiratory adaptations depending on the body height and the sport specificity: intensive and prolonged endurance training. These findings are interesting for clinical individual application to diagnose obstructive disease and test reversibility with bronchodilator drugs.
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Wang, Kangyu, Zixuan Zhang, Shaokun Li, Jian Hu, Tao Liu, Yang Jiang, Jun Wu, et al. "Transcriptome-Wide Analysis for Ginsenoside Rb3 Synthesis-Related Genes and Study on the Expression of Methyl Jasmonate Treatment in Panax ginseng." Life 11, no. 5 (April 25, 2021): 387. http://dx.doi.org/10.3390/life11050387.
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Panax ginseng C. A. Meyer is a kind of renascent herb that belongs to the genus Panax in the family Araliaceae. It is a traditional Chinese precious herbal medicine with a long history of medicinal use. Ginsenoside Rb3 is one of the important active ingredients in ginseng and has important physiological activity in the treatment of many diseases. In this study, we screened and systematically analyzed the candidate genes related to ginsenoside Rb3 synthesis through bioinformatics methods; discussed the functions, expression patterns, and interactions of the genes related to ginsenoside Rb3 synthesis; and finally, selected seven genes, mainly PgRb3, that directly contribute to the synthesis of ginsenoside Rb3. This study provides a reference for revealing the expression rules of ginsenoside Rb3 synthesis-related genes and elucidating the regulatory mechanism of methyl jasmonate, lays a theoretical foundation for the research of ginsenoside Rb3 synthesis, and provides theoretical and technical support for the factory production of ginsenoside monomer saponins.
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George, Daniel, Stéphane Pallu, Céline Bourzac, Rkia Wazzani, Rachele Allena, Yves Rémond, and Hugues Portier. "Prediction of Cortical Bone Thickness Variations in the Tibial Diaphysis of Running Rats." Life 12, no. 2 (February 3, 2022): 233. http://dx.doi.org/10.3390/life12020233.
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A cell-mechanobiological model is used for the prediction of bone density variation in rat tibiae under medium and high mechanical loads. The proposed theoretical-numerical model has only four parameters that need to be identified experimentally. It was used on three groups of male Wistar rats under sedentary, moderate intermittent and continuous running scenarios over an eight week period. The theoretical numerical model was able to predict an increase in bone density under intermittent running (medium intensity mechanical load) and a decrease of bone density under continuous running (higher intensity mechanical load). The numerical predictions were well correlated with the experimental observations of cortical bone thickness variations, and the experimental results of cell activity enabled us to validate the numerical results predictions. The proposed model shows a good capacity to predict bone density variation through medium and high mechanical loads. The mechanobiological balance between osteoblast and osteoclast activity seems to be validated and a foreseen prediction of bone density is made available.
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Shevchyk, L. O., N. Ya Kravets, H. M. Holineі, M. A. Kryzhanovska, and M. I. Parubok. "КРЕМЕНЕЦЬКИЙ ПЕРІОД ТВОРЧОСТІ ВІДОМОГО ВЧЕНОГО ТА ПЕДАГОГА – КОСТЯНТИНА АДРІАНОВИЧА ТАТАРИНОВА." Scientific Issue Ternopil Volodymyr Hnatiuk National Pedagogical University. Series: Biology 82, no. 3 (October 1, 2022): 66–71. http://dx.doi.org/10.25128/2078-2357.22.3.10.
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K. A. Tatarinov was a multifaceted personality, he made a significant contribution to the development of paleozoology, hunting science, ornithology and teriology in Ukraine. The article describes the main events of the Kremenets period of the scientist's life and work. The described period dates from August 1958 to August 1963. While working in Kremenets, he not only a scientist, but also develops as a manager, starting his career in August 1958 as a senior lecturer at the Department of Zoology Kremenets Pedagogical Institute, after two years - an associate professor, and since February 1961 - head of the specified department. Konstantin Adrianovych during his work at the Kremenets Pedagogical Institute, showed himself as a talented teacher with deep theoretical knowledge, hardworking and persistent scientist. Already at that time he understood the need for domestic and foreign creative scientific cooperation scientists with the aim of developing a unified program of stationary faunistic and zoogeographic studies. During the short 6 years of work at the Department of Zoology of the Kremenets Pedagogical Institute, Kostyantyn Adrianovych systematically organized annual educational field trips, worked on the creation and replenishment of the educational (museum) collection of bird and mammal skins, and conducted intensive speleozological research. At this time the scientist begins the cycle paleozoological studies, in particular the study of the fossil fauna of caves Podillia, modern and fossil vertebrate fauna of the mountain system Prykarpattia and Ukrainian Carpathians. In general, the field of scientific research in this period is very diverse from paleontology, zoogeography, zoology to phenology nature and ecology of vertebrates. During this time, he prepared and published the textbooks "Textbook of Zoology" and "Vertebrate Zoology", published a number of scientific works on fossil birds, small mammals and dolphins of Podillia (60 publications in total). Scientific results studies quite fully represent faunal diversity and faunal wealth of vertebrate animals of Kremenets and its surroundings and cover the forest massifs of the Eastern Carpathians and Hologoro-Kremenetskyi highlands, dry meadows, cave groups of mammals.
In his pedagogical activities, he pays a lot of attention to highlighting contemporary achievements of zoology, the role of Ukrainian scientists in the study of the species and zoogeographic diversity of the vertebrate fauna of Kremenech region.
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Miele, Ylenia, Gábor Holló, István Lagzi, and Federico Rossi. "Shape Deformation, Budding and Division of Giant Vesicles and Artificial Cells: A Review." Life 12, no. 6 (June 6, 2022): 841. http://dx.doi.org/10.3390/life12060841.
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The understanding of the shape-change dynamics leading to the budding and division of artificial cells has gained much attention in the past few decades due to an increased interest in designing stimuli-responsive synthetic systems and minimal models of biological self-reproduction. In this respect, membranes and their composition play a fundamental role in many aspects related to the stability of the vesicles: permeability, elasticity, rigidity, tunability and response to external changes. In this review, we summarise recent experimental and theoretical work dealing with shape deformation and division of (giant) vesicles made of phospholipids and/or fatty acids membranes. Following a classic approach, we divide the strategies used to destabilise the membranes into two different types, physical (osmotic stress, temperature and light) and chemical (addition of amphiphiles, the addition of reactive molecules and pH changes) even though they often act in synergy when leading to a complete division process. Finally, we review the most important theoretical methods employed to describe the equilibrium shapes of giant vesicles and how they provide ways to explain and control the morphological changes leading from one equilibrium structure to another.
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Kim, Chunghwan, Won June Choi, Yisha Ng, and Wonmo Kang. "Mechanically Induced Cavitation in Biological Systems." Life 11, no. 6 (June 10, 2021): 546. http://dx.doi.org/10.3390/life11060546.
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Cavitation bubbles form in soft biological systems when subjected to a negative pressure above a critical threshold, and dynamically change their size and shape in a violent manner. The critical threshold and dynamic response of these bubbles are known to be sensitive to the mechanical characteristics of highly compliant biological systems. Several recent studies have demonstrated different biological implications of cavitation events in biological systems, from therapeutic drug delivery and microsurgery to blunt injury mechanisms. Due to the rapidly increasing relevance of cavitation in biological and biomedical communities, it is necessary to review the current state-of-the-art theoretical framework, experimental techniques, and research trends with an emphasis on cavitation behavior in biologically relevant systems (e.g., tissue simulant and organs). In this review, we first introduce several theoretical models that predict bubble response in different types of biological systems and discuss the use of each model with physical interpretations. Then, we review the experimental techniques that allow the characterization of cavitation in biologically relevant systems with in-depth discussions of their unique advantages and disadvantages. Finally, we highlight key biological studies and findings, through the direct use of live cells or organs, for each experimental approach.
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Mitsuhashi, Hiromi, Ryota Morikawa, Yoh Noguchi, and Masako Takasu. "Dissipative Particle Dynamics Simulations for Shape Change of Growing Lipid Bilayer Vesicles." Life 13, no. 2 (January 22, 2023): 306. http://dx.doi.org/10.3390/life13020306.
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The characteristic shape changes observed in the growth and division of L-form cells have been explained by several theoretical studies and simulations using a vesicle model in which the membrane area increases with time. In those theoretical studies, characteristic shapes such as tubulation and budding were reproduced in a non-equilibrium state, but it was not possible to incorporate deformations that would change the topology of the membrane. We constructed a vesicle model in which the area of the membrane increases using coarse-grained particles and analyzed the changes in the shape of growing membrane by the dissipative particle dynamics (DPD) method. In the simulation, lipid molecules were added to the lipid membrane at regular time intervals to increase the surface area of the lipid membrane. As a result, it was found that the vesicle deformed into a tubular shape or a budding shape depending on the conditions for adding lipid molecules. This suggests that the difference in the place where new lipid molecules are incorporated into the cell membrane during the growth of L-form cells causes the difference in the transformation pathway of L-form cells.
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Campos, Néstor, Jesús Alcalá-Reygosa, Scott C. Watson, Ioannis Kougkoulos, Adolfo Quesada-Román, and Nelson Grima. "Modeling the retreat of the Aneto Glacier (Spanish Pyrenees) since the Little Ice Age, and its accelerated shrinkage over recent decades." Holocene 31, no. 8 (April 25, 2021): 1315–26. http://dx.doi.org/10.1177/09596836211011678.
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The Aneto, located on the Maladeta Massif (Central Pyrenees), is the largest glacier of the Pyrenees. The glacier is 675 m long, occupies an area of 48.64 ha and has a maximum altitude of 3269 m. In this study, we present a detailed area, volume, ice thickness, and Equilibrium Line Altitude reconstruction of the glacier for different periods (LIA, 1957, 1983, 2000, 2006, 2015, and 2017) and analyze its retreat. To estimate the glacier extent during the LIA, the moraines were mapped by using photo interpretation techniques whereas for the recent stages digital satellite images and aerial photographs were used. Moreover, we estimated the topography of the glacier using a simple steady-state model that assumes a perfectly plastic ice rheology, which allowed reconstructing the theoretical ice profiles of the glacier. To reconstruct the ice surface, a digital elevation model was created and combined with the bedrock topography in order to obtain the ice thickness of each stage. The results of the study reveal a considerable retreat of the Aneto Glacier since the LIA. The length of the glacier has reduced from 1970 to 675 m from LIA to2017, and its tongue has retreated from 2385 to 3029 m a.s.l. Furthermore, the glaciated area has been reduced from 245 to 48.64 ha from LIA to 2017 and the ELA has risen from 2919 to 3139 m a.s.l. The data obtained indicates that in the LIA–2017 period the glacier volume has been reduced from 82.57 m × 106 m3 to 3.48 m × 106 m3 and the maximum ice thickness from 95 to 27m. We also reconstructed the climatic conditions, showing an increase in temperature of ~1.14°C from LIA to 2017. These data reveal a vast retreat of the glacier since the LIA, which has accelerated since the 1980’s and even more since the year 2000.
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Halley, J. W. "Some Factors from Theory, Simulation, Experiment and Proteomes in the Current Biosphere Supporting Deep Oceans as the Location of the Origin of Terrestrial Life." Life 12, no. 9 (August 28, 2022): 1330. http://dx.doi.org/10.3390/life12091330.
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Some standard arguments are reviewed supporting deep ocean trenches as a likely location for the origin of terrestrial life. An analysis of proteomes of contemporary prokaryotes carried out by this group is cited as supporting evidence, indicating that the original proteins were formed by quenching from temperatures close to the boiling point of water. Coarse-grained simulations of the network formation process which agree quite well with experiments of such quenches both in drying and rapid fluid emission from a hot to a cold fluid are also described and cited as support for such a scenario. We suggest further experiments, observations and theoretical and simulation work to explore this hypothesis.
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Li, Huiyun, Jine Quan, Sohel Rana, Yanmei Wang, Zhi Li, Qifei Cai, Shuhong Ma, Xiaodong Geng, and Zhen Liu. "The Molecular Network behind Volatile Aroma Formation in Pear (Pyrus spp. Panguxiang) Revealed by Transcriptome Profiling via Fatty Acid Metabolic Pathways." Life 12, no. 10 (September 26, 2022): 1494. http://dx.doi.org/10.3390/life12101494.
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Pears are popular table fruits, grown and consumed worldwide for their excellent color, aroma, and taste. Volatile aroma is an important factor affecting fruit quality, and the fatty acid metabolism pathway is important in synthesizing volatile aromas. Most of the white pear varieties cultivated in China are not strongly scented, which significantly affects their overall quality. Panguxiang is a white pear cultivar, but its aroma has unique components and is strong. The study of the mechanisms by which aroma is formed in Panguxiang is, therefore, essential to improving the quality of the fruit. The study analyzed physiological and transcriptome factors to reveal the molecular network behind volatile aroma formation in Panguxiang. The samples of Panguxiang fruit were collected in two (fruit development at 60, 90, 120, and 147 days, and fruit storage at 0, 7, 14, 21, and 28 days) periods. A total of nine sample stages were used for RNA extraction and paired-end sequencing. In addition, RNA quantification and qualification, library preparation and sequencing, data analysis and gene annotation, gene co-expression network analysis, and validation of DEGs through quantitative real-time PCR (qRT-;PCR) were performed in this study. The WGCNA identified yellow functional modules and several biological and metabolic pathways related to fatty acid formation. Finally, we identified seven and eight hub genes in the fatty acid synthesis and fatty acid metabolism pathways, respectively. Further analysis of the co-expression network allowed us to identify several key transcription factors related to the volatile aroma, including AP2/ERF-ERF, C3H, MYB, NAC, C2H2, GRAS, and Trihelix, which may also be involved in the fatty acid synthesis. This study lays a theoretical foundation for studying volatile compounds in pear fruits and provides a theoretical basis for related research in other fruits.
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Regenauer-Lieb, Klaus, Manman Hu, Christoph Schrank, Xiao Chen, Santiago Peña Clavijo, Ulrich Kelka, Ali Karrech, et al. "Cross-diffusion waves resulting from multiscale, multiphysics instabilities: application to earthquakes." Solid Earth 12, no. 8 (August 16, 2021): 1829–49. http://dx.doi.org/10.5194/se-12-1829-2021.
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Abstract. Theoretical approaches to earthquake instabilities propose shear-dominated source mechanisms. Here we take a fresh look at the role of possible volumetric instabilities preceding a shear instability. We investigate the phenomena that may prepare earthquake instabilities using the coupling of thermo-hydro-mechano-chemical reaction–diffusion equations in a THMC diffusion matrix. We show that the off-diagonal cross-diffusivities can give rise to a new class of waves known as cross-diffusion or quasi-soliton waves. Their unique property is that for critical conditions cross-diffusion waves can funnel wave energy into a stationary wave focus from large to small scale. We show that the rich solution space of the reaction–cross-diffusion approach to earthquake instabilities can recover classical Turing instabilities (periodic in space instabilities), Hopf bifurcations (spring-slider-like earthquake models), and a new class of quasi-soliton waves. Only the quasi-soliton waves can lead to extreme focussing of the wave energy into short-wavelength instabilities of short duration. The equivalent extreme event in ocean waves and optical fibres leads to the appearance of “rogue waves” and high energy pulses of light in photonics. In the context of hydromechanical coupling, a rogue wave would appear as a sudden fluid pressure spike. This spike is likely to cause unstable slip on a pre-existing (near-critically stressed) fault acting as a trigger for the ultimate (shear) seismic moment release.
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Lipus, Martin Peter, Felix Schölderle, Thomas Reinsch, Christopher Wollin, Charlotte Krawczyk, Daniela Pfrang, and Kai Zosseder. "Dynamic motion monitoring of a 3.6 km long steel rod in a borehole during cold-water injection with distributed fiber-optic sensing." Solid Earth 13, no. 1 (January 19, 2022): 161–76. http://dx.doi.org/10.5194/se-13-161-2022.
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Abstract. Fiber-optic distributed acoustic sensing (DAS) data find many applications in wellbore monitoring such as flow monitoring, formation evaluation and well integrity studies. For horizontal or highly deviated wells, wellbore fiber-optic installations can be conducted by mounting the sensing cable to a rigid structure (casing/tubing) which allows for a controlled landing of the cable. We analyze a cold-water injection phase in a geothermal well with a 3.6 km long fiber-optic installation mounted to a 3/4 in. sucker rod by using both DAS and distributed temperature sensing (DTS) data. During cold-water injection, we observe distinct vibrational events (shock waves) which originate in the reservoir interval and migrate up- and downwards. We use temperature differences from the DTS data to determine the theoretical thermal contraction and integrated DAS data to estimate the actual deformation of the rod construction. The results suggest that the rod experiences thermal stresses along the installation length – partly in the compressional and partly in the extensional regime. We find strong evidence that the observed vibrational events originate from the release of the thermal stresses when the friction of the rod against the borehole wall is overcome. Within this study, we show the influence of temperature changes on the acquisition of distributed acoustic/strain sensing data along a fiber-optic cable suspended along a rigid but freely hanging rod. We show that observed vibrational events do not necessarily originate from induced seismicity in the reservoir but instead can originate from stick–slip behavior of the rod construction that holds the measurement equipment.
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Almowallad, Sanaa, Leena S. Alqahtani, and Mohammad Mobashir. "NF-kB in Signaling Patterns and Its Temporal Dynamics Encode/Decode Human Diseases." Life 12, no. 12 (December 2, 2022): 2012. http://dx.doi.org/10.3390/life12122012.
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Defects in signaling pathways are the root cause of many disorders. These malformations come in a wide variety of types, and their causes are also very diverse. Some of these flaws can be brought on by pathogenic organisms and viruses, many of which can obstruct signaling processes. Other illnesses are linked to malfunctions in the way that cell signaling pathways work. When thinking about how errors in signaling pathways might cause disease, the idea of signalosome remodeling is helpful. The signalosome may be conveniently divided into two types of defects: phenotypic remodeling and genotypic remodeling. The majority of significant illnesses that affect people, including high blood pressure, heart disease, diabetes, and many types of mental illness, appear to be caused by minute phenotypic changes in signaling pathways. Such phenotypic remodeling modifies cell behavior and subverts normal cellular processes, resulting in illness. There has not been much progress in creating efficient therapies since it has been challenging to definitively confirm this connection between signalosome remodeling and illness. The considerable redundancy included into cell signaling systems presents several potential for developing novel treatments for various disease conditions. One of the most important pathways, NF-κB, controls several aspects of innate and adaptive immune responses, is a key modulator of inflammatory reactions, and has been widely studied both from experimental and theoretical perspectives. NF-κB contributes to the control of inflammasomes and stimulates the expression of a number of pro-inflammatory genes, including those that produce cytokines and chemokines. Additionally, NF-κB is essential for controlling innate immune cells and inflammatory T cells’ survival, activation, and differentiation. As a result, aberrant NF-κB activation plays a role in the pathogenesis of several inflammatory illnesses. The activation and function of NF-κB in relation to inflammatory illnesses was covered here, and the advancement of treatment approaches based on NF-κB inhibition will be highlighted. This review presents the temporal behavior of NF-κB and its potential relevance in different human diseases which will be helpful not only for theoretical but also for experimental perspectives.
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Hordijk, Wim, Mike Steel, and Stuart Kauffman. "Autocatalytic Sets Arising in a Combinatorial Model of Chemical Evolution." Life 12, no. 11 (October 26, 2022): 1703. http://dx.doi.org/10.3390/life12111703.
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The idea that chemical evolution led to the origin of life is not new, but still leaves open the question of how exactly it could have led to a coherent and self-reproducing collective of molecules. One possible answer to this question was proposed in the form of the emergence of an autocatalytic set: a collection of molecules that mutually catalyze each other’s formation and that is self-sustaining given some basic “food” source. Building on previous work, here we investigate in more detail when and how autocatalytic sets can arise in a simple model of chemical evolution based on the idea of combinatorial innovation with random catalysis assignments. We derive theoretical results, and compare them with computer simulations. These results could suggest a possible step towards the (or an) origin of life.
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Schwichtenberg, Berit, Florian Fusseis, Ian B. Butler, and Edward Andò. "Biotite supports long-range diffusive transport in dissolution–precipitation creep in halite through small porosity fluctuations." Solid Earth 13, no. 1 (January 10, 2022): 41–64. http://dx.doi.org/10.5194/se-13-41-2022.
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Abstract. Phyllosilicates are generally regarded to have a reinforcing effect on chemical compaction by dissolution–precipitation creep (DPC) and thereby influence the evolution of hydraulic rock properties relevant to groundwater resources and geological repositories as well as fossil fuel reservoirs. We conducted oedometric compaction experiments on layered NaCl–biotite samples to test this assumption. In particular, we aim to analyse slow chemical compaction processes in the presence of biotite on the grain scale and determine the effects of chemical and mechanical feedbacks. We used time-resolved (4-D) microtomographic data to capture the dynamic evolution of the porosity in layered NaCl–NaCl/biotite samples over 1619 and 1932 h of compaction. Percolation analysis in combination with advanced digital volume correlation techniques showed that biotite grains influence the dynamic evolution of porosity in the sample by promoting a reduction of porosity in their vicinity. However, the lack of preferential strain localisation around phyllosilicates and a homogeneous distribution of axial shortening across the sample suggests that the porosity reduction is not achieved by pore collapse but by the precipitation of NaCl sourced from outside the NaCl–biotite layer. Our observations invite a renewed discussion of the effect of phyllosilicates on DPC, with a particular emphasis on the length scales of the processes involved. We propose that, in our experiments, the diffusive transport processes invoked in classical theoretical models of DPC are complemented by chemo-mechanical feedbacks that arise on longer length scales. These feedbacks drive NaCl diffusion from the marginal pure NaCl layers into the central NaCl–biotite mixture over distances of several hundred micrometres and several grain diameters. Such a mechanism was first postulated by Merino et al. (1983).
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Mishra, Sujeet Kumar, Kunhe Li, Simon Brauburger, Arnab Bhattacherjee, Nestor Norio Oiwa, and Dieter W. Heermann. "Superstructure Detection in Nucleosome Distribution Shows Common Pattern within a Chromosome and within the Genome." Life 12, no. 4 (April 6, 2022): 541. http://dx.doi.org/10.3390/life12040541.
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Nucleosome positioning plays an important role in crucial biological processes such as replication, transcription, and gene regulation. It has been widely used to predict the genome’s function and chromatin organisation. So far, the studies of patterns in nucleosome positioning have been limited to transcription start sites, CTCFs binding sites, and some promoter and loci regions. The genome-wide organisational pattern remains unknown. We have developed a theoretical model to coarse-grain nucleosome positioning data in order to obtain patterns in their distribution. Using hierarchical clustering on the auto-correlation function of this coarse-grained nucleosome positioning data, a genome-wide clustering is obtained for Candida albicans. The clustering shows the existence beyond hetero- and eu-chromatin inside the chromosomes. These non-trivial clusterings correspond to different nucleosome distributions and gene densities governing differential gene expression patterns. Moreover, these distribution patterns inside the chromosome appeared to be conserved throughout the genome and within species. The pipeline of the coarse grain nucleosome positioning sequence to identify underlying genomic organisation used in our study is novel, and the classifications obtained are unique and consistent.
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Dong, Haoran, Hui Chen, Bing Xu, Yingru Tan, Qun Ling, and Liang Shi. "Citric Acid Changes the Fingerprint of Flavonoids and Promotes Their Accumulation in Phellinus igniarius (L.) Quél." Life 13, no. 1 (December 26, 2022): 68. http://dx.doi.org/10.3390/life13010068.
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Phellinus igniarius is a valuable medicinal fungus. P. igniarius is rich in a variety of chemical compounds with medicinal value, among which are flavonoids. Therefore, increasing the content of flavonoids in P. igniarius is beneficial for its potential use in medicinal applications. This study demonstrated that exogenous treatment with citric acid (CA) could significantly increase flavonoid accumulation in P. igniarius. Additionally, we found that CA induced the biosynthesis of flavonoids in a concentration- and time-dependent manner. The flavonoid content could be increased up to 60.96 mg/g when using the treatment with 2.77 mM citric acid for 69.74 h, which was determined by using the response surface method. The changes in the fingerprint profiles of P. igniarius flavonoids with the treatment of CA as an exogenous inducer were also analyzed. In this study, the effect of citric acid as the exogenous inducer on the flavonoid content of P. igniarius was studied, and the processing conditions were optimized through the surface response curve. This approach provides novel insights and a theoretical basis for the production of high-quality P. igniarius.
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Xu, Qingshan, Qianqian Wei, Yali Kong, Lianfeng Zhu, Wenhao Tian, Jing Huang, Lin Pan, Qianyu Jin, Junhua Zhang, and Chunquan Zhu. "Unearthing the Alleviatory Mechanisms of Brassinolide in Cold Stress in Rice." Life 12, no. 6 (June 2, 2022): 833. http://dx.doi.org/10.3390/life12060833.
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Cold stress inhibits rice germination and seedling growth. Brassinolide (BR) plays key roles in plant growth, development, and stress responses. In this study, we explored the underlying mechanisms whereby BR helps alleviate cold stress in rice seedlings. BR application to the growth medium significantly increased seed germination and seedling growth of the early rice cultivar “Zhongzao 39” after three days of cold treatment. Specifically, BR significantly increased soluble protein and soluble sugar contents after three days of cold treatment. Moreover, BR stimulated the activity of superoxide dismutase, catalase, peroxidase, and ascorbate peroxidase; thereby alleviating cold-induced damage and increasing glutathione content and the GSH/GSSG ratio while concomitantly reducing H2O2 content. BR upregulated the expression levels of cold-response-related genes, including OsICE1, OsFer1, OsCOLD1, OsLti6a, OsSODB, OsMyb, and OsTERF2, and downregulated that of OsWRKY45, overall alleviating cold stress symptoms. Thus, BR not only upregulated cellular osmotic content and the antioxidant enzyme system to maintain the physiological balance of reactive oxygen species under cold but, additionally, it regulated the expression of cold-response-related genes to alleviate cold stress symptoms. These results provide a theoretical basis for rice breeding for cold resistance using young seedlings.
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Ma, Xiaolong, Xiaolin Fan, Gangzheng Wang, Ruiping Xu, Lianlian Yan, Yan Zhou, Yuhua Gong, Yang Xiao, and Yinbing Bian. "Enhanced Expression of Thaumatin-like Protein Gene (LeTLP1) Endows Resistance to Trichoderma atroviride in Lentinula edodes." Life 11, no. 8 (August 23, 2021): 863. http://dx.doi.org/10.3390/life11080863.
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Lentinula edodes (shiitake mushrooms) is heavily affected by the infection of Trichoderma atroviride, causing yield loss and decreases quality in shiitake mushrooms. The selection and breeding of fungal-resistant L. edodes species are an important approach to protecting L. edodes from T. atroviride infection. Herein, a highly resistant L. edodes strain (Y3334) and a susceptible strain (Y55) were obtained by using a resistance evaluation test. Transcriptome analyses and qRT-PCR detection showed that the expression level of LeTLP1 (LE01Gene05009) was strongly induced in response to T. atroviride infection in the resistant Y3334. Then, LeTLP1-silenced and LeTLP1-overexpression transformants were obtained. Overexpression of LeTLP1 resulted in resistance to T. atroviride. Compared with the parent strain Y3334, LeTLP1-silenced transformants had reduced resistance relative to T. atroviride. Additionally, the LeTLP1 protein (Y3334) exhibited significant antifungal activity against T. atroviride. These findings suggest that overexpression of LeTLP1 is a major mechanism for the resistance of L. edodes to T. atroviride. The molecular basis provides a theoretical basis for the breeding of resistant L. edodes strains and can eventually contribute to the mushroom cultivation industry and human health.
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German, R. Z. "Taxonomic Survivorship Curves." Short Courses in Paleontology 4 (1991): 175–84. http://dx.doi.org/10.1017/s247526300000218x.
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Taxonomic survivorship curves were derived from ecological and biomedical techniques for examining population structure and demographic trends. In simplest form, survivorship curves are graphical representations of the numbers or proportions of taxa that survive specific lengths of time. These curves provide a basis for calculating longevity, extinction rates, and other “life history” attributes of higher taxa. Survivorship curves have also been fruitful for comparative studies of contemporaneous higher taxa (e.g., cohorts), or among higher taxa that existed at different periods of geologic time. Various modifications of the concepts, both theoretical and methodological, have changed the way these curves are used to analyze paleontologic data.
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Fumero, Ascensión, Rosario J. Marrero, Teresa Olivares, Francisco Rivero, Yolanda Alvarez-Pérez, Carmen Pitti, and Wenceslao Peñate. "Neuronal Activity during Exposure to Specific Phobia through fMRI: Comparing Therapeutic Components of Cognitive Behavioral Therapy." Life 12, no. 8 (July 27, 2022): 1132. http://dx.doi.org/10.3390/life12081132.
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Cognitive behavioral therapy (CBT) packages for anxiety disorders, such as phobias, usually include gradual exposure to anxious contexts, positive self-verbalizations, and relaxation breathing. The objective of this research was to analyze the specific neural activation produced by the self-verbalizations (S) and breathing (B) included in CBT. Thirty participants with clinical levels of a specific phobia to small animals were randomly assigned to three fMRI conditions in which individuals were exposed to phobic stimuli in real images: a group underwent S as a technique to reduce anxiety; a second group underwent B; and a control group underwent exposure only (E). Simple effects showed higher brain activation comparing E > S, E > B, and S > B. In particular, in the E group, compared to the experimental conditions, an activation was observed in sensory-perceptive and prefrontal and in other regions involved in the triggering of emotion (i.e., amygdala, supplementary motor area, and cingulate gyrus) as well as an activation associated with interoceptive sensitivity (i.e., insula and cingulate cortex). According to the specific tool used, discrepancies in the neural changes of CBT efficacy were observed. We discuss the theoretical implications according to the dual model of CBT as a set of therapeutic tools that activate different processes.
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Peng, Cui, Yang Liu, Liangyong Shui, Zhongyi Zhao, Xinfang Mao, and Zhongyuan Liu. "Mechanisms of Action of the Antimicrobial Peptide Cecropin in the Killing of Candida albicans." Life 12, no. 10 (October 11, 2022): 1581. http://dx.doi.org/10.3390/life12101581.
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The development of drug resistance has caused fungal infections to become a global health concern. Antimicrobial peptides (AMPs) offer a viable solution to these pathogens due to their resistance to drug resistance and their diverse mechanisms of actions, which include direct killing and immunomodulatory properties. The peptide Cecropin, which is expressed by genetically engineered bacteria, has antifungal effects on Candida albicans. The minimal inhibitory concentration (MIC) and the minimal fungicidal concentration (MFC) of Candida albicans were 0.9 μg/mL and 1.8 μg/mL, respectively, detected by the micro-broth dilution method. According to the killing kinetics, the MFC of Cecropin could kill Candida albicans in 40 min. The electron microscope indicated that Cecropin could cause the cell wall to become rough and nicked, eventually killing Candida albicans. The effects of Cecropin on the cell membrane of treated C. albicans, using the 1,6-diphenyl-1,3,5-hexatriene and propidium iodide protocol, showed that they could change the permeability and fluidity, destroy it, and lead to cell necrosis. In addition, Cecropin can also induce cells to produce excessive reactive oxygen species, causing changes in the mitochondrial membrane potential. Therefore, this study provides a certain theoretical basis for the antifungal infection of new antifungal agents.
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Olivares-Hernández, Alejandro, Luis Figuero-Pérez, José Pablo Miramontes-González, Álvaro López-Gutiérrez, Rogelio González-Sarmiento, Juan Jesús Cruz-Hernández, and Emilio Fonseca-Sánchez. "Immune System Disorders, Cancer and Viral Infections: A New Treatment Opportunity for the Immune Checkpoint Inhibitors." Life 11, no. 12 (December 15, 2021): 1400. http://dx.doi.org/10.3390/life11121400.
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The relationship between viral infections and cancer is well known and has been established for decades. Multiple tumours are generated from alterations secondary to viral infections 2 resulting from a dysregulation of the immune system in many cases. Certain causal relationships, such as that between the Epstein–Barr virus (EBV) in nasopharyngeal cancer or hepatitis C and B viruses in hepatocarcinoma, have been clearly established, and their implications for the prognosis and treatment of solid tumours are currently unknown. Multiple studies have evaluated the role that these infections may have in the treatment of solid tumours using immunotherapy. A possible relationship between viral infections and an increased response to immune checkpoint inhibitors (ICIs) has been established at a theoretical level in solid neoplasms, such as EBV-positive cavum cancer and human papillomavirus (HPV)-positive and oropharyngeal cancer. These could yield a greater response associated with the activation of the immune system secondary to viral infection, the consequence of which is an increase in survival in these patients. That is why the objective of this review is to assess the different studies or clinical trials carried out in patients with solid tumours secondary to viral infections and their relationship to the response to ICIs.
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Savchenko, Tatyana, and Konstantin Tikhonov. "Oxidative Stress-Induced Alteration of Plant Central Metabolism." Life 11, no. 4 (April 1, 2021): 304. http://dx.doi.org/10.3390/life11040304.
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Oxidative stress is an integral component of various stress conditions in plants, and this fact largely determines the substantial overlap in physiological and molecular responses to biotic and abiotic environmental challenges. In this review, we discuss the alterations in central metabolism occurring in plants experiencing oxidative stress. To focus on the changes in metabolite profile associated with oxidative stress per se, we primarily analyzed the information generated in the studies based on the exogenous application of agents, inducing oxidative stress, and the analysis of mutants displaying altered oxidative stress response. Despite of the significant variation in oxidative stress responses among different plant species and tissues, the dynamic and transient character of stress-induced changes in metabolites, and the strong dependence of metabolic responses on the intensity of stress, specific characteristic changes in sugars, sugar derivatives, tricarboxylic acid cycle metabolites, and amino acids, associated with adaptation to oxidative stress have been detected. The presented analysis of the available data demonstrates the oxidative stress-induced redistribution of metabolic fluxes targeted at the enhancement of plant stress tolerance through the prevention of ROS accumulation, maintenance of the biosynthesis of indispensable metabolites, and production of protective compounds. This analysis provides a theoretical basis for the selection/generation of plants with improved tolerance to oxidative stress and the development of metabolic markers applicable in research and routine agricultural practice.
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Wu, Yanqing, Xiang Cai, and Yuhan Tang. "Outcomes of Low-Temperature Stress on Biological Alterations within Pothos (Epipremnum aureum) Leaves." Life 12, no. 9 (September 14, 2022): 1432. http://dx.doi.org/10.3390/life12091432.
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Pothos (Epipremnum aureum) is a commonly used indoor ornamental foliage, particularly in the middle and lower regions of the Yangtze River in China. It typically grows in the tropical area, and it is yet unclear whether prolonged winter temperatures cause plant damage and impact its development. In this study, the E. aureum chilling injury response was explored by maintaining it at 1 °C. Based on the acquired results, low-temperature stress (LTS) induced wilting and yellowing of leaves and diminished chloroplast pigment concentrations, particularly the chlorophyll b content. LTS also induced overproduction of reactive oxygen species (ROS) within E. aureum and enhanced the relative electrical conductivity and superoxide dismutase activity. In addition, with prolonged LTS, the anatomical structure of E. aureum was severely damaged, resulting in a marked reduction in the photochemical activity of the photosystem Ⅱ reaction center and suppressed photosynthesis. Moreover, results of the transcriptomic analysis revealed that LTS induced the expression of genes involved in the α-linolenic acid metabolic pathway, plant hormone network, host plant–pathogen association, and MAPK axis, suggesting that LTS would activate its resistant response to cold stress. These results unraveled the physiological and transcriptomical response of E. aureum to chilling injury, which would lay a theoretical foundation for the cultivation of low-temperature-tolerant varieties of E. aureum.
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Wang, Meiyao, Jun Zhou, Shengyan Su, Yongkai Tang, Gangchun Xu, Jianlin Li, Fan Yu, et al. "Comparative Transcriptome Analysis on the Regulatory Mechanism of Thoracic Ganglia in Eriocheir sinensis at Post-Molt and Inter-Molt Stages." Life 12, no. 8 (August 3, 2022): 1181. http://dx.doi.org/10.3390/life12081181.
Full textAbstract:
Eriocheir sinensis is an aquatic species found distributed worldwide. It is found in the Yangtze River of China, where the commercial fishing of this valuable catadromous aquatic species has been banned. As an important member of the phylum Arthropoda, E. sinensis grows by molting over its whole lifespan. The central nervous system of Eriocheir sinensis plays an important regulatory role in molting growth. Nevertheless, there are no reports on the regulatory mechanisms of the nervous system in E. sinensis during the molting cycle. In this study, a comparative transcriptome analysis of E. sinensis thoracic ganglia at post-molt and inter-molt stages was carried out for the first time to reveal the key regulatory pathways and functional genes operating at the post-molt stage. The results indicate that pathways and regulatory genes related to carapace development, tissue regeneration, glycolysis and lipolysis and immune and anti-stress responses were significantly differentially expressed at the post-molt stage. The results of this study lay a theoretical foundation for research on the regulatory network of the E. sinensis nervous system during the post-molt developmental period. Detailed knowledge of the regulatory network involved in E. sinensis molting can be used as a basis for breeding improved E. sinensis species, recovery of the wild E. sinensis population and prosperous development of the E. sinensis artificial breeding industry.
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Lee, Benjamin D., and Eugene V. Koonin. "Viroids and Viroid-like Circular RNAs: Do They Descend from Primordial Replicators?" Life 12, no. 1 (January 12, 2022): 103. http://dx.doi.org/10.3390/life12010103.
Full textAbstract:
Viroids are a unique class of plant pathogens that consist of small circular RNA molecules, between 220 and 450 nucleotides in size. Viroids encode no proteins and are the smallest known infectious agents. Viroids replicate via the rolling circle mechanism, producing multimeric intermediates which are cleaved to unit length either by ribozymes formed from both polarities of the viroid genomic RNA or by coopted host RNAses. Many viroid-like small circular RNAs are satellites of plant RNA viruses. Ribozyviruses, represented by human hepatitis delta virus, are larger viroid-like circular RNAs that additionally encode the viral nucleocapsid protein. It has been proposed that viroids are direct descendants of primordial RNA replicons that were present in the hypothetical RNA world. We argue, however, that much later origin of viroids, possibly, from recently discovered mobile genetic elements known as retrozymes, is a far more parsimonious evolutionary scenario. Nevertheless, viroids and viroid-like circular RNAs are minimal replicators that are likely to be close to the theoretical lower limit of replicator size and arguably comprise the paradigm for replicator emergence. Thus, although viroid-like replicators are unlikely to be direct descendants of primordial RNA replicators, the study of the diversity and evolution of these ultimate genetic parasites can yield insights into the earliest stages of the evolution of life.
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Paschek, Klaus, Kai Kohler, Ben K. D. Pearce, Kevin Lange, Thomas K. Henning, Oliver Trapp, Ralph E. Pudritz, and Dmitry A. Semenov. "Possible Ribose Synthesis in Carbonaceous Planetesimals." Life 12, no. 3 (March 10, 2022): 404. http://dx.doi.org/10.3390/life12030404.
Full textAbstract:
The origin of life might be sparked by the polymerization of the first RNA molecules in Darwinian ponds during wet-dry cycles. The key life-building block ribose was found in carbonaceous chondrites. Its exogenous delivery onto the Hadean Earth could be a crucial step toward the emergence of the RNA world. Here, we investigate the formation of ribose through a simplified version of the formose reaction inside carbonaceous chondrite parent bodies. Following up on our previous studies regarding nucleobases with the same coupled physico-chemical model, we calculate the abundance of ribose within planetesimals of different sizes and heating histories. We perform laboratory experiments using catalysts present in carbonaceous chondrites to infer the yield of ribose among all pentoses (5Cs) forming during the formose reaction. These laboratory yields are used to tune our theoretical model that can only predict the total abundance of 5Cs. We found that the calculated abundances of ribose were similar to the ones measured in carbonaceous chondrites. We discuss the possibilities of chemical decomposition and preservation of ribose and derived constraints on time and location in planetesimals. In conclusion, the aqueous formose reaction might produce most of the ribose in carbonaceous chondrites. Together with our previous studies on nucleobases, we found that life-building blocks of the RNA world could be synthesized inside parent bodies and later delivered onto the early Earth.
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Zeng, Xing, Tongtong Pei, Yongfeng Song, Pei Guo, Huilan Zhang, Xin Li, Hao Li, Hong Di, and Zhenhua Wang. "A Three-Year Plant Study of Salt-Tolerant Transgenic Maize Showed No Effects on Soil Enzyme Activity and Nematode Community." Life 12, no. 3 (March 11, 2022): 412. http://dx.doi.org/10.3390/life12030412.
Full textAbstract:
The environmental effects of genetically modified crops are now a global concern. It is important to monitor the potential environmental impact of transgenic corn after commercial release. In rhizosphere soil, plant roots interact with soil enzymes and microfauna, which can be affected by the transgenes of genetically modified crops. To determine the long-term impact of transgenic plant cultivation, we conducted a field study for 3 consecutive years (2018–2020) and observed the enzyme activities and nematode populations in plots planted with transgenic maize BQ-2, non-transgenic wild-type maize (Qi319), and inbred line B73. We took soil samples from three cornfields at four different growth stages (V3, V9, R1, and R6 stages); determined soil dehydrogenase, urease, and sucrase activities; and collected and identified soil nematodes to the genus level. The results demonstrated seasonal variations in dehydrogenase, urease, and sucrase activities. However, there was a consistent trend of change. The generic composition and diversity indices of the soil nematodes did not significantly differ, although significant seasonal variation was found in the individual densities of the principal trophic groups and the diversity indices of the nematodes in all three cornfields. The results of the study suggest that a 3-year cultivation of transgenic corn had no significant effects on soil enzyme activity and the soil nematode community. This study provides a theoretical basis for the environmental impact monitoring of transgenic corn.
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Zhou, Tong, Haiqi Zhang, Meng Chen, Yingping Zhang, Guobin Chen, Guiwei Zou, and Hongwei Liang. "Identification and Expression Analysis of Wnt2 Gene in the Sex Differentiation of the Chinese Soft-Shelled Turtle (Pelodiscus sinensis)." Life 13, no. 1 (January 9, 2023): 188. http://dx.doi.org/10.3390/life13010188.
Full textAbstract:
The Chinese soft-shelled turtle (Pelodiscus sinensis) is an important freshwater aquaculture animal in China. The Wnt gene family plays important regulatory roles in the development and growth of mammals. However, the precise function of these family genes has not been well understood in the sex differentiation of Chinese soft-shelled turtles. Here, we cloned a member of the Wnt family, Wnt2, which obtained a 1077 bp open reading frame that encoded a 358-aa protein. The putative amino acid sequences of proteins are exceeded 80% identical to other turtles. The expression level of Wnt2 peaked at the 14th stage both in female and male embryos during the early gonadal differentiation period of Chinese soft-shelled turtles, which occurred before gonadal differentiation. Wnt2 mRNA was expressed at higher levels in the brains and gonads of mature P. sinensis females compared with those in mature males. Wnt agonists significantly affected the expression level of Wnt2 during the gonadal differentiation period. After Wnt agonists (1.0 μg/μL, 2.5 μg/μL, 5.0 μg/μL) treatment, the expression level of the Wnt2 generally appeared to have an inverted-V trend over time in female embryonic gonads. The results suggested that Wnt2 may participate in the regulation of gonad development in P. sinensis during the early embryonic stages. These results could provide a theoretical basis for the reproduction process of the Chinese soft-shelled turtle.
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Du, Kun, Yang Yang, Jinping Li, Ming Wang, Jinjin Jiang, Jian Wu, Yujie Fang, Yang Xiang, and Youping Wang. "Functional Analysis of Bna-miR399c-PHO2 Regulatory Module Involved in Phosphorus Stress in Brassica napus." Life 13, no. 2 (January 22, 2023): 310. http://dx.doi.org/10.3390/life13020310.
Full textAbstract:
Phosphorus stress is one of the important factors restricting plant growth and development, and the microRNA (miRNA) family is involved in the regulation of the response to plant nutrient stress by repressing the expression of target genes at the post-transcriptional or translational level. miR399 is involved in the transportation of phosphate in multiple plants by improving tolerance to low Pi conditions. However, the effect of miR399 on the response of low Pi stress in rapeseed (Brassica napus L.) is unclear. The present study showed a significant increase in taproot length and lateral root number of plants overexpressing Bna-miR399c, while the biomass and Pi accumulation in shoots and roots increased, and the anthocyanin content decreased and chlorophyll content improved under low Pi stress. The results illustrate that Bna-miR399c could enhance the uptake and transportation of Pi in soil, thus making B. napus more tolerant to low Pi stress. Furthermore, we confirmed that BnPHO2 is one of the targets of Bna-miR399c, and the rejection of Pi in rapeseed seedlings increased due to the overexpression of BnPHO2. Hence, we suggest that miR399c-PHO2 module can effectively regulate the homeostasis of Pi in B. napus. Our study can also provide the theoretical basis for germplasm innovation and the design of intelligent crops with low nutrient input and high yield to achieve the dual objectives of income and yield increase and environmental protection in B. napus.