Subdiscipline Of Biology Research Articles

HEOM‐QUICK2: A general‐purpose simulator for fermionic many‐body open quantum systems—An update

AbstractMany‐body open quantum systems (OQSs) have a profound impact on various subdisciplines of physics, chemistry, and biology. Thus, the development of a computer program capable of accurately, efficiently, and versatilely simulating many‐body OQSs is highly desirable. In recent years, we have focused on the advancement of numerical algorithms based on the fermionic hierarchical equations of motion (HEOM) theory. Being in‐principle exact, this approach allows for the precise characterization of many‐body correlations, non‐Markovian memory, and non‐equilibrium thermodynamic conditions. These efforts now lead to the establishment of a new computer program, HEOM for QUantum Impurity with a Correlated Kernel, version 2 (HEOM‐QUICK2), which, to the best of our knowledge, is currently the only general‐purpose simulator for fermionic many‐body OQSs. Compared with version 1, the HEOM‐QUICK2 program features more efficient solvers for stationary states, more accurate treatment of non‐Markovian memory, and improved numerical stability for long‐time dissipative dynamics. Integrated with quantum chemistry software, HEOM‐QUICK2 has become a valuable theoretical tool for the precise simulation of realistic many‐body OQSs, particularly the single atomic or molecular junctions. Furthermore, the unprecedented precision achieved by HEOM‐QUICK2 enables accurate simulation of low‐energy spin excitations and coherent spin relaxation. The unique usefulness of HEOM‐QUICK2 is demonstrated through several examples of strongly correlated quantum impurity systems under non‐equilibrium conditions. Thus, the new HEOM‐QUICK2 program offers a powerful and comprehensive tool for studying many‐body OQSs with exotic quantum phenomena and exploring applications in various disciplines.This article is categorized under: Data Science > Computer Algorithms and Programming Software > Simulation Methods Theoretical and Physical Chemistry > Statistical Mechanics

Three-dimensional reconstruction of high latitude bamboo coral via X-ray microfocus Computed Tomography

The skeletons of long-lived bamboo coral (Family Keratoisididae) are promising archives for deep-water palaeoceanographic reconstructions as they can record environmental variation at sub-decadal resolution in locations where in-situ measurements lack temporal coverage. Yet, detailed three dimensional (3D) characterisations of bamboo coral skeletal architecture are not routinely available and non-destructive investigations into microscale variations in calcification are rare. Here, we provide high-resolution micro-focus computed tomography (µCT) data of skeletal density for two species of bamboo coral (Acanella arbuscula: 5 specimens, voxel size, 15 µm (central branch scans) and 50 µm (complete structure scan); Keratoisis sp.: 4 specimens, voxel size, 15 µm) collected from the Labrador Sea and Baffin Bay deep-water basins, Eastern Canadian Arctic. These data provide reference models useful for developing methods to assess structural integrity and other fine-scale complexities in many biological, geological, and industrial systems. This will be of wider value to those investigating structural composition, arrangement and/or composition of complex architecture within the fields and subdisciplines of biology, ecology, medicine, environmental geology, and structural engineering.

Cryptic or underworked? Taxonomic revision of the Antistrophus rufus species complex (Cynipoidea, Aulacideini)

Cryptic species present challenges across many subdisciplines of biology. Not all “cryptic” species, however, are truly cryptic; many are simply underexplored morphologically. We examined this idea for the Antistrophus rufus species complex, which previously contained three species thought to be morphologically cryptic. To determine whether the A. rufus complex are truly cryptic species, we assessed species boundaries of members of the A. rufus species complex using morphological, ecological, and DNA barcode data, and tested whether a set of 50 morphological characters could adequately diagnose these species. We revealed that this complex includes five species, and that there are useful phenotypic diagnostic characters for all members of this species complex. This enabled redescription of four species and the description of Antistrophus laurenae Nastasi, sp. nov., which induces externally inconspicuous galls in stems of Silphium integrifolium Michx., a host not associated with other members of the complex. We use these new diagnostic characters to construct a key to the five species of the rufus complex. We conclude that the A. rufus complex was not a true case of cryptic species. Our Bayesian analysis of DNA barcode data suggests possible cospeciation of members of the rufus complex and their Silphium host plants, but further study is necessary to better understand the evolution of host use in the lineage.

Symbiosis takes a front and center role in biology.

All animals and plants likely require interactions with microbes, often in strong, persistent symbiotic associations. While the recognition of this phenomenon has been slow in coming, it will impact most, if not all, subdisciplines of biology.

Integration Review of Project Based Learning in Biology Education: A Systematic Literature Synthesis of Education Levels, Biology Subdisciplines, Research Methodologies and Learning Competencies

Project-Based Learning (PjBL) has become an increasingly popular learning approach in many fields, including biology. The research conducted a systematic review of the literature on the implementation and effectiveness of PjBL in biology education, especially in the period 2019–2023. The study explores the use of PjBL in various subdisciplines of biology, education, and research methodologies, as well as integrating a variety of targeted learning and competence approaches. Colleges widely adopt PjBL, focusing on developing students' cognitive, affective, and psychomotor abilities. The study also highlights the various learning methods integrated into the pjBL, including laboratory experiments, field activities, and reflection. The findings confirm that PjBL is an effective educational strategy for improving student understanding of concepts, critical thinking skills, and learning motivation. This approach supports holistic and applied learning experiences, integrating theory with real practice, as well as developing skills essential to students in the 21st century. The study provides a comprehensive insight into the current trends and potential of PjBL in biology education, as well as recommending directions for future education research and practice.

Epistemology of synthetic biology: a new theoretical framework based on its potential objects and objectives.

Synthetic biology is a new research field which attempts to understand, modify, and create new biological entities by adopting a modular and systemic conception of the living organisms. The development of synthetic biology has generated a pluralism of different approaches, bringing together a set of heterogeneous practices and conceptualizations from various disciplines, which can lead to confusion within the synthetic biology community as well as with other biological disciplines. I present in this manuscript an epistemological analysis of synthetic biology in order to better define this new discipline in terms of objects of study and specific objectives. First, I present and analyze the principal research projects developed at the foundation of synthetic biology, in order to establish an overview of the practices in this new emerging discipline. Then, I analyze an important scientometric study on synthetic biology to complete this overview. Afterwards, considering this analysis, I suggest a three-level classification of the object of study for synthetic biology (which are different kinds of living entities that can be built in the laboratory), based on three successive criteria: structural hierarchy, structural origin, functional origin. Finally, I propose three successively linked objectives in which synthetic biology can contribute (where the achievement of one objective led to the development of the other): interdisciplinarity collaboration (between natural, artificial, and theoretical sciences), knowledge of natural living entities (past, present, future, and alternative), pragmatic definition of the concept of "living" (that can be used by biologists in different contexts). Considering this new theoretical framework, based on its potential objects and objectives, I take the position that synthetic biology has not only the potential to develop its own new approach (which includes methods, objects, and objectives), distinct from other subdisciplines in biology, but also the ability to develop new knowledge on living entities.

Integrative revision of species limits in the genus Schiffornis (Aves: Tityridae) reveals cryptic diversity in the Neotropics

Abstract Accurate species delimitation is essential for many biological subdisciplines. Nonetheless, current species diversity remains incompletely documented even in well-studied groups such as birds. Here, we take an integrative approach to examine species limits in the genus Schiffornis, a widespread group of dull-plumaged, whistle-voiced suboscine passerines of Neotropical humid-forest understory, currently considered to comprise seven species. We measured geographic variation in song, morphology, and mitochondrial and genome-wide nuclear markers to resolve the taxonomy of the genus. We show that Schiffornis comprises 13 separately evolving population lineages, of which most qualify as species taxa under all species definitions. These include a cryptic new species, several species splits, and the resurrection of a morphologically undifferentiated, but vocally and genetically distinct, taxon that was synonymized nearly a century ago in the Schiffornis turdina complex. We also found several hitherto unnoticed contact zones between diverging lineages and a leapfrog pattern of geographic song variation in the S. turdina complex, and we highlight potential avenues of further research of this genus.

The Whole Is Greater Than The Sum of Its Parts: Large-scale Phenomena Arising from Small-Scale Biophysical Processes.

The symposium "Large-scale biological phenomena arising from small-scale biophysical processes" at the SICB 2023 Annual General Meeting focused on the cross-disciplinary exploration of emergent phenomena in biology. Interactions between cells or organisms at small scales within a system can govern patterns occurring at larger scales in space, time, or biological complexity. This theme recurs in many sub-disciplines of biology, including cell and developmental biology, evolution, and ecology. This symposium, and the associated special issue introduced here, showcases a wide range of cross-disciplinary collaborations among biologists, physicists, and engineers. Technological advancements in microscopy and microfluidics, as well as complementary advances in mathematical modelling and associated theory demonstrate the timeliness of this issue. This introduction seeks to provide useful background information to place the studies within this issue in a broader biophysical context and highlight similarities in ideas and approaches across systems and sub-disciplines. We hope to demonstrate that cross-disciplinary research linking small-scale biophysics to larger-scale emergent phenomena can help us understand problems ranging from single-cell behaviors to tissue formation and function, evolution of form, and the dynamics of communities.

A new hub-and-spoke biology curriculum designed around interdisciplinary laboratory practical sessions to enhance student employability

A new hub-and-spoke (H&S) model for restructuring the traditional biological science curriculum is presented here. The H&S model emphasises the integration of sub-disciplines of biology and the integration of biology with other scientific disciplines. In this model, traditional undergraduate courses that include both theory and a stand-alone laboratory component are replaced with discovery-based research courses that act as the hub, servicing discipline-specific theory-only courses, which act as the spoke. The hub course includes an immersive laboratory experience, aimed to integrate all the spoke components that the hub unit serves. The H&S model also offers an opportunity to develop a new framework that will support active pedagogies such as inquiry-based and open-ended problem-based learning, where students work in groups to solve challenging problems and build their capacity to design and implement approaches to undertake their own investigation, thus enhancing students critical thinking as well as generic skills. Overall, this model offers higher interdisciplinary biological laboratory skills, and an integrative understanding of scientific projects thus enhancing the graduate’s employability. This curriculum model may be easily adapted for other branches of science, given the interdisciplinary nature of all sciences and the R&D innovation sector.

VIRUS: EVOLUSI, GENETIKA, DRIFT DAN SHIFT ANTIGEN

Viral evolution is a subdiscipline of evolutionary biology and virology that focuses on the evolution of viruses. Many viruses, especially RNA viruses, have relatively high mutation rates and short production durations (on the order of one point mutation or more per genome per round of replication). The rapid pace of viral mutation paired with natural selection enables viruses to rapidly adapt to changes in the host environment, despite the fact that the majority of viral mutations offer little benefit and frequently prove to be harmful. Additionally, because viruses often make several copies in an infected host, altered genes can be rapidly transmitted to a large number of offspring. The high mutation rates of RNA viruses, which are the result of an error-prone RNA-dependent RNA polymerase, make them a veritable gold mine for researchers interested in discovering evolutionary novelty and developing new methods to study evolution in action. There are two different forms of genetic changes: antigenic drift and antigenic shift. This article covers briefly the evolution of viruses in terms of genetic variation.

Universe Radius-Electron Relationship Shows Electron Creation is the Dark Energy Driving Quantized Universe Expansion

IJCAA publishes original hypotheses and discoveries in cosmology, astronomy, space science and technology, astrophysics, astrobiology, plasma physics, and Earth & planetary sciences. It covers multiple disciplines and sub-disciplines of biology, geology, physics, chemistry, extinction, the origin and evolution of life and Martian colonization and exploration. It mainly focuses on the conceptual problems of the current paradigm of early universe cosmology and astronomy, thus motivating exploration of the potential of string theory to provide a new paradigm.

The Core Concepts, Competencies, and Grand Challenges of Comparative Vertebrate Anatomy and Morphology.

SynopsisCore concepts offer coherence to the discourse of a scientific discipline and facilitate teaching by identifying large unifying themes that can be tailored to the level of the class and expertise of the instructor. This approach to teaching has been shown to encourage deeper learning that can be integrated across subdisciplines of biology and has been adopted by several other biology subdisciplines. However, Comparative Vertebrate Anatomy, although one of the oldest biological areas of study, has not had its core concepts identified. Here, we present five core concepts and seven competencies (skills) for Comparative Vertebrate Anatomy that came out of an iterative process of engagement with the broader community of vertebrate morphologists over a 3-year period. The core concepts are (A) evolution, (B) structure and function, (C) morphological development, (D) integration, and (E) human anatomy is the result of vertebrate evolution. The core competencies students should gain from the study of comparative vertebrate anatomy are (F) tree thinking, (G) observation, (H) dissection of specimens, (I) depiction of anatomy, (J) appreciation of the importance of natural history collections, (K) science communication, and (L) data integration. We offer a succinct description of each core concept and competency, examples of learning outcomes that could be used to assess teaching effectiveness, and examples of relevant resources for both instructors and students. Additionally, we pose a grand challenge to the community, arguing that the field of Comparative Vertebrate Anatomy needs to acknowledge racism, androcentrism, homophobia, genocide, slavery, and other influences in its history and address their lingering effects in order to move forward as a thriving discipline that is inclusive of all students and scientists and continues to generate unbiased knowledge for the betterment of humanity. Despite the rigorous process used to compile these core concepts and competencies, we anticipate that they will serve as a framework for an ongoing conversation that ensures Comparative Vertebrate Anatomy remains a relevant field in discovery, innovation, and training of future generations of scientists.

Satisfiable Cosmologies

IJCAA publishes original hypotheses and discoveries in cosmology, astronomy, space science and technology, astrophysics, astrobiology, plasma physics, and Earth & planetary sciences. It covers multiple disciplines and sub-disciplines of biology, geology, physics, chemistry, extinction, the origin and evolution of life and Martian colonization and exploration. It mainly focuses on the conceptual problems of the current paradigm of early universe cosmology and astronomy, thus motivating exploration of the potential of string theory to provide a new paradigm.

Anomalous Infrared Absorbance of S═O: A Perturbation Study of α-C-H/D.

Solvatochromic shifts of S═O vibrational probes describe the strength of the surrounding electric fields and the hydrogen bonding status. Herein, we demonstrated how the solvents alter the infrared (IR) spectra of the S═O vibrating mode. The experimental measurement of the involvement of α-H/D isotopic interactions with different solvents and their effects on the IR absorbance spectra of the vibrational probe provides detailed knowledge of the microsolvation environment despite the complexity of overlapping bands in the spectra. Herein, we discover how the solvents interact differently with DMSO and DMSO-d6, while being electronically and structurally the same. Interestingly, the IR spectrum of the S═O mode remains unaltered during α-isotopic replacement in the presence of aprotic solvents (acetone, acetonitrile, and dichloromethane), but in strongly coordinating polar solvents (D2O), it is altered remarkably. There is a lack of quantitative information about the influence of the α-H atom or α-isotopic substitution on the vibrational probe in the literature. Our experiments provide a detailed molecular understanding of the structure of DMSO in DMSO-solvent binary mixtures. As DMSO plays an important role in virtually all subdisciplines of chemistry and biology, we believe that our work will be of interest to a large diversity of studies in these fields.

Ring Forming Approaches to para-Quinones: Toward a General Diels–Alder Disconnection

Abstract para-Quinones feature extensively as targets and/or intermediates throughout a number of chemical and biological subdisciplines, highlighting the importance of efficient preparative methods. This Synpacts article provides an overview of ring forming approaches to para-hydroquinones and para-benzoquinones, concluding with our recent contribution concerning the development of 2,5-bis(tert-butyldimethylsilyloxy)furans as vicinal bisketene equivalents in the Diels–Alder reaction.1 Introduction2 Ring Forming Approaches to para-Quinones2.1 Hauser–Kraus Annulation2.2 Moore–Liebeskind Rearrangement2.3 Wulff–Dötz Reaction2.4 Oxidative Bergman Cyclization2.5 Diels–Alder Strategies2.5.1 Ketene–Enol Equivalents2.5.2 Bisketene Equivalents3 Toward an Improved Bisketene Equivalent4 Conclusion

Soap Bubbles on the Surface of a Liquid: A Playful Universe in 3+1 Dimensions, a Real Universe in 4+1 Dimensions

IJCAA publishes original hypotheses and discoveries in cosmology, astronomy, space science and technology, astrophysics, astrobiology, plasma physics, and Earth & planetary sciences. It covers multiple disciplines and sub-disciplines of biology, geology, physics, chemistry, extinction, the origin and evolution of life and Martian colonization and exploration. It mainly focuses on the conceptual problems of the current paradigm of early universe cosmology and astronomy, thus motivating exploration of the potential of string theory to provide a new paradigm.

A Margulian View of Symbiosis and Speciation: the Nasonia Wasp System

Species are fundamental units of biology that exemplify lineage diversification, while symbiosis of microbes and macrobial hosts exemplify lineage unification between the domains of life. While these conceptual differences between speciation and symbiosis often dominate the narrative of the respective fields, Lynn Margulis argued for interconnection between these two subdisciplines of biology in a manner that left a legacy for scholars and students alike to pursue, detail, and discover. The Margulian perspective has always been that host evolutionary processes such as speciation are more impacted by microbial symbioses than typically appreciated. In this article, we present and review the case system that she long envisioned, one in which layers of microbial symbiosis reduce species interbreeding and assist species diversification among a closely related group of small, metallic green, parasitoid wasps from the genus Nasonia.

The Physics of the Tresino Phase-Transition beneath the Solar Surface

IJCAA publishes original hypotheses and discoveries in cosmology, astronomy, space science and technology, astrophysics, astrobiology, plasma physics, and Earth & planetary sciences. It covers multiple disciplines and sub-disciplines of biology, geology, physics, chemistry, extinction, the origin and evolution of life and Martian colonization and exploration. It mainly focuses on the conceptual problems of the current paradigm of early universe cosmology and astronomy, thus motivating exploration of the potential of string theory to provide a new paradigm.

Publisher’s Note: Continued Publication of International Journal of Plant Biology by MDPI

The International Journal of Plant Biology (ISSN: 2037-0164) was launched in 2010 and publishes international and multidisciplinary research in the different subdisciplines of plant biology [...]

Welcome to the New Version of the International Journal of Plant Biology (IJPB)

With great pleasure, I welcome you to this new version of the International Journal of Plant Biology (IJPB), an international, peer-reviewed, open access journal about all different subdisciplines of plant biology published quarterly online by MDPI [...]