General Mechanism Research Articles

Variation in thermal physiology can drive the temperature-dependence of microbial community richness.

Predicting how species diversity changes along environmental gradients is an enduring problem in ecology. In microbes current theories tend to invoke energy availability and enzyme kinetics as the main drivers of temperature-richness relationships. Here we derive a general empirically-grounded theory that can explain this phenomenon by linking microbial species richness in competitive communities to variation in the temperature-dependence of their interaction and growth rates. Specifically, the shape of the microbial community temperature-richness relationship depends on how rapidly the strength of effective competition between species pairs changes with temperature relative to the variance of their growth rates. Furthermore, it predicts that a thermal specialist-generalist tradeoff in growth rates alters coexistence by shifting this balance, causing richness to peak at relatively higher temperatures. Finally, we show that the observed patterns of variation in thermal performance curves of metabolic traits across extant bacterial taxa is indeed sufficient to generate the variety of community-level temperature-richness responses observed in the real world. Our results provide a new and general mechanism that can help explain temperature-diversity gradients in microbial communities, and provide a quantitative framework for interlinking variation in the thermal physiology of microbial species to their community-level diversity.

Ferromagnetic quantum critical point protected by nonsymmorphic symmetry in a Kondo metal

Quantum critical points (QCPs), zero-temperature phase transitions, are windows to fundamental quantum-mechanical phenomena associated with universal behaviour. Magnetic QCPs have been extensively investigated in the vicinity of antiferromagnetic order. However, QCPs are rare in metallic ferromagnets due to the coupling of the order parameter to electronic soft modes. Recently, antisymmetric spin-orbit coupling in noncentrosymmetric systems was suggested to protect ferromagnetic QCPs. Nonetheless, multiple centrosymmetric materials host FM QCPs, suggesting a more general mechanism behind their protection. In this context, CeSi2-δ, a dense Kondo lattice crystallising in a centrosymmetric structure, exhibits ferromagnetic order when Si is replaced with Ag. We report that the Ag-substitution to CeSi1.97 linearly suppresses the ferromagnetic order towards a QCP, accompanied by concurrent strange-metal behaviour. Herein, we suggest that, despite the centrosymmetric structure, spin-orbit coupling arising from the local noncentrosymmetric structure, in combination with nonsymmorphic symmetry, can protect ferromagnetic QCPs. Our findings offer a general guideline for discovering new ferromagnetic QCPs and highlight one new family of materials within which the interplay of topology and quantum phase transitions can be investigated in the context of strongly correlated systems.

Controlled release of microorganisms from engineered living materials.

Probiotics offer therapeutic benefits and have the potential to treat complex diseases, but their persistence at the target site is often required for effective treatment. Although probiotic persistence can be achieved by repeated delivery, no biomaterial that releases metabolically active probiotics in a sustained manner has been developed yet. This work demonstrates a generic mechanism where stiff probiotics encapsulated within relatively less stiff hydrogels proliferate and induce hydrogel fracture. This allows a zero-order release of probiotics which can be easily controlled by adjusting the properties of the encapsulating matrices. This generic mechanism is applicable for a wide range of probiotics with different synthetic matrices and has the potential to be used in the treatment of a broad range of diseases.

Widespread Adaptive Introgression of Major Histocompatibility Complex Genes across Vertebrate Hybrid Zones.

Interspecific introgression is a potentially important source of novel variation of adaptive significance. Although multiple cases of adaptive introgression are well documented, broader generalizations about its targets and mechanisms are lacking. Multiallelic balancing selection, particularly when acting through rare allele advantage, is an evolutionary mechanism expected to favor adaptive introgression. This is because introgressed alleles are likely to confer an immediate selective advantage, facilitating their establishment in the recipient species even in the face of strong genomic barriers to introgression. Vertebrate major histocompatibility complex genes are well-established targets of long-term multiallelic balancing selection, so widespread adaptive major histocompatibility complex introgression is expected. Here, we evaluate this hypothesis using data from 29 hybrid zones formed by fish, amphibians, squamates, turtles, birds, and mammals at advanced stages of speciation. The key prediction of more extensive major histocompatibility complex introgression compared to genome-wide introgression was tested with three complementary statistical approaches. We found evidence for widespread adaptive introgression of major histocompatibility complex genes, providing a link between the process of adaptive introgression and an underlying mechanism. Our work identifies major histocompatibility complex introgression as a general mechanism by which species can acquire novel, and possibly regain previously lost, variation that may enhance defense against pathogens and increase adaptive potential.

The order of stimuli matters when learning second-order transitional probabilities.

The order of stimuli within sequences and the transitional probabilities (TPs) it generates are central information in sequence processing. However, less is known about what type of information and how it is extracted by general learning mechanisms. The present study focused on statistical learning of second-order TPs. Second-order TPs are involved when only the combination of two stimuli predicts the third. In a first experiment, TPs depended crucially on the order of presentation of a pair , which led to different predictions depending on the order of the stimuli (i.e., ABC vs.BAF). Eight visuomotor sequences governed by second-order TPs were used and response times (RTs) were recorded for each transition. The task included a learning phase followed by a switch phase during which the second-order TP were reversed (e.g., the sequences ABC and BAF became respectively ABF and BAC). A decrease of RTs between the second and the third stimulus during the learning phase and an increase of RTs during the switch phase suggested that variations of orders within second-order TPs could be learned. Further analyses, however, indicated that such learning was difficult for most participants. A second experiment showed that the difficulty of learning was not solely due to the difficulty to pick up the effect of order of presentation, but that learning second-order transitional probabilities in addition to order would be the main obstacle. These experiments suggest that statistical learning is capable of learning complex associations, even if this remains a challenge for human cognition.

Self‐organised pattern formation promotes consumer coexistence by fluctuation‐dependent mechanisms

Abstract In spatially extended ecosystems, habitat heterogeneity facilitates coexistence of species if each competitor experiences environmental conditions in a particular habitat that provide a growth advantage compared to other species, thereby making it locally competitively superior. If the competitive hierarchy among species is the same everywhere, heterogeneity‐facilitated coexistence is possible provided that superior competitors disperse maladaptively towards unfavourable habitats or if they hedge insufficiently against fluctuating environmental conditions. We use a generic two‐patch metacommunity model to show that the latter mechanisms also operate in metacommunities with homogeneous habitat quality when heterogeneous biomass distributions emerge from self‐organised pattern formation. The model consists of an abiotic resource, an autotroph producer and two competing heterotroph consumer species of which one is always competitively inferior to the other, irrespective of resource availability. If the induced biomass patterns are static in time, a lower dispersal rate can allow the inferior competitor to avoid competitive exclusion by retaining most of its biomass in the patch with the higher resource density. However, if the biomass patterns fluctuate spatio‐temporally, the inferior competitor must adopt a higher dispersal rate than the superior competitor to persist. This increased movement enables the inferior competitor to effectively distribute its biomass across space, thereby achieving a higher growth rate during periods of recovery from local population minima. Strikingly, we find a novel coexistence mechanism that emerges if the competitors differ in their abilities to induce pattern formation. Similar to relative nonlinearity in resource use (based e.g. on a gleaner–opportunist trade‐off), the dominant species modifies the spatial or spatio‐temporal variation in the distribution of the resource in a way that favours its competitor. This prevents competitive exclusion due to differently effective dispersal strategies. We conclude that while temporal instabilities that cause, for example, predator–prey oscillations are usually regarded as jeopardising species' persistence, spatial instabilities that give rise to self‐organised pattern formation should be interpreted more positively, as they provide a generic mechanisms for maintaining diversity in metacommunities without requiring a priori habitat heterogeneity. Read the free Plain Language Summary for this article on the Journal blog.

Nematic Superconductivity and Its Critical Vestigial Phases in the Quasicrystal.

We propose a general mechanism to realize nematic superconductivity (SC) and reveal its exotic vestigial phases in the quasicrystal (QC). Starting from a Penrose-Hubbard model, our microscopic studies suggest that the Kohn-Luttinger mechanism driven SC in the QC is usually gapless due to violation of Anderson's theorem, rendering that both chiral and nematic SCs are common. The nematic SC in the QC can support novel vestigial phases driven by pairing phase fluctuations above its T_{c}. Our combined renormalization group and MonteCarlo studies provide a phase diagram in which, besides the conventional charge-4e SC, two critical vestigial phases emerge, i.e., the quasinematic (QN) SC and QN metal. In the two QN phases, discrete lattice rotation symmetry is counterintuitively "quasibroken" with power-law decaying orientation correlation. They separate the phase diagram into various phases connected via Berezinskii-Kosterlitz-Thouless (BKT) transitions. These remarkable critical vestigial phases, which resemble the intermediate BKT phase in the q state (q≥5) clock model, are a consequence of the fivefold (or higher) anisotropy field brought about by the unique QC symmetry, which are absent in conventional crystalline materials.

Fundamentals and Exceptions of the LysR-type Transcriptional Regulators.

LysR-type transcriptional regulators (LTTRs) are emerging as a promising group of macromolecules for the field of biosensors. As the largest family of bacterial transcription factors, the LTTRs represent a vast and mostly untapped repertoire of sensor proteins. To fully harness these regulators for transcription factor-based biosensor development, it is crucial to understand their underlying mechanisms and functionalities. In the first part, this Review discusses the established model and features of LTTRs. As dual-function regulators, these inducible transcription factors exude precise control over their regulatory targets. In the second part of this Review, an overview is given of the exceptions to the "classic" LTTR model. While a general regulatory mechanism has helped elucidate the intricate regulation performed by LTTRs, it is essential to recognize the variations within the family. By combining this knowledge, characterization of new regulators can be done more efficiently and accurately, accelerating the expansion of transcriptional sensors for biosensor development. Unlocking the pool of LTTRs would significantly expand the currently limited range of detectable molecules and regulatory functions available for the implementation of novel synthetic genetic circuitry.

Molecular basis of TMED9 oligomerization and entrapment of misfolded protein cargo in the early secretory pathway.

Intracellular accumulation of misfolded proteins causes serious human proteinopathies. The transmembrane emp24 domain 9 (TMED9) cargo receptor promotes a general mechanism of cytotoxicity by entrapping misfolded protein cargos in the early secretory pathway. However, the molecular basis for this TMED9-mediated cargo retention remains elusive. Here, we report cryo-electron microscopy structures of TMED9, which reveal its unexpected self-oligomerization into octamers, dodecamers, and, by extension, even higher-order oligomers. The TMED9 oligomerization is driven by an intrinsic symmetry mismatch between the trimeric coiled coil domain and the tetrameric transmembrane domain. Using frameshifted Mucin 1 as an example of aggregated disease-related protein cargo, we implicate a mode of direct interaction with the TMED9 luminal Golgi-dynamics domain. The structures suggest and we confirm that TMED9 oligomerization favors the recruitment of coat protein I (COPI), but not COPII coatomers, facilitating retrograde transport and explaining the observed cargo entrapment. Our work thus reveals a molecular basis for TMED9-mediated misfolded protein retention in the early secretory pathway.

Review Research Paper of Feasibility study on Anti-Gravity Effect for Advance Propulsion system and technologies

The concept of anti-gravity, often portrayed in science fiction as a means to counteract or negate the effects of gravitational force, has intrigued scientists and enthusiasts alike for decades. This paper explores the feasibility of achieving anti-gravity effects through various theoretical and experimental perspectives. Firstly, theoretical frameworks such as general relativity and quantum mechanics are reviewed to understand gravity and its potential manipulation. While these theories provide foundational insights, they also highlight the immense challenges involved in directly counteracting gravitational forces due to their fundamental nature. Next, experimental efforts and hypothetical technologies proposed in scientific literature are examined. Concepts such as negative mass, exotic matter, and gravitational shielding are discussed in terms of their theoretical underpinnings and practical limitations. Experimental evidence, including anomalies in gravitational measurements and speculative engineering proposals, are scrutinized to evaluate their relevance to achieving anti-gravity effects. Furthermore, the paper addresses the technological and ethical implications of developing anti-gravity technology. Considerations such as energy requirements, environmental impact, and societal readiness are explored to provide a holistic perspective on the feasibility and desirability of pursuing anti-gravity research. Ultimately, while the idea of anti-gravity remains a captivating subject of scientific inquiry and fiction, current understanding and technological capabilities suggest significant hurdles that must be overcome before practical anti-gravity effects can be realized. This paper concludes by outlining potential avenues for future research and highlighting the interdisciplinary nature of addressing such a complex phenomenon.

Beyond self-healing: stabilizing and destabilizing photochemical adjustment of the ozone layer

Abstract. The ozone layer is often noted to exhibit self-healing, whereby depletion of ozone aloft induces ozone increases below, explained as resulting from enhanced ozone production due to the associated increase in ultraviolet (UV) radiation below. Similarly, ozone enhancement aloft can reduce ozone below (reverse self-healing). This paper considers self-healing and reverse self-healing to manifest a general mechanism we call photochemical adjustment, whereby ozone perturbations lead to a downward cascade of anomalies in UV and ozone. Conventional explanations for self-healing imply that photochemical adjustment is stabilizing, damping perturbations towards the surface. However, photochemical adjustment can be destabilizing if the enhanced UV disproportionately increases the ozone sink, as can occur if the enhanced UV photolyzes ozone to produce atomic oxygen, which speeds up catalytic destruction of ozone. We analyze photochemical adjustment in two linear ozone models (Cariolle v2.9 and LINOZ), finding that (1) photochemical adjustment is destabilizing above 40 km in the tropical stratosphere and (2) self-healing often represents only a small fraction of the total photochemical stabilization. The destabilizing regime above 40 km is reproduced in a much simpler model: the Chapman cycle augmented with destruction of O and O3 by generalized catalytic cycles and transport (the Chapman+2 model). The Chapman+2 model reveals that photochemical destabilization occurs where the ozone sink is more sensitive than the source to perturbations in overhead column ozone, which is found to occur when the window of overlapping absorption by O2 and O3 is optically unsaturated, i.e., when overhead slant column ozone is below approximately 1018 molec. cm−2.

Third Metal Ion Dictates the Catalytic Activity of the Two-Metal-Ion Pre-Ribosomal RNA-Processing Machinery.

Nucleic acid processing enzymes use a two-Mg2+-ion motif to promote the formation and cleavage of phosphodiester bonds. Yet, recent evidence demonstrates the presence of spatially conserved second-shell cations surrounding the catalytic architecture of proteinaceous and RNA-dependent enzymes. The RNase mitochondrial RNA processing (MRP) complex, which cleaves the ribosomal RNA (rRNA) precursor at the A3 cleavage site to yield mature 5'-end of 5.8S rRNA, hosts in the catalytic core one atypically-located Mg2+ ion, in addition to the ions forming the canonical catalytic motif. Here, we employ biased quantum classical molecular dynamics simulations of RNase MRP to discover that the third Mg2+ ion inhibits the catalytic process. Instead, its displacement in favour of a second-shell monovalent K+ ion propels phosphodiester bond cleavage by enabling the formation of a specific hydrogen bonding network that mediates the essential proton transfer step. This study points to a direct involvement of a transient K+ ion in the catalytic cleavage of the phosphodiester bond and implicates cation trafficking as a general mechanism in nucleic acid processing enzymes and ribozymes.

Polar targeting of proteins - a green perspective.

Cell polarity - the asymmetric distribution of molecules and cell structures within the cell - is a feature that almost all cells possess. Even though the cytoskeleton and other intracellular organelles can have a direction and guide protein distribution, the plasma membrane is, in many cases, essential for the asymmetric localization of proteins because it helps to concentrate proteins and restrict their localization. Indeed, many proteins that exhibit asymmetric or polarized localization are either embedded in the PM or located close to it in the cellular cortex. Such proteins, which we refer to here as 'polar proteins', use various mechanisms of membrane targeting, including vesicle trafficking, direct phospholipid binding, or membrane anchoring mediated by post-translational modifications or binding to other proteins. These mechanisms are often shared with non-polar proteins, yet the unique combinations of several mechanisms or protein-specific factors assure the asymmetric distribution of polar proteins. Although there is a relatively detailed understanding of polar protein membrane targeting mechanisms in animal and yeast models, knowledge in plants is more fragmented and focused on a limited number of known polar proteins in different contexts. In this Review, we combine the current knowledge of membrane targeting mechanisms and factors for known plant transmembrane and cortical proteins and compare these with the mechanisms elucidated in non-plant systems. We classify the known factors as general or polarity specific, and we highlight areas where more knowledge is needed to construct an understanding of general polar targeting mechanisms in plants or to resolve controversies.

Thermally activated damage recovery in ion‐irradiated Gd2Ti2‐yZryO7 pyrochlore

AbstractIonizing events having a wide variety of radiation‐induced effects can radically affect the kinetics of defect production or structural transformation in the pyrochlore structured oxides (A2B2O7). Therefore, a thorough understanding of the kinetics associated with cation ordering and disordering is required for various technological applications. The structural responses of Gd2Ti2‐yZryO7 (y = 0.4, 1.2, 1.6) pyrochlore series irradiated by 120 MeV Au9+ ions were investigated using in situ synchrotron x‐ray diffraction (SR‐XRD), micro‐Raman spectroscopy, and scanning electron microscopy (SEM). Each pyrochlore composition irradiated at the highest fluence, where structural modifications occur, was subsequently isochronally annealed from room temperature to 1000°C. The SR‐XRD results indicate that Ti‐rich composition (y = 0.4) retains its pre‐irradiated pyrochlore structure (Fdm) at 1000°C. In contrast, Zr‐rich compositions exhibit recrystallization to an intermediate defect‐fluorite phase (Fmm) above 500°C, and the pre‐irradiated pyrochlore superstructure does not recover even on annealing at 1000°C. These results reveal that recrystallization temperature strongly depends on the accumulated radiation damage, generally described with the cationic radius ratio (rA/rB). Thus, investigation of the thermal annealing behavior of irradiated pyrochlores helps better understanding the general mechanisms of radiation damage and recovery of pyrochlores, which is important for their use in nuclear applications.

Generation mechanism of behavioral risk for organizational decision-makers in financial institutions: organizational and human errors

This study investigates the mechanism behind the generation of behavioral risk among decision-makers in financial institutions. We start by examining the general mechanism of organizational decision-making behavior, then analyse organizational errors and human errors in the decision-making process, and subsequently define the connotations and types of organizational decision-makers’ behavioral risk. The study also identifies the necessary conditions for the emergence of decision-making behavioral risk. We construct a model to analyse the behavioral risk of decision-makers in financial institutions. We also develop motivation and utility functions for organizational decision-makers’ behavior, examine the relationship between factors in the utility function, and explore how organizational decision-makers adjust their behavior in various situations to maximize utility. The paper also analyses a case study involving the China Everbright Group (CEG). The study revealed the following: ① The conditions for the occurrence of organizational decision-makers’ behavioral risk in financial institutions mainly stem from the conflict between organizational interests and decision-makers’ interests, the failure of organizational contextual constraints, and the lack of organizational decision-making auditing and feedback mechanisms. ② Organizational decision-makers tend to exhibit inappropriate decision-making behaviors when they overestimate their own abilities in comparison to the benefits they expect. ③ Financial institutions should avoid organizational errors to reduce the likelihood of behavioral risk by increasing the cost of organizational decision-makers’ behavior. Our study proposes measures to mitigate the risk of inappropriate behavior by financial institutions through scientific decision-making.

Opposing neural processing modes alternate rhythmically during sustained auditory attention

During continuous tasks, humans show spontaneous fluctuations in performance, putatively caused by varying attentional resources allocated to process external information. If neural resources are used to process other, presumably “internal” information, sensory input can be missed and explain an apparent dichotomy of “internal” versus “external” attention. In the current study, we extract presumed neural signatures of these attentional modes in human electroencephalography (EEG): neural entrainment and α-oscillations (~10-Hz), linked to the processing and suppression of sensory information, respectively. We test whether they exhibit structured fluctuations over time, while listeners attend to an ecologically relevant stimulus, like speech, and complete a task that requires full and continuous attention. Results show an antagonistic relation between neural entrainment to speech and spontaneous α-oscillations in two distinct brain networks—one specialized in the processing of external information, the other reminiscent of the dorsal attention network. These opposing neural modes undergo slow, periodic fluctuations around ~0.07 Hz and are related to the detection of auditory targets. Our study might have tapped into a general attentional mechanism that is conserved across species and has important implications for situations in which sustained attention to sensory information is critical.

Indigo production identifies hotspots in cytochrome P450 BM3 for diversifying aromatic hydroxylation.

Evolution of P450 BM3 is a topic of extensive research, but screening the various substrate/reaction combinations remains a time-consuming process. Indigo production has the potential to serve as a simple high-throughput method for reaction screening, as bacterial colonies expressing indigo (+) variants can be visually identified via their blue phenotype. Indigo (+) single variants, indigo (-) single variants and a combinatorial library, containing mutations that enable the blue phenotype, were screened for their ability to hydroxylate a panel of 12 aromatic compounds using the 4-aminoantipyrine colorimetric assay. Recombination of indigo (+) single variants to create a multiple-variant library is a particularly useful strategy, as all top performing P450 BM3 variants with high hydroxylation activity were either indigo (+) single variants or contained multiple substitutions. Furthermore, active variants, as determined using the 4-AAP assay, were further characterized and several variants were identified that gave more than 90% conversion with 1,3-dichlorobenzene and predominantly formed 2,6-dichlorophenol; other variants showed significant substrate selectivity. This supports the hypothesis that substitution at positions that enable the indigo (+) phenotype, or hotspot residues, is a general mechanism for increasing aromatic hydroxylation activity. Overall, this research demonstrates that indigo (+) single variants, identified via colorimetric colony-based screening, may be recombined to generate a multiply-substituted variant library containing many variants with high aromatic hydroxylation activity. The combination of colony-based screening and other screening assays greatly accelerates enzyme engineering, as readily-identified indigo (+) single variants can be recombined to create a library of active multiple variants without extensive screening of single variants.

Theory of angular momentum transfer from light to molecules

We present a theory describing the interaction of structured light, such as light carrying orbital angular momentum, with molecules. The light-matter interaction Hamiltonian we derive is expressed through couplings between spherical gradients of the electric field and the (transition) electric multipole moments of a particle of any nontrivial rotation point group. Our model can therefore accommodate an arbitrary complexity of the molecular and electric field structure, and it can be straightforwardly extended to atoms or nanostructures. Applying this framework to rovibrational spectroscopy of molecules, we uncover the general mechanism of angular momentum exchange between the spin and orbital angular momenta of light, molecular rotation, and its center-of-mass motion. We show that the nonzero vorticity of Laguerre-Gaussian beams can strongly enhance certain rovibrational transitions that are considered forbidden in the case of nonhelical light. We discuss the experimental requirements for the observation of these forbidden transitions in state-of-the-art spatially resolved spectroscopy measurements. Published by the American Physical Society 2024

Energy-Saving Optimization of HVAC Systems Using an Ant Lion Optimizer with Enhancements

The complex and time-varying external climate conditions and multi-equipment variable coupling characteristics make it challenging to optimize the Heating, Ventilation, and Air Conditioning (HVAC) systems in existing buildings effectively. Additionally, the intricate energy exchange processes within HVAC systems present difficulties in developing accurate and generalizable energy consumption models. In response to these challenges, this paper proposes an Ant Lion Optimizer with Enhancements (ALOE) that can dynamically adjust the number of populations and the movement trend to improve the convergence speed and optimization ability, and randomly adjust the movement amplitude to enhance the local optimal escape ability. Finally, a case study of an office building in Hangzhou was carried out, and an overall energy consumption model of the HVAC system based on parameter identification and a general mechanism model was established. In this model, the energy-saving optimization effects of various advanced swarm intelligence optimization algorithms were compared. The experimental results demonstrate that under high, medium, and low load conditions, the ALOE algorithm achieves energy-saving rates of 28.16%, 28.26%, and 24.85%, respectively, the overall energy-saving rate for the entire day reaches 29.06%, which indicates the ALOE has significant superiority. This work will contribute to the development of energy-saving and emission-reduction technologies.

Cell swelling enhances ligand-driven β-adrenergic signaling

G protein-coupled receptors’ conformational landscape can be affected by their local, microscopic interactions within the cell plasma membrane. We employ here a pleiotropic stimulus, namely osmotic swelling, to alter the cortical environment within intact cells and monitor the response in terms of receptor function and downstream signaling. We observe that in osmotically swollen cells the β2-adrenergic receptor, a prototypical GPCR, favors an active conformation, resulting in cAMP transient responses to adrenergic stimulation that have increased amplitude. The results are validated in primary cell types such as adult cardiomyocytes, a model system where swelling occurs upon ischemia-reperfusion injury. Our results suggest that receptors’ function is finely modulated by their biophysical context, and specifically that osmotic swelling acts as a potentiator of downstream signaling, not only for the β2-adrenergic receptor, but also for other receptors, hinting at a more general regulatory mechanism.