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Introduction: Molecular markers are the examples of the contribution of genome technology to medicinal plant breeding through marker-assisted selection (MAS) for pharmaceutical quality.

Adipocyte dysfunction is a crucial driver of insulin resistance and type 2 diabetes. We identified EH domain-containing protein 2 (EHD2) as one of the most highly upregulated genes at the early stage of adipose-tissue expansion. EHD2 is a dynamin-related ATPase influencing several cellular processes, including membrane recycling, caveolae dynamics, and lipid metabolism. Here, we investigated the role of EHD2 in adipocyte insulin signaling and glucose transport. Using C57BL6/N EHD2 knockout mice under short-term high-fat diet conditions and 3T3-L1 adipocytes we demonstrate that EHD2 deficiency is associated with deterioration of insulin signal transduction and impaired insulin-stimulated GLUT4 translocation. Furthermore, we show that lack of EHD2 is linked with altered plasma membrane lipid and protein composition, reduced insulin receptor expression, and diminished insulin-dependent SNARE protein complex formation. In conclusion, these data highlight the importance of EHD2 for the integrity of the plasma membrane milieu, insulin receptor stability, and downstream insulin receptor signaling events, involved in glucose uptake and ultimately underscore its role in insulin resistance and obesity.

Genetic variation at the MTIF3 (Mitochondrial Translational Initiation Factor 3) locus has been robustly associated with obesity in humans, but the functional basis behind this association is not known. Here, we applied luciferase reporter assay to map potential functional variants in the haplotype block tagged by rs1885988 and used CRISPR-Cas9 to edit the potential functional variants to confirm the regulatory effects on MTIF3 expression. We further conducted functional studies on MTIF3-deficient differentiated human white adipocyte cell line (hWAs-iCas9), generated through inducible expression of CRISPR-Cas9 combined with delivery of synthetic MTIF3 -targeting guide RNA. We demonstrate that rs67785913-centered DNA fragment (in LD with rs1885988, r 2 > 0.8) enhances transcription in a luciferase reporter assay, and CRISPR-Cas9-edited rs67785913 CTCT cells show significantly higher MTIF3 expression than rs67785913 CT cells. Perturbed MTIF3 expression led to reduced mitochondrial respiration and endogenous fatty acid oxidation, as well as altered expression of mitochondrial DNA-encoded genes and proteins, and disturbed mitochondrial OXPHOS complex assembly. Furthermore, after glucose restriction, the MTIF3 knockout cells retained more triglycerides than control cells. This study demonstrates an adipocyte function-specific role of MTIF3 , which originates in the maintenance of mitochondrial function, providing potential explanations for why MTIF3 genetic variation at rs67785913 is associated with body corpulence and response to weight loss interventions., Competing Interests: MH, DC, HA, PS, AS, MC, HM, PF, SK No competing interests declared, (© 2023, Huang et al.)

Aquaglyceroporin 7 (AQP7) facilitates glycerol flux across the plasma membrane with a critical physiological role linked to metabolism, obesity, and associated diseases. Here, we present the single-particle cryo-EM structure of AQP7 determined at 2.55 Å resolution adopting two adhering tetramers, stabilized by extracellularly exposed loops, in a configuration like that of the well-characterized interaction of AQP0 tetramers. The central pore, in-between the four monomers, displays well-defined densities restricted by two leucine filters. Gas chromatography mass spectrometry (GC/MS) results show that the AQP7 sample contains glycerol 3-phosphate (Gro3P), which is compatible with the identified features in the central pore. AQP7 is shown to be highly expressed in human pancreatic α- and β- cells suggesting that the identified AQP7 octamer assembly, in addition to its function as glycerol channel, may serve as junction proteins within the endocrine pancreas., (© 2023. The Author(s).)

Clinical endocrinology entails an understanding of the mechanisms involved in the regulation of tumors that occur in the endocrine system. The exact cause of endocrine cancers remains an enigma, especially when discriminating malignant lesions from benign ones and early diagnosis. In the past few years, the concepts of personalized medicine and metabolomics have gained great popularity in cancer research. In this systematic review, we discussed the clinical metabolomics studies in the diagnosis of endocrine cancers within the last 12 years. Cancer metabolomic studies were largely conducted using nuclear magnetic resonance (NMR) and mass spectrometry (MS) combined with separation techniques such as gas chromatography (GC) and liquid chromatography (LC). Our findings revealed that the majority of the metabolomics studies were conducted on tissue, serum/plasma, and urine samples. Studies most frequently emphasized thyroid cancer, adrenal cancer, and pituitary cancer. Altogether, analytical hyphenated techniques and chemometrics are promising tools in unveiling biomarkers in endocrine cancer and its metabolism disorders.

Background: Medicinal plants are used to treat various disorders, including diabetes, globally in a range of formulations. While attention has mainly been on the aerial plant parts, there are only a few review studies to date that are focused on the natural constituents present in the plant roots with health benefits. Thus, the present study was performed to review in vivo studies investigating the antidiabetic potential of the natural compounds in plant roots., Methods: We sorted relevant data in 2001-2019 from scientific databases and search engines, including Web of Knowledge, PubMed, ScienceDirect, Medline, Reaxys, and Google Scholar. The class of phytochemicals, plant families, major compounds, active constituents, effective dosages, type of extracts, time of experiments, and type of diabetic induction were described., Results: In our literature review, we found 104 plants with determined antidiabetic activity in their root extracts. The biosynthesis pathways and mechanism of actions of the most frequent class of compounds were also proposed. The results of this review indicated that flavonoids, phenolic compounds, alkaloids, and phytosteroids are the most abundant natural compounds in plant roots with antidiabetic activity. Phytochemicals in plant roots possess different mechanisms of action to control diabetes, including inhibition of α -amylase and α -glucosidase enzymes, oxidative stress reduction, secretion of insulin, improvement of diabetic retinopathy/nephropathy, slow the starch digestion, and contribution against hyperglycemia., Conclusion: This review concludes that plant roots are a promising source of bioactive compounds which can be explored to develop against diabetes and diabetes-related complications., Competing Interests: Conflict of interestNone., (© The Author(s) 2021.)

The losses of honey bee colonies and declines of other insect pollinators have been associated with negative effects of pesticides. Honey bees as well as other pollinators are nectar and pollen foragers and thus are exposed to an extensive range of phytochemicals. Understanding the synergistic, additive, and antagonistic effects of plant secondary metabolites and pesticides in honey bees may help to protect honey bee colonies against agrochemicals. In this study, we used untargeted metabolomics to investigate the impact of dietary phytochemical composition on the residual concentration of three pesticides: imidacloprid, tau-fluvalinate and tebuconazole in exposed honey bees. Honey bees were given different diets based on pollen or nectar from four plants: Reseda odorata, Borago officinalis, Phacelia tanacetifolia, and Trifolium repens for two days. Thereafter, they were orally exposed to 10 ng/bee imidacloprid or contact-exposed to 0.9 μg/bee tau-fluvalinate or 5 μg/bee tebuconazole. After 1 h of oral exposure or 24 h of contact exposure, the honey bees were anaesthetised with CO 2 , sacrificed by freezing, extracted with a validated QuEChERS method, and residual pesticide concentrations were determined by LC-QTRAP-MS/MS. The phytochemical composition in the given diets were profiled with an UHPLC-Q Exactive-MS/MS. The results revealed that the dietary phytochemical composition has a noteworthy influence on the concentration of residual pesticides in honey bees. The correlation coefficient analysis demonstrated that flavonoids have a reducing effect on the residual concentration of imidacloprid and tau-fluvalinate in honey bees. The results also highlighted that exposure to imidacloprid impaired the metabolism of sugars in honey bees. Exploiting flavonoid-rich plants may protect honey bees against pesticides and hold promise as forage plants in future beekeeping., (Copyright © 2021 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

With the identification of novel antibiotics from nature being pivotal in the fight against human pathogenic bacteria, there is an urgent need for effective methodologies for expedited screening of crude extracts. Here we report the development and validation of a simple and dye-free antimicrobial assay in 96-well microplate format, for both determination of IC 50 values and high-resolution inhibition profiling to allow pin-pointing of bioactive constituents directly from crude extracts. While commonly used antimicrobial assays visualize cell viability using dyes, the developed and validated assay conveniently uses OD 600 measurements directly on the fermentation broth. The assay was validated with an investigation of the inhibitory activity of DMSO against Staphylococcus aureus , temperature robustness, interference by coloured crude extracts as well as inter-day reproducibility. The potential for high-resolution S. aureus growth inhibition profiling was evaluated on a crude extract of an inactive Alternaria sp., spiked with ciprofloxacin.

Honey bees are important pollinators and are subject to numerous stressors, such as changing floral resources, parasites, and agrochemical exposure. Pesticide exposure has been linked to the decline in the global honey bee population. We have limited knowledge of the metabolic pathways and synergistic effects of xenobiotics in bees. Quercetin is one of the most abundant phytochemicals in plants and is therefore abundant in the honey bee diet. Quercetin can upregulate the detoxification system in honey bees; however, it is still unknown to what extent quercetin ingestion can reduce the content of absorbed pesticides. In this study, we investigated the effect of dietary quercetin on the contents of three pesticides in honey bees: imidacloprid (insecticide), tebuconazole (fungicide), and tau-fluvalinate (insecticide and acaricide). Bees were divided into two main groups and fed either quercetin-sucrose paste or only sucrose for 72 h. Thereafter, they were orally exposed to ∼10 ng/bee imidacloprid or contact-exposed to ∼0.9 μg/bee tau-fluvalinate or ∼5.2 μg/bee tebuconazole. After 1 h of oral exposure or 24 h of contact exposure, the bees were anaesthetised with CO 2 , sacrificed by freezing, and extracted with a validated QuEChERS method. Subsequently, the concentrations of the three pesticides and quercetin in the bees were determined with a triple quadrupole tandem mass spectrometer coupled to an HPLC system. No significant effect on the concentration of tebuconazole or tau-fluvalinate was observed in bees fed quercetin. Intake of quercetin led to a reduction in the concentration of imidacloprid in honey bees. Quercetin-rich plants may be exploited in future beekeeping., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

Derivation and culture of small hepatocyte progenitor cells (SHPCs) capable of proliferating in vitro has been described in rodents and recently in humans. These cells are capable of engrafting in injured livers, however, they display de-differentiated morphology and reduced xenobiotic metabolism activity in culture over passages. Here we report that SHPCs derived from adult primary human hepatocytes (PHHs) and cultured on mouse embryonic fibroblasts (MEFs) not only display differentiated morphology and exhibit gene expression profiles similar to adult PHHs, but importantly, they retain their phenotype over several passages. Further, unlike previous reports, where extensive manipulations of culture conditions are required to convert SHPCs to metabolically functional hepatocytes, SHPCs in our co-culture system maintain expression of xenobiotic metabolism-associated genes. We show that SHPCs in co-culture are able to perform xenobiotic metabolism at rates equal to their parent PHHs as evidenced by the metabolism of acetaminophen to all of its major metabolites. In summary, we present an improved co-culture system that allows generation of SHPCs from adult PHHs that maintain their differentiated phenotype over multiple passages. Our findings would be useful for expansion of limited PHHs for use in studies of drug metabolism and toxicity testing., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2020 The Authors.)

Worldwide, 463 million people are affected by diabetes of which the majority is diagnosed with Type 2 Diabetes (T2D). T2D can ultimately lead to retinopathy, nephropathy, nerve damage, and amputation of the lower extremities. α-Glucosidase, responsible for converting starch to monosaccharides, is a key therapeutic target for the management of T2D. However, due to substantial side effects of currently marketed drugs, there is an urgent need for the discovery of new α-glucosidase inhibitors. In our ongoing efforts to identify novel α-glucosidase inhibitors from Nature, we are investigating the potential of endophytic filamentous fungi as sustainable sources of hits and/or leads for future antihyperglycemic drugs. Here we report one previously unreported xanthone (5) and two known xanthones (7 and 11) as α-glucosidase inhibitors, isolated from an endophytic Penicillium canescens, recovered from fruits of Juniperus polycarpos. The three xanthones 5, 7, and 11 showed inhibitory activities against α-glucosidase with IC 50 values of 38.80 ± 1.01 μM, 32.32 ± 1.01 μM, and 75.20 ± 1.02 μM, respectively. Further pharmacological characterization revealed a mixed-mode inhibition for 5, a competitive inhibition for 7, while 11 acted as a non-competitive inhibitor., Competing Interests: Declaration of Competing Interest The authors declare no conflict of interest., (Copyright © 2020 Elsevier B.V. All rights reserved.)

Peptic Ulcer Disease (PUD) is the most common disorder of the stomach and duodenum, which is associated with Helicobacter pylori infection. PUD occurs due to an imbalance between offensive and defensive factors and Proton Pump Inhibitors (PPI), Nonsteroidal Anti-Inflammatory Drugs (NSAIDs) and antibiotics are frequently used for the treatment. Recently, medicinal plants have emerged as efficacious, safe and widely available alternative therapies for PUD. The aim of this review was to study the medicinal plants and phytochemicals, which have been used for PUD treatment to evaluate the potential role of natural compounds to develop herbal remedies for PUD. Information was obtained using a literature search of electronic databases, such as Web of Science, Google Scholar, PubMed, Sci Finder, Reaxys and Cochrane. Common and scientific names of the plants and keywords such as 'peptic ulcer', 'gastric ulcer', 'stomach ulcer' and 'duodenal ulcer' were used for search. Eventually, 279 plants from 89 families were identified and information on the plant families, part of the plant used, chemical constituents, extracts, ulcer model used and dosage were abstracted. The results indicated that most of the anti-PUD plants were from Asteraceae (7.1%) and Fabaceae (6.8%) families while flavonoids (49%), tannins (13%), saponins (10%) and alkaloids (9%) were the most common natural compounds in plants with anti-PUD activity., (Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.net.)

Background: Recent studies have suggested that artichoke (Cynara scolymus L.) may reduce certain biochemical blood factors but the efficacy of this plant on blood pressure (BP) has not yet been investigated. In this study, we determined the clinical efficacy of C. scolymuson BP and body mass index (BMI) in hypertensive patients as an adjunctive to captopril for the first time., Methods: The total phenolic content and gas chromatography-mass spectrometry metabolite profiling in leaves of C. scolymus have been evaluated. A clinical trial was subsequently carried out on 40 patients to determine the effect of C. scolymus on BP and BMI in hypertensive patients. The treatment group received capsules containing C. scolymus(500 mg twice daily) and the placebo group received starch powder for 8 weeks. Systolic blood pressure (SBP), diastolic blood pressure, and BMI were determined before and after the study., Results: A significant improvement of the BMI was seen in the C. scolymus group compared with the placebo group (p = 0.04)., Conclusions: Our findings demonstrated that the consumption of C. scolymus powder as a rich source of phenolic and antioxidant compounds could potentially improve BMI and SBP in hypertensive patients. Therefore, more trials are needed to confirm or reject the antihypertensive impact of artichoke., (© 2019 S. Karger AG, Basel.)

Human-induced pluripotent stem cell (hiPSC)-derived hepatocytes (iHEP) offer an attractive alternative to primary human hepatocytes (PHH) for drug toxicity studies, as PHHs are limited in supply, vary in their metabolic activity between donors, and rapidly lose their functionality in vitro. However, one of the major drawbacks with iHEP cells in drug safety studies is their decreased phenotypic maturity, with lower liver specific enzyme activity compared with that of PHH. Here we evaluated the effects of 3D culture and non-parenchymal cells on the maturation of iHEPs. We describe a serum-free, chemically defined 3D in vitro model using iHEP cells, which is compatible with automation and conventional assay plates. The iHEP cells cultured in this model form polarized aggregates with functional bile canaliculi and strongly increased expression of albumin, urea and genes encoding phase I and II drug metabolism enzymes and bile transporters. Cytochrome P450-mediated metabolism is significantly higher in 3D iHEP aggregates compared to 2D iHEP culture. Furthermore, addition of human liver sinusoidal endothelial cells (sECs) and iPS-derived endothelial cells (iECs) improved mature hepatocyte function and CYP450 enzyme activity. Also, ECs formed endothelial networks within the hepatic 3D cultures, mimicking aspects of an in vivo architecture. Collectively, these results suggest that the iHEP/EC aggregates described here may have the potential to be used for many applications, including as an in vitro model to study liver diseases associated with sinusoidal endothelial cells. STATEMENT OF SIGNIFICANCE: iPS-derived hepatocytes provide an inexhaustible source of cells for drug screening, toxicology studies and cell-based therapies, but lack mature phenotype of adult primary human hepatocytes (PHH). Herein, we show that 3D culture of iPS-derived hepatocytes and their co-culture with human sinusoidal endothelial cells (sECs) to improve their maturity., (Copyright © 2019 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.)

Background: Beauty is a universal phenomenon and debate over what constitutes beauty particularly beauty to human body, has raged since philosophy began. The beauty of individual features depends on "ideal" proportions, and it is suggested that expressing beauty in terms of geometry is possible. Assessment of some used parameters in facial surgeries and harmony of various facial features are essential to surgeon, who requires facial analysis. One of these parameters, is nasolabial angle, in patients undergoing rhinoplasty. This study based on theoretical definitions of beauty and proportions performed the search for the application of this numerical proportions in modern cosmetic surgery., Methods: Twenty-three samples [16 (69.5%) female and 7 (30.5%)] male] were enrolled from patients who underwent rhinoplasty, by a single surgeon. The nasolabial angle was measured in these patients from their lateral profile photographs with adobe Photoshop, before and after surgery., Results: Ideal post-operative angle was 111.54±26.5 degrees from this study and 18.8 ◦ increase in male and 14.68 ◦ increase in female were seen. There was no significant difference between men and women., Conclusion: Our results showed that an ideal proportion can be very useful and practical to assess patient's preoperative expectations and to evaluate the results after surgery and satisfaction of cosmetic surgery process., Competing Interests: The authors declare no conflict of interest.

Objective: The aim of the present review is to give an overview about the role, biosynthesis, and characteristics of Podophyllotoxin (PTOX) as a potential antitumor agent with particular emphasis on key biosynthesis processes, function of related enzymes and characterization of genes encoding the enzymes., Materials and Methods: Google scholar, PubMed and Scopus were searched for literatures which have studied identification, characterization, fermentation and therapeutic effects of PTOX and published in English language until end of 2016., Results: PTOX is an important plant-derived natural product, has derivatives such as etoposide and teniposide, which have been used as therapies for cancers and venereal wart. PTOX structure is closely related to the aryltetralin lactone lignans that have antineoplastic and antiviral activities. Podophyllum emodi Wall. (syn. P. hexandrum ) and Podophyllum peltatum L. (Berberidaceae) are the major sources of PTOX. It has been shown that ferulic acid and methylenedioxy substituted cinnamic acid are the enzymes involved in PTOX synthesis. PTOX prevents cell growth via polymerization of tubulin, leading to cell cycle arrest and suppression of the formation of the mitotic-spindles microtubules., Conclusion: Several investigations have been performed in biosynthesis of PTOX such as cultivation of these plants, though they were unsuccessful. Thus, it is important to find alternative sources to satisfy the pharmaceutical demand for PTOX. Moreover, further preclinical studies are warranted to explore the molecular mechanisms of these agents in treatment of cancer and their possible potential to overcome chemoresistance of tumor cells.

A defined protocol for efficiently deriving endothelial cells from human pluripotent stem cells was established and vascular morphogenesis was used as a model system to understand how synthetic hydrogels influence global biological function compared with common 2D and 3D culture platforms. RNA sequencing demonstrated that gene expression profiles were similar for endothelial cells and pericytes cocultured in polyethylene glycol (PEG) hydrogels or Matrigel, while monoculture comparisons identified distinct vascular signatures for each cell type. Endothelial cells cultured on tissue-culture polystyrene adopted a proliferative phenotype compared with cells cultured on or encapsulated in PEG hydrogels. The proliferative phenotype correlated to increased FAK-ERK activity, and knockdown or inhibition of ERK signaling reduced proliferation and expression for cell-cycle genes while increasing expression for "3D-like" vasculature development genes. Our results provide insight into the influence of 2D and 3D culture formats on global biological processes that regulate cell function., (Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.)

Purpose: Carbohydrates are shown to have an important role in blood glucose control, type 2 diabetes and cardiovascular diseases risk. This is even more challenging when considering populations consuming refined grains diets. Bread and rice are staple foods which supply main proportion of Iranian calorie intake. This study was designed to investigate the effect of bread and rice intake on blood glucose control, lipid profile and anthropometric measurements in Iranian type 2 diabetic patients., Methods: 426 patients with type 2 diabetes were included in this study. Anthropometric measurements were done using standard methods. Dietary information was assessed by a valid and reliable food frequency questionnaire (FFQ). Fasting blood glucose (FBG), glycated hemoglobin (HbA1c), serum triglycride (TG), total cholesterol (TC), low density lipoprotein (LDL) and high density lipoprotein (HDL) cholesterol were examined after 12-hour fasting., Results: The results represented that people in the highest tertile compared to the lowest tertile of calorie adjusted total bread intake have higher FBG. FBG in the highest tertile of calorie adjusted total bread-rice intake was also significantly higher than the lowest. The association remained significant after adjusting for potential confounders. Rice intake showed no association with cardio-metabolic risk factors., Conclusion: We founded that higher total bread intake and total bread-rice intake were associated with FBG in type 2 diabetic patients whereas rice intake was not associated with glucose and lipid profile. This result should be confirmed in prospective studies, considering varieties, glycemic index (GI), glycemic load (GL) and cooking method of bread and rice., Competing Interests: The authors have declared that no competing interests exist.

Objective: Melissa officinalis is a perennial herb from the Lamiaceae family which has shown to have modulating effects on serum lipid profile. The aim of the current study is to explore the effects of M. officinalis supplementation on serum biochemical parameters of patients with borderline hyperlipidemia., Methods: 58 hyperlipidemic patients were allocated randomly to 2 groups: first group received capsules containing 1000mg M. officinalis leaf powder (MO group), and the second group received placebo capsules (P group) 3 times per day for 2 months. Fasting blood glucose (FBG), HDL, LDL, Triglyceride, Creatinine and liver function enzymes including AST and ALT were evaluated before and after study., Results: The mean of LDL in MO group significantly decreased compared with P group after the supplementation (P=0.02). Although the level of Cholesterol, FBG, HDL, Triglyceride, Creatinine and ALT did not show significant difference between two groups after 2 months (P≥0.05), the level of AST exhibited a significant difference between two groups (P=0.009)., Conclusions: Our findings demonstrated that M. officinalis supplementation as a rich source of antioxidants and bioactive compounds can be effective in remission of LDL and AST levels in patients with borderline hyperlipidemia., (Copyright © 2016 Elsevier Ltd. All rights reserved.)

Here, we describe an in vitro strategy to model vascular morphogenesis where human induced pluripotent stem cell-derived endothelial cells (iPSC-ECs) are encapsulated in peptide-functionalized poly(ethylene glycol) (PEG) hydrogels, either on standard well plates or within a passive pumping polydimethylsiloxane (PDMS) tri-channel microfluidic device. PEG hydrogels permissive towards cellular remodeling were fabricated using thiol-ene photopolymerization to incorporate matrix metalloproteinase (MMP)-degradable crosslinks and CRGDS cell adhesion peptide. Time lapse microscopy, immunofluorescence imaging, and RNA sequencing (RNA-Seq) demonstrated that iPSC-ECs formed vascular networks through mechanisms that were consistent with in vivo vasculogenesis and angiogenesis when cultured in PEG hydrogels. Migrating iPSC-ECs condensed into clusters, elongated into tubules, and formed polygonal networks through sprouting. Genes upregulated for iPSC-ECs cultured in PEG hydrogels relative to control cells on tissue culture polystyrene (TCP) surfaces included adhesion, matrix remodeling, and Notch signaling pathway genes relevant to in vivo vascular development. Vascular networks with lumens were stable for at least 14days when iPSC-ECs were encapsulated in PEG hydrogels that were polymerized within the central channel of the microfluidic device. Therefore, iPSC-ECs cultured in peptide-functionalized PEG hydrogels offer a defined platform for investigating vascular morphogenesis in vitro using both standard and microfluidic formats., Statement of Significance: Human induced pluripotent stem cell-derived endothelial cells (iPSC-ECs) cultured in synthetic hydrogels self-assemble into capillary networks through mechanisms consistent with in vivo vascular morphogenesis., (Copyright © 2016 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.)

The salamander has the remarkable ability to regenerate its limb after amputation. Cells at the site of amputation form a blastema and then proliferate and differentiate to regrow the limb. To better understand this process, we performed deep RNA sequencing of the blastema over a time course in the axolotl, a species whose genome has not been sequenced. Using a novel comparative approach to analyzing RNA-seq data, we characterized the transcriptional dynamics of the regenerating axolotl limb with respect to the human gene set. This approach involved de novo assembly of axolotl transcripts, RNA-seq transcript quantification without a reference genome, and transformation of abundances from axolotl contigs to human genes. We found a prominent burst in oncogene expression during the first day and blastemal/limb bud genes peaking at 7 to 14 days. In addition, we found that limb patterning genes, SALL genes, and genes involved in angiogenesis, wound healing, defense/immunity, and bone development are enriched during blastema formation and development. Finally, we identified a category of genes with no prior literature support for limb regeneration that are candidates for further evaluation based on their expression pattern during the regenerative process.