Data gaps in Biology

Representative open questions

Showing 30 of 418 — one per source paper, highest-quality first.

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

  References 67 and 68 establish that leukemia-initiating cells can reside in CD34− fractions in some AML patients and target self-renewing haematopoietic stem cells in chronic lymphocytic leukemia, yet the spatial localization patterns (metaphyseal versus central marrow) and niche dependencies of these phenotypically-distinct leukaemic stem cell populations remain uncharacterized.

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

  Pathogen diversity and virulence variation in M. phaseolina isolates affecting sesame have been incompletely characterized; systematic phenotypic and genotypic characterization of diverse pathogen isolates is needed to validate resistance loci and breeding markers across pathogenic variation.

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

  The Danish medical birth registry analysis was restricted to women born 1957–1973 who reached reproductive completion by age 45–61 years; extending this analysis to younger birth cohorts with ongoing reproductive histories would clarify whether PCOS genetic effects on completed family size persist across different reproductive windows.

• 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 gastruloids were cultured for a maximum of five days post-induction; extension of culture duration combined with proteomic profiling would reveal whether gastruloid development plateaus or recapitulates later stages of gastrulation and axial mesoderm patterning.

• 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

  The study integrated rumen and plasma metabolomic data to propose the rumen–plasma–sperm axis, but did not directly measure metabolite concentrations in seminal plasma or sperm cells themselves. Targeted lipidomic and metabolomic profiling of seminal plasma and isolated sperm would confirm whether the identified bioactive lipids and energy metabolites (N-decanoyl-L-homoserine lactone, glycerophospholipids, arginine) are actually bioavailable at the sperm compartment.

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

  While Bilifractor porci showed strong positive correlation with EGC ring fission metabolites, the specific metabolic enzymes and gene clusters in this organism responsible for generating these postbiotics have not been annotated; comparative genomic analysis with related species is needed to identify the functional genetic determinants.

• 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.

• 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.

• 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

  Aberrant mechanical loading triggers intervertebral disc degeneration through pyroptosis and nerve ingrowth, but quantitative biomechanical thresholds that initiate pyroptotic cascades in different disc regions and the metabolic consequences of sustained pyroptosis in nucleus pulposus cells require characterization.

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

  While the study established that elevated NETs expression in HNSCC tissues correlates with tumor progression, the specific spatial distribution of NETs within the tumor microenvironment (perivascular regions, tumor core versus invasive margin) and their heterogeneity across different HNSCC subtypes and stages remains uncharacterized.

• 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

  The role of the Lissencephaly-1-like gene in stem cell maintenance in planarian Schmidtea mediterranea (B124) has not been compared across different stem cell populations; whether this gene regulates self-renewal, proliferation, or differentiation in planarian stem cells requires mechanistic elucidation.

• 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

  While the paper demonstrates that organoid variability in developmental age signals can be quantified across 24 datasets (173 batches) using EGAD co-expression analysis, no investigation addresses whether specific culture conditions, growth factors, or passage numbers systematically bias age predictions; identifying these technical covariates would improve organoid standardization and comparability.

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

  The nucleofection efficiency for peptide delivery into K562 and HeLa cells is mentioned but not quantitatively reported; establishing baseline peptide nucleofection rates and cellular uptake kinetics would clarify the translational applicability of the Ku80-peptide for leukemogenic rearrangement prevention in primary hematopoietic cells.

• 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.

• Novel endogenous protein-based strategies to inhibit clinically relevant bacterial AB-type toxins including pertussis toxin (2026) · doi

  The screening and identification of endogenous protein/peptide inhibitors has been incomplete, with the authors noting that 'many potential inhibitors of bacterial toxins still need to be identified.' Systematic large-scale screening of the entire human proteome and peptidome against the panel of clinically relevant AB-type toxins (anthrax, cholera, Shiga toxins, C. difficile toxins) has not been comprehensively performed.

• The potential of metabolic engineering for sustainable phytosterol production (2026) · doi

  The paper proposes transferring phytosterol biosynthetic pathways into fast-growing microorganisms (bacteria, yeast, algae) as 'cell factories,' but does not specify which host organisms have been experimentally validated or how metabolic perturbations in these specific hosts affect sterol biosynthesis regulation and phytosterol yield optimization.

• The tiny germline chromosomes of Paramecium aurelia have an exceptionally high recombination rate and are capped by a new class of Helitrons (2026) · doi

  The dN/dS computation for full-size Helitron transposase copies in P. aurelia was initiated (phyML phylogenetic tree, MAFFT L-INS-i alignment), but the methods section ends abruptly without reporting the actual dN/dS values, selection pressure estimates, or comparison of transposase evolution rates across the 7 Paramecium species.

• On the potential origin of the zygote-like cancer stem cell with a focus on fusion for cell rescue (2026) · doi

  The relationship between genome doubling events and zygote-like cancer stem cell formation through fusion mechanisms requires systematic investigation with whole genome sequencing datasets. Pan-cancer analysis of genome doubling patterns across different cancer types needs to be integrated with fusion-derived stem cell markers to establish causal links to cancer evolution and prognosis.