Data gaps in Biology

Representative open questions

Showing 30 of 407 — one per source paper, highest-quality first.

• Longitudinal localization of leukaemic stem cells between the metaphysis and central marrow governs their behaviour (2026) · doi

  The study identifies N-cadherin+ vascular niche interactions with leukaemic stem cells (referenced in N-cad-tdTomato experiments), but the specific adhesion mechanisms governing metaphyseal versus central marrow localization and their differential response to N-cadherin-targeted therapy (reference 65: telmisartan/ADH-1 function) have not been systematically compared across AML subtypes.

• Selective elimination of circulating effector CD8 T cells via LTβR blockade separates anti-CD137 efficacy from toxicity (2026) · doi

  Adoptive cell transfer experiments transferred either total splenocytes or purified CD8 T cells, but the paper does not report whether effector CD8 T cell subsets (e.g., CD62L−CCR7− circulating effector versus tissue-resident memory cells) were differentially transferred to assess their specific contributions to anti-CD137 toxicity versus tumor control.

• The role of estrogen and its receptors in the regulation of ferroptosis and autophagy (2026) · doi

  While the review highlights the estrogen-autophagy-ferroptosis axis in endometriosis and endometrial cancer development, there is no direct experimental evidence comparing ferroptosis induction rates between estrogen-responsive versus estrogen-independent cancer cell lines under identical iron metabolism conditions.

• Charcoal rot in sesame: infection biology, host resistance mechanism, and genomic-enabled strategies for durable resistance breeding (2026) · doi

  Genotype × environment interactions (G×E), particularly under drought-linked disease pressure, have not been comprehensively characterized across sesame germplasm; robust, environment-stable QTL/loci for charcoal rot resistance across diverse geographic regions and climate conditions remain limited.

• Genomic analyses implicate hormonal and metabolic dysregulation in polycystic ovary syndrome (2026) · doi

  The Mendelian randomization analysis corrected for BMI using multivariate inverse-weighted methods, but sex-specific outcome data were not available for most tested outcomes; conducting sex-stratified MR analyses for PCOS-related hormonal and metabolic traits remains unexplored.

• Cancer-associated fibroblasts regulate DNA repair in pancreatic cancer through NDRG1-mediated R-loop processing (2026) · doi

  Mixed-effects regression models were optimized using the Ordered Quantile normalizing transformation, but the paper does not specify which datasets required normalization or provide sensitivity analyses comparing results from normalized versus non-normalized datasets in the context of NDRG1-mediated DNA repair quantification.

• Electrophilic compound screening identifies GPX4-dependent ferroptosis as a senescence vulnerability (2026) · doi

  SK-MEL-103 cells are the primary model for senescence-ferroptosis coupling in this proteomics study, but the generalizability of GPX4-dependent ferroptosis vulnerability to other senescent cell types (fibroblasts, epithelial cells) and additional senescence inducers beyond etoposide and tozasertib has not been systematically evaluated. Cell-type and inducer-specific differences in ferroptosis-related proteome signatures require investigation.

• The proteomic landscape and temporal dynamics of human and mouse gastruloid development (2026) · doi

  The proteomic temporal dynamics of gastruloids were sampled only at discrete timepoints (72 and 144 h for mouse gastruloids; 24 and 120 h for human RA-gastruloids). High-resolution kinetic profiling at intermediate timepoints would be needed to capture the complete proteomic trajectory and identify transient protein expression states during gastruloid differentiation.

• Decoding Rho GTPase signalling networks in directed cell migration (2026) · doi

  While multiple studies demonstrate that ubiquitination of IQGAP1 diminishes Cdc42 activation and that various phosphorylation events on GEFs like SOS1 modulate GTPase activity, the complete proteomic landscape of post-translational modifications regulating individual Rho family GTPases across different cell types and migration contexts has not been systematically mapped.

• Integrative transcriptomic analysis reveals miR-26a-5p downregulation and a potential predictive gene signature for the progression of metabolic liver disease (2026) · doi

  Larger cohorts with longitudinal histological assessment are needed to characterize the full spectrum of transcriptomic and histological changes across the progression from diet-induced metabolic perturbation to HCC, as the in vivo HCD model demonstrated only a relatively small sample size that was underpowered to capture comprehensive disease progression phenotypes.

• Dietary N-acetylcysteine enhances sperm motility by remodeling the rumen microbiome and its metabolic axis in goats (2026) · doi

  NAC supplementation enriched multiple lipid-related pathways including biosynthesis of unsaturated fatty acids, glycerophospholipid metabolism, and steroid hormone biosynthesis in the rumen microbiome, but the specific contribution of each pathway to systemic sperm motility enhancement was not quantitatively delineated. Pathway-selective inhibition studies would be required to determine which lipid metabolic alterations are necessary and sufficient for the observed phenotype.

• Gut microbiota-driven IL-17/PPAR axis mediates epigallocatechin-induced intestinal repair in weaned lambs (2026) · doi

  The downregulation of arachidonic acid metabolism and reduced prostaglandin F2α/I2 mediators in the LE group was observed via KEGG analysis, but the specific microbial taxa and metabolic enzymes responsible for suppressing this pro-inflammatory pathway have not been identified through targeted genomic or proteomic approaches.

• Proteogenomic decoding of chemotherapy resistance in patients with triple-negative breast cancer (2026) · doi

  The proteogenomic analysis integrated mRNA, protein, and phosphoprotein expression data, but did not incorporate genomic mutation data, copy number alterations, or epigenetic modifications; the contribution of these additional molecular layers to the identified chemotherapy resistance phenotypes remains unexplored.

• Adaptation of lipid metabolism of the polyextremophilic cyanobacterium Cyanobacterium aponinum PCC 10605 to adverse environmental conditions (2026) · doi

  The contribution of Fe, Zn, and Mn limitation to lipid remodeling during extended batch cultivation (42 days) has not been experimentally separated from the effects of general nutrient starvation and chlorosis. The paper identifies micronutrient depletion as evident after 14 days via ICP-OES, but does not conduct targeted supplementation experiments to determine whether restoring individual micronutrients (Fe, Zn, or Mn) can prevent or reverse the observed lipid accumulation patterns.

• Ethyl methanesulfonate mutagenesis in fungi: genetic mechanisms, applications, and implications for agricultural biotechnology (2026) · doi

  The comparative functional genomics gap between Aspergillus nidulans and Neurospora crassa secondary metabolite pathways identified through EMS and gene deletion approaches remains unresolved. Standardized comparative characterization of biosynthetic gene clusters across multiple Aspergillus and Neurospora species using EMS-derived mutants is lacking.

• Early transplantation reshapes desert soil microbiomes and inferred interactions, with irrigation as a stabilizing input (2026) · doi

  The study identified an aridity threshold beyond which abiotic factors override facilitative dynamics in desert soils, but the precise threshold value and its variability across plant species and soil types remain uncharacterized. Multi-site, longer-duration trials are needed to establish the generality of this threshold for restoration and to determine how plant identity and soil type modulate the stress gradient hypothesis in desert microbiomes.

• Comparative genomics identifies small interfering RNA with activity against all five human betacoronaviruses (2026) · doi

  Potential mechanisms underlying the loss of siRNA efficacy in replication-competent infection models compared to reporter assays include reduced target accessibility due to RNA secondary structures and shielding by viral nucleocapsid proteins. These hypotheses require direct experimental validation through structural probing of viral RNA secondary structures and nucleocapsid protein binding sites in the context of si117m, si123m, and si128m target regions.

• What causes self-sterility in Couroupita guianensis (Lecythidaceae)? (2026) · doi

  Although the study rules out embryo-expressed deleterious recessive alleles as the cause of self-sterility in C. guianensis, it does not investigate whether endosperm-expressed genetic incompatibilities (beyond malfunction) may trigger the observed fruit developmental failure. The role of endosperm gene dosage balance or parent-of-origin effects in the selfed fruit abortion phenotype requires specific investigation.

• The intrinsically disordered protein SPE-56 is required for acrosomal-like exocytosis and fertility in Caenorhabditis elegans (2026) · doi

  Live imaging of sperm activation in whole anesthetized worms using levamisole immobilization was performed only at 20°C; the effects of physiological temperature variation (37°C equivalent in C. elegans) on SPE-56-dependent MO fusion kinetics and pseudopod extension dynamics have not been investigated.

• Kidney angiopoietin-like protein 4 regulates fibrotic responses in diabetic kidney disease (2026) · doi

  The comparative efficacy of ANGPTL4 inhibition versus modulation of downstream effectors (such as STAT6 or cGAS-STING signaling) for attenuating kidney inflammation and fibrosis in diabetic nephropathy has not been systematically evaluated in head-to-head preclinical studies using identical disease models and outcome measures.

• Metabolic reprogramming in intervertebral disc degeneration: mechanisms and therapeutic opportunities (2026) · doi

  M1 macrophage-derived exosomes promote intervertebral disc degeneration through LCN2/NF-κB signaling in nucleus pulposus cells, but the quantitative relationship between exosome concentration, LCN2 expression levels, and the temporal kinetics of senescence induction in primary human disc cells remain uncharacterized.

• Cationic nanoparticles with disrupting neutrophil extracellular traps inhibit the progression of head and neck squamous cell carcinoma (2026) · doi

  While the study demonstrated that NET-DNA at 1 μg/mL significantly enhanced SCC9 cell migration in wound-healing assays, the concentration-dependent relationship between NET-DNA levels and tumor cell migratory capacity across different HNSCC cell lines remains unexplored, requiring additional migration and invasion assays at multiple NET-DNA concentrations.

• Ento-Linguistics: Language, Ambiguity, and Scientific Communication in Entomology: How Terminology Networks Shape Understanding of Insect Biology (And Vice-Versa) (2026) · doi

  The anthropomorphic term set 𝒜 (queen, king, slave, worker, soldier, nurse) is defined for social insects but lacks systematic extension to non-social entomological groups; the appropriateness penalty function for anthropomorphic language requires validation across colonial, solitary, and parasitic insect taxa.

• Society for Developmental Biology 70th Annual Meeting (2011) · doi

  Early stages of hematopoietic stem cell (HSC) maturation during mouse embryogenesis (B123) require identification of the specific signaling pathways and transcriptional regulators that govern HSC specification; the temporal dynamics of HSC emergence from mesoderm have not been fully mapped.

• Trajectory inference for a branching SDE model of cell differentiation via lineage tracing (2026) · doi

  The reweighting method for handling cell death and subsampling in scRNA-seq lineage tracing has only been validated numerically on synthetic branching SDE trajectories with simulated extinction and subsampling. Validation on real lineage-traced scRNA-seq datasets with measured or inferred death rates and actual experimental subsampling patterns is needed to assess the practical applicability of the theoretical bias corrections.

• Evaluating poultry by-product meal, tomato pomace, and azolla with or without Natuzyme supplementation as sustainable alternatives to fish meal for Nile tilapia (Oreochromis niloticus) (2026) · doi

  The paper lacks dose-response data comparing varying inclusion levels (e.g., 25%, 50%, 75%, 100% replacement) of poultry by-product meal combined with tomato pomace and azolla to determine the maximum sustainable replacement threshold for fish meal while maintaining growth performance and feed efficiency in Nile tilapia.

• Cell type-agnostic transcriptomic signatures enable uniform comparisons of neural maturation (2026) · doi

  The study restricted gene analysis to one-to-one mouse-human orthologs (9,460-9,615 genes), yet synapse-biased genes were explicitly tested only through inclusion/exclusion of SynGO genes; the contribution of other functionally specialized gene modules (e.g., mitochondrial genes, cell cycle regulators, metabolic enzymes) to developmental tempo estimates across species has not been systematically evaluated.

• Discovery of an Endonuclease G-inhibitory Ku80-peptide protecting against leukemogenic rearrangements at the MLL breakpoint cluster (2026) · doi

  While the study measured intrachromosomal recombination frequencies and DSB repair outcomes using extrachromosomal reporter plasmids with I-SceI-induced breaks, direct quantification of endogenous MLL breakpoint cluster rearrangements in primary leukemic cells or patient-derived samples was not performed.

• Development of the fluorescent probe CenSpark for labeling centrioles and cilia (2026) · doi

  EB3-GFP microtubule plus-end dynamics were simultaneously imaged with CenSpark-650 to visualize centriole-nucleated microtubule growth, but quantitative analysis of how centriolar positioning and orientation influence microtubule catastrophe and rescue events near the centrosome remains incomplete. Three-dimensional tracking of microtubule plus-ends relative to CenSpark-labeled centriole architecture during different cell cycle phases is needed.

• Stem cell activation in organ culture reveals novel transcriptional programs underlying metabolic, fibrotic, vascular, and immune dysregulation in uterine leiomyomas (2026) · doi

  The study focused exclusively on MED12-mutated leiomyomas, the most prevalent genetic subtype of uterine fibroids. Transcriptional programs and pathway dynamics must be characterized in other genetic subtypes (HMGA2-rearranged, FUBP1-mutated, or wild-type leiomyomas) to determine whether the metabolic, fibrotic, vascular, and immune dysregulation mechanisms are shared or distinct across leiomyoma subtypes.