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Biology subjects

De Jaeger, G.

Publications and source records attributed to De Jaeger, G..

At least 19 recordsLinked to original sources

Integration of SYT1 Interactomics and Dual-Localization Proteomics Links ER-PM Contacts to Lignin Deposition

Membrane contact sites (MCSs) are evolutionarily conserved intracellular nanodomains that physically bridge opposing lipid bilayers to facilitate non-vesicular communication and maintain cellular homeostasis. In plants, endoplasmic reticulum-plasma membrane (ER-PM) contact sites play fundamental roles in environmental adaptation, and are populated by specialized proteins which act as tethers such as Synaptotagmin 1 (SYT1). However, a comprehensive view of the molecular machinery governing processes at these junctions is still needed. In this work, we integrate affinity purification mass spectrometry, TurboID proximity labeling, and a dual-localization reanalysis of HyperLOPIT spatial proteomics to functionally map the protein interaction landscape of the ER-PM contact sites protein SYT1. Beyond recovering established ER-PM MCS functions, our analysis identified uncharacterized proteins as bona fide resident components of these junctions, and revealed that these nanodomains act as docking platforms that anchor the monolignol biosynthetic complex. By spatially organizing Membrane Steroid Binding Proteins and cytochrome P450 enzymes, our findings support a model where SYT1-mediated anchoring of this metabolon to ER-PM contact sites optimizes monolignol export required for stress-induced lignification. Ultimately, this proteomic framework expands the functional repertoire of ER-PM contact sites, opening new avenues to uncover hidden roles of MCSs across diverse eukaryotic systems.

molecular biology↗

The molecular architecture of the Arabidopsis callose synthase complex

ABSTRACTCallose synthase is responsible for the targeted deposition of the {beta}-1,3-glucan polymer, callose which underlines essential plant developmental processes, including cell division, pathogen defense or cell-cell communication. The architecture of the callose synthase complex (CALSC) as well as the molecular mechanisms of callose synthesis remain unknown. Here we report an integrative characterisation of the Arabidopsis CALS complex, with the most enriched subunits, CALS1, CALS2 and CALS3, forming its core. Structurally, CALSC assembles into a trimer, requiring the plant-specific Bag domain to mediate inter-subunit associations. The biological importance of CALSC assembly is highlighted by the simultaneous loss of CALS1 and CALS3, which abolishes plasmodesmal callose deposition and affects symplastic transport. Site-directed mutagenesis and molecular dynamics simulations depict the topology of the CALS1 active site in detail, including the components of the enzymatic reaction. We pinpoint the translocating tunnel through which the nascent glucan is delivered and mechanistically confirm the role of transmembrane helix 8 in regulating glucan export. Our work provides unprecedented insight into the molecular architecture of the CALSC and the distinct changes from maturation to activity at the plasma membrane, while showcasing the mechanisms involved in callose synthesis at the molecular level.

plant biology↗

TGA family of transcription factors are nitric oxide sensors in the root stem cell niche

Plant root development is tightly regulated and depends on the coordination among different cell types located in the root stem cell niche (SCN). A complex network of regulators includes the gasotransmitter nitric oxide (NO) known to inhibit primary root growth, modify root architecture and alter meristem organisation. However, little is known about the molecular targets and the mechanistic insights of this signalling molecule during root SCN homeostasis. Here, genetic, molecular and physiological evidence support that TGA transcription factors of the bZIP family, and specifically PERIANTHIA (PAN), contribute to NO-mediated root stem cell regulation. NO induces reversible S-nitrosylation of PAN, thereby inhibiting its binding to DNA and associated transcriptional activation. In turn, the protein-SNO reductase activity of TRXh5 is able to denitrosylate PAN. This switch on and off mechanism of PAN activation modulates WOX5 expression and quiescent centre activity, which alters columella stem cell maintenance through a NO-dependent mechanism. Different TGA members interact with PAN and are also S-nitrosylated, whose expression in the root SCN together with their accumulated mutations contribute to NO sensing during root apical meristem development. Collectively, these findings reveal a molecular framework where NO controls the ability of PAN to bind to its targets as a master regulator of the root SCN.

plant biology↗

Clathrin-coated vesicles are targeted for selective autophagy during osmotic stress.

Plants frequently encounter hyperosmotic stress due to drought and salinity, leading to rapid water loss, reduced turgor pressure, and decreased cell volume. This contraction drastically alters plasma membrane tension, a physical parameter that must be strictly maintained to support mechanosignaling and cell expansion. However, the mechanisms by which plants adjust their membrane surface area to match a shrinking cell volume remain poorly understood. Here, we identify selective autophagy dependent degradation of plasma membrane-derived clathrin-coated vesicles (CCVs) in response to hyperosmotic shock. This pathway involves the recruitment of the endocytic TPLATE complex (TPC) to autophagosomes in an osmotic-stress dependent manner. Through correlative light and electron microscopy (CLEM) and electron tomography (ET), we provide ultrastructural evidence of the physical association of CCVs with autophagosome membranes. These autophagosomes contain endocytic machinery, including TPC and clathrin, and are targeted to the vacuole. Mechanistically, we show that the conserved ATG8-interacting motifs (AIMs) in the AtEH1/Pan1 and AtEH2/Pan1 TPC subunits interact with ATG8, suggesting that they facilitate the recruitment of CCVs to autophagosomes. Using time-lapse imaging, we demonstrate that the acute induction of autophagy is precisely coupled to the reduction in cell volume under hyperosmolar conditions. Our results suggest that endocytic removal of excess plasma membrane to maintain membrane tension and cellular integrity is coupled to TPC-mediated CCV-phagy. These findings reveal a homeostatic mechanism that enables plants to adapt to the challenges of drought and salinity. Significance StatementAll living cells must maintain the physical integrity of their outer membrane. How cells can adapt their surface area to respond to rapid changes in cell volume, such as those caused by drought or salt stress, remains a fundamental question in biology. We identify a mechanism in plants involving autophagy - a cellular recycling pathway - where plasma membrane-derived vesicles are targeted for degradation following salt or osmotic stress. This pathway involves the TPLATE complex, an evolutionary ancient and essential endocytic complex in plants, which directly interacts with the autophagy protein ATG8. This discovery reveals how plants adapt to osmotic stress by modulating their membrane properties, supporting a framework for future improvement of crop resilience in response to salinity and drought.

plant biology↗

The structural scaffold of the TPLATE complex deforms the membrane during plant endocytosis

Summary paragraphEukaryotic cells maintain homeostasis of their outer membrane by controlled internalization of lipid and protein constituents via endocytosis1. Endocytosis is evolutionary conserved and utilizes similar structural folds. How these structural folds are combined into proteins and protein complexes however differs between eukaryotic kingdoms2. The TPLATE complex in plants is an evolutionary ancient protein module that combines several endocytic folds into a single octameric protein complex3-5. Its molecular architecture, lipid-nucleated condensate formation, and its requirement for clathrin cage curvature revealed its function in endocytosis initiation in plants6-8. Mechanistic understanding of how this complex drives membrane deformation during plant endocytosis is, however, lacking. Here, we used an integrative structural approach to obtain a precise molecular structure of the TPLATE complex. In addition, our approach allowed visualizing the structural flexibility that hallmarks this enigmatic complex. We prove that the intrinsic structural flexibility is required for its functionality and membrane recruitment. The membrane binding interface consists of several domains with differential lipid preferences. Finally, we show that the crescent shape of the structured part of the complex is sufficient for membrane curvature generation. Our mechanistic insight answers the long-standing question of how plants execute endocytosis without cytoskeletal-based force generation.

plant biology↗

The cell cycle controls spindle architecture in Arabidopsis by modulating the augmin pathway

To ensure an even segregation of chromosomes during somatic cell division, eukaryotes rely on specific microtubule structures called mitotic spindles. There are, however, striking differences in overall spindle organization among eukaryotic super groups, and in particular little is known about how spindle architecture is determined in plants. As a foundation for our work, we have measured prime characteristics of Arabidopsis mitotic spindles and built a three-dimensional dynamic model of the Arabidopsis mitotic spindle using Cytosim. Next, we identified the cell-cycle regulator CYCLIN-DEPENDENT KINASE B1 (CDKB1) together with its cyclin partner CYCB3;1 as key regulators of spindle shape and organization in Arabidopsis. Loss of CDKB1 function resulted in a high number of astral microtubules that are normally absent from plant spindles, as opposed to animal ones. We identified an augmin complex member, ENDOSPERM DEFECTIVE1 (EDE1), as a substrate of the CDKB1;1-CYCB3;1 complex. A non-phosphorylatable mutant of EDE1 displayed spindles with extended pole-to-pole distance, resembling the phenotypes of cycb3;1 and cdkb1 mutants. Moreover, we found that the mutated EDE1 version associated less efficiently with spindle microtubules. Consistently, reducing the level of augmin in Cytosim simulations largely recapitulated the spindle phenotypes observed in cycb3;1 and cdkb1 mutants. Our results emphasize the importance of cell cycle-dependent phospho-control of the mitotic spindle in plant cells. They also support the validity of our computational model as a framework for the exploration of mechanisms controlling the organization of the spindle in plants and in other species.

developmental biology↗

SnRK1 inhibits anthocyanin biosynthesis through both transcriptional regulation and direct phosphorylation and dissociation of the MYB/bHLH/TTG1 MBW complex.

Plants have evolved an extensive specialized secondary metabolism. The colorful flavonoid anthocyanins, for example, not only stimulate flower pollination and seed dispersal but also protect different tissues against high light, UV- and oxidative stress. Their biosynthesis is highly regulated by environmental and developmental cues and induced by high sucrose levels. Expression of the biosynthetic enzymes involved is controlled by a transcriptional MBW complex, comprising (R2R3) MYB- and bHLH-type transcription factors (TF) and the WD40 repeat protein TTG1. Anthocyanin biosynthesis is obviously useful but also carbon- and energy-intensive and non-vital. Consistently, the SnRK1 protein kinase, a metabolic sensor activated in carbon- and energy-depleting stress conditions, represses anthocyanin biosynthesis. Here we show that Arabidopsis SnRK1 represses MBW complex activity both at the transcriptional and post-translational level. In addition to repressing expression of the key transcription factor MYB75/PAP1, SnRK1 activity triggers MBW complex dissociation, associated with loss of target promoter binding, MYB75 protein degradation and nuclear export of TTG1. We also provide evidence for direct interaction with and phosphorylation of multiple MBW complex proteins. These results indicate that repression of expensive anthocyanin biosynthesis is an important strategy to save energy and redirect carbon flow to more essential processes for survival in metabolic stress conditions.

plant biology↗

Phase separation-based visualization of protein-protein interactions and kinase activities in plants

Protein activities depend heavily on protein complex formation and dynamic post-translational modifications, such as phosphorylation. Their dynamic nature is notoriously difficult to monitor in planta at cellular resolution, often requiring extensive optimization and high-end microscopy. Here, we generated and exploited the SYnthetic Multivalency in PLants (SYMPL)-vector set to study protein-protein interactions (PPIs) and kinase activities in planta based on phase separation. This technology enabled easy detection of inducible, binary and ternary protein-protein interactions among cytoplasmic, nuclear and plasma membrane proteins in plant cells via a robust image-based readout. Moreover, we applied the SYMPL toolbox to develop an in vivo reporter for SnRK1 kinase activity, allowing us to visualize tissue-specific, dynamic SnRK1 activation upon energy deprivation in stable transgenic Arabidopsis plants. The applications of the SYMPL cloning toolbox lay the foundation for the exploration of PPIs, phosphorylation and other post-translational modifications with unprecedented ease and sensitivity.

plant biology↗

Mapping the adaptor protein complex interaction network in Arabidopsis identifies P34 as a common stability regulator

Adaptor protein (AP) complexes are evolutionarily conserved vesicle transport regulators that recruit coat proteins, membrane cargos and coated vesicle accessory proteins. Since in plants endocytic and post-Golgi trafficking intersect at the trans-Golgi network, unique mechanisms for sorting cargos of overlapping vesicular routes are anticipated. The plant AP complexes are part of the sorting machinery, but despite some functional information, their cargoes, accessory proteins, and regulation remain largely unknown. Here, by means of various proteomics approaches, we generated the overall interactome of the five AP and the TPLATE complexes in Arabidopsis thaliana. The interactome converged on a number of hub proteins, including the thus far unknown adaptin binding-like protein, designated P34. P34 interacted with the clathrin-associated AP complexes, controlled their stability and, subsequently, influenced clathrin-mediated endocytosis and various post-Golgi trafficking routes. Altogether, the AP interactome network offers substantial resources for further discoveries of unknown endomembrane trafficking regulators in plant cells.

plant biology↗

The FANCC-FANCE-FANCF complex is evolutionarily conserved and regulates meiotic recombination

At meiosis, programmed meiotic DNA double-strand breaks are repaired via homologous recombination, resulting in crossovers (COs). From a large excess of DNA double-strand breaks that are formed, only a small proportion gets converted into COs because of active mechanisms that restrict CO formation. The Fanconi anemia (FA) complex proteins AtFANCM, MHF1, and MHF2 were previously identified in a genetic screen as anti-CO factors that function during meiosis in Arabidopsis thaliana. Here, pursuing the same screen, we identify FANCC as a new anti-CO gene. FANCC was previously only identified in mammals because of low primary sequence conservation. We show that FANCC, and its physical interaction with FANCE-FANCF, is conserved from vertebrates to plants. Further, we show that FANCC, together with its subcomplex partners FANCE and FANCF, regulates meiotic recombination. Mutations of any of these three genes partially rescues CO-defective mutants, which is particularly marked in female meiosis. Functional loss of FANCC, FANCE, or FANCF results in synthetic meiotic catastrophe with the pro-CO factor MUS81. This work reveals that FANCC is conserved outside mammals and has an anti-CO role during meiosis together with FANCE and FANCF.

genetics↗

AtEH/Pan1 proteins drive phase separation of the TPLATE complex and clathrin polymerisation during plant endocytosis

Clathrin-mediated endocytosis (CME) is an essential cellular internalisation pathway involving the dynamic assembly of clathrin and accessory proteins to form membrane-bound vesicles. In plants, the evolutionarily ancient TSET/TPLATE complex (TPC) plays an essential, but not well-defined role in CME. Here, we show that two highly disordered TPC subunits, AtEH1 and AtEH2 function as scaffolds to drive biomolecular condensation of the complex. These condensates specifically nucleate on the plasma membrane through interactions with anionic phospholipids, and facilitate the dynamic recruitment and assembly of clathrin, early-, and late-stage endocytic accessory proteins. Importantly, clathrin forms ordered assemblies within the condensate environment. Biomolecular condensation therefore acts to promote dynamic protein assemblies throughout clathrin-mediated endocytosis. Furthermore, the disordered region sequence properties of AtEH1 regulate the material properties of the endocytic condensates in vivo and alteration of these material properties influences endocytosis dynamics, and consequently plant adaptive growth. HighlightsO_LIAtEH subunits are endocytic scaffolds which drive condensation of the TPC C_LIO_LIAtEH1 condensates nucleate on the plasma membrane via lipid interactions C_LIO_LICondensation of AtEH1/TPC facilitates clathrin re-arrangement and assembly C_LIO_LIAtEH1 IDR1 composition controls condensate properties to regulate endocytosis C_LI

cell biology↗

TraB is a novel component of the ER-Mitochondria contact site (EMCS) with dual roles in ER-Mitochondrial tethering and mitophagy

ER-mitochondria contact sites (EMCSs) are important for mitochondrial function. Here, we have identified a novel eukaryotic EMCS complex, comprising a family of uncharacterised mitochondrial outer-membrane proteins, TraB1 and the ER protein, VAP27-1. In Arabidopsis, there are two TraB1 isoforms and the trab1a/trab1b double mutant exhibits abnormal mitochondrial morphology, strong starch accumulation and impaired energy metabolism, indicating that these proteins are essential for normal mitochondrial function. Moreover, TraB1 proteins also interact with ATG8 in order to regulate mitochondrial degradation (mitophagy). The turnover of depolarised mitochondria is significantly reduced in both trab1a/b and VAP27 mutants (vap27-1/3/4/6) under mitochondrial stress conditions, with an increased population of dysfunctional mitochondria present in the cytoplasm. Consequently, plant recovery after stress is significantly perturbed. A similar phenotype is found in both autophagy mutants (atg5 and atg7), suggesting that TraB1 regulated mitophagy and ER-mitochondrial tethering are two closely related processes, necessary for normal mitochondrial function. Taken together, we ascribe a dual role to TraB1 which is a novel component of the EMCS complex in eukaryotes, regulating both tethering of the mitochondria to the ER and mitophagy.

cell biology↗

Molecular convergence by differential domain acquisition is a hallmark of chromosomal passenger complex evolution

The chromosomal passenger complex (CPC) is a heterotetrameric regulator of eukaryotic cell division, consisting of an Aurora-type kinase and a scaffold built of INCENP, Borealin and Survivin. While most CPC components are conserved across eukaryotes, orthologs of the chromatin reader Survivin have previously only been found in animals and fungi, raising the question of how its essential role is carried out in other eukaryotes. By characterizing proteins that bind to the Arabidopsis Borealin ortholog, we identified BOREALIN RELATED INTERACTOR 1 and 2 (BORI1 and BORI2) as redundant Survivin-like proteins in the context of the CPC in plants. Loss of BORI function is lethal and a reduced expression of BORIs causes severe developmental defects. Similar to Survivin, we find that the BORIs bind to phosphorylated histone H3, relevant for correct CPC association with chromatin. However, this interaction is not mediated by a BIR domain as in previously recognized Survivin orthologs, but by an FHA domain, a widely conserved phosphate-binding module. We propose that the unifying criterion of Survivin-type proteins is a helix that facilitates complex formation with the other two scaffold components, and that the addition of a phosphate-binding domain, necessary for concentration at the inner centromere, evolved in parallel in different eukaryotic groups. Using sensitive similarity searches, we indeed find conservation of this helical domain between animals and plants, and identify the missing CPC component in most eukaryotic supergroups. Interestingly, we also detect Survivin orthologs without a defined phosphate-binding domain, possibly reflecting the situation in the last eukaryotic common ancestor. Significance StatementThe identification of two SURVIVIN-type genes in the model plant Arabidopsis unfolded the evolutionary trajectories of this central chromosomal passenger complex component and led to the identification of SURVIVIN orthologs in almost the entire eukaryotic kingdom. Our work indicates that the central most aspect of the SURVIVIN gene family is a helix to make contact with two other core chromosomal passenger complex members whereas the addition of a phosphate-binding domain shown to bind to chromatin in animals and plants evolved in parallel at least 3 times in different eukaryotic branches.

cell biology↗

A NET4-RabG3 couple mediate the link between actin and the tonoplast and is essential for normal actin cytoskeletal remodelling in stomatal closure to flg22

Members of the NETWORKED (NET) family are involved in actin-membrane interactions. They tether the cells plasma membrane (PM) to the actin network. Moreover, in a similar manner, they are also involved in the tethering of membrane bound organelles to the actin cytoskeleton; the endoplasmic reticulum (ER) and the ER to the PM. This raises the question as to whether NET proteins are involved in actin cytoskeletal remodelling. Here we show that two members of the NET family, NET4A and NET4B, are essential for normal guard cell actin reorganization, which is a process critical for stomatal closure in plant immunity. NET4 proteins interact with F-actin and with members of the Rab7 GTPase RABG3 family through two distinct domains, allowing for simultaneous localization to actin filaments and the tonoplast. NET4 proteins interact with GTP-bound, active RABG3 members, suggesting their function as downstream effectors. We also show that RABG3b is critical for stomatal closure induced by microbial patterns. Taken together, we conclude that the actin cytoskeletal remodelling during stomatal closure depends on a molecular link between actin filaments and the tonoplast, which is mediated by the NET4-RABG3b interaction. We propose that stomatal closure to microbial patterns involves the coordinated action of immune signalling events and proper actin cytoskeletal remodelling.

plant biology↗

Proteomic Characterization of Isolated Arabidopsis Clathrin-Coated Vesicles Reveals Evolutionarily Conserved and Plant Specific Components

In eukaryotes, clathrin-coated vesicles (CCVs) facilitate the internalization of material from the cell surface as well as the movement of cargo in post-Golgi trafficking pathways. This diversity of functions is partially provided by multiple monomeric and multimeric clathrin adaptor complexes that provide compartment and cargo selectivity. The adaptor- protein AP-1 complex operates as part of the secretory pathway at the trans-Golgi network, while the AP-2 complex and the TPLATE complex (TPC) jointly operate at the plasma membrane to execute clathrin-mediated endocytosis. Key to our further understanding of clathrin-mediated trafficking in plants will be the comprehensive identification and characterization of the network of evolutionarily conserved and plant- specific core and accessory machinery involved in the formation and targeting of CCVs. To facilitate these studies, we have analyzed the proteome of enriched trans-Golgi network/early endosome-derived and endocytic CCVs isolated from dividing and expanding suspension-cultured Arabidopsis cells. Tandem mass spectrometry analysis results were validated by differential chemical labeling experiments to identify proteins co-enriching with CCVs. Proteins enriched in CCVs included previously characterized CCV components and cargos such as the vacuolar sorting receptors in addition to conserved and plant-specific components whose function in clathrin-mediated trafficking has not been previously defined. Notably, in addition to AP-1 and AP-2, all subunits of the AP-4 complex, but not AP-3 or AP-5, were found to be in high abundance in the CCV proteome. The association of AP-4 with suspension-cultured Arabidopsis CCVs is further supported via additional biochemical data.

cell biology↗

SAMBA controls the rate of cell division in maize development through APC/C interaction

SAMBA has been identified as a plant-specific regulator of the anaphase-promoting complex (APC/C) which controls unidirectional cell cycle progression in Arabidopsis, but so far its role was not studied in monocots. Here, the association of SAMBA with APC/C was shown to be conserved in maize. Two samba CRISPR alleles showed growth defects that aggravated with plant age such as dwarfed plants due to shortened upper leaf length, erect leaf architecture, and reduced leaf size due to an altered cell division rate and cell expansion. Despite the fact that in both alleles the frameshift occurred at the same position, the two alleles differed in the severity and developmental onset of the phenotypes, because samba-1 represented a knock-out allele, while translation re-initiation in samba-3 resulted in a truncated protein that was still able to interact with the APC/C and regulate its function, albeit with altered APC/C activity or efficiency. Our data are consistent with a dosage-dependent role for SAMBA to control developmental processes for which a change in growth rate is pivotal.

plant biology↗

Arabidopsis Casein Kinase 2 triggers Stem Cell Exhaustion under Al Toxicity and Phosphate Deficiency Through activation of the DNA Damage Response pathway

Aluminum (Al) toxicity and inorganic phosphate (Pi) limitation are widespread chronic abiotic and mutually enhancing stresses that profoundly affect crop yield. Both stresses cause a strong inhibition of root growth, resulting from a progressive exhaustion of the stem cell niche. Here, we report on a casein kinase 2 (CK2) inhibitor identified by its capability to maintain a functional root stem cell niche under Al toxic conditions. CK2 operates through phosphorylation of the cell cycle checkpoint activator SUPPRESSOR OF GAMMA RADIATION1 (SOG1), priming its activity under DNA-damaging conditions. In addition to yielding Al tolerance, CK2 and SOG1 inactivation prevents meristem exhaustion under Pi starvation, revealing the existence of a low Pi-induced cell cycle checkpoint that depends on the DNA damage activator ATAXIA-TELANGIECTASIA MUTATED. Overall, our data reveal an important physiological role for the plant DNA damage response pathway under agriculturally limiting growth conditions, opening new avenues to cope with Pi limitation. ONE-SENTENCE SUMMARYCasein kinase 2 and DNA damage response regulators play a pivotal role in the control of Arabidopsis root growth in response to Al toxicity and phosphate limitation.

plant biology↗

The TPLATE subunit is essential for structural assembly of the endocytic TSET complex

All eukaryotic cells rely on endocytosis to regulate the plasma membrane proteome and lipidome. Most eukaryotic groups, with the exception of fungi and animals, have retained the evolutionary ancient TSET complex as a regulator of endocytosis. Despite the presence of similar building blocks in TSET, compared to other coatomer complexes, structural insight into this adaptor complex is lacking. Here, we elucidate the molecular architecture of the octameric plant TSET complex (TPLATE complex/TPC) using an integrative structural approach. This allowed us to describe a plant-specific connection between the TML subunit and the AtEH/Pan1 proteins and show a direct interaction between the complex and the plasma membrane without the need for any additional protein factors. Furthermore, we identify the appendage of TPLATE as crucial for complex assembly. Structural elucidation of this ancient adaptor complex vastly advances our functional as well as evolutionary insight into the process of endocytosis. Graphical abstract O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

cell biology↗