Functional Differentiation Research Articles

Identification and functional characterization of the diterpene synthase family in Pogostemon cablin (Blanco) Benth

Pogostemon cablin (Blanco) Benth (Patchouli) is an aromatic herb extensively used in pharmaceutical and cosmetic industries. Sesquiterpenes are the characteristic constitutes in patchouli which are synthesized in the glandular trichomes on leaves and stems. Gibberellic acid (GA), a tetracyclic diterpenoid, plays a crucial role in the formation of glandular trichome. However, the diterpene biosynthesis remains largely unknown in patchouli. Here we identified a small diterpene synthases (diTPSs) family comprising three class II diTPSs (PatCPS1-3) and three class I diTPSs (PatKSL1 and PatGLS1-2). These diTPSs are functionally characterized using a yeast heterologous expression system. PatCPS1 was identified as an ent-copalyl diphosphate synthase (ent-CPS), in combination with PatKSL1, yield ent-kaurene, the precursor of GA, indicating their involvement in primary metabolism. PatCPS2 converted GGPP into (+)-8, 13-copalyl diphosphate (CPP). No activity was detected for PatCPS3, PatGLS1 and PatGLS2. Three ohnologs of PatCPS1 were further characterized to explore the possible functional differentiation of ent-CPS during the evolution of tetraploid hybrid patchouli genome. GC-MS analysis showed all ohnologs are functional ent-CPSs, demonstrating the functional conservation of PatCPS1 during evolution. Expression profiling by qRT-PCR showed PatCPS1 and PatKSL1 are ubiquitously expressed in all tissues, consistent with their involvement in primary metabolism. Conversely, PatCPS2 and PatCPS3 were predominantly expressed in the above ground parts, indicating a role in specialized metabolism. In summary, these findings clarify the early stages of GA biosynthesis in patchouli and provide gene elements for further metabolic engineering of sesquiterpenes via diterpenoids.

High-resolution 7T fMRI reveals the visual zone of the human claustrum

Abstract The claustrum is a thin grey matter structure located between the insular cortex and the putamen. The function of the claustrum is largely unknown with diverse hypotheses ranging from multisensory integration and consciousness to attention and cognitive control. Much research on the function of the claustrum relies on invasive techniques in animal models, as the claustrum’s uniquely thin shape makes it difficult to image non-invasively in human subjects. In the current proof-of-concept study, we used high-resolution ultra-high field (7 Tesla) functional magnetic resonance imaging (fMRI) to measure activity in the human claustrum during the processing of naturalistic stimuli. We presented short video clips as visual only, auditory only or audiovisual conditions while participants performed a central fixation task. We found distinct visual responses in both the left and the right claustrum at a consistent spatial location across participants, hemispheres and sessions. We also found deactivations in response to auditory stimulation. These deactivations were confined to the right claustrum and did not overlap with visual activity. The deactivation in response to auditory stimulation demonstrates the complexity of claustrum’s functional organization and suggests functional differentiation within the claustrum. This is the first study to demonstrate sensory-specific effects within the human claustrum. It opens the possibility for studying the claustrum’s role in higher-level aspects of sensory processing in humans.

A novel iterative algorithm for nonlinear inelastic dynamic analysis of truss structures; MCB-Spline+Sp time integration method

The focus of this work is on the development of a novel algorithm for the nonlinear dynamic analysis of structures. In the sake of a general and easy-to-implement solution method, the tangential stiffness matrix is calculated by combining the Cauchy-Riemann equations derived from the differentiation of complex functions and using the nodal displacement perturbation vector. An implicit direct time integration method based on a cubic B-Spline is integrated with the incremental-iterative method using a quadrature rule based on the interpolation of spline functions, which is referred to as the MCB-Spline+Sp time integration method. A step-by-step algorithm for developing a computer code to implement this method is provided. The effectiveness of the proposed approach is evaluated through several nonlinear time history analyses, which demonstrate its accuracy and efficiency by observing less computational efforts and fast convergence rate. Moreover, a comparison is made between the developed method and well-established techniques such as the Newmark and Standard-Bathe time integration methods in combination with the iterative Newton-Raphson method.

Histone lactylation drives CD8+ T cell metabolism and function.

The activation and functional differentiation of CD8+ T cells are linked to metabolic pathways that result in the production of lactate. Lactylation is a lactate-derived histone post-translational modification; however, the relevance of histone lactylation in the context of CD8+ T cell activation and function is not known. Here, we show the enrichment of H3K18 lactylation (H3K18la) and H3K9 lactylation (H3K9la) in human and mouse CD8+ T cells, which act as transcription initiators of key genes regulating CD8+ T cell function. Further, we note distinct patterns of H3K18la and H3K9la in CD8+ T cell subsets linked to their specific metabolic profiles. Additionally, we find that modulation of H3K18la and H3K9la by targeting metabolic and epigenetic pathways influence CD8+ T cell effector function, including antitumor immunity, in preclinical models. Overall, our study uncovers the potential roles of H3K18la and H3K9la in CD8+ T cells.

Expression of laccase and ascorbate oxidase affects lignin composition in Arabidopsis thaliana stems.

Lignin is a phenolic polymer that is a major source of biomass. Oxidative enzymes, such as laccase and peroxidase, are required for lignin polymerisation. Laccase is a member of the multicopper oxidase family and has a high amino acid sequence similarity with ascorbate oxidase. However, the process of functional differentiation between the two enzymes remains poorly understood. In this study, the common ancestry sequence of laccase and ascorbate oxidase (AncMCO) was predicted via phylogenetic reconstruction, and its in vivo effect on lignin biosynthesis in Arabidopsis thaliana was assessed. The estimated AncMCO sequence conserved key residues that coordinate with copper ions, implying that the electron transfer system is likely to be conserved in AncMCO. However, multiple insertions/deletions corresponding to protein surface structures have been found between laccase, ascorbate oxidase, and AncMCO. The overexpression of canonical laccase (AtLAC4) and ascorbate oxidase (AtAAO1) in A. thaliana resulted in notable increases of syringyl/guaiacyl lignin unit ratio in stems, whereas, in contrast, the overexpression of AncMCO did not show any detectable change in lignin deposition. Transcriptomic analysis revealed that the AtAAO1-overexpressing line exhibited significant changes in the expression of a wide range of cell wall biosynthesis genes. These results highlight the importance of the molecular evolution of multicopper oxidase, which drives lignin biosynthesis during plant evolution.

COHERENCE AS A FACTOR IN THE EFFECTIVENESS OF JOINT ACTIVITIES OF OPEN-SOURCE DEVELOPERS

Coherence determines a team’s effectiveness, assuming an optimal combination of individual activities. To describe the content of coherence in teams of open-source software developers is the main aim of the study. A total of 114,016 sequences of interactions related to pull requests from 979 open-source projects make up the purposive sample of the research. An automated observation process utilising a large language model was used as a method of data analysis. According to the analysis, coherence as a characteristic of effective teams is defined by the unity of purpose, acceptance of functional differentiation between roles, and a high pace of software development. Each participant motivates one another to carry out the subsequent set of actions. Contributors make a clear addition, team members manage the procedure, respond quickly and approve the actions.

Astrocytes contribute to the functional differentiation of the hippocampal longitudinal axis during reward and aversion processing in the adult male rat

This study aims to investigate whether glial cells, in particular putative astrocytes, contribute to functional distinctions between the dorsal (DH), intermediate (IH), and ventral (VH) hippocampus. To evaluate this, we performed three different behavioral tasks (i.e., Morris water maze; MWM, Passive avoidance; PA, T-maze place preference; TPP) to determine whether the DH, IH, and VH are necessary for each task. Sensitivity of behavioral tasks was confirmed using lidocaine (2 %, 1 μl) reversible inactivation. Subsequently, we examined the effects of silencing astrocytes, using fluorocitrate (FC, 1 mM/1 μl), into the DH, IH, and VH on these tasks. The effects of drugs were examined separately. We observed that injection of FC into the DH resulted in a significant impairment in MWM performance. In contrast, while FC injections into the IH or VH did not prevent platform localization during the acquisition phase, rats showed difficulty recalling the target zone during the retrieval phase. In the PA test, FC injection into the VH impaired task learning and memory. During the acquisition phase, FC injection into the DH or IH did not differ from the control in the number of shocks; however, during retrieval, there was a significant decrease in the latency before entering the dark chamber. The TPP test performance was impaired by FC injection in the IH. In sum, we show that glial cells, especially astrocytes in specific functional regions of the hippocampus, play distinct roles in processing aversive and rewarding experiences and contribute to the functional organization of the hippocampal longitudinal axis.

Characterization and expression analysis of the MADS-box gene AGL8 in cotton: insights into gene function differentiation in plant growth and stress resistance.

AGAMOUS-LIKE 8 (AGL8) belongs to the MADS-box family, which plays important roles in transcriptional regulation, sequence-specific DNA binding and other biological processes and molecular functions. The genome of cotton, a representative polyploid plant, contains multiple AGL8 genes. However, their functional differentiation is still unclear. In this study, a comprehensive genomic analysis of AGL8 genes was conducted. Cotton AGL8s were subdivided into four subgroups (Groups 1, 2, 3, and 4) based on phylogenetic analysis, and different subgroups of AGL8s presented different characteristics, including different structures and conserved motifs. With respect to the promoter regions of the GhAGL8 genes, we successfully predicted cis-elements that respond to phytohormone signal transduction and the stress response of plants. Transcriptome data and real-time quantitative PCR validation indicated that three genes, namely, GH_D07G0744, GH_A03G0856 and GH_A07G0749, were highly induced by methyl jasmonate (MeJA), salicylic acid (SA), and abscisic acid (ABA), which indicated that they function in plant resistance to abiotic and biotic stresses. The information from the gene structure, number and types of conserved domains, tissue-specific expression levels, and expression patterns under different treatments highlights the differences in sequence and function of the cotton AGL8 genes. Different AGL8s play roles in vegetative growth, reproductive development, and plant stress resistance. These results lay a foundation for further study of GhAGL8s in cotton.

Comparative Effectiveness of Ascorbic Acid vs. Calcium Ascorbate Ingestion on Pharmacokinetic Profiles and Immune Biomarkers in Healthy Adults: A Preliminary Study.

Previous trials have displayed augmented intracellular vitamin C concentrations in the leukocytes at 24 h after acute supplementation with 1000 mg calcium ascorbate (CA), compared to ascorbic acid (AA). The primary objective was to evaluate comparative leukocyte vitamin C accumulation kinetics over 32 h following acute 250 mg or 500 mg doses from the two sources. Secondary objectives were to evaluate neutrophil phagocytic function and lymphocyte differentiation between the two sources of vitamin C. Ninety-three healthy females (250 mg, n = 27; 500 mg, n = 24) and males (250 mg, n = 19; 500 mg, n = 23) were assigned to ingest a single dose of CA or AA providing 250 mg or 500 mg of vitamin C in two separate double-blind, randomized crossover trials. There were no significant differences in the primary or secondary outcomes between the two treatments in the 250 mg low-dose study. Conversely, there was evidence that ingestion of 500 mg of CA increased DHA in plasma, increased neutrophil functionality during the first 8 h of the PK study, promoted increased natural killer cells, and altered weight-adjusted PK profiles, suggesting greater volume distribution and clearance from the blood. These findings indicate that 500 mg of CA may promote some immune benefits compared to 500 mg of AA ingestion.

Numerical differentiation of the piecewise smooth function by using Fourier extension method

Numerical differentiation of the piecewise smooth function is considered in this paper. To avoid the large error of numerical differentiation that may occur near potential non-smooth points, we identify the discontinuity points of the first or second derivative of the function. Then we divide the domain of the function into several sub-domains. For each sub-domain, the approximation is constructed by Fourier extension, and the global approximation of the piecewise smooth function is formed by superposition to improve accuracy. Some numerical experiments are conducted to further verify the efficacy of the method.

Accurate preference-based method to obtain the deterministically optimal and satisfactory fairness-efficiency trade-off

The resource allocation problem is a classic multi-objective challenge, particularly when balancing the fairness-efficiency trade-off. To achieve a deterministically optimal and satisfactory solution, researchers frequently employ preference-based methods, including selecting among Pareto solutions based on the decision-maker's a posteriori preference and using deterministic models incorporating a priori preferences. In this study, we address two main challenges—specifically, (1) the limitations in measuring the abstract concepts of fairness and efficiency and (2) finding a deterministically optimal and satisfactory balance between fairness and efficiency. We apply a Gini impurity index derived from the classification and regression tree to calculate fairness, ensuring the Gini index function's differentiability. Additionally, we unify the scales of fairness and efficiency to facilitate calculation. Using accurate preference information, we employ the extended interval goal programming method to solve the model and achieve a deterministically optimal and satisfactory solution. The comparative analysis results demonstrate that our model (1) efficiently addresses the real-world water resource allocation problem concerning the fairness-efficiency trade-off; and (2) generates fewer penalties, with an average improvement ratio of 8% in the case study, using more refined penalty functions that align closer to the decision-maker's real and nonlinear preferences.

The rhizosphere contributes disproportionately to free-living nitrogen fixation in subalpine forest soils

Root activity creates a unique microbial hotspot in the rhizosphere, profoundly regulating free-living nitrogen fixation (FLNF). However, empirical assessments of rhizosphere FLNF and its ecological consequences for nitrogen (N) budgets remain lacking, particularly for different root functional modules. Here, we separately collected rhizosphere soils attached to two root functional modules, absorptive roots and transport roots, and investigated the rates (15N2 incorporation) and regulators of rhizosphere FLNF in a N-limited subalpine coniferous forest. The measured rates were further extrapolated to annual fluxes based on the volume of the rhizosphere and the relationship between FLNF rate and temperature. We found that absorptive roots drove significantly higher rhizosphere FLNF rates than did transport roots (12.2 vs. 7.5 ng N g-1 d-1), with both rhizosphere compartments exhibiting rates well exceeding those in the bulk soil (0.9 ng N g-1 d-1). The FLNF rates were positively correlated with soil organic carbon content but showed no significant relationship with the abundance or composition of the diazotrophic community. Moreover, when extrapolated to the ecosystem level the FLNF fluxes were 2-fold greater in the rhizosphere of absorptive roots than in that of transport roots (0.13 vs. 0.04 kg N ha-1 yr-1). Taken together, despite representing only 6.0% of the soil volume, the two rhizosphere compartments contributed as much as 47.2% to the total soil FLNF fluxes. Overall, we provide empirical evidence that despite its limited volume, the rhizosphere contributes disproportionately to the FLNF in subalpine forest soils. Our findings also underscore the critical role of root functional differentiation in regulating rhizosphere FLNF, which is essential for integrating this process into the ecosystem-level N cycle.

Loss of STING impairs lactogenic differentiation.

Heightened energetic and nutrient demand during lactogenic differentiation of the mammary gland elicits upregulation of various stress responses to support cellular homeostasis. Here, we identify the stimulator of interferon genes (STING) as an immune supporter of the functional development of mouse mammary epithelial cells (MECs). An in vitro model of MEC differentiation revealed that STING is activated in a cGAS-independent manner to produce both type I interferons and proinflammatory cytokines in response to the accumulation of mitochondrial reactive oxygen species. Induction of STING activity was found to be dependent on the breast tumor suppressor gene single-minded 2 (SIM2). Using mouse models of lactation, we discovered that loss of STING activity results in early involution of #3 mammary glands, severely impairing lactational performance. Our data suggest that STING is required for successful functional differentiation of the mammary gland and bestows a differential lactogenic phenotype between #3 mammary glands and the traditionally explored inguinal 4|9 pair. These findings affirm unique development of mammary gland pairs that is essential to consider in future investigations into normal development and breast cancer initiation.

지수함수 미분법의 정당화에 관한 예비 교사들의 수학 내용 지식과 인식

The purpose of this paper is to examine pre-service teachers' mathematical content knowledge and perceptions regarding the justification of the differentiation of the exponential function in relation to the connection between school mathematics and university mathematics. We analyzed and categorized how pre-service teachers justified the differentiation of the exponential function through semi-structured interviews, examined whether the gaps in the learning trajectory in school mathematics were rigorously addressed, and surveyed their perceptions about these gaps. This study revealed that the justification methods of pre-service teachers could be categorized into seven types, and they had difficulty rigorously addressing the gaps. Many pre-service teachers were unaware of the gaps in the learning trajectory and agreed on the need for consistent learning trajectories between school and university mathematics. This study highlights the need to improve pre-service teacher education by examining the mathematical content knowledge required for mathematics teachers in connection to school mathematics.

Field theory with the Maxima computer algebra system

The Maxima computer algebra system, the open-source successor to MACSYMA, the first general-purpose computer algebra system that was initially developed at the Massachusetts Institute of Technology in the late 1960s and later distributed by the United States Department of Energy, has some remarkable capabilities, some of which are implemented in the form of add-on, “share” packages that are distributed along with the core Maxima system. One such share package is itensor, for indicial tensor manipulation. One of the more remarkable features of itensor is functional differentiation. Through this, it is possible to use itensor to develop a Lagrangian field theory and derive the corresponding field equations. In this paper, we demonstrate this capability by deriving Maxwell’s equations from the Maxwell Lagrangian, and exploring the properties of the system, including current conservation.

원삼국~백제 한성기 취락의 저장 양상 변화

In the process of state formation, storage methods can change according to political, economic, and social transformations. This study aims to identify such changes in storage methods, storage amounts, and stored crops by comparing and analyzing various types of archaeological evidence, such as crop remains, pottery, storage pits, and above-ground structures from sites of the central region of the Korean Peninsula dating the Proto-Three Kingdoms to Baekje’s Hanseong period. The results of the analysis revealed that, in the Gyeonggi region, the tendency to store crops indoors was weakened by the Hanseong period. However, in major settlements, this tendency persisted, and the use of external storage facilities increased, with rice becom-ing a significant crop for external storage. In the Yeongseo region, the change in indoor storage methods was not as distinct as in the Gyeonggi region, but there was a noticeable change in external storage patterns. Overall, the use of deep storage pits increased, new storage crops were added, and the use of external storage facilities increased somewhat in the Namhan River basin. Analyzing the reasons for these changes based on contemporary contexts, it was found that both the Gyeonggi and Yeongseo regions were influenced by changes in agricultural production methods. In the case of the Gyeonggi region, the in-creased complexity of society, such as the intensification of social stratification and the dif-ferentiation of site functions, also influenced storage strategies.

Sterol regulatory element-binding proteins mediate intrinsic fungicide tolerance and antagonism in the fungal biocontrol agent Clonostachys rosea IK726

Sterol regulatory element-binding proteins (SREBPs) are transcription factors governing various biological processes in fungi, including virulence and fungicide tolerance, by regulating ergosterol biosynthesis and homeostasis. While studied in model fungal species, their role in fungal species used for biocontrol remains elusive. This study delves into the biological and regulatory function of SREBPs in the fungal biocontrol agent (BCA) Clonostachys rosea IK726, with a specific focus on fungicide tolerance and antagonism. Clonostachys rosea genome contains two SREBP coding genes (sre1 and sre2) with distinct characteristics. Deletion of sre1 resulted in mutant strains with pleiotropic phenotypes, including reduced C. rosea growth on medium supplemented with prothioconazole and boscalid fungicides, hypoxia mimicking agent CoCl2 and cell wall stressor SDS, and altered antagonistic abilities against Botrytis cinerea and Rhizoctonia solani. However, Δsre2 strains showed no significant effect. Consistent with the gene deletion results, overexpression of sre1 in Saccharomyces cerevisiae enhanced tolerance to prothioconazole. The functional differentiation between SRE1 and SRE2 was elucidated by the yeast-two-hybridization assay, which showed an interaction between SREBP cleavage-activating protein (SCAP) and SRE1 but not between SRE2 and SCAP. Transcriptome analysis of the Δsre1 strain unveiled SRE1-mediated expression regulation of genes involved in lipid metabolism, respiration, and xenobiotic tolerance. Notably, genes coding for antimicrobial compounds chitinases and polyketide synthases were downregulated, aligning with the altered antagonism phenotype. This study uncovers the role of SREBPs in fungal BCAs, providing insights for C. rosea IK726 application into integrated pest management strategies.

Regenerative capacity of alveolar type 2 cells is proportionally reduced following disease progression in idiopathic pulmonary fibrosis-derived organoid cultures.

Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive lung disease that leads to respiratory failure and death due to irreversible scarring of the distal lung. While historically considered a chronic inflammatory disorder, the aberrant function of the alveolar epithelium is now recognized to play a central role in IPF pathophysiology. This study aimed to investigate the regenerative capacity of AT2 cells using IPF-derived alveolar organoids and to examine the effects of disease progression on this capacity. Lung tissues from 3 pneumothorax patients and 6 IPF patients (early and advanced stages) were obtained by VATS and lung transplantation. HTII-280+ cells were isolated from CD31-CD45-EpCAM+ cells in the distal lungs of IPF and pneumothorax patients using fluorescence-activated cell sorting (FACS) and resuspended in 48-well plates to establish IPF-derived alveolar organoids. Immuno-staining was used to confirm the presence of AT2 cells. FACS sorting yielded approximately 1% AT2 cells of the total cells in early IPF tissue, and the number decreased as the disease progressed, compared with 2.7% in pneumothorax. Additionally, the cultured organoids in the IPF groups were smaller in size and fewer in number compared to those from pneumothorax patients. The colony-forming efficiency decreased as the disease progressed. In immuno-staining results, the IPF organoids showed lower expression of SFTPC compared to the pneumothorax group and contained KRT5+ cells. This study confirmed that the regenerative capacity of AT2 cells in IPF decreases as the disease progresses, and IPF AT2 cells inherently exhibit functional abnormalities and altered differentiation plasticity.

A mathematical primer to classical deep learning

This manuscript synthesizes the statistical foundations of classical deep learning by integrating insights from eight seminal works. It covers matrix calculus, neuron layers, weight and bias indexing, cost functions, differentiation of neuron operations, activation functions, bias functions, gradient descent, and backpropagation algorithms. The synthesis aims to provide a comprehensive understanding of the mathematical and statistical principles underpinning deep learning models, facilitating their application and further development in various domains.

Nuclear dualism without extensive DNA elimination in the ciliate Loxodes magnus

Most eukaryotes have one nucleus and nuclear genome per cell. Ciliates have instead evolved distinct nuclei that coexist in each cell: a silent germline vs. transcriptionally active somatic nuclei. In the best-studied model species, both nuclei can divide asexually, but only germline nuclei undergo meiosis and karyogamy during sex. Thereafter, thousands of DNA segments, called internally eliminated sequences (IESs), are excised from copies of the germline genomes to produce the streamlined somatic genome. In Loxodes, however, somatic nuclei cannot divide but instead develop from germline copies even during asexual cell division, which would incur a huge overhead cost if genome editing was required. Here, we purified and sequenced both genomes in Loxodes magnus to see whether their nondividing somatic nuclei are associated with differences in genome architecture. Unlike in other ciliates studied to date, we did not find canonical germline-limited IESs, implying Loxodes does not extensively edit its genomes. Instead, both genomes appear large and equivalent, replete with retrotransposons and repetitive sequences, unlike the compact, gene-rich somatic genomes of other ciliates. Two other hallmarks of nuclear development in ciliates-domesticated DDE-family transposases and editing-associated small RNAs-were also not found. Thus, among the ciliates, Loxodes genomes most resemble those of conventional eukaryotes. Nonetheless, base modifications, histone marks, and nucleosome positioning of vegetative Loxodes nuclei are consistent with functional differentiation between actively transcribed somatic vs. inactive germline nuclei. Given their phylogenetic position, it is likely that editing was present in the ancestral ciliate but secondarily lost in the Loxodes lineage.