Biology subjects

Ge, H.

Publications and source records attributed to Ge, H..

At least 19 recordsLinked to original sources

bioRxiv2026

Small brown planthopper infestation enhances it reproduction and insecticide tolerance by manipulating glucose distribution and levels in rice

The evolutionary arms race between plants and insects involves not only direct defense and counter-defense but also sophisticated resource manipulation. However, how herbivorous insects respond to host nutritional signals to modulate their fitness traits remains unclear. This study investigates how the small brown planthopper (SBPH, Laodelphax striatellus) manipulates host plant carbohydrate allocation, and to elucidate the molecular mechanisms by which the acquired glucose enhances SBPH fecundity and insecticide tolerance. Using molecular, pharmacological, and biochemical approaches, we found that SBPH infestation induced systemic carbohydrate reallocation in rice, elevating whole-plant glucose levels by promoting aerial accumulation while depleting root reserves. Host-derived glucose enhanced SBPH fecundity by activating the target of rapamycin (TOR) pathway, upregulating juvenile hormone (JH) signaling, and increasing vitellogenin production. For imidacloprid tolerance, glucose boosted glutathione S-transferase (GST) activity via two synergistic mechanisms: by upregulating glutamate cysteine ligase (GCL) to increase glutathione synthesis, and transcriptionally via the glucose-TOR-JH axis to induce LsGSTe1 (SBPH epsilon class GST) and LsGSTo1 (SBPH omega class GST) expression. Our findings establish host-derived glucose as a central signaling molecule that SBPH utilizes to modulate conserved pathways for simultaneous optimization of reproduction and insecticide resistance. This reveals a multifaceted nutrient-responsive mechanism in insect pests and identifies the glucose-TOR-JH axis as critical molecular targets for developing nutrient-based pest control strategies, such as disrupting insect nutrient-sensing pathways or modulating host carbohydrate metabolism. HighlightsO_LISBPH infestation elevates whole-plant glucose levels by promoting aerial accumulation while suppressing root abundance. C_LIO_LISBPH-induced glucose in the rice aerial tissues boosts reproduction of SBPH via TOR-JH-Vg pathway. C_LIO_LISBPH-induced glucose in the rice aerial tissues enhances imidacloprid tolerance of SBPH through GCL-GSH-GST and TOR-JH-GST axis. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=152 SRC="FIGDIR/small/701313v2_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@39e084org.highwire.dtl.DTLVardef@1c310cborg.highwire.dtl.DTLVardef@1838575org.highwire.dtl.DTLVardef@1aedebe_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2025

Prolactin links psychological stress to psoriasis via a fibroblast-chemokine pathway

Psoriasis is a chronic inflammatory skin disease that forms a vicious cycle with psychological stress. Whether and how the hypothalamic-pituitary (HP) axis-mediated neuroendocrine system regulates psoriasis remains obscure. Here, we report elevated levels of the pituitary hormone prolactin (PRL) in both psoriasis patients and imiquimod (IMQ)-induced psoriasis mice. Mechanistically, PRL acts on dermal PRLR-expressing fibroblasts to promote the production of the chemokines CCL2 and CCL7, which then recruit monocytes/macrophages into psoriatic lesional skin, thereby activating local IL-17A-producing T cells. Accordingly, pharmacological targeting of PRL signaling inhibits the recruitment of monocytes/macrophages, decreases the frequency of IL-17A-producing T cells, and alleviates IMQ-induced psoriasis in mice. In summary, our results delineate a mechanism by which the neuroendocrine hormone PRL aggravates psoriasis and highlight a potential therapeutic strategy of inhibiting PRL-PRLR signaling, particularly in psoriasis patients experiencing psychological stress.

immunology↗

bioRxiv2025

scDIAGRAM: Detecting Chromatin Compartments from Individual Single-Cell Hi-C Matrix without Imputation or Reference Features

Single-cell Hi-C (scHi-C) provides unprecedented insight into 3D genome organization, but its sparse and noisy data pose challenges in accurately detecting A/B compartments, which are crucial for understanding chromatin structure and gene regulation. We presented scDIAGRAM, a data-driven method for annotating A/B compartments in single cells using direct statistical modeling and graph community detection. Unlike existing approaches, scDIAGRAM operates without relying on external information, such as the CpG density or imputation techniques, and preserves cell-to-cell heterogeneity. Accuracy and robustness of scDIAGRAM were illustrated through simulated scHi-C datasets and a human cell line. We applied scDIAGRAM to real scHi-C datasets from the mouse brain cortex, mouse embryonic development, and human acute myeloid leukemia (AML), demonstrating its ability to capture compartmental shifts associated with transcriptional variation. This robust framework offers new insights into the functional roles of chromatin compartments at single-cell resolution across various biological contexts.

bioinformatics↗

bioRxiv2025

Beach sand beneath our feet: an overlooked reservoir of antibiotic resistance genes and pathogens, revealed by metagenomic evidence from Qingdao's recreational beaches

Coastal beach environments, especially those with heavy tourist activity, represent a dynamic interface between terrestrial and marine microbiomes. However, beach sand is rarely considered in surveillance of antibiotic resistance. In this study, we combined 16S rRNA gene sequencing and shotgun metagenomics to characterize microbial communities and antibiotic resistance genes (ARGs) at four popular recreational beaches in Qingdao, China. We show that beach sands harbor highly diverse bacterial communities with significantly greater richness than adjacent seawater. Beach sand near sewage discharge points had microbial profiles intermediate between raw sewage and open-ocean water, reflecting contributions from both sources. Metagenomic analysis identified a broad "resistome" of over 300 distinct ARGs in these beach and water samples, spanning 33 antibiotic classes and 6 resistance mechanism categories. Notably, the rifampicin resistance gene rpoB2 was the most abundant ARG, and genes conferring resistance to peptide antibiotics were prevalent. Sewage outfalls were found to be major contributors of ARGs, with waste-influenced sand containing a larger and more diverse ARG pool than sand farther from pollution sources. We also detected a high diversity of bacterial virulence factor genes, particularly in sand. Our findings highlight that tourist beaches can serve as reservoirs and mixing zones for antibiotic-resistant and potentially pathogenic bacteria from land-based pollution. This underscores the need to include beach sand in environmental monitoring for antibiotic resistance and to improve wastewater management at recreational coastlines to mitigate public health risks. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=198 SRC="FIGDIR/small/661489v1_ufig1.gif" ALT="Figure 1"> View larger version (84K): org.highwire.dtl.DTLVardef@18705f3org.highwire.dtl.DTLVardef@1979f8forg.highwire.dtl.DTLVardef@16c9029org.highwire.dtl.DTLVardef@6c778d_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2024

Mesoscale chromatin confinement facilitates target search of pioneer transcription factors in live cells

Pioneer transcription factors (PTFs) possess the unique capability to access closed chromatin regions and initiate cell fate changes, yet the underlying mechanisms remain elusive. Here, we characterized the single-molecule dynamics of PTFs targeting chromatin in living cells, revealing a notable "confined target search" mechanism. PTFs like FOXA1, FOXA2, SOX2, OCT4 and KLF4 sampled chromatin more frequently than non-pioneer factor MYC, alternating between fast free diffusion in the nucleus and slower confined diffusion within mesoscale zones. Super-resolved microscopy showed closed chromatin organized as mesoscale nucleosome-dense domains, confining FOXA2 diffusion locally and enriching its binding. We pinpointed specific histone-interacting disordered regions, distinct from DNA-binding domain, crucial for confined target search kinetics and pioneer activity within closed chromatin. Fusion to other factors enhanced pioneer activity. Kinetic simulations suggested transient confinement could increase target association rate by shortening search time and binding repeatedly. Our findings illuminate how PTFs recognize and exploit closed chromatin organization to access targets, revealing a pivotal aspect of gene regulation.

molecular biology↗

bioRxiv2024

Natural killer cell migration in HIV-infected individuals is inhibited by impairment of HIF-1alpha-mediated glycolysis

Natural killer (NK) cells serve as the first line of defense of the immune system and play a crucial role in fighting against HIV infection. The effective function of NK cells is closely related to their migration ability, but the status of NK cell migration in HIV-infected individuals and the regulation mechanism for NK cell migration remains unknown. Here, we found that NK cell migration was significantly impaired in HIV-infected individuals, lower in immune non-responders (INRs) compared with immune responders (IRs), and positively correlated with CD4+ T cell counts. Further investigations showed that the decreased NK cell migration in HIV infection was caused by the impairment of glycolysis. Mechanistically, we found that NK cell migration was regulated by HIF-1 pathway, and inhibitory receptor TIGIT restrained HIF-1 expression by inhibiting PI3K/AKT/mTORC1 or ERK signaling pathway, consequently weakening the glycolysis of NK cells in HIV-infected individuals, and ultimately leading to down-regulation of migration. Collectively, we uncovered a mechanism of reduced NK cell migration in HIV infection and provided a new insight for immunotherapy in HIV infection. In BriefThe effective function of NK cells is closely related to its migration ability. The authors show that impaired NK cell migration in HIV-infected individuals is caused by TIGIT inhibiting HIF-1-mediated glycolysis via PI3K/AKT/mTORC1 or ERK pathway.

immunology↗

bioRxiv2023

DNA-protein interaction is dominated by short anchoring elements

To understand the regulation of gene expression, it is essential to elucidate the binding mechanism of DNA binding domain (DBD) of transcription factors (TFs), and predict the location of transcription factor binding sites (TFBSs). For an exhaustive search of TFBSs, we have investigated four typical TFs with diverse origins, such as WRKY, PU.1, GLUCOCORTICOID RECEPTOR (GR), and MYC2 by using a newly developed method, KaScape. During KaScape experiments, we identified short sequences (3-4 bases) or "anchoring element" (AE) for the four TFs that dominated the bound population of DNA-DBD binding. We further developed the AEEscape (AE Energy landscape) algorithm to detect and confirm the AE and derived its binding energy landscape for all possible sequences. Our analysis of the energy landscape revealed an energetic funnel around the TFBS, which is related to the AE density gradient in the region surrounding the TFBS. Our results provide novel insights into the mechanism of TF binding to TFBSs.

biophysics↗

bioRxiv2022

FCGRT, a cancer-derived immunoglobulin G binding protein, mediates the malignant phenotype of glioma

CIgG has received increasing attention, and was first discovered by our group to indicate poor prognosis in glioma. Furthermore, by protein mass spectrometry, we found that FCGRT can combine with CIgG. However, the study of FCGRT in glioma has not been reported. We used the CGGA325, TCGA dataset and immunohistochemistry to verify the importance of FCGRT on the prognosis of glioma patients. Single cell sequencing data analysis evaluated that the role of FCGRT in the microenvironment of glioma. Estimate, ssGSEA, EPIC and xCell were used for immune infiltration analysis. FCGRT was knocked down in U251 cells to detect the effect of FCGRT on the malignant development of glioma. These results showed that patients with higher FCGRT expression had a shorter overall survival. FCGRT was closely related to the tumor microenvironment, especially to macrophages in the tumor microenvironment (r=0.743, p<0.001). Interestingly we also found that FCGRT was positively correlated with IGHG1. Finally, we found that knock-down of FCGRT resulted in a decrease in proliferation, migration and invasion of U251 cells. Taken together, we believe that FCGRT is an independent prognostic factor for glioma patients, and its possible mechanism is to promote proliferation and invasion of tumor cells by interacting with CIgG.

bioinformatics↗

bioRxiv2021

Direct Reconstruction of Gene Regulatory Networks underlying Cellular state Transitions without Pseudo-time Inference

Nowadays the advanced technology for single-cell transcriptional profiling enables people to routinely generate thousands of single-cell expression data, in which data from different cell states or time points are derived from different samples. Without transferring such time-stamped cross-sectional data into pseudo-time series, we propose COSLIR (COvariance restricted Sparse LInear Regression) for directly reconstructing the gene regulatory networks (GRN) that drives the cell-state transition. The differential gene expression between adjacent cell states is modeled as a linear combination of gene expressions in the previous cell state, and the GRN is reconstructed through solving an optimization problem only based on the first and second moments of the sample distributions. We apply the bootstrap strategy as well as the clip threshold method to increase the precision and stability of the estimation. Simulations indicate the perfect accuracy of COSLIR in the oracle case as well as its good performance and stability in the sample case. We apply COSLIR separately to two cell lineages in a published single-cell qPCR dataset during mouse early embryo development. Nearly half of the inferred gene-gene interactions have already been experimentally reported and some of them were even discovered during the past decade after the dataset was published, indicating the power of COSLIR. Furthermore, COSLIR is also evaluated on several single-cell RNA-seq datasets, and the performance is comparable with other methods relying on the pseudo-time reconstruction.

bioinformatics↗

bioRxiv2021

Molecular mechanism behind the involvement of apple flavonoid glycosyltransferase gene MdGT1 in the color of apple leaves

Nowadays, the plant family 1 UDP-glycosyltransferases (UGTs) are more and more investigated owing to their contribution to the plant secondary metabolism and diverse biological roles. Apple (Malus domestica) is one of the most widely cultivated fruit trees with great economical importance. However, poor knowledge is known about the apple UGTs. In this study, we identified 229 members of family 1 through a genome-wide analysis of the apple UGTs, which were clustered into 18 groups, from A to R. We also performed detailed analysis to 34 apple UGTs with quantitavive RT-PCR, and discovered a number of stress-regulated UGTs. Among them, we characterized the role of MD09G1064900, also named as MdUGT83L3, which is significantly induced by salt and cold. In vivo analysis showed that it has high activity towards cyanidin, and moderate activity towards quercetin and keampferol. The transgenic callus and regenerated apple plants overexpressing MdUGT83L3 showed enhanced tolerance to salt and cold treatments. Overexpression of MdUGT83L3 also increased anthocyanin accumulation in the callus tissues and enhanced ROS clearing upon exposed to salt and cold stresses. Futhermore, via yeast-two-hybrid assay, EMSA and CHIP analysis, we also found that MdUGT83L3 could be directly regualted by MdMYB88. Our study indicated that MdUGT83L3, under the regulation of MdMYB88, plays important roles in salt and cold stress adaptation via modulating flavonoid metabolism in apple.

molecular biology↗

bioRxiv2020

A Fast Detection Method for Wheat Mould Based on Biophotons

Mould is a common phenomenon in stored wheat. First, mould will decrease the quality of wheat kernels. Second, the mycotoxins metabolized by mycetes are very harmful for humans. Therefore, the fast and accurate examination of wheat mould is vitally important to evaluating its storage quality and subsequent processing safety. Existing methods for examining wheat mould mainly rely on chemical methods, which always involve complex and long pretreatment processes, and the auxiliary chemical materials used in these methods may pollute our environment. To improve the determination of wheat mould, this paper proposed a type of green and nondestructive determination method based on biophotons. The specific implementation process is as follows: first, the ultra-weak luminescence between healthy and mouldy wheat samples are measured repeatedly by a biophotonic analyser, and then, the approximate entropy and multiscale approximate entropy are separately introduced as the main classification features. Finally, the classification performances have been tested using the support vector machine(SVM). The ROC curve of the newly established classification model shows that the highest recognition rate can reach 93.6%, which shows that our proposed classification model is feasible and promising for detecting wheat mould.

microbiology↗

bioRxiv2020

Opposing neural signals of CaV1-encoded peptides are tuned by C-terminus mediated inhibition

L-type calcium (CaV1) channels regulate gene expressions via the cascade of excitation-transcription coupling, or directly as standalone CCAT (Calcium Channel Associated Transcriptional-regulator) peptides encoding distal carboxyl-terminus (DCT) of CaV1, both evidenced in dendritogenesis signaling in neurons. We here discover that DCT peptides opposedly mediate these two sets of transcription signals, all tunable in accordance to C-terminus mediated inhibition (CMI) of Ca2+/CaV1 influx. By electrophysiology, neurite morphology, and FRET 2-hybrid binding analyses, we systematically examined native and derived DCT peptides across CaV1, unveiling that the overall balance between cytosolic inhibition versus nuclear facilitation is spatially and temporally tuned by CMI of each DCT variant. Our findings not only resolve several controversies existing to DCT variants, but also propose a de novo scheme of CaV1-centric gene regulation: two concurrent routes of transcription signals initiated from either membrane CaV1 channels or nuclear CaV1-encoded peptides are subject to autonomous feedback tuning by peptide/channel interactions.

neuroscience↗

bioRxiv2020

The Nonequilibrium Mechanism of Noise Enhancer synergizing with Activator in HIV Latency Reactivation

Reactivating HIV latency and then simultaneously eliminating it by antiretroviral therapy has become a leading strategy in curing HIV. Recently, single-cell screening experiments have shown the drug synergy between two categories of biomolecules, Activators (AC) and Noise Enhancers (NE): NE can amplify the reactivation of latent HIV induced by AC, although NE itself cannot reactivate HIV latency. Based on an established LTR-two-state effective model, we uncover two necessary conditions for this type of drug synergy: The decreasing of the turning-on rate of LTR induced by NE is highly inhibited when presented with AC; The timescale of LTR turning off without AC/NE presented should be no slower than the timescale of Tat transactivation. Then we propose a detailed LTR-four-state mechanistic model with both AC/NE regulation kinetics and Tat transactivation circuit. We show that, in order to achieve drug synergy, the system of HIV gene state transition must operate out of thermodynamic equilibrium, which is caused by energy input. The direction of energy input determines whether the inhibition of NE upon the reactivation rate of LTR-off states (unbinding of RNAP) can be successfully prevented in the presence of AC. The drug synergy can also be significantly enhanced if the energy input is appropriately distributed to more than one reaction. Our model reveals a generic nonequilibrium mechanism underpinning the noise enhanced drug synergy, which may apply to identify the same drug synergy on reactivating a diverse class of lentivirus latency. Significance StatementThe "kick and kill" strategy has become a promising way to cure HIV by eliminating latent HIV reservoirs, the main barrier to a clinical cure. Two categories of biomolecules, Activators (AC) and Noise Enhancers (NE), have been found to have synergy on reactivating latent HIV (kick strategy). We uncover the underlying non-equilibrium mechanism of such drug synergy by developing mathematical models based on genetic regulatory kinetics. We find that controlling the magnitude and direction of energy input into genetic regulatory kinetics can prevent NE from reducing the turn-on rate of the inactivated gene state in the presence of AC, which produces the synergy. This general nonequilibrium mechanism can be useful for identifying other drug synergies on lentivirus latency reactivation.

systems biology↗

bioRxiv2019

SCRIBE: a new approach to dropout imputation and batch effects correction for single-cell RNA-seq data

Single-cell RNA sequencing technologies are widely used in recent years as a powerful tool allowing the observation of gene expression at the resolution of single cells. Two of the major challenges in scRNA-seq data analysis are dropout events and batch effects. The inflation of zero(dropout rate) varies substantially across single cells. Evidence has shown that technical noise, including batch effects, explains a notable proportion of this cell-to-cell variation. To capture biological variation, it is necessary to quantify and remove technical variation. Here, we introduce SCRIBE (Single-Cell Recovery Imputation with Batch Effects), a principled framework that imputes dropout events and corrects batch effects simultaneously. We demonstrate, through real examples, that SCRIBE outperforms existing scRNA-seq data analysis tools in recovering cell-specific gene expression patterns, removing batch effects and retaining biological variation across cells. Our software is freely available online at https://github.com/YiliangTracyZhang/SCRIBE.

bioinformatics↗

bioRxiv2019

Identification of the Repressive Domain of the Negative Circadian Clock Component CHRONO

Circadian rhythm is an endogenous, self-sustainable oscillation that participates in regulating organisms physiological activities. Key to this oscillation is a negative feedback by main clock components Periods and Cryptochromes that repress transcriptional activity of BMAL1/CLOCK complexes. In addition, a novel repressor, CHRONO, has been identified recently, but details of CHRONOs function during repressing the circadian cycle remain unclear. Here we report that a domain of CHRONO mainly composed of -helixes is critical to repression through the exploitation of protein-protein interactions according to luciferase reporter assays, co-immunoprecipitation, immunofluorescence, genome editing and structural information analysis via circular dichroism spectroscopy. This repression is fulfilled by interactions between CHRONO with a region on the BMAL1 C-terminus where Cryptochrome and CBP bind. Our results indicate that CHRONO and PER differentially function as BMALA/CLOCK-dependent repressors. We further suggest a repression model of how PER, CRY and CHRONO proteins associate with BMAL1, respectively.

molecular biology↗

bioRxiv2018

Limited differential expression of miRNAs and other small RNAs in LPS-stimulated human monocytes

Monocytes are a distinct subset of myeloid cells with diverse functions in early inflammatory immune modulation. While previous studies have surveyed the role of microRNA regulation on different myeloid cell lines and primary cultures, the time-dependent kinetics of inflammatory stimulation on miRNA expression and the relationship between miRNA-to-target-RNA expression have not been comprehensively profiled in monocytes. In this study, we use next-generation sequencing and RT-PCR assays to analyze the non-coding small RNA transcriptome of unstimulated and lipopolysaccharide (LPS)-stimulated monocytes at 6 and 24 hours. We identified a miRNA signature consisting of five mature miRNAs (hsa-mir-146a, hsa-mir-155, hsa-mir-9, hsa-mir-147b, and hsa-mir-193a) upregulated by LPS-stimulated monocytes after 6 hours and found that most miRNAs were also upregulated after 24 hours of stimulation. Only one miRNA gene was down-regulated and no other small RNAs were found dysregulated in monocytes after LPS treatment. In addition, novel tRNA-derived fragments were also discovered in monocytes, although none showed significant changes upon LPS stimulation. Interrogation of validated miRNA targets by transcriptomic analysis revealed that the majority of differential mRNA expression was maintained in LPS-stimulated monocytes although few of miRNA targets seemed to obtain heterogeneous expression pattern along the treatment. Our findings reveal a potential role by which selective miRNA upregulation and stable expression of other small RNAs enable monocytes to develop finely tuned cellular responses during acute inflammation.

genomics↗

bioRxiv2018

Expression of novel fusion antiviral proteins Ricin A Chain-Pokeweed Antiviral Proteins (RTA-PAPs) in Escherichia coli and their inhibition of protein synthesis and of hepatitis B virus in vitro

Ricin A chain (RTA) and Pokeweed antiviral proteins (PAPs) are plant-derived N-glycosidase ribosomal-inactivating proteins (RIPs) isolated from Ricinus communis and Phytolacca Americana respectively. This study was to investigate the potential antiviral value of novel fusion proteins between RTA and PAPs (RTA-PAPs). In brief, RTA-Pokeweed antiviral protein isoform 1 from seeds (RTA-PAPS1) was produced in E. coli in vivo expression system, purified from inclusion bodies using gel filtration chromatography and protein synthesis inhibitory activity assayed by comparison to the production of a control protein Luciferase. The antiviral activity of the RTA-PAPS1 against Hepatitis B virus (HBV) in HepAD38 cells was then determined using a dose response assay by quantifying supernatant HBV DNA compared to control virus infected HepAD38 cells. The cytotoxicity in HepAD38 cells was determined by measuring cell viability using a tetrazolium dye uptake assay. Results showed that RTA-PAPS1 could effectively be recovered and purified from inclusion bodies. The refolded protein was bioactive with 50% protein synthesis inhibitory concentration (IC50) of 0.06nM (3.63ng/ml). The results also showed that RTA-PAPS1 had a synergetic activity against HBV with a half-maximal response concentration value (EC50) of 0.03nM (1.82ng/ml) and a therapeutic index of >21818. The fusion protein was further optimized using in silico tools, produced in E. coli in vivo expression system, purified by three-step process from soluble lysate and protein synthesis inhibition activity assayed. Results showed that the optimized protein RTA mutant-Pokeweed antiviral protein isoform 1 from leaves (RTAM-PAP1) could be recovered and purified from soluble lysates with gain of function activity on protein synthesis inhibition with an IC50 of 0.03nM (1.82ng/ml). Collectively, our results demonstrate that RTA-PAPs are amenable to effective production and purification in native form, possess significant antiviral activity against HBV in vitro with a high therapeutic index and, thus, meriting further development as potential antiviral agents against chronic HBV infection.

synthetic biology↗

bioRxiv2018

Structure for Energy Cycle: A unique status of Second Law of Thermodynamics for living systems

Distinguishing things from beings, or matters from lives, is a fundamental question. Extending E. Schrodingers neg-entropy and I. Prigogines dissipative structure, we propose a chemical kinetic view that the earliest \"live\" process is essentially a special interaction between a pair of specific components under a corresponding, particular environmental conditions. The interaction exists as an inter-molecular-force-bond complex (IMFBC) that couples two separate chemical processes: One is the spontaneous formation of an IMFBC driven by the decrease of Gibbs free energy as a dissipative process; while the other is the disassembly of the IMFBC driven thermodynamically by free energy input from the environment. The two processes that are coupled by the IMFBC were originated independently and considered non-living on Earth, but the IMFBC coupling of the two can be considered as the earliest form of metabolism: This forms the first landmark on the path from things to a being. The dynamic formation and dissemblance of the IMFBCs, as composite individuals, follows a principle designated as \"... structure for energy for structure for energy...\", the cycle continues, shortly \"structure for energy cycle\". With additional features derived from an IMFBC, such as multiple intermediates, autocatalytic ability of one individual upon the formation of another, aqueous medium, and mutual beneficial relationship between formation of polypeptides and nucleic acids, etc., the IMFBC-centered \"live\" process spontaneously evolved into more complex living organisms with the characteristics one currently knows.

evolutionary biology↗