Disciplines / Research questions
Biology
98 research topics · 322 questions
Why are leguminous plants able to perform symbiotic nitrogen fixation?7 questions
Duplication history and molecular determinants of NFP-type Nod factor receptor specialization in the nitrogen-fixing clade of plants
Testing the symbiosome-stability hypothesis of legume nodulation: nodule-type-dependent losses in Papilionoideae, the functional role of the fixation-thread wall, and the genomic and diversification consequences of the fixation-thread-to-symbiosome transition
Direct NIN→NF-YA1 regulation and the ancestry of the NIN–NF-YA1 transcriptional module in nitrogen-fixing nodule symbiosis: the Parasponia test and the NF-YA1 infection regulon
Molecular mechanism of Symbiosis Determinant 1 (SD1)-dependent signaling by the NFR1 Nod factor receptor: binding partners and coordination of infection and organogenesis
Mechanism of co-option of the ancient common symbiosis pathway for root-nodule symbiosis
The MtAHL1/MtAHL2 AHL transcription-factor regulatory module in legume nodules: direct targets beyond NCR genes, essentiality for nitrogen fixation, complex architecture, and conservation across nodule types
The molecular and genetic identity of the cryptic potentiating precursor of symbiotic nitrogen fixation in the angiosperm nitrogen-fixing clade
Why does amyotrophic lateral sclerosis occur?4 questions
C9ORF72 loss-of-function mechanisms in repeat-expansion ALS/FTD: neuronal GTPase substrates and autophagy steps, the in-vivo causal hierarchy, environmental modifiers, and function-preserving therapeutics
Pathogenic driver, protective sequestration, or secondary phenomenon: the causal significance of TDP-43 accumulation in ALS and frontotemporal lobar degeneration
Completing the pathway and cell-type map of genetic risk in amyotrophic lateral sclerosis: rare, regulatory, and non-European variation
DNA-break-triggered homology-directed-repair-mediated large expansions of the C9orf72 G4C2 repeat: spontaneous-lesion relevance in vivo, pathway identity, mouse-human differences, outcome determinants, and editing safety
Why does auxin have different functions in somatic embryogenesis?8 questions
Stage-specific auxin transport machinery of somatic embryogenesis: which influx and efflux carriers operate from embryo identity acquisition to somatic embryo patterning, and how do they explain the distinct behaviors of 2,4-D and IAA?
Mechanism of stage- and domain-specific auxin and cytokinin response partitioning underlying embryonic shoot–root axis establishment during somatic embryogenesis
Ethylene-mediated repression of YUCCA auxin biosynthesis genes during somatic embryogenesis induction in Arabidopsis: perception components and molecular mechanism
Downstream regulatory mechanisms of OsBBM1-triggered somatic embryogenesis in rice: LAFL network involvement, auxin-cytokinin interplay, and the requirement for endogenous OsYUC-mediated auxin biosynthesis
Mechanistic basis of 2,4-D-triggered acquisition and endogenous-IAA-maintained embryonic identity during Arabidopsis somatic embryogenesis
Auxin-dosage-dependent methylation control of embryogenic competence in Arabidopsis somatic embryogenesis: linking the 2,4-D concentration window to LEC1/LEC2/BBM/WUS/AGL15 promoter methylation
Mechanistic basis of the divergence between auxinic activity and somatic-embryogenesis induction among 2,4-D analogues: why the very active auxin MCPA weakly induces somatic embryogenesis in Arabidopsis thaliana
Functional distinction between phenylacetic acid and indole auxins, and the signalling mechanisms underlying endogenous phytohormone dynamics, during Norway spruce somatic embryogenesis
Why are some viruses non-pathogenic?3 questions
Unresolved mechanism and evolutionary fate of host cooperative metabolic defenses that convert lethal Citrobacter rodentium infection into asymptomatic carriage (iron–insulin resistance–intestinal glucose circuit, Sanchez et al. 2018)
Mechanisms of spontaneous long-term control of HIV-1 infection: the unidentified CD8+ non-cytolytic antiviral factor and the host-versus-virus determinants of the long-term survivor state
Natural history of four novel Magellanic penguin picornaviruses (Sphenifaro, Sphenigellan, Sphenimaju, and Sphenilena viruses): host range, transmission, pathogenic potential, and population connectivity
Why do some enzymes have very high optimal temperatures for catalysis while others have very low ones?3 questions
Distinguishing a rate-determining-step change from conformational-equilibrium coupling in the high-temperature kinetics of MalL
Mechanistic origins of variation in macromolecular-rate-theory temperature-sensitivity traits (, , ) of soil microbial enzymes
Mechanism or history? Establishing the basis, molecular origin, and generality of the enzyme stability-activity trade-off
Why do some plants need to undergo a period of low temperature before they can flower?7 questions
Cis- versus trans-regulation of the two determinants of vernalization requirement in Brassica rapa: steady-state BrFLC expression and cold-repression kinetics
Mechanistic basis of the nucleation, spreading, and maintenance phases of H3K27me3 Polycomb memory at Arabidopsis FLC, and how such silencing can be established without DNA replication
Evolutionary origins of the vernalization requirement: conditions for its gain and loss, and the constrained-versus-reinvented genetic logic of cold-induced flowering competence
Molecular identification of the fast thermosensory inputs (current-temperature element C and short-term warm-spike memory element S) to VIN3 in the Arabidopsis vernalization network
Molecular machinery of the vernalization-memory reset cycle in wheat: cold-induced TaVRN1 activation, embryonic silencing, and light-triggered TaVRN2 reactivation
Completing the growth-dilution mechanism of long-term cold sensing in Arabidopsis: the nuclear activation route of NTL8 and the generality of reduced-dilution thermosensing
How COOLAIR antisense transcription represses Arabidopsis FLC in cis during vernalization: molecular mechanism, necessity of the antisense transcript, and the genome-wide generality of 3′-end antisense regulation
Why can plant pollen tubes accurately enter the embryo sac?8 questions
Signal-transduction mechanism of the LIP1/LIP2 receptor-like cytoplasmic kinases downstream of AtLURE1 perception in Arabidopsis pollen-tube guidance
Molecular identification of the female signals implementing pollen tube emergence, adhesion, and the funicular polytubey block in one-to-one pollen tube guidance of Arabidopsis
Signal transduction and quantitative gradient sensing in Arabidopsis ovule-directed pollen tube guidance
Molecular coupling of ovule-derived attractant perception to MLO5/MLO9-dependent Ca2+ channel delivery in pollen tube guidance
Open components of the AtLURE1 pollen-tube attractant system in Arabidopsis: non-cell-autonomous regulation of synergid attractant production, post-attraction species-specific barriers, and the evolutionary forces shaping the AtLURE1 gene cluster
Completing the LURE-centered mechanism of pollen-tube guidance: additional guidance cues, LURE perception, competence and other synergid cysteine-rich peptides, and species-preferential recognition
Decoding synergid Ca spiking during pollen tube reception: the residual cascade from RALF–FER–LRE–NORTIA-mediated calcium influx to pollen-tube rupture and synergid cell death in Arabidopsis
Molecular mechanism of pollen tube entry into and rupture within the receptive synergid via the peritubular membrane
Why do plant roots grow in the direction of gravity?5 questions
Simultaneous integration of gravitropic, phototropic, and hydrotropic signaling in plant roots
Molecular mechanism by which the HEAT-repeat protein Creeping Stem 1 (CS1) enables amyloplast sedimentation and directional auxin transport in soybean
Formulating an integrated quantitative theory of root gravitropism: linking statolith sedimentation, PIN polarization, auxin asymmetry, and angle-dependent curvature
Mechanism and generality of centrifugation-induced diagravitropism and resultant-law violation in plant roots
Evolutionary assembly of the fast root gravitropic mechanism in land plants: homology versus convergence of the PIN2-type auxin-transport module
How is the highly ordered organization of the cell nucleus related to the function of the genome?3 questions
Determinants and transcriptional consequences of mechanical coupling between nuclear condensates and chromatin
Determinants of CTCF insulating potency, mechanisms of CTCF-independent enhancer–promoter communication, and locus-general rules for structural-variant effects on TAD architecture
Causal directionality between nuclear lamina association, genome compartmentalization, and gene expression across cell lineages
How do cells integrate and manage metabolic processes?3 questions
Completing the division of labor in metabolic regulation: which mechanisms control the metabolic reactions unassigned to transcription, translation, acetylation, and phosphorylation?
Molecular mechanism of metabolite sensing by nuclear hormone receptors in the C. elegans dietary response: how perturbed mitochondrial metabolic flux signals to NHR-10, NHR-68, and NHR-114
How metabolic regulation and hierarchical gene-expression regulation combine to coordinate Escherichia coli central metabolism
Homeostatic balance mechanisms of cellular signal transduction networks2 questions
Molecular mechanisms and scope of the parallel adaptive expression feedback that stabilizes the Ca2+ signaling system (STIM, SERCA, PMCA)
Network-level crosstalk compensation as a general design principle of gene networks: generalization beyond the two-input in vitro demonstration and discovery of natural crosstalk-compensation motifs
Do bacteria communicate with each other (quorum sensing)?3 questions
Biosynthetic origin, bacterial detection mechanism, and in vivo function of the mammalian epithelial autoinducer-2 mimic (L-xylosone/L-xylulose) in host-bacteria quorum-sensing crosstalk
Molecular mechanism of AI-2 sensing and AI-2-controlled energetic coupling between Desulfovibrio vulgaris and Clostridium acetobutylicum under nutritional stress
Molecular, structural, and physiological basis of autoinducer-2 sensing through dCache_1-domain receptors in prokaryotes
What great mysteries are hidden in small sialic acids?1 questions
How did the panda's "pseudo-thumb" evolve?1 questions
How do depression and schizophrenia occur?1 questions
The biological basis of consciousness and intelligence2 questions
Open core of the Cogitate adversarial test of consciousness theories: causal necessity of prefrontal cortex and the missing ignition and posterior-synchronization mechanisms
From correlation to mechanism: replication, causal direction, and mediating neurocircuitry of the trait-wisdom by moral-condition brain-activation interaction
Is gamete fusion during double fertilization in flowering plants random?3 questions
Regulation of the sperm fusogen GCS1/HAP2 in Arabidopsis double fertilization: female-side interactors, DMP8/DMP9-dependent control, in vivo trimerization dynamics, and the quantitative basis of fusion competence
Sperm-side perception and signaling of egg-cell-secreted EC1 peptides during double fertilization in flowering plants
Mechanism of sperm-egg versus sperm-central-cell fusion preference in angiosperm double fertilization, and the source of opposite fusion biases among single sperm-like cells
How did language and the brain evolve?4 questions
Functional consequences and phenotypic targets of positive selection in language-impairment and dyslexia genes (FOXP2, CNTNAP2, ROBO1, ROBO2, KIAA0319)
The precursor-assembly problem in the self-domestication account of language evolution: why do domesticated species other than humans exhibit only isolated language precursor traits?
Causal functions and anatomical validation of the tractography-derived divergence of human language pathways: arcuate fasciculus versus extreme capsule and inferior fronto-occipital fasciculus
Mechanism by which the human-specific FOXP2 substitutions reshape cortico-basal ganglia circuits: direct in-vivo transcriptional targets and the dopamine phenotype in humanized Foxp2 mice
How to use computer simulations to understand the computational mechanisms of animal sensory systems?2 questions
Biological plausibility of interneuron gradient computation in whole-body Caenorhabditis elegans chemotaxis simulation: naturalistic optimization without teaching signals
Implementation and functional significance of composite receptive fields generated by sparseness and divisive normalization in high-order auditory circuits
What is the mechanism or material basis of long-term memory?1 questions
Who are the ancestors of fungi?5 questions
Robust resolution of the remaining deep nodes of the Opisthokonta tree of life: the root of unicellular Holozoa, the placement of Tunicaraptor, early fungal branching, the position of Olpidium, and the position of Placozoa
Fungal affinity, taxonomic placement, and geographic extent of the ~635 Ma fungus-like microfossils in karstic sheet-cavities of the Doushantuo cap dolostone, South China
Fungal affinity of the 2.4-billion-year-old mycelium-like filaments in the Ongeluk Formation basalt, South Africa
Resolving the early evolution of Fungi: deep basal relationships, independent losses of the flagellum, and the ancestral nutritional mode and habitat
Unresolved deep nodes in the early diversification of fungi: the placement of Glomeromycota and the root of Microsporidia
Plant aging and its regulation4 questions
Molecular identity of the pheophorbide a-dependent retrograde signal linking chloroplast chlorophyll-catabolite status to jasmonate signaling during dark-induced senescence
Mechanistic basis of antagonistic SCOOP10 versus SCOOP12 signaling through the MIK2 receptor-like kinase during Arabidopsis leaf senescence
Direct molecular mechanism linking the MADS-box transcription factor HuCMB1 to downstream senescence effectors in pitaya (Hylocereus undatus) fruit
Constraints or adaptations in plant ageing: the evolutionary roles of clonality, organ durability, programmed death, and adventitious shoot formation, and whether adventitious shoot formation prevents senescence from meristem ageing
How is the plant cell wall formed?2 questions
Open questions in plant cellulose synthase complex assembly and regulation: the PCR-interface ligand, the in vivo oligomeric organization of CesA isoforms, phosphorylation function, and the rosette-to-microfibril chain-number relationship
Unresolved quantitative questions in cellulose synthase complex dynamics during secondary cell wall deposition: delivery versus residence time, per-complex synthesis rate, and targeting to microtubule-band domains
How did plant sexual and asexual reproduction originate and evolve?3 questions
Apogamous apomixis in the fern Dryopteris affinis: functional roles of candidate genes and the molecular pathway from unreduced spore to apogamous embryo
The unresolved origin of the apomictic Ranunculus cassubicus complex: the causal mechanism linking hybridization and polyploidization to the switch to apomixis, its reticulate ancestry, and the age of the asexual lineages
Testing the Muralidhar–Haig model for the origin of triploid apomicts in Taraxacum: euploid-pollen back-transmission, tetraploid intermediates, clonal-fitness dynamics, realistic genetic architecture, and empirical validation
How does DNA conformation affect gene expression?3 questions
Molecular mechanism of transcriptional repression by accumulated negative DNA supercoiling in the human genome
Cell-state-resolved activity and causal role of conserved Z-flipons in transcription reinitiation
Mechanism of G-quadruplex-dependent transcriptional regulation at the Dele and Cdc6 CpG islands