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Biomedical subjects

Jian Chen

Publications and source records attributed to Jian Chen.

At least 19 recordsLinked to original sources

Pathogen Species-Specific Differences in Induction of the Maize Polyubiquitin Gene Promoter in Transgenic Wheat.

The maize polyubiquitin promoter (ZmUbi) is a mainstay in molecular biology for transgene expression and is used for constitutive expression of defense-related gene products. Transgenic wheat lines were produced expressing a ZmUbi-RUBY reporter gene that produces the red pigment betalain. Some lines showed transgene silencing with reduced RUBY transcript accumulation and chimeric sectors of betalain. Infection of these plants with Blumeria graminis, Puccinia graminis f. sp. tritici (Pgt), or P. triticina (Pt) each resulted in localized betalain accumulation at infection sites and increased RUBY transcript accumulation. In contrast, two isolates of P. striiformis f. sp. tritici (Pst) caused no detectable RUBY transcript accumulation and no visible betalain accumulation at infection sites, although a modest betalain increase was detected in infected tissue extracts. Compared with Pst, Pgt more strongly induced host genes involved in transcriptional and post-transcriptional regulatory processes, although no obvious pathogen-induced changes in ZmUbi promoter methylation were observed. ZmUbi-GUS transgenic wheat plants were also pathogen challenged, and, unlike Pst, both Pgt and Pt induced localized GUS staining at infection sites. Database mining showed that the endogenous maize polyubiquitin gene from which ZmUbi is derived was pathogen inducible, albeit in a species-specific fashion. These pathogen differences in ZmUbi induction have implications when using this regulatory element to express defense-related transgenes in wheat. Comparing the resistance efficacy of transgenes against different pathogens using this promoter is potentially influenced by significant, localized expression differences occurring at infection sites of different pathogen species. [Formula: see text] Copyright © 2026 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Promoter Regions, Genetic↗

Urinary Small Extracellular Vesicle DNA as a Biomarker for the Non-Invasive Diagnosis of Bladder Cancer.

Existing diagnostic technologies for bladder cancer (BC) suffer from low sensitivity, low specificity, or a lack of validation. Therefore, validated, non-invasive diagnostic biomarkers with high sensitivity and specificity for early detection of BC are needed to complement and improve upon the limitations of existing diagnostic methods. We used low-pass whole genome sequencing (LP-WGS) technology to detect copy number variations (CNVs) in small extracellular vesicle (sEV) DNA isolated from urine samples of patients. Based on these results, we constructed and validated a diagnostic model to differentiate between benign and malignant bladder lesions. We conducted a receiver operating characteristic analysis and calculated the area under the curve (AUC) to evaluate the performance of the diagnostic model. The urine sEV-DNA LP-WGS data revealed CNV differences between benign and malignant samples. The diagnostic model achieved an AUC of 0.953, a sensitivity of 86.7%, and a specificity of 100% in the training cohort and an AUC of 0.985, a sensitivity of 90%, and a specificity of 100% in the validation cohort. Even at the lowest coverage depth of 0.01X, the performance of the diagnostic model remained relatively robust. Notably, the performance of this diagnostic model surpassed that of the biomarker neuron-specific enolase (sensitivity: 85.7% vs. 64.3%; specificity: 100% vs. 87.5%) and urinary cytology (sensitivity: 100% vs. 66.7%; specificity: 100% vs. 94.1%). Our study demonstrates that urine sEV-DNA exhibits high discriminatory power in distinguishing between benign and malignant bladder lesions, making it a promising tool for auxiliary diagnosis of BC.

Humans↗

Synergistic engineering of Casδ nuclease for robust genome editing.

Casδ is a recently identified evolutionary transitional CRISPR system characterized by its compact size (~900 amino acids), broad temperature tolerance, and guidance by a short crRNA without the requirement of a tracrRNA. However, the low editing efficiency of Casδ in eukaryotic cells limits its application. Here, we have developed a hierarchical engineering strategy to improve the genome editing activity of Casδ-1, with optimization focused on enhancing its interactions with the crRNA, the protospacer adjacent motif (PAM) duplex, the single-stranded DNA substrate, and the RNA-DNA heteroduplex. Through this strategy, we successfully generated an activity-enhanced Casδ-1 variant, designated enCasδ, which harbors 9 amino acid substitutions that synergistically augment its editing efficiency. In human cell lines, enCasδ showed 1.3- to 29.3-fold higher editing activity than the wild-type Casδ-1 across ten tested genomic loci, with an average editing efficiency of 54.6%. In addition, enCasδ also mediated robust genome editing in maize; its editing efficiency increased by an average of 5.3-fold relative to Casδ-1, and reached up to an average of 80% at the TS4 and PSY1 loci in stable transgenic lines. The overall editing performance of enCasδ was comparable to that of Streptococcus pyogenes Cas9 (SpCas9) and other Cas12 nucleases. Collectively, enCasδ represents a highly optimized Casδ-1 variant that broadens the applicability of the Casδ CRISPR system and facilitates robust genome editing in both animal cells and plants.

Gene Editing↗

COG6 is an essential host factor for influenza A virus infection.

Influenza A virus (IAV) relies on the host cellular machinery to support its replication. Understanding these host dependencies can inform the development of novel antiviral strategies. In this study, we identified conserved oligomeric Golgi complex subunit 6 (COG6) as a novel host factor critical for IAV replication through a genome-wide clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) knockout screen. Disruption of COG6 significantly impaired viral replication. Mechanistically, COG6 supports IAV replication via two distinct means. First, consistent with the role of the COG complex in Golgi homeostasis, COG6 is required for the proper presentation of surface sialic acids, the primary receptor for IAV entry. Second, COG6 deficiency unexpectedly led to lysosome-dependent degradation of viral proteins. Notably, lysosomal activity was also upregulated in IAV-infected wild-type cells, albeit to a lesser extent than in COG6-deficient cells. Treatment with lysosomal inhibitors rescued viral protein stability in COG6 knockout cells. Protein interaction analysis further demonstrated that COG6-mediated stabilization of viral proteins did not rely on viral protein-COG6 interaction, refuting the hypothesis that COG6 acts as a shield factor to protect viral protein from lysosomal degradation. Moreover, knockout of other COG subunits produced similar antiviral effects, suggesting that an intact COG complex is required for IAV replication. Together, these findings uncover a critical role of the COG complex in regulating IAV replication and highlight a previously unappreciated functional link between the Golgi and lysosomes that could be exploited for treating IAV infections.IMPORTANCEDespite advances in virology, numerous host determinants facilitating influenza A virus (IAV) pathogenesis remain uncharacterized. Our study establishes conserved oligomeric Golgi complex subunit 6 (COG6) as a critical host factor promoting IAV infection through complementary mechanisms: receptor modulation and viral protein stabilization. This represents the first demonstration that the COG complex regulates viral pathogenesis through proteostasis mechanisms, fundamentally expanding our understanding of host-virus interactions at the organelle interface. These findings not only provide new perspectives on viral exploitation of Golgi trafficking networks but also identify potential therapeutic targets against evolving influenza strains.

Influenza A virus↗

Dominant negative ATP5F1A variants disrupt oxidative phosphorylation causing neurological disorders.

ATP5F1A encodes the α-subunit of complex V of the respiratory chain, which is responsible for mitochondrial ATP synthesis. We describe 6 probands with heterozygous de novo missense ATP5F1A variants that presented with developmental delay, intellectual disability, and movement disorders. All variants were located at the contact points between the α- and β-subunits. Functional studies in C. elegans revealed that the variants were damaging via a dominant negative genetic mechanism. Biochemical and proteomics studies of proband-derived cells showed a marked reduction in complex V abundance and activity. Mitochondrial physiology studies revealed increased oxygen consumption, yet decreased mitochondrial membrane potential and ATP levels indicative of uncoupled oxidative phosphorylation as a pathophysiologic mechanism. Our findings contrast with the previously reported ATP5F1A variant, p.Arg207His, indicating a different pathological mechanism. This study expands the phenotypic and genotypic spectrum of ATP5F1A-associated conditions and highlights how functional studies can provide an understanding of the genetic, molecular, and cellular mechanisms of ATP5F1A variants of uncertain significance. With 12 heterozygous individuals now reported, ATP5F1A is the most frequent nuclear genome cause of complex V deficiency.

Humans↗

Comprehensive discovery and functional characterization of the noncanonical proteome.

The systematic identification and functional characterization of noncanonical translation products, such as novel peptides, will facilitate the understanding of the human genome and provide new insights into cell biology. Here, we constructed a high-coverage peptide sequencing reference library with 11,668,944 open reading frames and employed an ultrafiltration tandem mass spectrometry assay to identify novel peptides. Through these methods, we discovered 8945 previously unannotated peptides from normal gastric tissues, gastric cancer tissues and cell lines, nearly half of which were derived from noncoding RNAs. Moreover, our CRISPR screening revealed that 1161 peptides are involved in tumor cell proliferation. The presence and physiological function of a subset of these peptides, selected based on screening scores, amino acid length, and various indicators, were verified through Flag-knockin and multiple other methods. To further characterize the potential regulatory mechanisms involved, we constructed a framework based on artificial intelligence structure prediction and peptide‒protein interaction network analysis for the top 100 candidates and revealed that these cancer-related peptides have diverse subcellular locations and participate in organelle-specific processes. Further investigation verified the interacting partners of pep1-nc-OLMALINC, pep5-nc-TRHDE-AS1, pep-nc-ZNF436-AS1 and pep2-nc-AC027045.3, and the functions of these peptides in mitochondrial complex assembly, energy metabolism, and cholesterol metabolism, respectively. We showed that pep5-nc-TRHDE-AS1 and pep2-nc-AC027045.3 had substantial impacts on tumor growth in xenograft models. Furthermore, the dysregulation of these four peptides is closely correlated with clinical prognosis. Taken together, our study provides a comprehensive characterization of the noncanonical proteome, and highlights critical roles of these previously unannotated peptides in cancer biology.

Humans↗

Dominant negative variants in KIF5B cause osteogenesis imperfecta via down regulation of mTOR signaling.

BACKGROUND: Kinesin motor proteins transport intracellular cargo, including mRNA, proteins, and organelles. Pathogenic variants in kinesin-related genes have been implicated in neurodevelopmental disorders and skeletal dysplasias. We identified de novo, heterozygous variants in KIF5B, encoding a kinesin-1 subunit, in four individuals with osteogenesis imperfecta. The variants cluster within the highly conserved kinesin motor domain and are predicted to interfere with nucleotide binding, although the mechanistic consequences on cell signaling and function are unknown. METHODS: To understand the in vivo genetic mechanism of KIF5B variants, we modeled the p.Thr87Ile variant that was found in two patients in the C. elegans ortholog, unc-116, at the corresponding position (Thr90Ile) by CRISPR/Cas9 editing and performed functional analysis. Next, we studied the cellular and molecular consequences of the recurrent p.Thr87Ile variant by microscopy, RNA and protein analysis in NIH3T3 cells, primary human fibroblasts and bone biopsy. RESULTS: C. elegans heterozygous for the unc-116 Thr90Ile variant displayed abnormal body length and motility phenotypes that were suppressed by additional copies of the wild type allele, consistent with a dominant negative mechanism. Time-lapse imaging of GFP-tagged mitochondria showed defective mitochondria transport in unc-116 Thr90Ile neurons providing strong evidence for disrupted kinesin motor function. Microscopy studies in human cells showed dilated endoplasmic reticulum, multiple intracellular vacuoles, and abnormal distribution of the Golgi complex, supporting an intracellular trafficking defect. RNA sequencing, proteomic analysis, and bone immunohistochemistry demonstrated down regulation of the mTOR signaling pathway that was partially rescued with leucine supplementation in patient cells. CONCLUSION: We report dominant negative variants in the KIF5B kinesin motor domain in individuals with osteogenesis imperfecta. This study expands the spectrum of kinesin-related disorders and identifies dysregulated signaling targets for KIF5B in skeletal development.

Animals↗

Enhancement of pyruvate production by osmotic-tolerant mutant of Torulopsis glabrata.

Pyruvate production by Torulopsis glabrata was used as a model to study the mechanism of product inhibition and the strategy for enhancing pyruvate production. It was found that the concentration of cell growth and pyruvate deceased with the increase of NaCl and sorbitol concentrations. To enhance the osmotic stress resistance of the strain, an NaCl-tolerant mutant RS23 was screened and selected through a pH-controlled continuous culture with 70 g/L NaCl as the selective criterion. Compared with the parent strain, mutant RS23 could grow well on the medium containing 70 g/L NaCl or 0.6 mol/L sorbitol. Pyruvate concentration by the mutant strain RS23 reached 94.3 g/L at 82 h (yield on glucose 0.635 g/g) in a 7-l fermentor with 150 g/L glucose as carbon source. Pyruvate concentration and yield of mutant RS23 were 41.1% and 11.1% higher than those of the parent strain, respectively. The strategy for enhancing pyruvate production by increasing osmotic stress resistance may provide an alternative approach to enhance organic acids production with yeast.

Candida glabrata↗

Study and improvement of the conditions for production of a novel alkali stable catalase.

Catalase (CAT) is an enzyme capable of catalyzing the conversion of H(2)O(2) to O(2) and H(2)O. It has recently acquired interest due to its attractive potential application in the textile industries. In a previous study, a bacterium with slight halophilic and alkaliphilic characteristics, Bacillus sp. F26, was isolated and found to produce high-level alkaline CAT. In the present study, the effects of culture conditions on the CAT production were investigated. The results showed that the highest activity of CAT (13.9 U/mg protein) was obtained when glucose (15 g/L) was used as carbon source. The utilization of the mixture of corn steep liquid and beef extract stimulated both bacterial growth and CAT synthesis. The highest biomass (4.5 g/L) and activity of CAT (16.5 U/mg protein) were found synchronously when 10 g/L corn steep liquid and 10 g/L beef extract were used as nitrogen source. The addition of H(2)O(2) as an oxidative stress was used to enhance CAT production in the flasks. It was found that the activity of CAT was increased by 51.3-22.8 U/mg protein compared with the control when 2 mmol/L H(2)O(2) was added at later exponential phases (16 h), although the cell growth was significantly inhibited. Based on the above, an exponential H(2)O(2) feed strategy was developed, in which the feed rate of H(2)O(2) was controlled according to specific cell growth rate (mu). In this way, the maximum CAT production (29.9 U/mL) was obtained, which was 92.8 and 20.7% higher than that in batch and constant rate fed-batch fermentation, respectively.

Bacillus↗

Synchronized and sustained release of multiple components in silymarin from erodible glyceryl monostearate matrix system.

Development of sustained delivery systems for herbal medicines was very difficult because of their complexity in composition. The concept of synchronized release from sustained release systems, which is characterized by release of multiple components in their original ratio that defines a herbal medicine, served as the basis for keeping the original pharmacological activity. In this study, erodible matrix systems based on glyceryl monostearate and polyethylene glycol 6000 or poloxamer 188 were prepared to perform strict control on synchronized release of the five active components of silymarin, i.e. taxifolin, silychrystin, silydianin, isosilybin and silybin. The matrix system was prepared by a melt fusion method. Synchronized release was achieved with high similarity factor f(2) values between each two of the five components. Erosion profiles of the matrix were in good correlation with release profiles of the five components, showing erosion-controlled release mechanisms. Through tuning some of the formulation variables, the system can be adjusted for synchronized and sustained release of silymarin for oral administration. In vitro hemolysis study indicated that the synchronized release samples showed a much better stabilizing effect on erythrocyte membrane.

Animals↗

Expression of human DNA methyltransferase 1 in colorectal cancer tissues and their corresponding distant normal tissues.

BACKGROUND AND AIM: DNA methylation plays an important role during colorectal cancer (CRC) carcinogenesis. DNA methyltransferase 1 (DNMT1) is responsible for maintaining DNA methylation. We addressed the significance of DNMT1 expression in CRC. MATERIALS AND METHODS: We measured the expression of DNMT1 in CRC tissues and in their corresponding distal normal colorectal mucosa using reverse transcriptase-polymerase chain reaction and immunohistochemical analysis. RESULTS: The mean +/- SD of DNMT1 mRNA in CRC tissues was 1.04 +/- 0.36, which was significantly higher than that in their corresponding distal normal colorectal mucosa (0.58 +/- 0.44, P < 0.05). Fifty-eight out of 77 (75.3%) CRC tissues and only 30 out of 77 (39%) corresponding distant normal colorectal mucosa showed immunoreactivity (P < 0.001). We also found that the immunoreactivity of DNMT1 was higher in mucosa adjacent to cancer than in corresponding normal colorectal mucosa; high immunoreactivity was significantly correlated with poor differentiation in CRC tissues (P = 0.008). No significant associations were found between DNMT1 immunoreactivity and the following variables: age, sex, locations of cancer, Duke's phase, and the presence of lymph-node metastasis. CONCLUSION: These findings suggested that DNMT1 was associated with the malignant phenotype, and dysregulation of DNMT1 expression was present in tumor cells of CRC.

Adult↗

Changes of soil organic carbon in an intensively cultivated agricultural region: a denitrification-decomposition (DNDC) modelling approach.

Regional modelling of soil organic carbon (SOC) dynamics is important for predicting large-scale patterns in carbon cycling and for assessing potential responses of soil carbon pools to land-use change. However, data uncertainties related to both spatial heterogeneity and small-scale differences in farming practice related to cropping systems affect the accuracy of regional models. A case study is presented from Quzhou County in the North China Plain, an area characterized by highly intensive farming. For this county, the DNDC model was validated using sampling data from 68 sites around the county under generalized farm practices. Unique modelling units based on soil type, soil texture and crop type were created and then used to model the spatial change of SOC under different farming practices. Considering the main factors affecting SOC sequestration, the results indicate that the DNDC model delivers acceptable modelling results at county level. The results show that there is a great potential for SOC sequestration in Quzhou County in its central, southern and eastern parts. Changes in farming practices show a strong effect on carbon sequestration. A very efficient and environmental friendly sequestration of SOC pools could be achieved even by decreasing nitrogen fertilizer inputs, when the amount of straw returned to the field is greatly increased.

Agriculture↗

Expression, purification and characterization of a three-domain Kazal-type inhibitor from silkworm pupae (Bombyx mori).

Serine protease inhibitors are essential for host physiological and immunological activities in insects. Analyzing the amino-acid sequence of a cDNA coding for a serine protease inhibitor in Bombyx mori (BmSPI), we found that BmSPI contained three homologous domains with a conserved sequence of C-X(3)-C-X(9)-C-X(6)-Y-X(7)-C-X(3)-C-X(11)-C similar to that of Kazal-type serine protease inhibitors, suggesting BmSPI as a new member of the Kazal-type serine protease inhibitor family. To characterize the three-domain Kazal-type inhibitor from silkworm pupae, the recombinant protein was expressed in Escherichia coli BL21 (DE3) Star. After purification with affinity and reversed-phase chromatographies, the recombinant BmSPI with a molecular mass of 33.642 Da was shown to be a specific subtilisin A inhibitor. Further studies indicated that the K(i) value of the recombinant BmSPI was 3.35 nM and the inhibitor seemed to form a 1:1 complex with subtilisin A. This is a first description of the structure and characterization of Kazal-type inhibitor with three domains cloned from silkworm pupae, B. mori.

Amino Acid Sequence↗

TRB3 interacts with CtIP and is overexpressed in certain cancers.

TRB3, a human homolog of Drosophila Tribbles, has been recently shown as a critical negative regulator of Akt and S6 kinase activation in a number of cellular processes. Here we found that TRB3 interacted with an important cell cycle regulator CtIP (CtBP-interacting protein) and the interaction involved the C-terminus of both proteins. Interestingly, TRB3 and CtIP co-localized to the nucleus in HeLa cells and exhibited a unique dot-like pattern. Finally, we demonstrated that TRB3 was overexpressed in multiple tumor tissues. Since CtIP plays important roles in cell cycle checkpoint control and it has been implicated in tumorigenesis, our data suggest that TRB3 may be involved in these biological processes through interacting with CtIP.

B-Lymphocytes↗

High operative risk of cool-tip radiofrequency ablation for unresectable pancreatic head cancer.

BACKGROUND AND OBJECTIVES: To report and discuss the effect, complications and mortality of cool-tip radiofrequency ablation (RFA) for unresectable pancreatic cancer. METHODS: During October 2003 to July 2004, sixteen patients with unresectable pancreatic cancer were treated by open cool-tip RFA. One-half of the 16 patients had tumors located in the pancreatic head. A 5-mm minimum safe distance between RFA site and major peripancreatic vessels was kept to avoid injury to the vessels. RESULTS: Six of twelve patients with back pain got pain relief postoperatively. Pancreatic fistula occurred in three patients (18.8%) and healed smoothly in 7-10 days with routine abdominal drainage. The mortality was 25% (4/16). In the four death cases, tumors were all located in the pancreatic head; three patients with tumor close to portal vein died suddenly of massive gastrointestinal hemorrhage on the 4th, 30th, 40th postoperative day respectively and a 79-year-old patient died of acute renal failure on the 2nd postoperative day. CONCLUSIONS: Standard use of cool-tip RFA was dangerous for pancreatic head cancer close to portal vein, in which a 5-mm minimum safe distance between RFA site and major peripancreatic vessels might not be enough to avoid injury to the vessels.

Acute Kidney Injury↗

Effects of extraction solvent mixtures on antioxidant activity evaluation and their extraction capacity and selectivity for free phenolic compounds in barley (Hordeum vulgare L.).

Four kinds of solvent extracts from three Chinese barley varieties (Ken-3, KA4B, and Gan-3) were used to examine the effects of extraction solvent mixtures on antioxidant activity evaluation and their extraction capacity and selectivity for free phenolic compounds in barley through free radical scavenging activity, reducing power and metal chelating activity, and individual and total phenolic contents. Results showed that extraction solvent mixtures had significant impacts on antioxidant activity estimation, as well as different extraction capacity and selectivity for free phenolic compounds in barley. The highest DPPH* and ABTS*+ scavenging activities and reducing power were found in 80% acetone extracts, whereas the strongest *OH scavenging activity, O2*- scavenging activity, and metal chelating activity were found in 80% ethanol, 80% methanol, and water extracts, respectively. Additionally, 80% acetone showed the highest extraction capacity for (+)-catechin and ferulic, caffeic, vanillic, and p-coumaric acids, 80% methanol for (-)-epicatechin and syringic acid, and water for protocatechuic and gallic acids. Furthermore, correlations analysis revealed that TPC, reducing power, DPPH* and ABTS*+ scavenging activities were well positively correlated with each other (p < 0.01). Thus, for routine screening of barley varieties with higher antioxidant activity, 80% acetone was recommended to extract free phenolic compounds from barley. DPPH* scavenging activity and ABTS*+ scavenging activity or reducing power could be used to assess barley antioxidant activity.

Acetone↗

Genetic variation of Chinese PRRSV strains based on ORF5 sequence.

Thirteen isolates of porcine reproductive and respiratory syndrome virus (PRRSV) from different provinces of China were studied and compared with several PRRSV isolates from other countries. Phylogenetic analysis shows that all Chinese isolates of PRRSV in this study belong to the American genotype, except for one strain, B13, which clustered as a European genotype. Sequence analysis revealed that PRRSV Chinese isolates of the American genotype were highly similar in the ORF5 sequence and could be classified into two subclades. One contains PRRSV isolates that are more closely related to the American vaccine strain MLV Resp and its parent strain VR-2332, and the other contains ones only distantly related to them. Within the Chinese isolates slight genetic variation occurred, and some strains may originate directly from the vaccine virus.

Amino Acid Sequence↗

Redistribution of carbon flux in Torulopsis glabrata by altering vitamin and calcium level.

Manipulation of cofactor (thiamine, biotin and Ca(2+)) levels as a potential tool to redistribute carbon flux was studied in Torulopsis glabrata. With sub-optimization of vitamin in fermentation medium, the carbon flux was blocked at the key node of pyruvate, and 69 g/L pyruvate was accumulated. Increasing the concentrations of thiamine and biotin could selectively open the valve of carbon flux from pyruvate to pyruvate dehydrogenase complex, the pyruvate carboxylase (PC) pathway and the channel into the TCA cycle, leading to the over-production of alpha-ketoglutarate. In addition, the activity of PC was enhanced with Ca(2+) present in fermentation medium. By combining high concentration's vitamins and CaCO(3) as the pH buffer, a batch culture was conducted in a 7-L fermentor, with the pyruvate concentration decreased to 21.8 g/L while alpha-ketoglutarate concentration increased to 43.7 g/L. Our study indicated that the metabolic flux could be redistributed to overproduce desired metabolites with manipulating the cofactor levels. Furthermore, the manipulation of vitamin level provided an alternative tool to realize metabolic engineering goals.

Biotin↗