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Biomedical subjects

Jun Yin

Publications and source records attributed to Jun Yin.

At least 37 records · Page 2Linked to original sources

Single-cell FRET imaging of transferrin receptor trafficking dynamics by Sfp-catalyzed, site-specific protein labeling.

Fluorescence imaging of living cells depends on an efficient and specific method for labeling the target cellular protein with fluorophores. Here we show that Sfp phosphopantetheinyl transferase-catalyzed protein labeling is suitable for fluorescence imaging of membrane proteins that spend at least part of their membrane trafficking cycle at the cell surface. In this study, transferrin receptor 1 (TfR1) was fused to peptide carrier protein (PCP), and the TfR1-PCP fusion protein was specifically labeled with fluorophore Alexa 488 by Sfp. The trafficking of transferrin-TfR1-PCP complex during the process of transferrin-mediated iron uptake was imaged by fluorescence resonance energy transfer between the fluorescently labeled transferrin ligand and TfR1 receptor. We thus demonstrated that Sfp-catalyzed small molecule labeling of the PCP tag represents a practical and efficient tool for molecular imaging studies in living cells.

Bacterial Proteins↗

Long-term operation of biofilters for biological removal of ammonia.

Biological removal of ammonia was investigated using two types of packing materials, compost and sludge in laboratory-scale biofilters (8l reactor volume). The aim of this study is to investigate the potential of unit systems packed with these supports in terms of ammonia emissions treatment. Experimental tests and measurements included analysis of removal efficiency, metabolic products, and results of long-term operation. The inlet concentration of ammonia applied was 20-200 mg m-3. The ammonia loading rates of 24.9-566 g NH3 m-3 d-1 to compost biofilter (BF3) and 24.9-472 g NH3 m-3 d-1 to sludge biofilter (BF4) were applied for 210 days, respectively. Removal efficiencies of the compost and sludge biofilters were in the range of 97-99% and 95-99%, respectively when the inlet concentration of ammonia was below 110 mg m-3, and the maximum elimination capacities were 288 and 243 g NH3m-3d-1, respectively. However, removal efficiency and elimination capacity of both biofilters significantly decreased as the inlet concentration increased to above 110 mg m-3. By using kinetic analysis, the maximum removal rate of ammonia, Vm, and the saturation constant, Ks, were determined for both packing materials and the value of Vm for compost was found to be larger. Periodic analysis of the biofilter packing materials showed the accumulation of the nitrification product NO3- in the operation. During the experiment, the pressure drops measured were very low. The use of both packing materials requires neither nutritive aqueous solution nor buffer solution.

Air Pollutants↗

An initial investigation of the association between the SARS outbreak and weather: with the view of the environmental temperature and its variation.

OBJECTIVE: To understand the association between the SARS outbreak and the environmental temperature, and to provide a scientific basis for prevention and control measures against it. METHODS: The daily numbers of the probable SARS patients and the daily meteorological factors during the SARS outbreak period in Hong Kong, Guangzhou, Beijing, and Taiyuan were used in the data analysis. Ecological analysis was conducted to explore the association between the daily numbers of probable SARS patients and the environmental temperature and its variations. RESULTS: There was a significant correlation between the SARS cases and the environmental temperature seven days before the onset and the seven day time lag corresponds well with the known incubation period for SARS. The optimum environmental temperature associated with the SARS cases was between 16 degrees C to 28 degrees C, which may encourage virus growth. A sharp rise or decrease in the environmental temperature related to the cold spell led to an increase of the SARS cases because of the possible influence of the weather on the human immune system. This study provided some evidence that there is a higher possibility for SARS to reoccur in spring than that in autumn and winter. CONCLUSION: Current knowledge based on case studies of the SARS outbreak in the four cities suggested that the SARS outbreaks were significantly associated with the temperature and its variations. However, because the fallacy and the uncontrolled confounding effects might have biased the results, the possibility of other meteorological factors having an affect on the SARS outbreaks deserves further investigation.

China↗

A combination of soft-shell turtle powder and essential oil of a unicellular chorophyte prevents bone loss and decreased bone strength in ovariectomized rats.

The effects of soft-shell turtle (Trionyx sinensis) powder (SST) on the proximal tibiae of ovariectomized (OVX) rats were investigated using peripheral quantitative computed tomography (pQCT) and examination of serum biochemical markers. Considering the relationship between the antioxidative property and antiosteoporotic activity, the synergistic effects of a mixture of SST and essential oil of the microalgae Haematococcus pluvialis (OHP) with strong antioxidant activity were also examined. Oral administration of SST (100, 200 mg/kg) or a mixture of SST (100, 200 mg/kg) and OHP (13, 26 mg/kg) three times weekly prevented the decrease in bone mineral content (BMC) in total bone, BMC and bone mineral density (BMD) in cortical bone, and bone strength indices induced by ovariectomy in a dose-dependent manner without uterine side effects. However, OHP alone showed no significant effects.

Animals↗

[Evaluation of TTC and INT-electron transport system activity tests for heavy metal inhibition of activated sludge].

The effects of Cu2+, Zn2+, Cd2+, Hg2+, Ni2+, Pb2+ and Ag+ on TTC and INT-electron transport system activity are studied and the sensitivities of TTC and INT-electron transport system activity to seven tested heavy metals are compared to evaluate both the parameters for assessing heavy metal inhibition of activated sludge. The median inhibitory concentration (IC50) of seven tested heavy metals measured via TTC-electron transport system activity is less than that measured via INT-electron transport system activity, which indicates that the INT-electron transport system activity is less sensitive to heavy metals than the TTC-electron transport system activity. The ranking of tested heavy metals in order of decreasing toxicity based on TTC-electron transport system activity was Hg2+, Cd2+, Cu2+, Ag+, Zn2+, Ni2+ and Pb2+ , and the ranking based on INT-electron transport system activity was Hg2+, Ag+, Cu2+, Cd2+, Zn2+, Ni2+ and Pb2+.

Bacteria↗

[Screen of differentially expressed genes between gastrula embryos and tail bud embryos in gynogenetic gibel carp (Carassius auratus gibelio)].

Suppression subtractive hybridization (SSH) cDNA plasmid libraries were constructed between gastrula embryos and tail bud embryos in gynogenetic gibel carp (Carassius auratus gibelio). 739 and 816 PCR positive clones were respectively selected to perform dot blot, and 72 dot blot positive clones and 98 dot blot positive clones were obtained from the SSH plasmid libraries specific for gastrula embryos and tail bud embryos. Sequencing analysis and database searches indicated that there were 19 known genes and 31 unknown/cDNA fragments in the sequenced 72 dot blot positive clones specific for gastrula embryos, and 52 known genes and 37 unknown cDNA fragments in the sequenced 98 dot blot positive clones specific for tail bud embryos. Moreover,specific expressions of partial genes were further confirmed by virtual Northern blots and RT-PCR. The screen of these differentially expressed genes will help us to understand the molecular mechanism in gibel carp embryogenesis.

Animals↗

[Recombinant design and expression of human three-domain antibody against BoNTa].

VH and Vkappa genes were amplified from human ScFv B17 specific against botulinum neurotoxin serotype A (BoNTa). Gene sequence encoding 5'-terminal 12 amino acid of heavy chain constant region CH1, as a linker, linked VH and Vkappa to construct a new three-domain antibody molecule VH/Vkappa. VH/Vkappa was expressed at high level over 34% of total host cell proteins in E. coli. Recombinant protein were purified up to 95% by affinity column. As a result, recombinant VH/Vkappa could recognize and bind specific to BoNTa in ELISA. However, comparing with its parent ScFv, VH/Vkappa has higher relative affinity and stability.

Antibodies, Monoclonal↗

[Improved biochemical characteristics of human disulfide-stabilized Fv fragment to rabies virus].

This study is (1) to improve the stabilization of human scFv to rabies virus; (2) to prepare active human dsFv fragment; and (3) to evaluate the biological activities of dsFv. The dsFv V(H) and VL were separately expressed in PET22b(+)/BL21 (DE3), solublized and combined in appropriate molar ratio in refolding solution. The resultant dsFv fragments were evaluated for its protection against rabies virus, its affinity and stability, in reference to the cognate scFv. The dsFv was found to bind specifically to Vero vaccine of rabies virus. Compared to the scFv, the dsFv was more stable, had higher affinity, and was able to inhibit the infection of Rabies virus to Vero cell. This established a solid basis for the clinical application of dsFv to rabies virus.

Antibodies, Viral↗

Factor X Shanghai and disruption of translocation to the endoplasmic reticulum.

BACKGROUND AND OBJECTIVES: Most secreted proteins, including coagulation factor X (FX), are synthesized with a signal peptide, which is necessary for targeting the nascent polypeptide into the endoplasmic reticulum. Characterization of naturally occurring mutations may provide insights into the functional roles of the amino acids in the signal peptide. DESIGN AND METHODS: A 52-year old male patient with type I FX deficiency was studied. Mutations were searched for by FX gene (F10) sequencing. The wild-type and the mutant FX proteins were expressed in transfected cells and then immunological assays were performed. Pulse-chase experiments and cell-free expression studies were conducted to determine the cellular fate of the mutant FX molecules. RESULTS: The patient we studied was homozygous for a substitution of arginine for serine at codon -30 in the signal sequence of F10. Immunoassays detected low FX antigen levels in both the conditioned media and lysates of the cells expressing the mutant protein. Pulse-chase analysis showed that only trace amounts of the mutant FX protein were detectable in the conditioned media, and that the mutant molecules did not accumulate inside the cells either. The results of cell-free expression studies showed that although the transcription and translation of the mutant construct were normal, no post-translational processing, such as N-linked glycosylation, occurred in the presence of microsomes. INTERPRETATION AND CONCLUSIONS: These findings suggest that substitution of a neutral polar amino acid, serine by arginine, in the hydrophobic core of FX signal peptide severely impairs the ability of the protein to enter the endoplasmic reticulum and results in FX deficiency.

Amino Acid Substitution↗

Porphyrin distortion during affinity maturation of a ferrochelatase antibody, monitored by Resonance Raman spectroscopy.

Resonance Raman (RR) spectra are reported for mesoporphyrin IX bound to the Fab fragment of the ferrochelatase antibody 7G12. Binding induces activation of a Raman band at 680 cm(-1), which is assigned to an out-of-plane porphyrin vibration, gamma15. This is exactly the predicted effect of distorting mesoporphyrin to the geometry of N-methylmesoporphyrin IX, the 7G12 hapten, based on DFT/CIS modeling of the RR spectrum. The modeling also shows that the pyrrole ring that is tilted out of the porphyrin plane bears a nitrogen lone pair, which is therefore available for coordination by an incoming metal ion. The 680 cm(-1) band intensity is approximately 3 times higher for the affinity-matured antibody than for the germline precursor antibody, while intermediate values are found for variants in which germline residues are mutated to mature residues or vice versa. Thus, RR spectroscopy reveals an evolution from weak substrate distortion in the germline antibody to strong substrate distortion in the affinity-matured antibody, and supports the view that catalysis involves a substrate strain mechanism.

Computer Simulation↗

Phagemid encoded small molecules for high throughput screening of chemical libraries.

A new strategy for monovalently displaying small molecules on phage surfaces was developed and applied to high throughput screening for molecules with high binding affinity to the target protein. Peptidyl carrier protein (PCP) excised from nonribosomal peptide synthetase was monovalently displayed on the surface of M13 phage as pIII fusion proteins. Small molecules of diverse structures were conjugated to coenzyme A (CoA) and then covalently attached to the phage displayed PCP by Sfp phosphopantetheinyl transferase. Because Sfp is broadly promiscuous for the transfer of small molecule linked phosphopantetheinyl moieties to apo PCP domains, this approach will enable displaying libraries of small molecules on phage surfaces. Unique 20-base-pair (bp) DNA sequences were also incorporated into the phagemid DNA so that each compound displayed on the phage surface was encoded by a DNA bar code encapsulated inside the phage coat protein. Single round selection of phage displayed small molecules achieved more than 2000-fold enrichment of small molecules with nM binding affinity to the target protein. The selection process is further accelerated by the use of DNA decoding arrays for identifying the selected small molecules.

Bacterial Proteins↗

Labeling proteins with small molecules by site-specific posttranslational modification.

We report here the development of a general strategy for site-specific labeling of proteins with small molecules by posttranslational modification enzyme, phosphopantetheinyl transferase Sfp. The target proteins are expressed as fusions to the peptide carrier protein (PCP) excised from nonribosomal peptide synthetase, and Sfp catalyzes the covalent modification of a specific serine residue on PCP by the small molecule-phosphopantetheinyl conjugate. The labeling reaction proceeds with high specificity and efficiency, targeting PCP fusion proteins in the cell lysate. The PCP tag has been shown to be compatible with various proteins, and Sfp-catalyzed PCP modification, compatible with various small-molecule probes conjugated to coenzyme A, highlighting the potential of the PCP tag for site-specific protein labeling with small molecules.

Avidin↗

Lmx1b controls the differentiation and migration of the superficial dorsal horn neurons of the spinal cord.

The differentiation and migration of superficial dorsal horn neurons and subsequent ingrowth of cutaneous afferents are crucial events in the formation of somatosensory circuitry in the dorsal spinal cord. We report that the differentiation and migration of the superficial dorsal horn neurons are regulated by the LIM homeobox gene Lmx1b, and its downstream targets Rnx and Drg11, two transcription factors implicated in the development of dorsal horn circuitry. An analysis of Lmx1b mutants shows that Lmx1b normally acts to maintain the expression of the Ebf genes and to repress the Zic genes. Lmx1b mutants also exhibit the disruption of the cutaneous afferent ingrowth, suggesting that the dorsal horn cells might provide important cues guiding sensory axons into the dorsal spinal cord. Our results thus indicate that Lmx1b has a pivotal role in genetic cascades that control the assembly of circuitry in the superficial dorsal horn.

Animals↗

A catalysis-based selection for peroxidase antibodies with increased activity.

A biotin-tyramine conjugate (1) was found to covalently cross-link with peroxidase antibody 7G12 upon the catalytic oxidation of the tyramine moiety in the presence of hydrogen peroxide (H2O2). On the basis of this observation, a novel strategy was developed to select mutants of 7G12 Fab with enhanced peroxidase activity from a library of phage displayed antibodies. In such a selection, tyramine is oxidized by hydrogen peroxide in a process catalyzed by peroxidase antibodies displayed on phage. Antibodies with higher peroxidase activity are preferentially labeled with biotin through irreversible adduct formation between oxidized biotin-linked tyramine molecules and phenolic side chains of the antibody. The corresponding phage particles can then be selected via biotin-streptavidin interactions. Using this strategy, phage displayed libraries of antibody 7G12 were selected for higher peroxidase activity. As a result, mutations of antibody 7G12 that led to 10 to 20-fold increases in the peroxidase activity (kcat/Km) were identified, suggesting the validity of this method for the evolution of peroxidase antibodies based directly on catalytic turnover.

Antibodies, Catalytic↗

A role for DNA polymerase V in G --> T mutations from the major benzo[a]pyrene N2-dG adduct when studied in a 5'-TGT sequence in E. coli.

Benzo[a]pyrene (B[a]P), a potent mutagen/carcinogen, is metabolically activated to (+)-anti-B[a]PDE, which induces a full spectrum of mutations (e.g. GC --> TA, GC --> AT, etc.) principally via its major adduct [+ta]-B[a]P-N2-dG. Recent findings suggest that different lesion bypass DNA polymerases may be involved in different mutagenic pathways, which is the subject of this report. [+ta]-B[a]P-N2-dG built into a plasmid in a 5'-TGT sequence gives approximately equal numbers of G --> T and G --> A mutations when host E. coli are UV irradiated prior to transformation, so this sequence context was chosen to investigate what DNA polymerases are involved in G --> T versus G --> A mutations. G --> T mutations decline (>10-fold) if E. coli either are not UV-irradiated or are deficient in DNA polymerase V ((delta)umuD/C), demonstrating a role for damage-inducible DNA Pol V in a G --> T pathway. G --> T mutations are not affected by transformation into E. coli deficient in either DNA polymerases II or IV. While the work herein was in progress, Lenne-Samuel et al. [Mol. Microbiol. 38 (2000) 299] built the same adduct into a plasmid in a 5'-GGA sequence, and showed that the frequency of G --> T mutations was similar in UV-irradiated and unirradiated host E. coli cells, suggesting no involvement by damage-inducible, lesion bypass DNA polymerases (i.e., not II, IV or V); furthermore, a role for DNA Pol V was explicitly ruled out. The easiest way to reconcile the findings of Lenne-Samuel et al. with the findings herein is if two G --> T mutagenic pathways exist for [+ta]-B[a]P-N2-dG, where sequence context dictates which pathway is followed. In contrast to the G --> T mutations, herein G --> A mutations from [+ta]-B[a]P-N2-dG in the 5'-TGT sequence context are shown not to be affected by UV-irradiation of host E. coli, and are not dependent on DNA Pol V, or Pol II, Pol IV, or the damage-inducible, but SOS-independent UVM system. Published studies, however, have shown that G --> A mutations are usually enhanced by UV-irradiation of host E. coli prior to the introduction of plasmids either site-specifically modified with [+ta]-B[a]P-N2-dG or randomly adducted with (+)-anti-B[a]PDE; both findings imply the involvement of a lesion-bypass DNA polymerase. These disparate results suggest the existence of two G --> A mutagenic pathways for [+ta]-B[a]P-N2-dG as well, although confirmation of this awaits further study. In conclusion, a comparison between the evidence presented herein and published findings suggests the existence of two distinct mutagenic pathways for both G --> T and G --> A mutations from [+ta]-B[a]P-N2-dG, where in each case one pathway is not damage-inducible and not dependent on a lesion-bypass DNA polymerase, while the second pathway is damage-inducible and dependent on a lesion-bypass DNA polymerase. Furthermore, DNA sequence context appears to dictate which pathway (as defined by the involvement of different DNA polymerases) is followed in each case.

Benzopyrenes↗

Protein dynamics and the immunological evolution of molecular recognition.

While it is accepted that protein flexibility plays a role in protein folding, catalysis, and molecular recognition, few techniques are capable of the rigorous measurement of protein motions required to quantify flexibility. Three-pulse photon echo shift spectroscopy can be used to measure the time scale of protein motions, and we have used this technique, along with steady-state spectroscopy and binding and structural data, to examine the immunological evolution of protein flexibility in an anti-fluorescein antibody. Two light chain somatic mutations increase affinity for fluorescein by 12-fold but also significantly affect flexibility. Specifically, a rigidification of the protein is seen in each of three observable motions; two slower motions undergo decreased amplitudes of displacement, by 3- and 20-fold, respectively, in response to an applied force, and the distribution associated with the amplitude of a faster motion is narrowed upon somatic mutation. The somatic mutations appear to rigidify the antibody-fluorescein complex by more strongly anchoring fluorescein to the protein and by more tightly packing the complex. The data demonstrate that in addition to affinity, antibody dynamics are systematically manipulated during affinity maturation, and they imply that the evolution of protein flexibility may be a central component of the immune response. The results also reflect the type of protein rigidification that may be important for other biological interactions, such as protein-protein, protein-ligand or protein-drug, and enzyme-substrate recognition.

5' Untranslated Regions↗

New diarylheptanoids from the rhizomes of Dioscorea spongiosa and their antiosteoporotic activity.

Bioassay-guided fractionation of the water extract of the rhizomes of Dioscorea spongiosa led to the isolation and identification of new diarylheptanoids, diospongins A - C, together with three known lignans. Their structures, including absolute stereochemistry, were determined by analyses of NMR data, chemical conversions and CD spectrum. The isolated compounds, except for diospongin A, exerted potent inhibitory activities on bone resorption induced by parathyroid hormone in a bone organ culture system.

Animals↗

In vivo antiosteoporotic activity of a fraction of Dioscorea spongiosa and its constituent, 22-O-methylprotodioscin.

The antiosteoporotic activity of the 90 % EtOH fraction of the water extract of rhizomes of Dioscorea spongiosa and methylprotodioscin, its major constituent, were examined in the model of postmenopausal bone loss using ovariectomized (OVX) rats or mice. After 6 weeks treatment, the proximal tibia of rats or mice and the distal femora of mice were scanned by peripheral quantitative computed tomography (pQCT). Both the 90 % EtOH fraction (100 mg/kg/d) and methylprotodioscin (50 mg/kg/d) significantly inhibited bone loss in bone mineral content (BMC) and bone mineral density (BMD) in total, cancellous and cortical bones, and the decrease in bone strength indexes induced by OVX, without side effect on the uterus.

Animals↗