Biomedical subjects

Dan Wu

Publications and source records attributed to Dan Wu.

At least 19 recordsLinked to original sources

PubMed2026

Development and evaluation of a multiplex PCR-based dual-platform targeted sequencing framework for precise differentiation of lumpy skin disease virus.

BACKGROUND: Lumpy skin disease virus (LSDV) shares over 96% genomic identity with goatpox and sheeppox viruses, presenting severe diagnostic challenges due to cross-reactivity. METHODS: To address this bottleneck, we established a targeted sequencing framework integrating multiplex PCR with short-read and long-read platforms. By sequentially screening target pathogens, identifying low-homology genes, and designing short and gradient long-fragment primer pools, we evaluated these dual-platform panels using highly homologous poxvirus samples. RESULTS: The short-read panel stably detected target viruses at inputs as low as 5.26 ×101 copies/μL. Under strict alignment criteria, LSDV mapping rates reached 42.91%, suppressing non-target signals to 3.05%. The Nanopore-Targeted Sequencing (NTS) long-amplicon strategy successfully eliminated homologous interference. By applying length-dependent diagnostic thresholds (≥ 100 reads for short amplicons; ≥ 50 reads for long amplicons), precise species-level identification was achieved, maintaining near-zero cross-reads (0-5) in ultra-long regions. Crucially, the field-deployable NTS workflow enabled complete detection in approximately 4 h. CONCLUSION: This complementary strategy seamlessly meets both laboratory demands for high-sensitivity enrichment and frontline requirements for rapid typing, providing a reliable tool for LSDV surveillance, mutation tracking, and outbreak control.

Capripoxvirus differentiation↗

PubMed2026

Light regulates capsaicinoid biosynthesis via the CaHY5-CaBBX2-CaACS8 module in pepper.

Capsaicinoids are a class of unique alkaloids that confer the pungent taste to pepper fruits. However, it remains largely unknown how light regulates the biosynthesis of capsaicinoids. We conducted a metabolic analysis on light- and dark-adapted pepper fruits. The results showed that dark-adapted pepper fruits had lower capsaicinoid contents and correspondingly downregulated transcription of capsaicinoid biosynthetic genes (CBGs), indicating that light plays a crucial role in capsaicinoid biosynthesis. Furthermore, silencing of CaHY5, a pivotal transcription factor gene in the light signaling pathway, decreased the content of capsaicinoid and suppressed the expression of CBGs, whereas transient overexpression of CaHY5 generated exactly opposite results. CaHY5 can bind to the G-box motif in the promoters of CaBBX2 and CaACS8, thereby enhancing their transcriptional levels. The activated CaBBX2 then binds to the T/G-box in the CaACS8 promoter to stimulate its expression. CaBBX2 or CaACS8 silencing led to decreased levels of capsaicinoids, while their transient overexpression produced increased capsaicinoid contents. Collectively, our results indicated that the light-activated CaHY5-CaBBX2-CaACS8 regulatory module plays a pivotal role in capsaicinoid biosynthesis. These findings provide new insights into the influence of light on capsaicinoid biosynthesis and potential targets for activation of this biosynthetic pathway in pepper.

Capsicum↗

PubMed2006

EMBL Nucleotide Sequence Database in 2006.

The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl) at the EMBL European Bioinformatics Institute, UK, offers a large and freely accessible collection of nucleotide sequences and accompanying annotation. The database is maintained in collaboration with DDBJ and GenBank. Data are exchanged between the collaborating databases on a daily basis to achieve optimal synchrony. Webin is the preferred tool for individual submissions of nucleotide sequences, including Third Party Annotation, alignments and bulk data. Automated procedures are provided for submissions from large-scale sequencing projects and data from the European Patent Office. In 2006, the volume of data has continued to grow exponentially. Access to the data is provided via SRS, ftp and variety of other methods. Extensive external and internal cross-references enable users to search for related information across other databases and within the database. All available resources can be accessed via the EBI home page at http://www.ebi.ac.uk/. Changes over the past year include changes to the file format, further development of the EMBLCDS dataset and developments to the XML format.

Base Sequence↗

PubMed2006

Aggregation behaviors of gelatin with cationic gemini surfactant at air/water interface.

The dilational rheological properties of gelatin with cationic gemini surfactant 1,2-ethane bis(dimethyl dodecyl ammonium bromide) (C(12)C(2)C(12)) at air/water interface were investigated using oscillating barriers method at low frequency (0.005-0.1 Hz), which was compared with single-chain surfactant dodecyltrimethyl ammonium bromide (DTAB). The results indicate that the maximum dilational modulus and the film stability of gelatin-C(12)C(2)C(12) are higher than those of gelatin-DTAB. At high concentration of C(12)C(2)C(12) or DTAB, the dilational modulus of gelatin-surfactant system becomes close to that corresponding to pure surfactant, suggesting gelatin at interface is replaced by surfactant. This replacement is also observed by surface tension measurement. However, it is found that gelatin-C(12)C(2)C(12) system has two obvious breaks but gelatin-DTAB has not in surface tension isotherms. These phenomena are ascribed to the double charges and strong hydrophobicity of C(12)C(2)C(12). Based on these experimental results, a mechanism of gelatin-surfactant interaction at air/water interface is proposed.

Air↗

PubMed2006

A simple and accurate method for quantification of magnetosomes in magnetotactic bacteria by common spectrophotometer.

A simple apparatus for measuring the magnetism of magnetotactic bacteria was developed with a common laboratory spectrophotometer, which was based on measuring the change in light scattering resulting from cell alignment in a magnetic field. A multiple coils were built around the cuvette holder of the spectrophotometer to compensate geomagnetic field and to generate two mutually perpendicular magnetic fields. In addition, we defined a novel magnetism parameter, R(mag), by modifying the definition of C(mag) to a normalized parameter with the culture absorbance obtained without application of magnetic field. The number of magnetosomes in each cell was determined by transmission electron microscopy to assess the relationship between the two magnetism parameters and the distribution of magnetosomes in the cells. We found that both R(mag) and C(mag) were linearly correlated rather with the percentage of magnetosome-containing bacteria than with the average magnetosome numbers, and R(mag) exhibited a better linearity than C(mag) with respect to the percentage of magnetosome-containing bacteria.

Electromagnetic Phenomena↗

PubMed2006

Mean-field coupling of calcium oscillations in a multicellular system of rat hepatocytes.

In a multicellular system of rat hepatocytes and even in an intact liver, cytoplasmic calcium oscillations are synchronized and highly coordinated. In this paper, the mean-field coupling term has been introduced to describe the coupling flux, which is more efficient than gap junctional coupling terms. An optimal coupling strength and an optimal stimulation level for the synchronization of the coupled system have been observed in this paper. Moreover, it has been proved that these results are independent of the cells number. Interestingly, it has been observed that the intracellular noise and the extracellular noise have different effects on the synchronization of the coupled system.

Animals↗

PubMed2006

Brownian motor with time-delayed feedback.

An inertial Brownian motor with time-delayed feedback driven by an unbiased time-periodic force is investigated. It is found that the mean velocity and the rectification efficiency are decreased when the noise intensity is increased. While the shape of the mean velocity and the rectification efficiency can be changed from one peak to two peaks when the time delay is increased, the symmetry in the velocity probability distribution function is broken when the delay time is increased.

Biological Clocks↗

PubMed2006

Sonochemical synthesis of polyaniline nanofibers.

Conventionally, micro-sized irregular polyaniline (PANI) particles were synthesized by dropwise addition of the ammonium persulfate (APS) solution into the aniline (ANI) solution with mechanical stirring. By replacing the mechanical stirring with an ultrasonic irradiation, PANI nanofibers in diameters of approximately 50 nm and lengths of 200 nm to several micrometers were prepared. Transmission electron microscopy (TEM) and scanning electron microscopy (SEM) showed that at the early stage of polymerization, the polymers formed in both the mechanical stirred and ultrasonicated systems are in the form of nanofiber. However, with continuing of the reaction, these primary nanofibers grow and agglomerate into irregular shaped PANI particles in the mechanical stirred system, while in the case of the ultrasonic irradiation, the growth and agglomeration are effectively prevented, preserving thus the PANI nanofibers in the final product. By increasing the APS/ANI molar ratio from 0.5 to 2.5, the aspect ratios of the PANI nanofibers decreased. The PANI nanofibers exhibit higher solubility than the irregular shaped PANI particles. Although the yield, as well as the conductivity of the ultrasonic synthesized PANI nanofibers, was slightly lower than the irregular shaped PANI particles, the ultrasonic synthesis approach is one of the facile and scalable approaches in synthesizing PANI nanofibers in comparison with other ones without use of templates (e.g., the interfacial polymerization and rapid mixing polymerization). UV-Vis and Fourier transformed infrared (FTIR) spectra indicated ultrasound had no significant effect on the chemical structure of the PANI.

Aniline Compounds↗

PubMed2006

Polarization and experimental configuration analyses of sum frequency generation vibrational spectra, structure, and orientational motion of the air/water interface.

Here we report a detailed study on spectroscopy, structure, and orientational distribution, as well as orientational motion, of water molecules at the air/water interface, investigated with sum frequency generation vibrational spectroscopy (SFG-VS). Quantitative polarization and experimental configuration analyses of the SFG data in different polarizations with four sets of experimental configurations can shed new light on our present understanding of the air/water interface. Firstly, we concluded that the orientational motion of the interfacial water molecules can only be in a limited angular range, instead of rapidly varying over a broad angular range in the vibrational relaxation time as suggested previously. Secondly, because different vibrational modes of different molecular species at the interface has different symmetry properties, polarization and symmetry analyses of the SFG-VS spectral features can help the assignment of the SFG-VS spectra peaks to different interfacial species. These analyses concluded that the narrow 3693 cm(-1) and broad 3550 cm(-1) peaks belong to C(infinityv) symmetry, while the broad 3250 and 3450 cm(-1) peaks belong to the symmetric stretching modes with C2v symmetry. Thus, the 3693 cm(-1) peak is assigned to the free OH, the 3550 cm(-1) peak is assigned to the singly hydrogen-bonded OH stretching mode, and the 3250 and 3450 cm(-1) peaks are assigned to interfacial water molecules as two hydrogen donors for hydrogen bonding (with C2v symmetry), respectively. Thirdly, analysis of the SFG-VS spectra concluded that the singly hydrogen-bonded water molecules at the air/water interface have their dipole vector directed almost parallel to the interface and is with a very narrow orientational distribution. The doubly hydrogen-bonded donor water molecules have their dipole vector pointing away from the liquid phase.

Journal Article↗

PubMed2006

Removal of p-xylene from an air stream in a hybrid biofilter.

Biofiltration of an air stream containing p-xylene has been studied in a laboratory hybrid biofilter packed with a mixture of mature pig compost, forest soil and the packing material which was made of polyethylene (PE) and used in the moving bed biological reactor (MBBR) in wastewater treatment. Three flow rates, 9.17, 19.87 and 40.66 m(3)m(-2)h(-1), were investigated for p-xylene inlet concentration ranging from 0.1 to 3.3 g m(-3). A high elimination capacity of 80 g m(-3)h(-1) corresponding to removal efficiency of 96% was obtained at a flow rate of 9.17 m(3)m(-2)h(-1) (empty bed residence time of 132 s). At a flow rate of 40.66 m(3)m(-2)h(-1) (empty bed residence time of 30s), the maximum elimination capacity for p-xylene was 40 g m(-3)h(-1) and removal efficiencies were in the range of 47-100%. The production of carbon dioxide (P(CO(2))) is proportional to elimination capacity (EC) and the linear relation was formulated as P(CO(2))=1.65EC+15.58. Stable pH values ranging from 6.3 to 7.6 and low pressure drop values less than 0.2 cm H(2)O (19.6 Pa) of packing media in compost-based biofilter of hybrid biofilter were observed, which avoided acidification and compaction of packing media and sustained the activity of microorganism populations.

Air↗

PubMed2006

EMBL Nucleotide Sequence Database: developments in 2005.

The EMBL Nucleotide Sequence Database (www.ebi.ac.uk/embl) at the EMBL European Bioinformatics Institute, UK, offers a comprehensive set of publicly available nucleotide sequence and annotation, freely accessible to all. Maintained in collaboration with partners DDBJ and GenBank, coverage includes whole genome sequencing project data, directly submitted sequence, sequence recorded in support of patent applications and much more. The database continues to offer submission tools, data retrieval facilities and user support. In 2005, the volume of data offered has continued to grow exponentially. In addition to the newly presented data, the database encompasses a range of new data types generated by novel technologies, offers enhanced presentation and searchability of the data and has greater integration with other data resources offered at the EBI and elsewhere. In stride with these developing data types, the database has continued to develop submission and retrieval tools to maximise the information content of submitted data and to offer the simplest possible submission routes for data producers. New developments, the submission process, data retrieval and access to support are presented in this paper, along with links to sources of further information.

Animals↗

PubMed2006

Liquid chromatographic/tandem mass spectrometric method for the quantitation of tranilast in human plasma.

An analytical method for the determination of tranilast in human plasma using tramadol as the internal standard has been developed based on liquid chromatography/tandem mass spectrometry. Sample preparation involved protein precipitation with methanol. Separation by reversed-phase high-performance liquid chromatography using methanol/10 mM ammonium acetate (70: 30, v/v) as mobile phase was complete in a run time of 2.4 min. Detection on a Q TRAP system used multiple reaction monitoring. The method was linear in the range 0.06-20 microg/mL with intra- and inter-day precisions (as relative standard deviation) of 2.2-2.6% and 2.3-2.9%, respectively. Accuracy (as relative error) was <-2.5%. The method was applied in a pharmacokinetic study in healthy volunteers treated with a single 80 mg oral dose of tranilast.

Administration, Oral↗

PubMed2006

Effect of CTCF-binding motif on regulation of PAX6 transcription.

PURPOSE: Previous studies indicate that the CCCTC binding transcription factor (CTCF) regulates homeobox PAX6 gene transcription in corneal epithelial cells. In the present study, the effect was investigated of CTCF activity on PAX6 transcription through interaction with five essential motifs located in an 80-bp region upstream from the PAX6 P0 promoter. METHODS: An electrophoretic mobility shift assay (EMSA) was used to determine the interaction between CTCF and DNA binding motifs. DNA mutagenesis was applied in identification of DNA motif functions. Immunohistochemistry and Western blot analyses were performed to detect the stress-induced effect on CTCF activity. RESULTS: The five identified CTCF-binding motifs were mutated one by one or in different combinations. Interactions of CTCF with these mutated motifs were determined by EMSA and DNA-binding competitions. All five CCCTC motifs were functional for the CTCF binding and DNA-binding activity of CTCF was proportionally decreased after increases in mutations of motif numbers. In addition, ultraviolet (UV) irradiation and epidermal growth factor (EGF) induced suppression and activation of CTCF expression, respectively. Effects of UV and EGF induction were due to alterations in CTCF expression and activity resulting in changes in CTCF DNA binding activity to the PAX6 promoter region detected by EMSA. CONCLUSIONS: These findings indicate that CTCF regulates PAX6 expression in response to stress-induced conditions and that the molecular base of CTCF controlling PAX6 expression is through five functional and specific motifs in the region upstream from the PAX6 P0 promoter in corneal epithelial cells.

Animals↗

PubMed2006

A highly sensitive and rapid assay for protein determination in human urine and penicillin using a Rayleigh light-scattering technique with benzeneazo-8-acetylamino-1-naphthol-3,6-disulfonic acid sodium salt.

A simple and sensitive method was conducted for the determination of trace amounts of proteins with benzeneazo-8-acetylamino-1-naphthol-3,6-disulfonic acid sodium salt (azophloxine, AP) using a Rayleigh light-scattering (RLS) technique. At pH 2.60 and in the presence of an emulsifier OP microemulsion, the RLS of AP can be greatly enhanced by proteins, owing to the interaction between AP and protein. The enhanced intensity is proportional to the concentration of proteins. Four proteins, including bovine serum albumin (BSA), human serum albumin (HSA), lysozyme (Lys) and gamma globulin (gamma-G) have been tested. For example, the linear range of BSA was 0 - 0.06 microg mL(-1) with detection limits of 2.38 ng mL(-1). The method was applied to the analysis of protein in human urine and penicillin samples with satisfactory results. The relative standard deviation was in all instances less than 4.0%, and the recovery was in the range of 97.5 - 104%.

Azo Compounds↗

PubMed2005

Tissue distribution and plasma clearance of heparin-binding EGF-like growth factor (HB-EGF) in adult and newborn rats.

Heparin-binding EGF-like growth factor (HB-EGF), a member of the epidermal growth factor (EGF) family, can protect intestinal epithelial cells from various forms of injury in vitro and attenuate intestinal ischemia/reperfusion damage in vivo. With the goal of eventual clinical use of HB-EGF to protect the intestines from injury in neonates, children, and adults, the pharmacokinetics and biodistribution of 125I-labeled HB-EGF were investigated. After intravenous bolus, HB-EGF had a distribution half-life of 0.8 min and an elimination half-life of 26.67 min. After gastric administration, the bioavailability was 7.8%, with a 2.38 h half-life in the absorption phase and an 11.13 h half-life in the elimination phase. After intravenous dosing, most radioactivity was found in the plasma, liver, kidneys, bile, and urine, whereas it was mainly distributed in the gastrointestinal tract after intragastric administration. The degradation of 125I-HB-EGF in plasma from newborn rats was lower than that in adult rats after gastric administration. This supports the feasibility of enteral administration of HB-EGF in the treatment of gastrointestinal diseases, including newborns afflicted with necrotizing enterocolitis.

Animals↗

PubMed2005

Quenching of the intrinsic fluorescence of bovine serum albumin by phenylfluorone-Mo(VI) complex as a probe.

In this paper, the binding characteristics of bovine serum albumin (BSA) and phenylfluorone (PF)-molybdenum (Mo(VI)) complex have been studied by fluorophotometry. The binding constants are calculated at different temperatures. The binding distance and the energy transfer efficiency between PF-Mo(VI) complex and protein are obtained on the basis of the theory of Forster energy transfer. DeltaH and DeltaS are calculated to be -7.11 kJ mol-1 and 70.30 J mol-1 K-1, which indicate that electrostatic force plays major role in the interaction of PF-Mo(VI) complex and BSA. The experimental results show that BSA and PF-Mo(VI) complex have strong interactions and the mechanism of quenching belongs to static quenching.

Animals↗

PubMed2005

Interaction of m-nitrophenylfluorone-Mo(VI) complex as a probe with human serum albumin: a fluorescence quenching study.

In this paper, the binding characteristics of human serum albumin (HSA) and m-nitrophenylfluorone (m-NPF)-molybdenum (Mo(VI)) complex have been studied by fluorophotometry. The binding constants are measured at different temperature. Based on the theory of Forster energy transfer, the binding distance and the energy transfer efficiency between m-nitrophenylfluorone-Mo(VI) complex and protein are obtained. According to the thermodynamic parameters, the main sort of binding force can be judged. The results indicate that HSA and m-NPF-Mo(VI) complex have strong interactions. The mechanism of quenching belongs to static quenching and the main sort of binding force is electrostatic gravitation.

Energy Transfer↗

PubMed2005

Determination of structure and energetics for gibbs surface adsorption layers of binary liquid mixture 1. Acetone + water.

The orientation, structure, and energetics of the vapor/acetone-water interface are studied with sum frequency generation vibrational spectroscopy (SFG-VS). We used the polarization null angle (PNA) method in SFG-VS to accurately determine the interfacial acetone molecule orientation, and we found that the acetone molecule has its C=O group pointing into bulk phase, one CH3 group pointing up from the bulk, and the other CH3 group pointing into the bulk phase. This well-ordered interface layer induces an antiparallel structure in the second layer through dimer formation from either dipolar or hydrogen bond interactions. With a double-layer adsorption model (DAM) and Langmuir isotherm, the adsorption free energies for the first and second layer are determined as deltaG degrees (ads,1) = - 1.9 +/- 0.2 kcal /mol and deltaG degrees (ads,2) = - 0.9 +/- 0.2 kcal /mol, respectively. Since deltaG degrees (ads,1) is much larger than the thermal energy kT = 0.59 kcal /mol, and deltaG degrees (ads,2) is close to kT, the second layer has to be less ordered. Without either strong dipolar or hydrogen bonding interactions between the second and the third layer, the third layer should be randomly thermalized as in the bulk liquid. Therefore, the thickness of the interface is not more than two layers thick. These results are consistent with previous MD simulations for the vapor/pure acetone interface, and undoubtedly provide direct microscopic structural evidences and new insight for the understanding of liquid and liquid mixture interfaces. The experimental techniques and quantitative analysis methodology used for detailed measurement of the liquid mixture interfaces in this report can also be applied to liquid interfaces, as well as other molecular interfaces in general.

Journal Article↗