Biology subjects

Khan, N. A.

Publications and source records attributed to Khan, N. A..

15 recordsLinked to original sources

bioRxiv2026

GDF15 modifies NAD+ salvage pathway and dampens immune response in mitochondrial disease

Mitochondrial integrated stress response (ISRmt) is a main mammalian metabolic stress pathway, with local ISRmt and a systemic response via circulating metabokines GDF15 and FGF21 as early signs of the response in mitochondrial diseases. FGF21 has been reported to regulate ISRmt progression and nutrient homeostasis, but the roles of GDF15 have remained unclear. Here, we explored the effects of inactivation of FGF21 or GDF15 or them together in Deletor mice. These mice endogenously activate the full ISRmt and metabokines as part of their mitochondrial muscle disease. GDF15 inactivity upregulated the skeletal muscle enzyme NMRK2, which converts nicotinamide riboside (NR) to nicotinamide mononucleotide (NMN) and NAD+. FGF21 was required for glutathione homeostasis. GDF15 inactivation also induced immune cell invasion in the muscle, aggravated by FGF21 loss, suggesting synergistic anti-inflammatory effects. Our findings indicate that in addition to their systemic effects, FGF21 and GDF15 are autocrine controllers of redox homeostasis in mitochondrial disease muscle.

cell biology↗

bioRxiv2026

Establishment of a cochlear lymphatic vascular network and immune surveillance system following cochlear implantation

Hearing loss is a highly prevalent sensory abnormality often addressed with cochlear implants (CI) that provide auditory rehabilitation for deaf patients. However, a universal inflammatory foreign body response (FBR) to the implanted materials negatively impacts CI outcomes. The mechanistic basis for immune cell infiltration and propagation of the FBR directed against CIs is not defined. Using mouse CI models and quantitative, highly tractable reporters for lymphatics, blood vessels, and immune cells, we identify inner ear lymphatic vessels and changes to the immune surveillance system following cochlear implantation. Histopathological analysis of implanted temporal bones from human subjects shows that both blood vessels and lymphatics are evident within the scala tympani of the implanted cochlea. Our data reveal a rich lymphatic vascular network in the inner ear, closely associated with the perilymphatic and endolymphatic spaces. Lymphatics proliferate within the perilymphatic space of the implanted cochleae and appear to traffic immune cells. Together, our data provide direct evidence that concurrent proliferation of blood vessels and recruitment of blood-borne immune cells comprise an 'immune surveillance system' in the implanted cochleae that promotes the FBR. Our findings also highlight potential opportunities to limit adverse FBR outcomes following cochlear implantation.

systems biology↗

bioRxiv2026

Reconstituting Mouse Embryogenesis Ex Utero from Gastrulation to Fetal Development Reveals Maternally Independent Metabolic Programs

Mammalian development takes place inside the maternal uterus, creating technological constraints that make difficult the study of embryogenesis in live developing embryos. A central challenge for understanding the role of metabolism in mammalian development is discriminating placental and uterine-regulated signals from embryo-intrinsic processes independent of maternal influence, a process that until now has remained inseparable during gastrulation and organogenesis1-3. Ex utero culture systems allowing continuous growth of embryos during pre-gastrulation to organogenesis4,5 offer a promising solution to this challenge. Here, we present optimized ex utero culture platforms that support faithful development of mouse embryos from gastrulation (embryonic day 6.5/7.5) through the fetal period (embryonic day [~]12.5) and harnessed these platforms for dissecting metabolic transitions in vivo during embryogenesis independently of uterus and placenta. We characterized the metabolome of in utero and ex utero whole embryos, fetal organs and culture medium between embryonic days E6.5 and E12.5 by liquid chromatography mass-spectrometry (LC-MS) metabolomics, isotope tracing, and single cell transcriptomics. These datasets present a comprehensive overview of the dynamic embryonic metabolism during gastrulation and organogenesis in utero and ex utero. This analysis revealed that the midgestational metabolic switch occurring at E10.5-E11.5 is faithfully recapitulated ex utero, indicating that this transition is intrinsically programmed in embryonic tissues and does not require direct maternal or placental cues. Notably, oxygen availability modulated the extent of this transition, but elevated oxygen was insufficient to induce it prematurely, demonstrating that the switch is developmentally timed and only partially environmental-responsive. We further harnessed the ex utero platform for identifying and perturbing a mitochondrial redox shift at E7.5-E8.5 that is critical for developmental progress after gastrulation. These findings uncover the remarkable metabolic plasticity of the mammalian embryo, demonstrating its capacity to sustain growth independently of maternal inputs from the establishment of the body plan through the onset of the fetal period. Moreover, they highlight the use of long-term ex utero culture as a unique framework for dissecting the mechanisms that shape embryogenesis under physiological and experimentally perturbed conditions, while functionally uncoupling embryonic programs from maternal and placental influences.

developmental biology↗

bioRxiv2026

Midgestation metabolic constraint in purine metabolism drives distinct strategies for placenta and fetal growth

Purine nucleotides are essential for mammalian development1,2. Purine monophosphates support cell signaling and proliferation and are synthesized by cells through either de novo synthesis or a salvage pathway3. We previously identified a midgestational metabolic transition in mice (gestational days gd10.5-11.5) characterized by changes in purine metabolism4. Midgestation is a period of rapid growth for placenta and embryo, yet it remains unclear how the placental tissues expand without directly competing with the embryo for biosynthetic resources. Here, we show that this midgestational metabolic transition is associated with a marked reduction in embryonic expression of purine salvage enzymes, which constrains embryonic metabolism and leads to different strategies for purine synthesis between the placenta and embryo. Midgestation embryos are unable to engage the purine salvage pathway even when de novo purine synthesis is blocked either in vivo or in ex utero embryo culture, whereas placental tissue and trophoblasts retain the capacity to use either pathway. Disruption of de novo purine synthesis in mice causes reduced embryonic growth, impaired axial elongation, and abnormal brain and placental development, which are only partially rescued by supplementation with purine salvage precursors. In human placenta, trophoblast stem cells readily switch between the de novo and salvage pathways based on nutrient availability, and syncytiotrophoblasts (STB) preferentially rely on the salvage pathway. We identified guanosine monophosphate (GMP) as a metabolic checkpoint regulating STB differentiation, with insufficient GMP levels causing degradation of the small GTPase Rheb and failure of mTOR activation. Supplementation of purine salvage substrates restored GMP synthesis and STB differentiation in humans, but not mice. Further, in vivo measurements in humans revealed that maternal circulating hypoxanthine decreases during pregnancy and is further reduced in women with clinically small placentas, highlighting the role of hypoxanthine in supporting placental growth. These results uncover compartmentalized purine salvage between the embryo and placenta as a mechanism that limits competition for biosynthetic resources and enables coordinated growth during mammalian development.

developmental biology↗

bioRxiv2025

Integrative metabolome-genome analysis reveals the genetic architecture of metabolic diversity in sorghum grain

Natural variation in the grain metabolome plays a central role in shaping nutritional quality and end-use traits in grass crops. Understanding the genetic basis of this metabolic diversity is therefore essential, yet population-scale integration of metabolomics and genomics remains limited in sorghum, a climate-resilient C4 crop renowned for its exceptional heat and drought tolerance. Here, we integrated large-scale untargeted metabolomic profiling, population genomics, and artificial intelligence (AI)-based machine learning to systematically dissect grain metabolic diversity and its genetic architecture in sorghum. Untargeted metabolomic profiling of mature grains of the Sorghum Association Panel (SAP) identified 4,877 compounds, revealing extensive quantitative variation relevant to grain nutritional improvement. Metabolite-based genome-wide association studies (mGWAS) identified [~]4.15 million significant SNP-metabolite associations, revealing the heterogeneous genetic architecture of metabolic traits. Associated variants were enriched in genic and regulatory regions but depleted in intergenic regions, consistent with functional constraint. A total of 38 metabolite gene clusters revealed coordinated genetic control of core metabolic pathways. We further applied machine learning to identify key metabolites that underlie grain color variation and to prioritize associated candidate genes, demonstrating the utility of predictive models integrating genotype, metabolome, and end trait. Collectively, this work establishes a population-scale atlas of sorghum grain metabolomic and genetic diversity, available through the Sorghum Grain Metabolite Diversity Atlas (SorGMDA). This resource enables integrated metabolomics and genomic analyses and supports systems-level breeding strategies for improving grain nutritional quality.

genomics↗

bioRxiv2025

NAD+ precursor treatment prevents cardiomyopathybut disrupts erythroid maturation in mitochondrial progeria

Nicotinamide adenine dinucleotide (NAD+) plays a central role in energy metabolism, and its decline is linked to various degenerative diseases. While NAD+ restoration holds therapeutic promise, its long term, tissue-specific consequences remain poorly understood. We investigated effects of nicotinamide riboside (NR) supplementation for "mutator" mice manifesting mitochondrial progeria. Our results reveal strikingly divergent outcomes: in proliferative bone marrow, NR-treated mutators show reductive stress with accumulation of NADH/NADPH, altered amino acid, nucleotide, folate levels and impaired heme biosynthesis. In blood, erythrocyte maturation defects are aggravated, exacerbating anemia. Conversely, in postmitotic cardiac tissue, NR enhanced contractility, reduces stress response markers and normalized metabolic profile. These findings indicate that while being beneficial for heart, chronic NAD+ boosting can compromise erythrocyte maturation in the context of mitochondrial disease. The data emphasize importance of evaluating systemic effects of NAD+ boosting therapies beyond the primary affected tissues and development of tissue-specific metabolic interventions for degenerative diseases. HighlightsO_LIChronic nicotinamide riboside supplementation exacerbates anemia and disrupts erythroid maturation in progeric mice. C_LIO_LIIn proliferative bone marrow cells, NR induces redox imbalance and drives profound metabolic dysregulation. C_LIO_LINR suppresses heme biosynthesis and iron transport pathways in the bone marrow. C_LIO_LIIn the heart, NR restores NAD+ levels, enhances cardiac function, and reduces metabolic stress. C_LI

physiology↗

bioRxiv2025

Nutrient-dependent pathology in mitochondrial hypertrophic cardiomyopathy model

ObjectiveMitochondrial translation defects are a major cause of early childhood hypertrophic cardiomyopathy (CMP). While the genetic basis of these disorders is being increasingly uncovered, the downstream molecular mechanisms driving disease pathogenesis remain poorly understood. In this study, we investigated the consequences of defects in mitochondrial ribosomal large subunit protein 44 (MRPL44), associated with infantile-onset CMP in human cardiomyocytes, in nutrient environments relevant to cardiac development. MethodsInduced pluripotent stem cell line with MRPL44 patient mutation and controls were differentiated to cardiomyocytes and grown in glucose or lipid-enriched medium reflecting prenatal or postnatal fuel preferences, respectively. Mitochondrial, lipid metabolic and cellular characteristics were studied by immunofluorescence and cellular transcriptome by RNA-sequencing. ResultsIn glucose-rich medium, patient-derived cardiomyocytes exhibit increased mitochondrial DNA (mtDNA) content and elevated mitochondrial transcripts. In contrast the lipid-enriched medium triggered both mitochondrial and endoplasmic reticulum -related stress responses, disrupted lipid and cholesterol homeostasis, accompanied by remodeling of the central biosynthetic pathway of one carbon metabolism. The cells accumulated lipids while also inducing lipid uptake and synthesis genes, suggesting maladaptive metabolic rewiring. ConclusionOur findings indicate that glucose and lipids, the latter being the postnatally favored cardiac fuel, exert remarkably different consequences in MRPL44 deficient cardiomyocytes. The lipid enriched medium elicited robust activation of metabolic stress responses, with chronic upregulation of anabolic biosynthesis pathways and lipid accumulation indicative of conflicting metabolic homeostasis. These observations provide a mechanistic basis for postnatal disease manifestation and highlight nutrient metabolism as a key driver in development of infantile-onset mitochondrial hypertrophic cardiomyopathy. HighlightsO_LIMRPL44 deficiency impairs mitochondrial translation but induces mtDNA replication and transcription in iPSC-derived cardiomyocytes. C_LIO_LIIn glucose conditions, MRPL44 mutant cardiomyocytes upregulate mitochondrial replication and transcription program, but not translation. C_LIO_LILipid-enriched nutrient conditions exacerbate disease phenotype, inducing mitochondrial and ER stress responses in MRPL44 deficiency. C_LIO_LIMitochondrial ribosome defect disrupts lipid homeostasis in cardiomyocytes causing impaired fatty acid oxidation, lipid accumulation and altered cholesterol metabolism. C_LI

molecular biology↗

bioRxiv2025

Novel fat-taste enhancers modulate functional connectivity of the reward system following sustained activation of gustatory pathways in mice

Humans and rodents exhibit an innate preference for dietary fat, and dysfunction of lingual fat-taste receptors CD36 and GPR120 in obesity suggests that impaired oro-sensory lipid detection may contribute to its development. Rodent models with reduced fat-taste sensitivity display increased fat intake, highlighting the role of taste perception in dietary regulation. The newly developed NKS-3 and NKS-5, high-affinity agonists for CD36 and CD36/GPR120 receptors, respectively, induce early fat satiation and reduce both fat-rich food intake and body weight gain in diet-induced obese mice. However, the neural mechanisms underlying these effects remain unclear. Here, we investigated the response of the reward system to a sustained activation of CD36 and GPR120 via fat-taste enhancers NKS-3 and NKS-5 compared to linoleic acid (LA). Male C57BL/6JRj mice (N=88) received oral administration of vehicle, 0.2% LA, 50 {micro}M NKS-3 or 75 {micro}M NKS-5 for 10 days. The immunohistochemical analysis of cerebral FosB neuronal expression revealed a reorganization of the functional network connectivity. Behavioral assessments over an additional 10-day period in a second cohort of animals detected no adverse motivational, compulsive-like, depressive or anxiogenic effect of the treatments. Our findings suggest that our fat-taste enhancers may offer a promising therapeutic strategy against obesity, leveraging the oral-gut-brain axis to regulate fat-rich food intake.

neuroscience↗

bioRxiv2024

Supervised Automation of Cell Counting in Confocal Microscopic Cochlear Imaging Datasets Using Macro in Imaris

Analyzing confocal microscopic data of biological samples using the Imaris software poses challenges due to its time-consuming nature involving tedious multiple steps and possibility of human errors. Here, we developed a supervised automation protocol to minimize manual input in cell and spot counting on confocal images obtained from mouse cochlear sections. The protocol increases efficiency by incorporating image recognition and object-oriented macros. Moreover, the protocol being adaptable allows scientists in diverse other fields to customize it for their specific needs. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=196 SRC="FIGDIR/small/604970v1_ufig1.gif" ALT="Figure 1"> View larger version (64K): org.highwire.dtl.DTLVardef@11b4aa0org.highwire.dtl.DTLVardef@c08c7dorg.highwire.dtl.DTLVardef@1479b59org.highwire.dtl.DTLVardef@280227_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2023

Computational Insights on Xenobiotic Nuclear Receptor-Air Pollutant Interactions Through Molecular Docking and Dynamics Simulations

Air pollution is a major global health risk, contributing to millions of deaths each year. Exposure to air pollutants can lead to a variety of adverse health effects, including oxidative stress, inflammation, and DNA damage. The nuclear receptor pregnane X receptor (PXR) is a xenobiotic sensor that plays a key role in the detoxification of environmental chemicals and air pollutants can activate these receptors, leading to the expression of genes involved in drug metabolism and detoxification. Elucidating the structural interactions of air pollutants with PXR provides insights into the mechanisms by which these pollutants exert their toxic effects. Using computational techniques, we screened 124 air pollutants toxic compounds from (APDB) against PXR and identified priority compounds for molecular dynamics simulation that revealed the dynamic binding mechanisms and structural conformations involved in PXR activation. Furthermore, the root mean square deviation (RMSD) and root mean square fluctuation (RMSF) analyses characterized the stability and flexibility of PXR-pollutant complexes. Together, these computational approaches provide unprecedented insights into the molecular basis of PXR activation by air pollutants. By enabling high-throughput screening and multi-faceted biophysical characterization of PXR interactions, this work elucidates the structural mechanisms linking air pollution to impaired xenobiotic metabolism. Integration of virtual screening, molecular dynamics, and rigorous biophysical analyses represents a powerful computational systems pharmacology pipeline for assessing health risks posed by ubiquitous environmental toxicants.

bioinformatics↗

bioRxiv2023

Fecal metagenomics to identify biomarkers of food intake in healthy adults: Findings from randomized, controlled, nutrition trials

BackgroundUndigested components of the human diet affect the composition and function of the microorganisms present in the gastrointestinal tract. Techniques like metagenomic analyses allow researchers to study functional capacity, thus, revealing the potential of using metagenomic data for developing objective biomarkers of food intake. ObjectiveAs a continuation of our previous work using 16S and metabolomic datasets, we aimed to utilize a computationally intensive, multivariate, machine learning approach to identify fecal Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology (KO) categories as biomarkers that accurately classify food intake. DesignData were aggregated from five controlled feeding studies that studied the individual impact of almonds, avocados, broccoli, walnuts, barley, and oats on the adult gastrointestinal microbiota. DNA from pre-and post-intervention fecal samples underwent shotgun genomic sequencing. After pre-processing, sequences were aligned and functionally annotated with DIAMOND v2.0.11.149 and MEGAN v6.12.2, respectively. After count normalization, the log of the fold change ratio for resulting KOs between pre-and post-intervention of the treatment group against its corresponding control was utilized to conduct differential abundance analysis. Differentially abundant KOs were used to train machine learning models examining potential biomarkers in both single-food and multi-food models. ResultsWe identified differentially abundant KOs in the almond (n = 54), broccoli (n = 2,474), and walnut (n = 732) groups (q < 0.20), which demonstrated classification accuracies of 80%, 87%, and 86% for the almond, broccoli, and walnut groups, respectively, using a random forest model to classify food intake into each food groups respective treatment and control arms. The mixed-food random forest achieved 81% accuracy. ConclusionsOur findings reveal promise in utilizing fecal metagenomics to objectively complement self-reported measures of food intake. Future research on various foods and dietary patterns will expand these exploratory analyses for eventual use in feeding study compliance and clinical settings.

bioinformatics↗

bioRxiv2023

Effect of growing regions on morphological characteristics, protein nutrition, rumen degradation and molecular structures of various whole-plant silage corn cultivars

Little information exists on the variation of morphological characteristics, nutritional value, ruminal degradability, and molecular structural makeup of diverse whole-plant silage corn (WPSC) cultivars among different growing regions. This study investigated the between-regions discrepancies in five widely used WPSC cultivars in China (FKBN, YQ889, YQ23, DK301 and ZD958) in terms of 1) morphological characteristics; 2) crude protein (CP) chemical profile; 3) Cornell Net Carbohydrate and Protein System (CNCPS) CP subfractions; 4) in situ CP degradation kinetics; and 5) CP molecular structures. Our results revealed that significant difference were observed on growing region and WPSC cultivar interaction for all estimated morphological characteristics (P < 0.001), CP chemical profile (P < 0.001), CNCPS subfractions (P < 0.001) and CP molecular structural features (P < 0.05). Except ear weight (P = 0.18), all measured morphological characteristics varied among different growing regions (P < 0.001). Besides, WPSC cultivars planted in different areas had remarkably different (P < 0.01) CP chemical profiles and CNCPS subfractions. All spectral parameters of protein primary structure of WPSC differed (P < 0.05) due to the various growing regions, except amide II area (P = 0.28). Finally, the area ratio of amide I to II was negatively correlated with the contents of soluble CP ({delta} = -0.66; P = 0.002), CP ({delta} = - 0.61; P = 0.006), non-protein N ({delta} = -0.56; P = 0.004) and acid detergent insoluble CP ({delta} = - 0.43; P = 0.008), in conjunction with positively correlated with moderately degradable CP (PB1;{delta} = 0.58; P = 0.01). In conclusion, the current study suggested that even for the same WPSC cultivar, the morphological characteristics, protein nutritional values and rumen degradability significantly varied among different grown regions due to distinguished molecular structures. Author summaryAs the major roughage source, whole plant silage corn plays an essential role in ruminant feed industry. The quality and quantity of it largely influenced by environmental and climate conditions except genetic factors. However, there was limited information to systematically analyze whole plant silage corn from morphological characteristics, nutritional components, rumen degradation to its inherent molecular structures. Thus, this study was conducted to investigate the discrepancies of various silage-corn cultivars grown in different regions from internal structure to phenotype based novel technology - fourier transform infrared spectroscopy.

biochemistry↗

bioRxiv2019

Role of nitric oxide in improving seed germination and alleviation of copper-induced photosynthetic inhibition in Indian mustard

Heavy metal stress limits crop production through its effects on seed germination and photosynthesis. Nitric oxide (NO), a versatile signaling molecule, plays a significant role in heavy metal stress tolerance. In the present investigation, the efficacy of NO application in the alleviation of copper (Cu) induced adverse impact on seed germination and photosynthesis of mustard plant (Brassica juncea L.) was evaluated. Pretreatment with NO donor sodium nitroprusside (SNP), significantly improved seed germination and alleviated Cu-accrued oxidative stress in B. juncea seeds. However, in the absence of NO, Cu showed a higher reduction in seed germination rate. Further, NO modulated the activities of antioxidant enzymes and sustained the lower level of lipid peroxidation by reducing H2O2, and thiobarbituric acid reactive substances (TBARS), thereby elevated the antioxidative capacity in Cu-exposed seeds. Seeds pretreated with NO also retained higher amylase activities for the proper seed germination when compared with control. NO mitigated Cu toxicity through an improved antioxidant system, and reducing Cu-induced accumulation of reactive oxygen species (ROS), reduction in lipid peroxidation improving photosynthetic efficiency and growth of the mustard plant. It may concluded that NO improved amylase activity, modulated activity of antioxidant enzymes, and enhanced the germination rate seeds under Cu stress, thereby improved photosynthesis and growth.

plant biology↗

bioRxiv2019

Injectable nanoclay gels for angiogenesis

The retention and sustained activity of therapeutic proteins at delivery sites are goals of regenerative medicine. Vascular endothelial growth factor (VEGF) has significant potential in promoting the growth and regeneration of blood vessels but is intrinsically labile. This is exacerbated by the inflammatory microenvironments at sites requiring regeneration. For VEGF to be efficacious it may require a carrier that stabilises it, protects it from degradation and retains it at a site of interest. In this study we tested the hypothesis that injectable nanoclay gels composed of Laponite XLG can stabilise VEGF and retain it in active form for therapeutic delivery. To achieve this, VEGF was incorporated in Laponite gels and its activity tested at a range of concentrations using in vivo cell culture tubulogenesis assays and in vivo angiogenesis assays. We found that VEGF-Laponite gels enhanced tubulogenesis in a dose-dependent manner in vivo. When administered subcutaneously in vivo Laponite was retained at an injection site for up to a period of three weeks and promoted a 4-fold increase in blood vessel formation compared with alginate or vehicle controls as confirmed by CD31 staining. Notably, in contrast to alginate, Laponite gels did not release VEGF, indicating a strong interaction between the growth factor and the nanoclay, and suggesting that Laponite enhancement of VEGF efficacy is due to its retention at an implantation site over a prolonged period. Our approach provides a robust method for delivery of bioactive recombinant VEGF without the necessity for complex hydrogel or protein engineering.

bioengineering↗

bioRxiv2018

Vaccinomics strategy for developing a unique multi-epitope monovalent vaccine against Marburg marburgvirus

Marburg virus causes severe hemorrhagic fever in both humans and non-human primates with high degree of infectivity and lethality. To date no approved treatment is available for Marburg virus infection. A study was employed to design a novel chimeric vaccine against Marburg virus by adopting reverse vaccinology approach. Envelope glycoprotein and matrix protein VP40 were identified as most antigenic viral proteins which generated a plethora of antigenic epitopes. Results showed that vaccine construct V1 was superior in terms of various physicochemical properties and structural stability. Molecular docking analysis of the refined vaccine with different MHCs and human immune TLR8 receptor demonstrated higher binding affinity. Moreover, complexed structure of the modeled vaccine and TLR8 indicated minimal deformability at molecular level. Translational potency and microbial expression of the modeled vaccine within E. coli strain K12 by pET28a(+) vector were also biologically significant. However, further in vitro and in vivo investigation could be implemented for the acceptance and validation of the designed vaccine against Marburg virus.

bioinformatics↗