Biological World Research Articles

Histones: The critical players in innate immunity.

The highly conserved histones in different species seem to represent a very ancient and universal innate host defense system against microorganisms in the biological world. Histones are the essential part of nuclear matter and act as a control switch for DNA transcription. However, histones are also found in the cytoplasm, cell membranes, and extracellular fluid, where they function as host defenses and promote inflammatory responses. In some cases, extracellular histones can act as damage-associated molecular patterns (DAMPs) and bind to pattern recognition receptors (PRRs), thereby triggering innate immune responses and causing initial organ damage. Histones and their fragments serve as antimicrobial peptides (AMPs) to directly eliminate bacteria, viruses, fungi, and parasites in vitro and in vivo. Histones are also involved in phagocytes-related innate immune response as components of neutrophil extracellular traps (NETs), neutrophil activators, and plasminogen receptors. In addition, as a considerable part of epigenetic regulation, histone modifications play a vital role in regulating the innate immune response and expression of corresponding defense genes. Here, we review the regulatory role of histones in innate immune response, which provides a new strategy for the development of antibiotics and the use of histones as therapeutic targets for inflammatory diseases, sepsis, autoimmune diseases, and COVID-19.

Operant conditioning of stochastic chemical reaction networks.

Adapting one's behavior to environmental conditions and past experience is a key trait of living systems. In the biological world, there is evidence for adaptive behaviors such as learning even in naturally occurring, non-neural, single-celled organisms. In the bioengineered world, advances in synthetic cell engineering and biorobotics have created the possibility of implementing lifelike systems engineered from the bottom up. This will require the development of programmable control circuitry for such biomimetic systems that is capable of realizing such non-trivial and adaptive behavior, including modification of subsequent behavior in response to environmental feedback. To this end, we report the design of novel stochastic chemical reaction networks capable of probabilistic decision-making in response to stimuli. We show that a simple chemical reaction network motif can be tuned to produce arbitrary decision probabilities when choosing between two or more responses to a stimulus signal. We further show that simple feedback mechanisms from the environment can modify these probabilities over time, enabling the system to adapt its behavior dynamically in response to positive or negative reinforcement based on its decisions. This system thus acts as a form of operant conditioning of the chemical circuit, in the sense that feedback provided based on decisions taken by the circuit form the basis of the learning process. Our work thus demonstrates that simple chemical systems can be used to implement lifelike behavior in engineered biomimetic systems.

Innovation versus novelty in microbial systems.

Innovation versus novelty in microbial systems.

Sequence-Activity Relationship of ATCUN Peptides in the Context of Alzheimer's Disease.

Amino-terminal CuII and NiII (ATCUN) binding sequences are widespread in the biological world. Here, we report on the study of eight ATCUN peptides aimed at targeting copper ions and stopping the associated formation of reactive oxygen species (ROS). This study was actually more focused on Cu(Aβ)-induced ROS production in which the Aβ peptide is the "villain" linked to Alzheimer's disease. The full characterization of CuII binding to the ATCUN peptides, the CuII extraction from CuII(Aβ), and the ability of the peptides to prevent and/or stop ROS formation are described in the relevant biological conditions. We highlighted in this research that all the ATCUN motifs studied formed the same thermodynamic complex but that the addition of a second histidine in position 1 or 2 allowed for an improvement in the CuII uptake kinetics. This kinetic rate was directly related to the ability of the peptide to stop the CuII(Aβ)-induced production of ROS, with the most efficient motifs being HWHG and HGHW.

Circadian clocks signal future states of affairs

On receiver-based teleosemantic theories of representation, the chemical states of the circadian clocks in animal, plant and cyanobacterial cells constitute signals of future states of affairs, often the rising and setting of the sun. This signalling is much more rigid than sophisticated representational systems like human language, but it is not simple on all dimensions. In most organisms the clock regulates many different circadian rhythms. The process of entrainment ensures that the mapping between chemical states of the clock and the daily light-dark cycle is adjusted to deal with seasonal changes. In regulating anticipatory behaviour, the states of the clock look forward both to the time the behaviour is supposed to happen and the later time when the anticipated circumstances are supposed to arise. The case of the circadian clock shows that purely indicative signals can arise in very basic biological systems and brings into sharp relief the trade-offs involved in characterizing representational systems. On receiver-based teleosemantic theories, future-directed signals are not restricted to complex multicellular organisms but are ubiquitous in the biological world.

Small Non-Coding RNAs in Human Cancer.

Small non-coding RNAs are widespread in the biological world and have been extensively explored over the past decades. Their fundamental roles in human health and disease are increasingly appreciated. Furthermore, a growing number of studies have investigated the functions of small non-coding RNAs in cancer initiation and progression. In this review, we provide an overview of the biogenesis of small non-coding RNAs with a focus on microRNAs, PIWI-interacting RNAs, and a new class of tRNA-derived small RNAs. We discuss their biological functions in human cancer and highlight their clinical application as molecular biomarkers or therapeutic targets.

GOD AND A WORLD OF NATURAL EVIL: THEOLOGY AND SCIENCE IN HARD CONVERSATION

AbstractThis is the text of the 2022 Boyle Lecture. After some acknowledgements, it introduces the theological problem of the suffering of nonhuman creatures in the natural world as described by evolutionary science. It sets aside the neo‐Cartesian objection that this suffering should not be considered real. The lecture then considers, and initially rejects, theodicies based on some form of fall event. An account is offered based on the premise that Darwinian evolution was the only way God could have given rise to a biological world containing the sorts of values we observe. Although this remains the preferred basis for an evolutionary theodicy, consideration is finally given to the extent to which certain phenomena, such as parasitism, cancers, and viral infections, might be thought to exhibit a resistance to the divine will. The tentative suggestion is made that this resistance might derive from temptation by spiritual powers, thus incorporating into an overall only‐way account an element of angelic fallenness.

Inertialess gyrating engines.

A typical model for a gyrating engine consists of an inertial wheel powered by an energy source that generates an angle-dependent torque. Examples of such engines include a pendulum with an externally applied torque, Stirling engines, and the Brownian gyrating engine. Variations in the torque are averaged out by the inertia of the system to produce limit cycle oscillations. While torque generating mechanisms are also ubiquitous in the biological world, where they typically feed on chemical gradients, inertia is not a property that one naturally associates with such processes. In the present work, seeking ways to dispense of the need for inertial effects, we study an inertia-less concept where the combined effect of coupled torque-producing components averages out variations in the ambient potential and helps overcome dissipative forces to allow sustained operation for vanishingly small inertia. We exemplify this inertia-less concept through analysis of two of the aforementioned engines, the Stirling engine, and the Brownian gyrating engine. An analogous principle may be sought in biomolecular processes as well as in modern-day technological engines, where for the latter, the coupled torque-producing components reduce vibrations that stem from the variability of the generated torque.

The Matic Exploratory of Content Marketing for the Fourth Industrial Revolution

The marketing world is a dynamic and constantly changing environment that never stagnates. The fourth industrial revolution refers to a set of new technologies that are integrating the physical, digital, and biological worlds, affecting all disciplines, economies, and sectors, and even questioning what it is to be human. The purpose of this paper is to investigate and analyzed, how important is a content marketing strategy to the customers in the era of the fourth industrial revolution. The presented paper consists of three parts, the first part of the paper focuses on theoretical aspects of content marketing. The second part focuses on methods of data collection that are needed to perform analysis. This research work makes use of secondary data. Relevant data for this study was collected from already published/online materials, articles, Newspapers, journals, archives, web postings as well as editorials. The method of analysis that was employed in this study is systematic qualitative content analysis. The result of this paper is a comprehensive overview of thematic exploratory content marketing strategy that can be used to influence user interests in the global market and how important is communication with customers.

A hypothetical improvement of the quadruple helix model of innovation

Orientation: Innovation is forged by sub-revolutions as described by the quadruple helix (QH) model. Research purpose: Innovation model formation is complex, and the useful QH model can develop and improve to be exemplary. Motivation for the study: The rationale of the study is to validate and improve the QH model with additional concepts, fresh perspectives of experts and the investigation of the primary sub-revolutions forging innovation. Research design, approach and method: A conceptual and critical review approach implied narrative data of the model from secondary sources; a convenience sample of five innovation experts for critical reviews was thematically analysed. Main findings: Ultimately, the improved QH model must accommodate the legal, moral and ethical world to merge with the physical, biological and digital worlds; appropriate terminology for QH innovation leadership is needed, and triple technology theory (TTT) should be incorporated with the triple management theory (TMT) dimension of the model; the review conformed the sub-revolutions of innovation with respect to (1) innovation leadership, upscaling agility and innovation essentials, (2) the triple helix (TH) ecosystems sub-revolution and epochal society and (3) the new technological paradigm, technology intensity and TMT. Practical/managerial implications: The already useful QH model is confirmed and may develop to become exemplary with respect to the hypothetical improvements suggested. Contribution/value-add: A fresh and improved QH model is suggested in the context of complex innovation model formation and the paucity of literature.

Imaging and Editing the Phospholipidome.

Membranes are multifunctional supramolecular assemblies that encapsulate our cells and the organelles within them. Glycerophospholipids are the most abundant component of membranes. They make up the majority of the lipid bilayer and play both structural and functional roles. Each organelle has a different phospholipid composition critical for its function that results from dynamic interplay and regulation of numerous lipid-metabolizing enzymes and lipid transporters. Because lipid structures and localizations are not directly genetically encoded, chemistry has much to offer to the world of lipid biology in the form of precision tools for visualizing lipid localization and abundance, manipulating lipid composition, and in general decoding the functions of lipids in cells.In this Account, we provide an overview of our recent efforts in this space focused on two overarching and complementary goals: imaging and editing the phospholipidome. On the imaging front, we have harnessed the power of bioorthogonal chemistry to develop fluorescent reporters of specific lipid pathways. Substantial efforts have centered on phospholipase D (PLD) signaling, which generates the humble lipid phosphatidic acid (PA) that acts variably as a biosynthetic intermediate and signaling agent. Though PLD is a hydrolase that generates PA from abundant phosphatidylcholine (PC) lipids, we have exploited its transphosphatidylation activity with exogenous clickable alcohols followed by bioorthogonal tagging to generate fluorescent lipid reporters of PLD signaling in a set of methods termed IMPACT.IMPACT and its variants have facilitated many biological discoveries. Using the rapid and fluorogenic tetrazine ligation, it has revealed the spatiotemporal dynamics of disease-relevant G protein-coupled receptor signaling and interorganelle lipid transport. IMPACT using diazirine photo-cross-linkers has enabled identification of lipid-protein interactions relevant to alcohol-related diseases. Varying the alcohol reporter can allow for organelle-selective labeling, and varying the bioorthogonal detection reagent can afford super-resolution lipid imaging via expansion microscopy. Combination of IMPACT with genome-wide CRISPR screening has revealed genes that regulate physiological PLD signaling.PLD enzymes themselves can also act as tools for precision editing of the phospholipid content of membranes. An optogenetic PLD for conditional blue-light-stimulated synthesis of PA on defined organelle compartments led to the discovery of the role of organelle-specific pools of PA in regulating oncogenic Hippo signaling. Directed enzyme evolution of PLD, enabled by IMPACT, has yielded highly active superPLDs with broad substrate tolerance and an ability to edit membrane phospholipid content and synthesize designer phospholipids in vitro. Finally, azobenzene-containing PA analogues represent an alternative, all-chemical strategy for light-mediated control of PA signaling.Collectively, the strategies described here summarize our progress to date in tackling the challenge of assigning precise functions to defined pools of phospholipids in cells. They also point to new challenges and directions for future study, including extension of imaging and membrane editing tools to other classes of lipids. We envision that continued application of bioorthogonal chemistry, optogenetics, and directed evolution will yield new tools and discoveries to interrogate the phospholipidome and reveal new mechanisms regulating phospholipid homeostasis and roles for phospholipids in cell signaling.

“I try to encourage my students to think, read, and talk science” intelligible identities in university teachers' figured worlds of higher education biology

AbstractHigher education biology is often imagined, perceived, and described as having reached gender equality in terms of who gets to participate in disciplinary practices. However, like any other natural science discipline, higher education biology is a world whose landscapes are shaped by (re)productions of historical, cultural, and social norms. We explore these norms through the lens of identity, asking what identities are recognized by university biology teachers at a large Swedish university, analyzing 94 teaching statements written when applying for faculty positions in biology. We argue that in and through teaching statements, university biology teachers negotiate and perform overarching academic and disciplinary norms and discourses with the goal to present themselves as intelligible candidates. As statements of value, they thereby display implicit and explicit identities recognized in worlds of higher education biology. Using a discourse analytical framework, we identified two university teacher identities imagined as intelligible: Research Science Teachers and Facilitating Science Teachers. Research Science Teachers position research and associated masculine‐coded competences as anchor points of biology practice. They consider researchers to be ultimate knowers and consequently to be best suitable for university teaching with the goal to recruit students into research. Facilitating Science Teachers, even though aware of the hegemonic position of research, disentangle imaginaries of what makes a researcher from what makes a university teacher. They transgress dominant imaginaries of research as the ultimate competence for themselves and students, and create spaces for alternative identity work. These findings contribute to a more nuanced understanding of (re)productive processes in science education, providing perspectives of how to together infract intergenerational (re)productions of hegemonic norms of doing science. Additionally, this study provides further evidence that higher education biology is not a gender‐neutral higher education landscape.

Gregor Mendel: The father of genetics who opened a biological world full of wonders

A few giants in science once made discoveries that opened doors for us to enter a world never seen before. As the father of modern genetics, Gregor Mendel is considered one of these giants owing to his discovery of the basic principles of inheritance. Retrospectively, it can be argued that the greatest century of discovery in biology was a period from the 1850s/1860s to the 1950s/1960s. Two of the giants in biological sciences at the beginning of this century of discoveries, on whose shoulders we stand, are Charles Darwin, who published On the Origin of Species in 1859 with geographic and biological observations from his 5-year voyage on HMS Beagle that lead to his macro-concept of evolution by natural selection (Darwin, 1859), and Gregor Mendel, who did 10-year crossing and counting experiments using the humble garden pea, leading to the establishment of the principle of inheritance as explained in his seminal paper “Experiments on Plant Hybrids” in 1865 (Mendel, 1866).

A vision towards integrated 6G communication networks: Promising technologies, architecture, and use-cases

The evolution of the previous mobile communication generations has led to innovative goals of the Internet of Everything (IoE) in the 5G. However, addressing all IoE-associated problems in 5G is difficult and a long-term process. As the key performance indicators (KPIs) of the 5G services are highly diverse, it is an intimidating task to develop a single platform enabling all KPIs. The vision of next-generation 6G wireless communications lies not only in enhancing these targets but also in providing new services. Numerous extensively envisaged future services, including life-critical services and wireless brain–computer interactions, will be critically dependent on an instant, virtually unlimited wireless connectivity. In this direction, the 6G is envisioned to have primely five service objectives; further-enhanced mobile broadband (FeMBB), ultra-massive machine type communication (umMTC), extremely reliable low latency communication (ERLLC), long-distance and high-mobility communications (LDHMC), and extremely low-power communications (ELPC). The 3D global integration of the wireless communication networks is lacking in the 5G, which is targeted by the future 6G. In this paper, we present an exhaustive review of the 6G wireless communication network. We explore the various existing mobile communication generations concerning data rate, frequency band, bandwidth allotted, latency, and applications. We also highlight various current trends and issues in the 5G communication network, which drives research for the 6G communication network. Our focus is to provide a comprehensive survey on the future 6G. So, we explored the objectives and design principles for 6G. This paper highlights the key 6G technology drivers. This paper also proposes an architectural design for 6G. Moreover, we carry out a case-study of 6G architecture operational design and compare the result with previous generation architecture designs. Further, 6G envisioned open research challenges, research directions, and recent advancements are also highlighted in this paper. Furthermore, we discuss possible use-cases in terms of real-time interactions of the biological, physical, and digital world, and also how these use-cases are going to serve in 6G.

Terahertz topological photonic integrated circuits for 6G and beyond: A Perspective

The development of terahertz integrated circuits is vital for realizing sixth-generation (6G) wireless communication, high-speed on-chip interconnects, high-resolution imaging, on-chip biosensors, and fingerprint chemical detection. Nonetheless, the existing terahertz on-chip devices suffer from reflection, and scattering losses at sharp bends or defects. Recently discovered topological phases of light endow the photonics devices with extraordinary properties, such as reflectionless propagation and robustness against impurities or defects, which is vital for terahertz integrated devices. Leveraging the robustness of topological edge states combined with a low-loss silicon platform is poised to offer a remarkable performance of the terahertz devices providing a breakthrough in the field of terahertz integrated circuits and high-speed interconnects. In this Perspective, we present a brief outlook of various terahertz functional devices enabled by a photonic topological insulator that will pave the path for augmentation of complementary metal oxide semiconductor compatible terahertz technologies, essential for accelerating the vision of 6G communication and beyond to enable ubiquitous connectivity and massive digital cloning of physical and biological worlds.

Fluorescent and Phosphorescent Nitrogen-Containing Heterocycles and Crown Ethers: Biological and Pharmaceutical Applications.

Fluorescent molecules absorb photons of specific wavelengths and emit a longer wavelength photon within nanoseconds. Recently, fluorescent materials have been widely used in the life and material sciences. Fluorescently labelled heterocyclic compounds are useful in bioanalytical applications, including in vivo imaging, high throughput screening, diagnostics, and light-emitting diodes. These compounds have various therapeutic properties, including antifungal, antitumor, antimalarial, anti-inflammatory, and analgesic activities. Different neutral fluorescent markers containing nitrogen heterocycles (quinolones, azafluoranthenes, pyrazoloquinolines, etc.) have several electrochemical, biological, and nonlinear optic applications. Photodynamic therapy (PDT), which destroys tumors and keeps normal tissues safe, works in the presence of molecular oxygen with light and a photosensitizing drugs (dye) to obtain a therapeutic effect. These compounds can potentially be effective templates for producing devices used in biological research. Blending crown compounds with fluorescent residues to create sensors has been frequently investigated. Florescent heterocyclic compounds (crown ether) increase metal solubility in non-aqueous fluids, broadening the application window. Fluorescent supramolecular polymers have widespread use in fluorescent materials, fluorescence probing, data storage, bio-imaging, drug administration, reproduction, biocatalysis, and cancer treatment. The employment of fluorophores, including organic chromophores and crown ethers, which have high selectivity, sensitivity, and stability constants, opens up new avenues for research. Fluorescent organic compounds are gaining importance in the biological world daily because of their diverse functionality with remarkable structural features and positive properties in the fields of medicine, photochemistry, and spectroscopy.

The expanding vistas of spatial transcriptomics.

The formation and maintenance of tissue integrity requires complex, coordinated activities by thousands of genes and their encoded products. Until recently, transcript levels could only be quantified for a few genes in tissues, but advances in DNA sequencing, oligonucleotide synthesis and fluorescence microscopy have enabled the invention of a suite of spatial transcriptomics technologies capable of measuring the expression of many, or all, genes in situ. These technologies have evolved rapidly in sensitivity, multiplexing and throughput. As such, they have enabled the determination of the cell-type architecture of tissues, the querying of cell-cell interactions and the monitoring of molecular interactions between tissue components. The rapidly evolving spatial genomics landscape will enable generalized high-throughput genomic measurements and perturbations to be performed in the context of tissues. These advances will empower hypothesis generation and biological discovery and bridge the worlds of tissue biology and genomics.

The expanding world of noncoding RNA biology

The expanding world of noncoding RNA biology

Enantioselective [2+2]-cycloadditions with triplet photoenzymes.

Naturally evolved enzymes, despite their astonishingly large variety and functional diversity, operate predominantly through thermochemical activation. Integrating prominent photocatalysis modes into proteins, such as triplet energy transfer, could create artificial photoenzymes that expand the scope of natural biocatalysis1-3. Here, we exploit genetically reprogrammed, chemically evolved photoenzymes embedded with a synthetic triplet photosensitizer that are capable of excited-state enantio-induction4-6. Structural optimization through four rounds of directed evolution afforded proficient variants for the enantioselective intramolecular [2+2]-photocycloaddition of indole derivatives with good substrate generality and excellent enantioselectivities (up to 99% enantiomeric excess). A crystal structure of the photoenzyme-substrate complex elucidated the non-covalent interactions that mediate the reaction stereochemistry. This study expands the energy transfer reactivity7-10 of artificial triplet photoenzymes in a supramolecular protein cavity and unlocks an integrated approach to valuable enantioselective photochemical synthesis that is not accessible with either the synthetic or the biological world alone.

Historic and charming <italic>Monascus</italic> spp.

<p indent="0mm"><italic>Monascus</italic> species are well-known as fermentation strains in food and pharmaceutical industries in China. <italic>Monascus</italic> spp. have a long application history for more than <sc>2000 years.</sc> Red mold rice (RMR), also known as anka and Hongqu in China, is the fermented product of steamed rice inoculated with certain <italic>Monascus</italic> strains. Nowadays, RMR and its related products have been extensively applied in food and medicine industries. In these RMR products, <italic>Monascus</italic> strains produce two kinds of the most well-known secondary metabolites (SMs) <italic>Monascus</italic> pigments (MPs) and monacolin K (MK). MPs have been employed as natural food colorant in Southeast Asia over one thousand years. MK (also known as lovastatin), an anticholesterol compound, has been developed to be a hypolipidemic drug and food supplements. Today, RMR and its relative products mainly yielded in China are not only applied in Southeast Asia, but also exported to Europe and America. It is estimated that more than one billion people, around the world, eat RMR and other relative products in their daily life. Therefore, <italic>Monascus</italic> species are considered as one of the historic and charming fermentation strains in China. Theoretical researches and product development of <italic>Monascus</italic> strains have attracted wide attention and made fruitful scientific achievements, especially in recent <sc>30 years.</sc> In-depth studies regarding RMR have revealed that <italic>Monascus</italic> spp. not only produce beneficial SMs, MPs and MK, but also a mycotoxin citrinin (CIT). A substantial amount of researches has been successfully made to elucidate the biosynthetic pathways of these SMs and their regulation mechanism. These achievements not only serve as models of fungal SMs biosynthesis, but also provide a roadmap for metabolic engineering and synthetic biology towards the selective production of the more valuable components. Furthermore, <italic>Monascus</italic> spp. also are unique objects for researching fungal reproduction regulation and magnetic and/or light responses because <italic>Monascus</italic> spp. are found to be significantly different from the known filamentous fungi in these two fields. The progress on reproduction regulation of <italic>Monascus</italic> spp. revealed that the well-established conidiation central regulation in <italic>Aspergillus</italic> species is not applicable in their <italic>Monascus</italic> relatives. On the other hand, <italic>M</italic>.<italic> ruber</italic> M7 genome contains one red-light and two green-light receptors, but not any blue-light receptor ortholog is present in<italic> M</italic>.<italic> ruber </italic>M7 and other <italic>Monascus</italic> species, indicating a biologically significant difference between <italic>Monascus</italic> species and other filamentous fungi. Because of the unique reproduction mechanism, light and magnetic response and abundant SMs biosynthesis of <italic>Monascus</italic> spp., it is expected to enrich the theoretical understanding of filamentous fungi and even the biological world through further research on <italic>Monascus</italic> spp. Therefore, it demonstrates a great potential for developing <italic>Monascus</italic> spp. into a model microorganism. The key discussions and future prospects are also proposed from the aspects of faced challenge on <italic>Monascus</italic> spp. investigation and their products development.