Application gaps in Biology

Representative open questions

Showing 30 of 208 — one per source paper, highest-quality first.

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

  While reference 66 demonstrates that manipulating niche composition (using Cxcl12fl/fl and Scf fl/fl mice) protects haematopoietic stem cells during infection, the extent to which these niche modifications differentially affect leukaemic stem cell behavior in metaphyseal versus central marrow compartments—and whether this translates to improved chemotherapy sensitivity in AML—remains experimentally unaddressed.

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

  High-throughput phenotyping and AI-based analytics platforms for scaling charcoal rot screening in sesame require development and validation; integration of automated image analysis with disease severity assessment under controlled and field conditions has not been demonstrated in sesame breeding pipelines.

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

  The regulation of LARG/ARHGEF12 in leukemia and ARHGEF15 overexpression in pancreatic cancer show enhanced cell motility, but direct comparison of how different GEF families (ARHGEF, DBL, TIAM families) compete for or collaborate in activating Rho GTPases during invasion specifically in three-dimensional extracellular matrix environments has not been systematically investigated.

• ​​Integrating machine learning and spatial transcriptomics uncovers shared immunomodulatory deubiquitinases in MAFLD and HCC (2026) · doi

  The EIF3F-ACSL4 axis-mediated CD8+ T cell exclusion and functional exhaustion requires investigation in MAFLD-related immunosuppression. While this immunosuppressive mechanism has been demonstrated in HCC, its activation status and therapeutic reversal potential specifically in the MAFLD microenvironment before malignant transformation has not been characterized.

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

  The protective effects of EGC have been validated only in weaned lambs; the generalizability of the gut microbiota-driven IL-17/PPAR axis mechanism to other ruminant species (calves, goats) and different weaning ages/feed transition protocols remains unexplored and requires species-comparative and age-dependent studies.

• Jellyfish bioactive compounds fueling marine biotechnology in blue economy and biomedicine (2026) · doi

  Proteomic investigations of Nemopilema nomurai jellyfish venom identified cardiotoxic and anticancer targets in HepG2 hepatocarcinoma cells, but the mechanism of action and selectivity of these venom components against other cancer cell lines (breast, lung, colon) and their therapeutic window have not been established.

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

  Mutation stability and phenotypic reversion rates in EMS-derived fungal strains are inadequately characterized beyond laboratory conditions. Field-level performance testing and long-term stability assessments are required to evaluate whether mutations remain stable across multiple generations and diverse agricultural environments before strain deployment.

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

  The chemical modification pattern of the siRNAs is based on clinically validated designs and showed in vivo protection against SARS-CoV-2 for up to four weeks after single dose. In vivo pharmacokinetics and protective efficacy of si117m, si123m, and si128m must be evaluated in animal models following respiratory tract delivery to support clinical translation.

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

  The discursive framing network function F(D,T) and cross-domain mapping strength M_ij are introduced with mathematical notation but lack empirical case studies demonstrating how terminology networks reshape understanding across the six ento-linguistic domains; specific examples of domain-dependent ambiguity propagation are absent.

• 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

  Long-term feeding trials (beyond the typical 8-12 week experimental period) are needed to evaluate the sustained effects of Natuzyme-supplemented diets containing azolla, poultry by-product meal, and tomato pomace on organ development, lipid metabolism, and reproductive performance in Nile tilapia broodstock.

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

  The compositional versus cell-autonomous age prediction analysis was conducted only across three tissue types (mouse brain, organoid, and fetal human brain); the generalizability of compositional age predictions driven by astrocyte-progenitor dynamics to other neural tissue contexts (e.g., postnatal brain, adult neural stem cell niches, or brain tumors with altered cellular composition) has not been evaluated.

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

  α1AT-containing drugs are already approved for α1AT deficiency treatment, but their therapeutic efficacy as off-label inhibitors of pertussis toxin has not been evaluated in clinical or preclinical in vivo studies. Systematic investigation of α1AT pharmacokinetics and toxin-neutralizing capacity specifically in pertussis toxin-mediated disease models is needed.

• Fast hospital discharge rates blur within-hospital ‘transmission footprint’ in bacterial genomes, as showcased with Staphylococcus aureus (2026) · doi

  Phylodynamic approaches could assess how external intervention factors (such as hospital control strategies implemented after detecting initial bacterial infections) influence S. aureus transmission within surrounding communities. However, robust phylodynamic analyses testing intervention impacts would require larger empirical datasets with detailed temporal records of control measure implementation and corresponding genomic sampling.

• Engineered exosome biomedical technologies for precision diagnosis and therapy in orthopedic diseases (2026) · doi

  Engineered exosomes with controlled release of pro-mineralization factors (BMP2 mRNA, hypoxia-specific gene delivery) have been integrated into hydrogel scaffolds for craniofacial bone healing without cell transplantation, but comparative efficacy against standard bone regeneration approaches in large-animal models and human clinical trials is absent.

• Elovanoid neuroprotection targets cell transcriptomics and proteomics to sustain synaptic integrity after brain injury (2026) · doi

  The translation of elovanoid neuroprotection from rodent traumatic brain injury models to larger animal models (primates, swine) and clinical application requires validation of species-specific differences in ELOVL4 expression, elovanoid biosynthesis capacity, and brain injury response pathways. Studies in these models are needed before human clinical trials.

• A Mathematical Model for Smooth Muscle Cell Phenotype Switching In Atherosclerotic Plaque (2026) · doi

  The model incorporates SMC population initiation from progenitor cells after 5-6 weeks based on the Misra et al. (2018) murine lineage tracing study, but the generalizability of this temporal dynamics to human atherosclerotic plaque development remains unexplored. The study does not address whether SMC recruitment and proliferation kinetics differ between murine models and human plaques of varying ages and stages.

• SARS-CoV-2 pseudoparticles preferentially infect ectoderm in human embryonic tissues (2026) · doi

  Although aprotinin and Dyngo4a showed variable efficacy across different cell types tested, future studies must test drug combinations over a range of doses to assess synergy, additivity, and antagonism while establishing in vivo pharmacokinetics and placental transfer rates of these endocytosis and serine protease inhibitors in the context of preventing SARS-CoV-2 vertical transmission.

• An animal component-free bioprocess for synthesizing 3D human matrix scaffolds using mesenchymal stromal cells (2026) · doi

  While Chen et al. (2025) demonstrated in vivo efficacy of MSC spheroid-derived 3D decellularized ECM in traumatic brain injury models, the present paper does not include in vivo functional validation of the animal component-free synthesized scaffolds or tissue regeneration capacity in relevant disease models.

• Clonal Signatures of Telomere Biology Disorders (2026) · doi

  The shared genetic predisposition between rheumatoid arthritis-interstitial lung disease and familial pulmonary fibrosis (reference 77) linked to telomere biology genes requires investigation into how telomerase-associated protein mutations (NHP2, NOP10) and poly(A)-specific ribonuclease deficiency contribute to autoimmune manifestations in addition to pulmonary fibrosis phenotypes.

• In silico molecular docking, molecular dynamics, and ADMET analysis of metabolites from Strychnos cocculoides as potential therapeutics for erectile dysfunction: a comparative study with sildenafil (2026) · doi

  L4 exhibits comparatively lower LD₅₀ values and multiple toxicity alerts despite favorable binding affinity to PDE5/PDE6; structure–activity relationship (SAR) and derivative optimization studies are required to systematically reduce the moderate hepatotoxic tendencies while maintaining potency comparable to sildenafil.

• Non-coding RNA delivery via lipid nanoparticles: a novel strategy for cancer immunotherapy (2026) · doi

  The POST modular platform for organ-specific LNP surface modification has been proposed theoretically but lacks comprehensive experimental validation across multiple cancer types; specific studies comparing targeting efficacy of different surface modifications (ligands, antibodies, peptides) for selective accumulation in pancreatic cancer, colorectal cancer, and cholangiocarcinoma tissues are needed.

• Fine-tuned GPT-based foundation models effectively reconstruct bacterial transcriptional regulatory networks from literature (2026) · doi

  While the authors propose applying the BERN2-based algorithm with species-specific transcription factor and regulated element dictionaries to reconstruct TRNs in diverse bacterial species, no evaluation has been performed on non-Salmonella bacteria. The scalability and accuracy of the fine-tuned GPT approach across clinically and biologically relevant bacteria with different regulatory mechanisms, genetic organization, and literature coverage patterns requires empirical validation.

• Transcriptional regulation in cardiovascular aging (2026) · doi

  SIRT2 activators have not been systematically screened or developed for cardiovascular aging applications. The paper identifies SIRT2 as a key epigenetic modifier but lacks concrete chemical development pipelines or candidate compounds for clinical translation targeting age-related cardiovascular disease.

• Phytochemical profiling and multi-target pharmacological evaluation of Symphyotrichum squamatum unveils its potential as a source of antidiabetic and anti-inflammatory agents (2026) · doi

  While kaempferol 3-O-glucoside (K3G) from related species showed MAPK and Nrf2/HO-1 pathway activation in microglial cells, the anti-inflammatory mechanism of S. squamatum's kaempferol glycosides in neuroinflammatory models has not been tested, limiting assessment of potential neuroprotective applications.

• Ethnobotanical study of wild edible plants in Dabat District, Ethiopia (2026) · doi

  The inverse relationship between literacy status and wild edible plant knowledge (illiterate 4.1±1.9 vs. literate 1.9±1.3) indicates a need to experimentally design and test integration frameworks that embed ethnobotanical content into formal education curricula, field-based learning modules, and community training programs to measure knowledge retention outcomes.

• RNA-based next-generation sequencing strategy for screening MDM2-amplified sarcomas (2026) · doi

  MDM2 expression levels (TPM) vary widely in confirmed DDLPS cases (ranging from 103.44 to 1564.01), yet the biological and prognostic significance of this variation, and whether the 100 TPM threshold optimally discriminates MDM2-amplified DDLPS from non-amplified sarcomas, are not systematically evaluated.

• Exploring the mechanism of baicalein on choroid melanoma based on network pharmacology, transcriptomics and experimental verification (2026) · doi

  Comprehensive pharmacokinetic/pharmacodynamic (PK/PD) profiling and GLP-compliant toxicity testing were not performed for baicalein in the choroidal melanoma model, and the compound's known limitations of low oral bioavailability and short half-life require specific drug delivery system optimization before clinical translation.

• Postbiotics and phage synergy in precision oral microbiome engineering: systems biology strategies targeting Streptococcus mutans in dental caries (2026) · doi

  Digital twin computational models integrating multi-omics datasets (metagenomics, metatranscriptomics, metabolomics, virome profiling) with host immune parameters to forecast caries risk and predict postbiotic-phage combination outcomes have not been clinically validated or benchmarked against conventional caries risk assessment tools.

• Exosomes and extracellular vesicles: Rethinking the essential values in cancer biology (2021) · doi

  The reciprocal cell competition mechanisms between cancer cells and normal cells mediated by secretory microRNAs and extracellular vesicles have been identified; systematic investigation of how EV-mediated competitive interactions influence cancer prevention and suppression of preneoplastic cell populations in intact mammary and prostate tissue is needed.

• Aquaporin membrane channels in the hepatobiliary tract: a model of complexity and clinical implications in health and disease (2026) · doi

  Aquaporin-8's involvement in hepatocyte lipid synthesis and cholesterol biosynthesis through SREBP signaling has been shown in isolated cell studies, but the functional significance of AQP8-SREBP interactions in non-alcoholic fatty liver disease (NAFLD) progression, particularly in high-fat diet models or in genetically obese animal strains beyond db/db mice, requires investigation.