Biomedical subjects

Haifeng Wang

Publications and source records attributed to Haifeng Wang.

18 recordsLinked to original sources

PubMed2026

Chemotactic sensing of extracellular antibiotic resistance genes enables their efficient removal by Stutzerimonas stutzeri.

The dissemination of antibiotic resistance genes (ARGs) in wastewater environments poses a severe threat to public health. Extracellular ARGs (eARGs) persist as free DNA fragments that are refractory to efficient removal by conventional physicochemical treatment technologies. Here, we isolated Stutzerimonas stutzeri CHY07 from municipal sewage and demonstrated that extracellular DNA fragments, including eARGs, can serve as chemoattractants for environmental bacteria. Through genomic mining, molecular docking, surface plasmon resonance (SPR), isothermal titration calorimetry (ITC) and protein-ligand interaction profiling, we identified the chemoreceptor Mcp16 as the primary sensor of extracellular DNA and revealed that it achieves sequence-independent recognition of the DNA phosphate backbone. We further established the endogenous pentapeptide VRSVR as a methylation substrate for CheR and constructed the engineered strain CHY07-2 (mcp16::VRSVR) using an SSB/CRISPR-Cas9 ribonucleoprotein (RNP) system. This strain exhibited significantly enhanced chemotactic responsiveness, achieving 72-h removal efficiencies of 96.56% and 91.60% for low- and high-molecular-weight eARGs in non-sterile WWTP secondary effluent; conversely, mcp16 deletion markedly attenuated both chemotaxis and removal, whereas in situ complementation restored them. These findings reveal a "chemotaxis-contact-removal" cascade - with a proposed self-reinforcing loop - in eARG-removing bacteria, providing both a theoretical framework and a technical paradigm for enhancing pollutant removal through targeted amplification of microbial chemotaxis.

Chemotaxis↗

PubMed2026

Efficient and precise programmable DNA knock-in without double-strand breaks.

Programmable gene knock-in holds substantial promise for treating genetic diseases and advancing cell therapies. However, achieving precise and efficient kilobase-scale DNA fragment integration remains challenging1,2. Here we report CRISPR kilobase-scale nickase-targeting (KNIT) editing for efficient, precise and programmable kilobase-scale DNA insertion without double-strand DNA cleavage, which is enabled through the coupling of a Cas9 nickase with a DNA donor recruiting system. KNIT editing facilitates programmable integration of DNA fragments from 0.7 kb to more than 10 kb and is effective across genomic loci and cell types. It achieves up to 89% efficiency and markedly reduces unintended insertion-deletion mutation (indels) rates, translocations and off-target editing. The system supports repeated insertion editing and multiloci gene knock-in with minimal translocations. Its enhanced version, KNIT editor 2, further improves efficiency via a single transfection. Moreover, in mutant cells with a pathological mutation, KNIT editing restores normal gene expression by inserting a therapeutic gene into a safe harbour locus or its native locus. Notably, KNIT editing enables non-viral and programmable chimeric antigen receptor T cell (CAR-T cell) engineering without double-strand breaks and with clinically relevant efficiencies. Moreover, the engineered CAR-T cells exhibit effective antitumour activity in vitro and in mouse models. Therefore, by achieving programmable and site-specific kilobase-scale DNA insertions without double-strand breaks while reducing unintended outcomes, KNIT editing provides a versatile platform for advancing personalized medicine.

Animals↗

PubMed2026

SurvGRN: a multi-feature fusion framework for bladder cancer survival prediction.

Bladder cancer survival outcomes exhibit significant heterogeneity, influenced by multifaceted factors. While digital pathology-based survival models leveraging artificial intelligence show promise, they often overlook complementary data sources. Conversely, imaging lacks cellular detail, and genomics/proteomics entail complexity and cost. To integrate multidimensional data for enhanced survival prediction, we propose SurvGRN, a multi-feature fusion framework. SurvGRN synergistically combines clinical variables, transcriptomics, and digital pathology slides using a gated residual network architecture. Pathological features are extracted via multiple instance learning, while clinical and transcriptomic data are processed as static inputs. These features are dynamically fused using a long short-term memory (LSTM) network for comprehensive survival risk assessment. Evaluated on 400 bladder cancer patients, SurvGRN significantly outperformed existing methods: improving the C-index by 12.6% over DeepMISL; 20.6% and 7.1% over graph-based models (DeepGraphConv and Patch-GCN); and 5.4% and 4.0% over attention-based approaches (Surformer and HVTSurv). Ablation studies confirmed the contributions of pathology features (extracted via ResNet-50 pre-trained on bladder tissue), clinical/transcriptomic data, and the LSTM fusion. SurvGRN also enabled significant stratification of patients into distinct risk cohorts. This work demonstrates that holistic integration of multi-source data through tailored fusion architectures substantially improves bladder cancer survival prediction.

bladder cancer↗

PubMed2025

Comparative analysis of antibiotic resistance genes between fresh pig manure and composted pig manure in winter, China.

Antibiotic resistance is a critical global public health issue. The gut microbiome acts as a reservoir for numerous antibiotic resistance genes (ARGs), which influence both existing and future microbial populations within a community or ecosystem. However, the differences in ARG expression between fresh and composted feces remain poorly understood. In this study, we collected eight samples from a farm in Kaifeng City, China, comprising both fresh and composted pig manure. Using a high-throughput quantitative PCR array, we analyzed differences in ARG expression between these two types of manure. Our findings revealed significant differences in ARG profiles, as demonstrated by principal coordinate analysis (PCoA). Further analysis identified 39 ARGs (log2FC > 1, p < 0.05) in composted pig manure, with 25 genes downregulated and 14 upregulated. Notably, tetB-01, blaOCH, and blaOXY were the most abundant in composted pig manure compared to fresh manure. Additionally, 16S rRNA species profiling revealed that the composting process significantly altered the microbial community structure, with an increased abundance of Firmicutes and a decreased abundance of Bacteroidetes in composted pig manure. In summary, composting substantially transforms both the microbial community structure and the ARG profile in pig manure, underscoring its potential role in modulating the dynamics of ARGs in agricultural environments.

Animals↗

PubMed2006

In situ visualization of paclitaxel distribution and release by coherent anti-Stokes Raman scattering microscopy.

Visualization of three-dimensional distribution of drug molecules and subsequent changes during the release process is critical for understanding drug delivery mechanisms as well as designing tailor-made release profiles. This study utilized coherent anti-Stokes Raman scattering (CARS) imaging to examine paclitaxel distribution in various polymer films with lateral resolution of 0.3 microm and depth resolution of 0.9 microm. Raman bands in the CH stretch vibration and fingerprint regions were used to distinguish paclitaxel from the polymers. The detection sensitivity was measured to be 29 mM by imaging paclitaxel molecules dissolved in N,N-dimethylformamide solution. Release of paclitaxel from a polymer matrix was monitored at an acquisition speed of 1 frame/s. Our results show that CARS microscopy can be used effectively for in situ imaging of native drug molecules in a delivery system.

Microscopy↗

PubMed2006

Enhancement of polyunsaturated fatty acid production by Tn5 transposon in Shewanella baltica.

Transposon Tn5 mutagenesis was used to generate random mutations in Shewanella baltica MAC1, a polyunsaturated fatty acid (PUFA)-producing bacterium. Three mutants produced 3-5 times more eicosapentaenoic acid (EPA 20:5 n-3) compared to the wild type at 10 degrees C. One of the mutants produced 0.3 mg EPA g(-1) when grown at high temperature (30 degrees C). Moreover, 2 mg docosahexaenoic acid (DHA 22:6 n-3) g(-1) was produced by S. baltica mutants at 4 degrees C. Sequencing of insertion mutation(s) showed 96% homology to trimethylamine N-oxide (TMAO) reductase gene and 85% homology to rRNA operons of E. coli. Tn5 transposon mutagenesis therefore is a suitable technique to increase PUFA formation in bacteria.

DNA Transposable Elements↗

PubMed2006

Coherent anti-Stokes Raman scattering imaging with a laser source delivered by a photonic crystal fiber.

We demonstrate laser-scanning coherent anti-Stokes Raman scattering (CARS) imaging with two excitation laser beams delivered by a large-mode-area photonic crystal fiber. The group-velocity dispersion and self-phase modulation effects are largely suppressed due to the large mode area of the fiber and the use of picosecond pulses. The fiber delivery preserves the signal level and image spatial resolution well. High-quality images of live spinal cord tissues are acquired using the fiber-delivered laser source. Our method provides a basic platform for developing a flexible and compact CARS imaging system.

Equipment Design↗

PubMed2006

Linkage disequilibrium sharing and haplotype-tagged SNP portability between populations.

The discovery of the block-like structure of linkage disequilibrium (LD) in human populations holds the promise of delineating the etiology of common diseases. However, understanding the magnitude, mechanism, and utility of between-population LD sharing is critical for future genome-wide association studies. In this study, substantial LD sharing between six non-African populations was observed, although much less between African-American and non-African, based on 20,000 SNPs of chromosome 21. We also demonstrated the respective roles of recombination and demographic events in shaping LD sharing. Furthermore, we showed that the haplotype-tagged SNPs chosen from one population are portable to the others in East Asia. Therefore, we concluded that the magnitude of LD sharing between human populations justifies the use of representative populations for selecting haplotype-tagged SNPs in genome-wide association studies of complex diseases.

Africa↗

PubMed2005

Easy and rapid method for the determination of gene expression in cumulus cells incubated for oocyte maturation.

BACKGROUND: The objectives of this study were to develop an easy and rapid method for measuring gene expression in a small number of cells by real-time PCR without RNA extraction and purification, and to use this method to determine more precisely IGF-I gene expression in the cumulus cells surrounding oocytes. METHODS: First, after small numbers of cumulus cells were lysed in cell lysis buffer, they were digested with various concentrations of DNase I for different periods at 37 degrees C to determine the optimal conditions for digestion of genomic DNA in the lysate. Since nonspecific amplification was liable to occur when the non-purified RT product of the cell lysate was used for real-time PCR with the given primers, the optimal conditions for Mg2+ and annealing temperature were well investigated. Further, to create the same conditions as in the actual sample reaction for measurement by real-time PCR, RT-minus product was added to the reaction mixture of the standard curve, and then the amplification efficiency was assessed. Next, IGF-I gene expression in cumulus cells collected from cumulus oocyte complexes (COCs) every 4 h during maturation was determined using the developed method. RESULTS: The optimal conditions for measuring gene expression using the cell lysate from a small number of cells were as follows: incubation of the cell lysate with 0.16 U/microL DNase I with 10 U/microL for 30 min, an Mg concentration of 1.5 mM for amplification of target gene by real-time PCR using RT-product of the cell lysate. When the RT-minus products added to the reaction mixture for the standard curve, which was prepared for purified 18SrRNA plasmid, the PCR efficiency was similar between the sample and the standard. The IGF-I gene expression in the cumulus cells was elevated up through the first 8 h of the culture and then declined gradually by the end of maturation, with the maximal gene expression (778-fold) seen at 8 h. CONCLUSION: It can be concluded that the method developed here, in which equivalent to cumulus cells collected from 0.03-0.075 COCs were employed per reaction, permits rapid and easy determination of target gene expression in a limited number of cells using real-time PCR without RNA extraction.

Animals↗

PubMed2005

In vitro and in vivo two-photon luminescence imaging of single gold nanorods.

Gold nanorods excited at 830 nm on a far-field laser-scanning microscope produced strong two-photon luminescence (TPL) intensities, with a cos(4) dependence on the incident polarization. The TPL excitation spectrum can be superimposed onto the longitudinal plasmon band, indicating a plasmon-enhanced two-photon absorption cross section. The TPL signal from a single nanorod is 58 times that of the two-photon fluorescence signal from a single rhodamine molecule. The application of gold nanorods as TPL imaging agents is demonstrated by in vivo imaging of single nanorods flowing in mouse ear blood vessels.

Animals↗

PubMed2005

Quantitative coherent anti-Stokes Raman scattering imaging of lipid distribution in coexisting domains.

We demonstrate quantitative vibrational imaging of specific lipid molecules in single bilayers using laser-scanning coherent anti-Stokes Raman scattering (CARS) microscopy with a lateral resolution of 0.25 mum. A lipid is spectrally separated from other molecules by using deuterated acyl chains that provide a large CARS signal from the symmetric CD(2) stretch vibration around 2100 cm(-1). Our temperature control experiments show that d62-DPPC has similar bilayer phase segregation property as DPPC when mixing with DOPC. By using epi-detection and optimizing excitation and detection conditions, we are able to generate a clear vibrational contrast from d62-DPPC of 10% molar fraction in a single bilayer of DPPC/d62-DPPC mixture. We have developed and experimentally verified an image analysis model that can derive the relative molecular concentration from the difference of the two CARS intensities measured at the peak and dip frequencies of a CARS band. With the above strategies, we have measured the molar density of d62-DPPC in the coexisting domains inside the DOPC/d62-DPPC (1:1) supported bilayers incorporated with 0-40% cholesterol. The observed interesting changes of phospholipid organization upon addition of cholesterol to the bilayer are discussed.

1,2-Dipalmitoylphosphatidylcholine↗

PubMed2005

Coherent anti-stokes Raman scattering imaging of axonal myelin in live spinal tissues.

We present a vibrational imaging study of axonal myelin under physiological conditions by laser-scanning coherent anti-Stokes Raman scattering (CARS) microscopy. We use spinal cord white matter strips that are isolated from guinea pigs and kept alive in oxygen bubbled Krebs' solution. Both forward- and epi-detected CARS are used to probe the parallel axons in the spinal tissue with a high vibrational contrast. With the CARS signal from CH2 vibration, we have measured the ordering degree and the spectral profile of myelin lipids. Via comparison with the ordering degrees of lipids in myelin figures formed of controlled lipid composition, we show that the majority of the myelin membrane is in the liquid ordered phase. By measuring the myelin thickness and axon diameter, the value of g ratio is determined to be 0.68 with forward- and 0.63 with epi-detected CARS. Detailed structures of the node of Ranvier and Schmidt-Lanterman incisure are resolved. We have also visualized the ordering of water molecules between adjacent bilayers inside the myelin. Our observations provide new insights into myelin organization, complementary to the knowledge from light and electron microscopy studies of fixed and dehydrated tissues. In addition, we have demonstrated simultaneous CARS imaging of myelin and two-photon excitation fluorescence imaging of intra- and extraaxonal Ca2+. The current work opens up a new approach to the study of spinal cord injury and demyelinating diseases.

1,2-Dipalmitoylphosphatidylcholine↗

PubMed2005

Probiotics down-regulate flaA sigma28 promoter in Campylobacter jejuni.

Lactobacilli and bifidobacteria are important members of the gastrointestinal microflora of humans and animals and are thought to have positive effects on human health. Therefore, there is an increasing interest in using these microorganisms as probiotics to be incorporated into either fermented dairy products or tablets. However, convincing scientific data that support claims of their health benefits are scarce. The effect of cell-free extracts of milk fermented by 10 probiotic bacteria (five Bifidobacterium strains and five Lactobacillus strains) on the expression of the flaA gene of Campylobacter jejuni was assessed using a fusion between the flaA sigma28 promoter and a promoterless luxCDABE cassette carried on the plasmid pRYluxCDABE, which resulted in strains with quantifiable luminescence linked to flaA sigma28 promoter activity. Cell-free extracts of milk fermented by all of the tested probiotic strains inhibited the growth of the C. jejuni and down-regulatedflaA sigma28 promoter activity. Two nonprobiotic lactic acid bacterial strains, Lactococcus lactis and Streptococcus thermophilus, were less inhibitory.

Animals↗

PubMed2004

Electromechanical properties of fine-grain, 0.7 Pb(Mg(1/3)Nb(2/3))O3-0.3PbTiO3 ceramics.

A fine grain, relaxor-based piezoelectric ceramic 0.7 Pb(Mg(1/3)Nb(2/3))O3-0.3PbTiO3 (PMN-30% PT) has been investigated, which was fabricated using the columbite precursor method. The complete set of electromechanical properties of the piezoceramic at room temperature is determined using a combination of ultrasonic and resonance techniques. This fine-grain ceramic (grain size < or = 2.5 microm) exhibits ultra-high dielectric permittivity (epsilon33(T)/epsilon0 approximately 7000) and a high coupling coefficient k(33) (= 0.78). Ultrasonic spectroscopy was used to measure the dispersion of the phase velocity and attenuation for the longitudinal wave propagating in the poling direction. Lower attenuation and smaller velocity dispersion were observed compared to modified Pb(Zr(x)Ti(1-x)O3 (PZT-5H) ceramics. The measurement results show that this fine-grain PMN-30% PT ceramic is a very good material for making ultrasonic array transducers.

Journal Article↗

PubMed2004

Characterizing ultra-thin matching layers of high-frequency ultrasonic transducer based on impedance matching principle.

The quarter-wavelength (lambda/4) acoustic matching layer is a vital component in medical ultrasonic transducers, which can compensate for the large acoustic impedance mismatch between the piezoelectric material and the human body. At high frequencies (approximately 100 MHz), the lambda/4 matching layers become extremely thin, and the characterization of their properties becomes very challenging. We report a method to measure the phase velocity and attenuation of ultra-thin layers using the lambda/4 matching principle, in which the acoustic impedance of the thin layer is between the substrate and water. The method has been successfully used to characterize epoxy films on glass substrate. The experimental results show good agreement in the phase-velocity measurement between our proposed method and the conventional ultrasonic spectroscopy method, but the attenuation measurement is sensitive to the properties of the substrate and water medium as well as the alignment of the sample.

Journal Article↗

PubMed2003

Purification and characterization of an extracellular alkaline serine protease with dehairing function from Bacillus pumilus.

An extracellular alkaline serine protease (called DHAP), produced by a Bacillus pumilus strain, demonstrates significant dehairing function. This protease is purified by hydrophobic interaction chromatography, ion exchange, and gel filtration. DHAP had a pI of 9.0 and a molecular weight of approximately 32,000 Dalton. It shows maximal activity at pH 10 and with a temperature of 55 degrees C; the enzyme activity can be completely inhibited by phenylmethylsulfonyl fluoride (PMSF) and diisopropyl fluorophosphates (DFP). The first 20 amino acid residues of the purified DHAP have been determined with a sequence of AQTVPYGIPQIKAPAVHAQG. Alignment of this sequence with other alkaline protease demonstrates its high homology with protease from another B. pumilus strain.

Amino Acid Sequence↗

PubMed2002

Phase-shifting apodizers for increasing focal depth.

We propose the use of a phase-shifting apodizers to increase focal depth, and we study the axial and radial behavior of this kind of apodizer under the condition that the axial intensity distribution is optimized for high focal depth.

Journal Article↗

PubMed2002

Transcription regulation in thermophilic bacteria: high resolution contact probing of Bacillus stearothermophilus and Thermotoga neapolitana arginine repressor-operator interactions.

Arginine-mediated regulation is remarkably well conserved in very divergent bacteria, and shows a number of unusual features that distinguish arginine regulation from other transcriptional control mechanisms. The arginine repressor subunit consists of a basic N-terminal DNA-binding domain, which belongs to the winged helix-turn-helix family, connected through a flexible linker to an acidic C-terminal domain responsible for binding of arginine and assembly of the high-affinity holohexamer, which binds an approximately 40 bp target. To gain further insight into the molecular details of arginine repressor-operator interactions we have established a high resolution contact map of the argC operator from Bacillus stearothermophilus, a moderate thermophilic Gram-positive bacterium, and the argR operator from Thermotoga neapolitana, a Gram-negative hyperthermophile, with the corresponding ArgR proteins. Enzymatic and chemical footprinting have been combined with missing contact, pre-modification, base substitution, and small ligand binding interference techniques to gather information on backbone and base-specific contacts with major and minor groove determinants of the operators. Wild-type and mutant argC operators have been compared for their interaction with the repressor, using both in vivo and in vitro approaches. Our results indicate that the operators of B. stearothermophilus and T. neapolitana consist of two ARG box-like sequences, 18 bp imperfect palindromes, separated by two and three base-pairs, respectively, and that the repressors from thermophilic origin establish base-specific contacts with two major groove segments and the intervening minor groove of each ARG box, all aligned on one face of the helix. In contrast, no specific contacts are established in the minor groove facing the repressor in the centre of the operator, nevertheless this region plays a crucial structural role in complex formation, as indicated by mutant studies. This picture is reminiscent of arginine repressor binding in Escherichia coli, and therefore reinforces the uniform view of arginine regulation, but also reveals a number of striking differences at particular positions of the boxes and in the length and base-pair composition of the spacer connecting two ARG boxes in the operator. These might be responsible, in part, for subtle but important functional and mechanistic differences in the way species-specific repressors interact with their cognate target sites. These variations are underlined by the different behaviour of the repressors from E. coli, B. stearothermophilus and T. neapolitana in their potential to bind heterologous operators, their requirement for arginine, and the resistance of complex formation to non-specific competitor DNA. Our findings are discussed in view of the crystal structure of the arginine repressor from B. stearothermophilus.

Aldehyde Oxidoreductases↗