Biomedical subjects

Ting Guo

Publications and source records attributed to Ting Guo.

At least 19 recordsLinked to original sources

PubMed2025

Intratumoral fungus Neurospora crassa is associated with worsened prognosis in ovarian cancer via modulation of extracellular matrix.

Landmark studies on intratumoral fungi (ITF) have raised concerns due to irreproducible results and data-analysis errors. We aimed to determine whether ITF exist in ovarian cancer (OvCa) and, if so, whether they play a role in disease biology. Formalin-fixed, paraffin-embedded OvCa samples and multiple controls underwent operational decontamination, qPCR, internal transcribed spacer sequencing, and post-hoc data decontamination. We also leveraged updated fungal reads from The Cancer Genome Atlas generated by the TCMbio group, which addressed human-read contamination and artificial inflation, to validate findings and assess prognostic associations. A murine syngeneic model established using mouse ovarian cancer cell line (OVHM) with intratumoral Neurospora crassa injection was established. Transcriptomic and metabolomic analyses were performed to explore mechanisms. Tumor-containing blocks harbored significantly higher fungal loads than environmental controls but had loads comparable to paraffin controls. Applying a two-pass decontamination filter reduced raw sequence features from 9289 amplicon sequence variants (ASVs) to 659 ASVs. We focused on high-abundance features present in human tissues but absent from xenografts and paraffin controls and identified one candidate, N. crassa, associated with unfavorable prognosis in OvCa. Integrating human and murine data, we found Neurospora correlated with eosinophils, whereas N. crassa itself was not immune-related. Neurospora crassa promoted OvCa progression with downregulation of integrin-linked kinase and decreased extracellular matrix-receptor interaction. Most ITF signals are likely contaminants. We identified N. crassa as associated with unfavorable prognosis in OvCa, potentially via modulation of the extracellular matrix.

Neurospora crassa↗

PubMed2024

DNA polymerase delta governs parental histone transfer to DNA replication lagging strand.

Chromatin replication is intricately intertwined with the recycling of parental histones to the newly duplicated DNA strands for faithful genetic and epigenetic inheritance. The transfer of parental histones occurs through two distinct pathways: leading strand deposition, mediated by the DNA polymerase ε subunits Dpb3/Dpb4, and lagging strand deposition, facilitated by the MCM helicase subunit Mcm2. However, the mechanism of the facilitation of Mcm2 transferring parental histones to the lagging strand while moving along the leading strand remains unclear. Here, we show that the deletion of Pol32, a nonessential subunit of major lagging-strand DNA polymerase δ, results in a predominant transfer of parental histone H3-H4 to the leading strand during replication. Biochemical analyses further demonstrate that Pol32 can bind histone H3-H4 both in vivo and in vitro. The interaction of Pol32 with parental histone H3-H4 is disrupted through the mutation of the histone H3-H4 binding domain within Mcm2. Our findings identify the DNA polymerase δ subunit Pol32 as a critical histone chaperone downstream of Mcm2, mediating the transfer of parental histones to the lagging strand during DNA replication.

DNA Polymerase III↗

PubMed2006

Synthesis of tubular gold and silver nanoshells using silica nanowire core templates.

We report the synthesis of tubular gold and silver nanoshells on silica nanowire core templates in solution. Silica nanowires were synthesized and characterized with optical and NMR methods. Gold nanoparticle seeds (2 to 3 nm) with weak repulsive surfactants such as tetrakis-hydroxymethyl-phosphonium chloride (THPC) were conjugated to the surface of these nanowires. A regrowth process was initiated from these nanoparticles on the surface of the silica nanowires dispersed in gold or silver stock solutions in the presence of reducing agents. Micrometers-long gold and silver tubular nanoshells (80-150 nm o.d.) were made, fully covering the silica nanowires.

Journal Article↗

PubMed2006

Complexin is able to bind to SNARE core complexes in different assembled states with distinct affinity.

The formation of the functional SNARE complex in vivo is central to the fast neurotransmitter release at the neuronal terminal. Numerous studies revealed that this process involves progressive assembly of an alpha-helical bundle and is dynamically reversible. So far many proteins directly or indirectly take part in this process. Complexin, one of such factors, has revealed rapid association with the SNARE complex, however, whether or not complexin can interact with partially assembled SNARE complex is critical and yet unknown. Here, we present evidence that complexin is able to bind to various mutant versions of the SNARE complex mimicking its quaternary structure at different assembly stages. In addition, the affinity of complexin for the SNARE complex is correlated with the extent to which the SNARE complex is assembled. These results suggest that complexin is able to bind to SNARE complex before its complete formation.

Adaptor Proteins, Vesicular Transport↗

PubMed2006

Silica nanocoils.

We report here the results of nanoparticle-catalyzed synthesis of a variety of silica nanocoils (SiNCs) under similar growth conditions to those of making regular straight silica/silicon nanowires (SiNWs). Synthesis of individual SiNCs with alternating coiled and straight segments was achieved with cobalt nanoparticle catalysts at alternating temperatures. In addition, a variety of SiNCs, including multiple SiNCs sharing the same nanoparticle catalyst, SiNC double helices, and individual SiNCs with varying pitches and diameters were made.

Journal Article↗

PubMed2006

Visualization and navigation system development and application for stereotactic deep-brain neurosurgeries.

We present the development of a visualization and navigation system and its application in pre-operative planning and intra-operative guidance of stereotactic deep-brain neurosurgical procedures for the treatment of Parkinson's disease, chronic pain, and essential tremor. This system incorporates a variety of standardized functional and anatomical information, and is capable of non-rigid registration, interactive manipulation, and processing of clinical image data. The integration of a digitized and segmented brain atlas, an electrophysiological database, and collections of final surgical targets from previous patients facilitates the delineation of surgical targets and surrounding structures, as well as functional borders. We conducted studies to compare the surgical target locations identified by an experienced stereotactic neurosurgeon using multiple electrophysiological exploratory trajectories with those located by a non-expert using this system on 70 thalamotomy, pallidotomy, thalamic deep-brain stimulation (DBS), and subthalamic nucleus (STN) DBS procedures. The average displacement between the surgical target locations in both groups was 1.95 +/- 0.86 mm, 1.83 +/- 1.07 mm, 1.88 +/- 0.89 mm and 1.61 +/- 0.67 mm for each category of surgeries, respectively, indicating the potential value of our system in stereotactic deep-brain neurosurgical procedures, and demonstrating its capability for accurate surgical target initiation.

Adult↗

PubMed2005

Crystal structures, Raman spectroscopy, and magnetic properties of Ba7.5Al13Si29 and Eu0.27Ba7.22Al13Si29.

The framework-deficient clathrate phases Ba7.5Al13Si29 and Eu0.27Ba7.22Al13Si29 were prepared using a molten Al flux. Single-crystal X-ray diffraction confirmed the two phases to be clathrate type I (space group Pmn). For Eu0.27Ba7.22Al13Si29, single-crystal X-ray diffraction revealed the Eu to partially occupy the 2a position. Microprobe analysis of single crystals provided the stoichiometry, and Raman spectroscopy was used to investigate the guest framework interactions. The Raman spectra are consistent with both Ba7.5Al13Si29 and Eu0.27Ba7.22Al13Si29 having minimal guest-host interactions. Magnetic susceptibility data for Eu0.27Ba7.22Al13Si29 imply weak magnetic ordering and indicate a 2+ oxidation state for the Eu ion.

Journal Article↗

PubMed2005

Porous chitosan-gelatin scaffold containing plasmid DNA encoding transforming growth factor-beta1 for chondrocytes proliferation.

Cartilage defects as a result of disease or injury have a very limited ability to heal spontaneously. Recently, tissue engineering and local therapeutic gene delivery systems have been paid much attention in the cartilage natural healing process. Gene-activated matrix (GAM) blends these two strategies, serving as local bioreactor with therapeutic agents expression and also providing a structural template to fill the lesion defects for cell adhesion, proliferation and synthesis of extracellular matrix (ECM). In the current study, we used chitosan-gelatin complex as biomaterials to fabricate three-dimensional scaffolds and plasmid DNA were entrapped in the scaffolds encoding transforming growth factor-beta1 (TGF-beta1), which has been proposed as a promoter of cartilage regeneration for its effect on the synthesis of matrix molecules and cell proliferation. The plasmid DNA incorporated in the scaffolds showed a burst release in the first week and a sustained release for the other 2 weeks. The gene transfectd into chondrocytes expresses TGF-beta1 protein stably in 3 weeks. The histological and immunohistochemical results confirmed that the primary chondrocytes cultured into the chitosan-gelatin scaffold maintained round and owned characters of high secretion of specific ECM. From this study, it can be concluded that this gene-activated chitosan-gelatins matrix has a potential in the application of cartilage defects regeneration.

Animals↗

PubMed2005

Synthesis and self-assembled ring structures of Ni nanocrystals.

Narrow size distribution Ni nanocrystals with average diameters from 5 to 13 nm ( approximately 20% standard deviation) and a face-centered cubic (fcc) structure were synthesized via rapid thermo-decomposition in the presence of surfactants in solution. Transmission electron microscopy (TEM) and X-ray diffraction (XRD) were used to characterize these nanocrystals. It was found that the solvent determined the rate of the decomposition of Ni precursors, while the surfactants controlled the size and shape of Ni nanocrystals. A three-step process was proposed to explain the synthesis. The purified Ni nanocrystals readily formed micrometer-sized ring structures on TEM grids after solvent evaporation (hexanes), and the magnetic field was found to increase the density of the rings.

Journal Article↗

PubMed2005

Ultrafast selected energy x-ray absorption spectroscopy investigations of Ni and Zn species.

The results of ultrafast selected energy x-ray absorption spectroscopy (USEXAS) investigations of Ni and Zn species are presented. The USEXAS measurements described here employed characteristic x-ray radiation of L(alpha) and L(beta) from an ultrafast laser-driven W x-ray target to probe the K absorption edges of Ni and Zn, respectively. Static x-ray absorption edge spectra of six Ni and Zn species in either solid or solution form were obtained. Simulations of near-edge x-ray absorption spectra of these Ni and Zn species were carried out with FEFF. The results of USEXAS measurements were in general agreement with the theoretically simulated spectra and those measured with synchrotron x-ray radiation.

Clinical Laboratory Techniques↗

PubMed2005

Enhanced relaxation of nanoparticle-bound supercoiled DNA in X-ray radiation.

A therapeutic methodology was developed based on the large X-ray absorption cross-section of gold nanoparticles at high photon energies (>81 keV). Experimental results showed that the amounts of the relaxed circular supercoiled DNA (scDNA) for gold nanoparticle-bound scDNA were more than doubled compared to that for free scDNA under otherwise identical radiation conditions.

DNA, Superhelical↗

PubMed2005

Atomic tungsten for ultrafast hard X-ray generation.

High-resolution X-ray absorption measurements (with an accuracy of +/-0.3 eV) of ZnSO(4) (aq) were performed with ultrafast selected energy X-ray absorption spectroscopy (USEXAS) using a laser-driven tungsten target X-ray source. The results were used to determine the absolute spectral positions of characteristic emission lines. By comparing these positions to those predicted for the line emission from tungsten of different oxidation states using the Dirac-Fock formula, the tungsten species responsible for ultrafast hard X-ray generation were found to be tungsten atoms. This finding provides the first direct evidence to support the mechanism of X-ray generation via high-energy electrons interacting with tungsten atoms in the solid target.

Journal Article↗

PubMed2005

A novel statistical ligand-binding site predictor: application to ATP-binding sites.

Structural genomics initiatives are leading to rapid growth in newly determined protein 3D structures, the functional characterization of which may still be inadequate. As an attempt to provide insights into the possible roles of the emerging proteins whose structures are available and/or to complement biochemical research, a variety of computational methods have been developed for the screening and prediction of ligand-binding sites in raw structural data, including statistical pattern classification techniques. In this paper, we report a novel statistical descriptor (the Oriented Shell Model) for protein ligand-binding sites, which utilizes the distance and angular position distribution of various structural and physicochemical features present in immediate proximity to the center of a binding site. Using the support vector machine (SVM) as the classifier, our model identified 69% of the ATP-binding sites in whole-protein scanning tests and in eukaryotic proteins the accuracy is particularly high. We propose that this feature extraction and machine learning procedure can screen out ligand-binding-capable protein candidates and can yield valuable biochemical information for individual proteins.

Adenosine Triphosphate↗

PubMed2005

Determination of CoSi2 self-aligned nanostructures with grazing incidence X-ray absorption spectroscopy.

Self-aligned nanostructures (SAN) made by reacting Co nanoparticles with crystalline Si substrates at high temperatures were studied with grazing incidence X-ray absorption spectroscopy (GI-XAS). The results from extended X-ray absorption fine structure (EXAFS) analysis and X-ray absorption near-edge spectroscopy (XANES) were used to identify SAN as crystalline CoSi2. Theoretical calculations of EXAFS and XANES spectra of several crystalline cobalt silicides were performed with the FEFF8 package. On the basis of these studies, the SAN samples were determined to contain nearly pure CoSi2.

Journal Article↗

PubMed2005

Silicon-based nanowires from silicon wafers catalyzed by cobalt nanoparticles in a hydrogen environment.

We present here the synthesis of silicon-based nanowires directly from silicon wafers at high temperatures and in the presence of cobalt nanoparticles and hydrogen gas. All three ingredients were critical to the growth of Si-based nanowires, which were between 5-60 nm in diameter and microm-mm long. Both heavily coiled and straight Si-based nanowires were made. Experimental evidence suggested that the sources of silicon for the nanowires growth were in the gas phase.

Journal Article↗

PubMed2005

Laser-driven hard-x-ray generation based on ultrafast selected energy X-ray absorption spectroscopy measurements of Ni compounds.

Three Ni compounds were studied by ultrafast selected energy x-ray absorption spectroscopy using a laser-driven electron x-ray source with a tungsten target. The measured K edges of these Ni compounds using this self-referencing method were made identical to those measured with synchrotron x-ray sources. This enabled us to determine the absolute peak positions of tungsten Lalpha(1) and Lalpha(2) emitted from this source to be within 1 eV of those from the neutral tungsten atoms, which strongly suggested that the x rays were emitted from high energy electrons interacting with tungsten atoms in the solid target. This is the best evidence to date that directly supports the cold atom x-ray generation theory.

Journal Article↗

PubMed2005

Development and application of functional databases for planning deep-brain neurosurgical procedures.

This work presents the development and application of a visualization and navigation system for planning deep-brain neurosurgeries. This system, which incorporates a digitized and segmented brain atlas, an electrophysiological database, and collections of final surgical targets of previous patients, provides assistance for non-rigid registration, navigation, and reconstruction of clinical image data. The fusion of standardized anatomical and functional data, once registered to individual patient images, facilitates the delineation of surgical targets. Our preliminary studies compared the target locations identified by a non-expert using this system with those located by an experienced neurosurgeon using regular technique on 8 patients who had undergone subthalamic nucleus (STN) deep-brain stimulations (DBS). The average displacement between the surgical target locations in both groups was 0.58 mm +/- 0.49 mm, 0.70 mm +/- 0.37 mm, and 0.69 mm +/- 0.34 mm in x, y, and z directions respectively, indicating the capability of accurate surgical target initiation of our system, which has also shown promise in planning and guidance for other stereotactic deep-brain neurosurgical procedures.

Artificial Intelligence↗

PubMed2005

[Cloning and transcriptional regulation analysis of amelogenin promoter in different cells].

PURPOSE: To clone different promoter region of amelogenin gene and analyze their transcriptional activity. METHODS: The upstream regulation sequences of amelogenin gene were retrieved and analyzed. Amplified by PCR from the genomic DNA of mouse C57BL/6J and digested with restriction endonucleases enzyme, different transcriptional regulation sequences of 5'flanking of amelogenin gene including the basal promoter were cloned and ligated with luciferase gene in PGL3-Basic vector. These report vectors were transiently transfected into CHO, Hela and UMR-106 cells and luciferase assay was performed to analyse the transcription activation of these promoters. RESULTS: 6 promoters different in length were cloned. The activity of luciferase was very strong in Hela cells. On the contrary, the CHO and UMR-106 cells showed weak fluorescence. Luciferase activity fluctuated with the different promoter lengths in Hela cell as well as in CHO and UMR-106 cells. 975 bp and 532 bp of amelogenin 5'flanking DNA had a strong transcriptional activation, but 285 bp of amelogenin 5'flanking DNA had a weaker transcriptional activation. CONCLUSION: The sequence of amelogenin promoter can be activated in Hela cell. Hela cell can be used as a good model to study the transcriptional regulation of amelogenin promoter. According to the different activities of different lengths, it is suggested that there were some potential siliencer located between -975 and -532, and some potential activator in the region between -532 and -285.

Amelogenin↗