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Yong Yu

Publications and source records attributed to Yong Yu.

At least 19 recordsLinked to original sources
PubMed2026

Extreme climatic events drive consistent and predictable shifts in soil antibiotic resistance genes.

Antimicrobial resistance (AMR) is a growing One Health challenge, and as climate warming intensifies extreme events, it remains unclear how these disturbances affect soil antibiotic resistance genes (ARGs). Here we analyzed the data from a controlled experiment using soils from 30 grassland sites across ten European countries, which simulated drought, flooding, freeze-thaw, and heatwaves to explore ARG dynamics. Overall, ARGs exhibited relatively small but highly consistent shifts across treatments. Heatwaves caused the strongest reductions in ARG abundance and in their linkages with mobile genetic elements (MGEs), a pattern that may reflect a hypothesized metabolic-genetic trade-off, in which microbial investment may shift from core metabolism toward stress signaling and structural maintenance. ARG dynamics during and after disturbance were governed by distinct soil physicochemical properties, with temperature and nutrient status determining acute responses, whereas soil moisture and seasonal variability in temperature and precipitation shaped longer-term legacy effects. Cross-validated random-forest models showed positive predictive performance for Bray-Curtis-based compositional responses within the environmental range represented by the 30 grassland sites. Our findings enhance the understanding of how soil ARGs respond to extreme climatic events and provide a step toward predicting extreme-event impacts on soil resistomes with relevance to One Health.

Soil Microbiology↗
PubMed2026

Unveiling microbial communities and biogeochemical cycles in Antarctic colored snow.

Snow cover, the extensive terrestrial habitat in Antarctica, sometimes exhibits vivid coloration, yet the structure and function of its microbial communities remain poorly characterized. Using metagenomic sequencing of red snow (RS) and green snow (GS) from the Fildes Peninsula, we found that bacterial, eukaryotic, and archaeal relative abundances were 85.82%, 13.52% and 0.16%, respectively. &#x3b2;-Diversity differed significantly between RS and GS across these three domains (P&#x2009;<&#x2009;0.05). Dominant bacterial phyla included Bacteroidota (RS: 62.61%; GS: 38.72%) and Pseudomonadota (RS: 32.80%; GS: 54.10%). Among eukaryotes, Chlorophyta (RS: 58.10%; GS: 52.98%) and Basidiomycota (RS: 14.80%; GS: 8.08%) were prevalent. Nanobdellota dominated archaea, with lower abundance in RS than GS. In the algal community, Sanguina, Gonium and Chloromonas were significantly enriched in red snow, while Chlorella and Micractinium were enriched in green snow (P&#x2009;<&#x2009;0.05). Marker genes associated with carbon (C), nitrogen (N), phosphorus (P) and sulfur (S) cycles were identified in green and red snow. Aerobic respiration and phosphate regulation were significantly enriched in red snow, while CO oxidation, fermentation, and denitrification were significantly enriched in green snow. Key microbial genera associated with these functional pathways also varied. In the denitrification of red snow, Stutzerimonas was the most abundant genus, while Janthinobacterium was abundant in green snow. Nitrification-related genes were detected only in red snow based on the present metagenomic data. The network of the red snow microbial community was potentially more complex and resistant based on topology, which not only benefited its own long-term survival but might also have potentially influenced the positive feedback effect of snowmelt by maintaining a low-albedo snow surface. This provided an ecological implication under climate warming: the expansion of red snow patches showed the potential to the increase nitrate runoff export, which would affect nitrogen nutrient levels in coastal Antarctic waters. Overall, this study used metagenomics to compare the multidomain (bacteria, archaea and eukaryotes) composition and diversity between red snow and green snow, and directly linked key microbial taxa with functional genes of biogeochemical cycles. This study provided new insights into the biological characteristics and functional potential of Antarctic colored snow.

Snow↗
PubMed2007

Polycyclic aromatic hydrocarbons in the surface sediments from Yellow River, China.

Fourteen surface sediment samples were collected from Lanzhou Reach of Yellow River, China in July 2005. The concentrations of 16 priority polycyclic aromatic hydrocarbons (PAHs) were determined by gas chromatography equipped with a mass spectrometry detector (GC-MS). Total concentrations of the PAHs ranged from 464 to 2621 ng/g dry weight. Sediment samples with the highest PAH concentrations appeared at the downstream of Lanzhou City, where there was the biggest wastewater discharge pipeline from Lanzhou Oil Refinery Factory and Lanzhou Chemical Industry Company. Municipal sewage also contributed to the PAH contamination in the sediments. A correlation existed between the sediment organic carbon content (f(oc)) and the total PAH concentrations (r(2)=0.57), suggesting that sediment organic carbon content played an important role in controlling the PAHs levels in the sediments. According to the observed molecular indices, PAHs contamination in Lanzhou Reach of Yellow River originated both from the high-temperature pyrolytic processes and from the petrogenic source, showing a mixed PAH input pattern, which was also confirmed by the results of a principal component analysis (PCA). According to the numerical effect-based sediment quality guidelines (SQGs) of the United States, the levels of PAHs at most studied sites in Lanzhou Reach of Yellow River should not exert adverse biological effects. Although at some sites (such as S10, S12, etc.) one PAH may exceed the effects range low (ERL), individual PAH did not exceed the effects range median (ERM). The results indicated that sediments in all sites should have potential biological impact, but should have no impairment.

China↗
PubMed2006

Congestion-gradient driven transport on complex networks.

We present a study of transport on complex networks with routing based on local information. Particles hop from one node of the network to another according to a set of routing rules with different degrees of congestion awareness, ranging from random diffusion to rigid congestion-gradient driven flow. Each node can be either source or destination for particles and all nodes have the same routing capacity, which are features of ad hoc wireless networks. It is shown that the transport capacity increases when a small amount of congestion awareness is present in the routing rules, and that it then decreases as the routing rules become too rigid when the flow becomes strictly congestion-gradient driven. Therefore, an optimum value of the congestion awareness exists in the routing rules. It is also shown that, in the limit of a large number of nodes, networks using routing based on local information jam at any nonzero load. Finally, we study the correlation between congestion at node level and a betweenness centrality measure.

Journal Article↗
PubMed2006

Optimal transport on complex networks.

We present a heuristic algorithm for the optimization of transport on complex networks. Previously proposed network transport optimization algorithms aim at avoiding or reducing link overload. Our algorithm balances traffic on a network by minimizing the maximum node betweenness with as little path lengthening as possible, thus being useful in cases when networks are jamming due to node congestion. By using the resulting routing, a network can sustain significantly higher traffic without jamming than in the case of shortest path routing.

Journal Article↗
PubMed2006

Engineering a novel, stable dimeric streptavidin with lower isoelectric point.

We have engineered a soluble, stable two-chain dimeric streptavidin (TCD) in Escherchia coli. Examination of the three-dimensional structure of streptavidin aided by empirical binding free-energy calculations helped us to select mutations at subunit interfaces that dissociate the native tetramer and stabilize the desired dimer. We chose positions W120, L124, V125 and H127 and mutated them to 120D/124D/125D/127D (TCD-1); 120D/124N/125S/127D (TCD-2); and 120D/124D/125S/127D (TCD-3). The H127D mutation creates electrostatic repulsion that disrupts the dimer-dimer interface, but leaves it very hydrophobic. Therefore, W120, L124 and V125 were mutated to hydrophilic residues to increase dimer solubility. Among the three candidates, TCD-2 gave the best result: a stable, active dimer with K(d) for biotin of approximately 1x10(-7)M after purification by gel-filtration chromatography. The experimental results confirm the possibility of rational engineering of low-pI dimeric streptavidins. Reduced-size streptavidin mutants with a net negative charge may be more suitable than antibodies or wild-type streptavidin for the targeting step in radioimmunotherapy because they should clear faster from the bloodstream and the kidney.

Bacterial Proteins↗
PubMed2006

Rapid analysis of the essential oils from dried Illicium verum Hook. f. and Zingiber officinale Rosc. by improved solvent-free microwave extraction with three types of microwave-absorption medium.

A new method of extracting essential oils from dried plant materials has been studied. By adding a microwave-absorption medium (MAM) to a reactor, solvent-free microwave extraction (SFME) was improved and can be used to extract essential oils from dried plant material without pretreatment. With a microwave irradiation power of 85 W it took only approximately 30 min to extract the essential oils completely. The whole extraction process is simple, rapid, and economical. Three types of MAM, iron carbonyl powder (ICP), graphite powder (GP), and activated carbon powder (ACP), and two types of dried plant material, Illicium verum Hook. f. and Zingiber officinale Rosc., were studied. The results were compared with those obtained by use of conventional SFME, microwave-assisted hydrodistillation (MAHD), and conventional hydrodistillation (HD), and the conclusion drawn was that improved SFME was a feasible means of extracting essential oils from dried plant materials, because there were few differences between the composition of the essential oils extracted by improved SFME and by the other methods.

Adsorption↗
PubMed2006

Promising clinical outcome of stereotactic body radiation therapy for patients with inoperable Stage I/II non-small-cell lung cancer.

PURPOSE: To evaluate the efficacy and toxicity of hypofractionated stereotactic body radiotherapy in patients with Stage I/II non-small-cell lung cancer. METHODS AND MATERIALS: Forty-three patients with inoperable Stage I/II non-small-cell lung cancer underwent treatment prospectively using the stereotactic gamma-ray whole-body therapeutic system (body gamma-knife radiosurgery) with 30 rotary conical-surface Co(60) sources focused on the target volume. Low-speed computed tomography simulation was conducted, which was followed by three-dimensional conformal radiotherapy planning. A total dose of 50 Gy was delivered at 5 Gy/fraction to the 50% isodose line covering the planning target volume, whereas a total dose of 70 Gy was delivered at 7 Gy/fraction to the gross target volume. The median follow-up duration was 27 months. RESULTS: Three to 6 months after treatment, the complete response rate for body-gamma knife radiosurgery was 63%, and the overall response rate was 95%. The 1-year, 2-year, and 3-year local control rates were all 95% in all patients. The 1-year, 2-year, and 3-year overall survival rates were 100%, 91%, and 91%, respectively, in patients with Stage I disease and 73%, 64%, and 64%, respectively, in those with Stage II disease. Only 2.3% (1/43) of the patients had Grade 3 pneumonitis. CONCLUSION: Our highly focused stereotactic body radiotherapy method resulted in promising local control and survival with minimal toxicity.

Adenocarcinoma↗
PubMed2006

Hexaferrocenylbenzene.

Hexaferrocenylbenzene has been synthesized by six-fold Negishi type ferrocenylation of hexabromo- or hexaiodobenzene.

Journal Article↗
PubMed2006

Fast complementation of split fluorescent protein triggered by DNA hybridization.

Fluorescent proteins have proven to be excellent reporters and biochemical sensors with a wide range of applications. In a split form, they are not fluorescent, but their fluorescence can be restored by supplementary protein-protein or protein-nucleic acid interactions that reassemble the split polypeptides. However, in prior studies, it took hours to restore the fluorescence of a split fluorescent protein because the formation of the protein chromophore slowly occurred de novo concurrently with reassembly. Here we provide evidence that a fluorogenic chromophore can self-catalytically form within an isolated N-terminal fragment of the enhanced green fluorescent protein (EGFP). We show that restoration of the split protein fluorescence can be driven by nucleic acid complementary interactions. In our assay, fluorescence development is fast (within a few minutes) when complementary oligonucleotide-linked fragments of the split EGFP are combined. The ability of our EGFP system to respond quickly to DNA hybridization should be useful for detecting the kinetics of many other types of pairwise interactions both in vitro and in living cells.

DNA↗
PubMed2006

[Expression of alpha-tubulin and gamma-tubulin in premalignant lesion and carcinoma of breast and the significance thereof].

OBJECTIVE: To investigate the expression of alpha-tubulin and gamma-tubulin, 2 kinds of centrosome proteins, in premalignant lesion and carcinoma of breast and the significance thereof. METHODS: Forty specimens of premalignant lesions of breast, 40 specimens of infiltrating ductal carcinoma of breast, 40 specimens of intraductal carcinoma (IDC), and 30 specimens of normal breast tissues were obtained during operation. Immunohistochemistry was used to analyze the protein expression of alpha-tubulin and gamma-tubulin, and the percentages of ki67 positive cells. Western blotting was used to examine the mRNA expression of alpha-tubulin and gamma-tubulin. RESULTS: The protein and mRNA expression values of alpha-tubulin and gamma-tubulin in breast carcinoma were higher than those in the premalignant lesions and normal breast tissues with significant differences between the premalignant lesions and normal breast torques and without significant differences between infiltrating ductal carcinoma of breast and IDC. The ki67 positive rates of the infiltrating ductal carcinoma of breast group, IDC group, premalignant lesion group, and normal breast tissues group were 16.0%, 37.0%, 53.6%, and 67.8% (P = 0.001). A positive correlation existed between the expression of alpha-tubulin and the expression of gamma-tubulin in the same case and the same group (all P = 0.00) and there was no significant correlation between the expression of alpha-tubulin and the expression of gamma-tubulin in the same case and the same group (all P > 0.05). Both the expression of alpha-tubulin and the expression of gamma-tubulin were significantly associated with the prognosis. CONCLUSIONS: Centrosome protein is one of the distinct phenotypes of breast cancer cells. Aberration of centrosome proteins may be used to screen high risk cases of breast carcinoma and to estimate the prognosis.

Blotting, Western↗
PubMed2006

Glaciecola psychrophila sp. nov., a novel psychrophilic bacterium isolated from the Arctic.

A novel bacterial strain, designated 170(T), was collected from high latitude Arctic locations (77 degrees 30' N to approximately 81 degrees 12' N), including the Canadian Basin and Greenland Sea. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that strain 170(T) was related to members of the genus Glaciecola and had the highest 16S rRNA gene sequence similarity to Glaciecola mesophila. Cells were Gram-negative, psychrophilic, motile rods. The temperature range for growth was 4-15 degrees C, with optimum growth at 12 degrees C and at approximately pH 6.0-9.0. Strain 170(T) contained C(16 : 1)omega7c, C(16 : 0), C(12 : 1) 3-OH and C(18 : 1)omega7c as major fatty acids. The genomic DNA G+C content was 42.9 mol%. On the basis of phenotypic characterization, phylogenetic analysis and DNA-DNA relatedness data, strain 170(T) is considered to represent a novel species of the genus Glaciecola, for which the name Glaciecola psychrophila is proposed. The type strain is 170(T) (=CGMCC 1.6130(T)=JCM 13954(T)).

Alteromonadaceae↗
PubMed2006

Study on modeling of multispectral emissivity and optimization algorithm.

Target's spectral emissivity changes variously, and how to obtain target's continuous spectral emissivity is a difficult problem to be well solved nowadays. In this letter, an activation-function-tunable neural network is established, and a multistep searching method which can be used to train the model is proposed. The proposed method can effectively calculate the object's continuous spectral emissivity from the multispectral radiation information. It is a universal method, which can be used to realize on-line emissivity demarcation.

Letter↗
PubMed2006

[Inhibitory effect of CVB3-VP1 siRNA on CVB3 replication].

AIM: To inhibit the expression of CVB3 VP1 protein and the replication of CVB3 with synthesized siRNAs. METHODS: According to the sequence and secondary structure of CVB3 VP1 protein, four pieces of siRNAs were designed following the requirement from Journal of Nature Cell Biology were synthesized in Shanghai GeneChem Company. Then they were transfected into HeLa cells by liposome (Lipofectamine 2000), but the non-transfected cells and non-specific siRNAs were taken as control. 48 hours later, the patho-morphous changes were observed, virus titer changes were examined by TCID50, CVB3-VP1 protein expression were detected by immunofluorescence with FITC dyeing, and CVB3-RNA level was tested by semi-quantitative RT-PCR. RESULTS: Two pieces of the four specific synthesized siRNAs (VP1-1 and VP1-2) were found to have obvious inhibitory effect on CVB3 replication and VP1 protein expression were reduced greatly. Besides, the changes of pathological cells were obviously mitigated. CONCLUSION: Specific siRNAs can effectively inhibit the expression of CVB3 VP1 protein and the replication of CVB3 in HeLa cells.

China↗
PubMed2006

[Phylogenetic analysis of bacterial diversity in Pacific Arctic sediments].

Using PCR-DGGE (denaturing gradient gel electrophoresis) methods, bacterial phylogenetic diversity in three Pacific Arctic sediment samples were investigated, taken from different depths in the range of 47 m to 3850 m. DGGE profiles of different layers in the same sediment sample are not completely same. 16S rDNA sequences corresponding to 50 excised bands from three sediment samples were analyzed and fell into seven lineages of the domain Bacteria: alpha- beta-, gamma-, delta-, epsilon- Proteobacteria, the Cytophaga-Flavobacterium-Bacteroides (CFB) group and Actinobacteria. However, the composition of bacterial phylotypes in three sediments is different. Fourteen sequences obtained from sediment B78 collected from the Canadian Basin belong to beta-, gamma- Proteobacteria, Comamonadaceae and Acidobacteria. Bacterial phylotypes in submarine plateau sediment P24 are alpha-, gamma-, delta-Proteobacteria; While seventeen sequences from sediment S11 colleted from continental slop in the Chukchi Sea are grouped into alpha-, gamma-, delta-, epsilon-Proteobacteria, the Cytophaga-Flavobacterium-Bacteroides (CFB) group and Actinobacteria. It is suggested the different characteristics of three sediments may cause the difference in the composition of bacterial phylotypes. 16S rDNA sequences from members of gamma-Proteobacteria dominated three sediments samples. The majority of the sequences were most closely related to uncultured marine environmental sequences, especially marine sediment environmental sequences (88% - 100%).

Arctic Regions↗
PubMed2006

[Phylogenetic diversity and cold-adaptive hydrolytic enzymes of culturable psychrophilic bacteria associated with sea ice from high latitude ocean, Artic].

The phylogenetic diversity of culturable psychrophilic bacteria associated with sea ice from high latitude sea (77 degrees 30'N - 81 degrees 12'N), Canadian Basin and Greenland sea Arctic, was investigated. A total of 37 psychrophilic strains were isolated using three different methods of ( i ) spread plate method: 100 microL of each dilution ice-melt sample was spreaded onto the surface of Marine 2216 agar (DIFCO laboratories, Detroit, MI) and incubated for 2 to 6 weeks at 4 degrees C; ( ii ) bath culture and spread plate method: 1 mL of sample was added to 9mL of NSW (unamended natural seawater, 0.2 microm prefiltered and autoclaved) and incubated for 1 months at - 1 degrees C, then spread plate method was used to isolate bacterial strains from the pre-cultured samples; ( iii ) cold shock, bath culture and spread plate method: samples were exposed to - 20 degrees C for 24h, then bacterial strains isolated by bath culture and spread plate method under aerobic conditions. Nearly half of psychrophilic strains are isolated by using method iii . 16S rDNA nearly full-length sequence analysis reveal that psychrophilic strains fall in two phylogenetic divisions, gamma-proteobacteria (in the genera Colwellia, Marinobacter, Shewanella, Thalassomonas, Glaciecola, Marinomonas and Pseudoalteromonas) and Cytophaga-Flexibacter-Bacteroides (in the genera Flavobacterium and Psychroflexus). Nine of bacterial isolates (BSi20007, BSi20497, BSi20517, BSi20537, BSi20170, BSi20001, BSi20002, BSi20675 and BSi20101) quite likely represent novel species (16S rDNA sequence similarity below 97%). One of strains (BSi20002) from Canadian Basin shows 100% sequence similarity to the Antarctic Weddell sea ice isolate Marinobacter sp. ANT8277, suggesting bacteria may have a bipolar distribution at the species level. AF283859 sequences were submitted to the BLAST search program of the National Center for Biotechnology Information website (NCBI, http://www. ncbi. nlm.nih. gov). Twenty sequences showing 100% similarity each other are retrieved from the database, eleven from Antarctic seawater bacteria, three from Antarctic sea-ice bacteria, one from Spitzbergen sea-ice bacteria, two from Chukchi Sea sea-ice bacteria, two from Canadian Basin sea-ice bacteria (in this study) and one from uncultured bacterium clone PDA-OTU11 associated with the coral Pocillopora damicornis from the Great Barrier Reef. These may indicate that the physiological and geographic barriers appear to be permeable and some bacterial species can survive in different environment. The majority of the bacterial strains are able to secrete diversity cold-adaptive hydrolytic enzymes into the medium at 4 degrees C. The isolates that are able to degrade Tween-80, glutin, and starch account for, respectively, 62.6%, 51.4% and 40.5%.

Arctic Regions↗
PubMed2005

Antiviral effects of sophoridine against coxsackievirus B3 and its pharmacokinetics in rats.

Coxsackievirus B3 (CVB3) is a major pathogen for acute and chronic viral myocarditis. The aim of this study was to investigate the antiviral effects of sophoridine, an alkaloid extracted from Chinese medicinal herb, Sophora flavescens, against CVB3, and the underlying pharmacokinetics. First, we determined the antiviral effects of sophoridine against CVB3 in in vitro (primarily cultured myocardial cells), in vivo (BALB/c mice) and serum pharmacological experiments. Then, we determined the pharmacokinetic behavior in serum samples of SD rats after oral administration by HPLC. Finally, we determined the effects of sophoridine on the production of cytokines in a murine viral myocarditis model by measuring mRNA expression of some important cytokines in hearts of infected BALB/c mice by RT-PCR. We found that sophoridine exhibited obvious antiviral effects both in vitro and in vivo, and serum samples obtained from rats with oral administration of sophoridine reduced the virus titers in infected myocardial cells. The serum concentration profile correlated closely with antiviral activity profile. Moreover, sophoridine significantly enhanced mRNA expression of IL-10 and IFN-gamma, but decreased TNF-alpha mRNA expression. In conclusion, sophoridine possesses antiviral activities against CVB3, by regulating cytokine expression, and it is likely that sophoridine itself, not its metabolites, is mainly responsible for the antiviral activities. Therefore, sophoridine may represent a potential therapeutic agent for viral myocarditis.

Alkaloids↗