Elevated nitrate enriches microbial functional genes for potential bioremediation of complexly contaminated sediments

Nitrate is an important nutrient and electron acceptor for microorganisms, having a key role in nitrogen (N) cycling and electron transfer in anoxic sediments. High-nitrate inputs into sediments could have a significant effect on N cycling and its associated microbial processes. However, few studies have been focused on the effect of nitrate addition on the functional diversity, composition, structure and dynamics of sediment microbial communities in contaminated aquatic ecosystems with persistent organic pollutants (POPs). Here we analyzed sediment microbial communities from a field-scale in situ bioremediation site, a creek in Pearl River Delta containing a variety of contaminants including polybrominated diphenyl ethers (PBDEs) and polycyclic aromatic hydrocarbons (PAHs), before and after nitrate injection using a comprehensive functional gene array (GeoChip 4.0). Our results showed that the sediment microbial community functional composition and structure were markedly altered, and that functional genes involved in N-, carbon (C)-, sulfur (S)-and phosphorus (P)- cycling processes were highly enriched after nitrate injection, especially those microorganisms with diverse metabolic capabilities, leading to potential in situ bioremediation of the contaminated sediment, such as PBDE and PAH reduction/degradation. This study provides new insights into our understanding of sediment microbial community responses to nitrate addition, suggesting that indigenous microorganisms could be successfully stimulated for in situ bioremediation of POPs in contaminated sediments with nitrate addition.

GeoChip 4: a functional gene-array-based high-throughput environmental technology for microbial community analysis

Micro-organisms play critical roles in many important biogeochemical processes in the Earth's biosphere. However, understanding and characterizing the functional capacity of microbial communities are still difficult due to the extremely diverse and often uncultivable nature of most micro-organisms. In this study, we developed a new functional gene array, GeoChip 4, for analysing the functional diversity, composition, structure, metabolic potential/activity and dynamics of microbial communities. GeoChip 4 contained approximately 82 000 probes covering 141 995 coding sequences from 410 functional gene families related to microbial carbon (C), nitrogen (N), sulphur (S), and phosphorus (P) cycling, energy metabolism, antibiotic resistance, metal resistance/reduction, organic remediation, stress responses, bacteriophage and virulence. A total of 173 archaeal, 4138 bacterial, 404 eukaryotic and 252 viral strains were targeted, providing the ability to analyse targeted functional gene families of micro-organisms included in all four domains. Experimental assessment using different amounts of DNA suggested that as little as 500 ng environmental DNA was required for good hybridization, and the signal intensities detected were well correlated with the DNA amount used. GeoChip 4 was then applied to study the effect of long-term warming on soil microbial communities at a Central Oklahoma site, with results indicating that microbial communities respond to long-term warming by enriching carbon degradation, nutrient cycling (nitrogen and phosphorous) and stress response gene families. To the best of our knowledge, GeoChip 4 is the most comprehensive functional gene array for microbial community analysis.

Development of HuMiChip for functional profiling of human microbiomes

Understanding the diversity, composition, structure, function, and dynamics of human microbiomes in individual human hosts is crucial to reveal human-microbial interactions, especially for patients with microbially mediated disorders, but challenging due to the high diversity of the human microbiome. Here we have developed a functional gene-based microarray for profiling human microbiomes (HuMiChip) with 36,802 probes targeting 50,007 protein coding sequences for 139 key functional gene families. Computational evaluation suggested all probes included are highly specific to their target sequences. HuMiChip was used to analyze human oral and gut microbiomes, showing significantly different functional gene profiles between oral and gut microbiome. Obvious shifts of microbial functional structure and composition were observed for both patients with dental caries and periodontitis from moderate to advanced stages, suggesting a progressive change of microbial communities in response to the diseases. Consistent gene family profiles were observed by both HuMiChip and next generation sequencing technologies. Additionally, HuMiChip was able to detect gene families at as low as 0.001% relative abundance. The results indicate that the developed HuMiChip is a useful and effective tool for functional profiling of human microbiomes.

Observation of electron neutrino appearance in a muon neutrino beam

The T2K experiment has observed electron neutrino appearance in a muon neutrino beam produced 295 km from the Super-Kamiokande detector with a peak energy of 0.6 GeV. A total of 28 electron neutrino events were detected with an energy distribution consistent with an appearance signal, corresponding to a significance of 7.3σ when compared to 4.92±0.55 expected background events. In the Pontecorvo-Maki-Nakagawa-Sakata mixing model, the electron neutrino appearance signal depends on several parameters including three mixing angles θ12, θ23, θ13, a mass difference Δm(32)(2) and a CP violating phase δ(CP). In this neutrino oscillation scenario, assuming |Δm(32)(2)|=2.4×10(-3)  eV(2), sin(2)θ(23)=0.5, and Δm322>0 (Δm(32)(2)<0), a best-fit value of sin(2)2θ(13)=0.140(-0.032)(+0.038) (0.170(-0.037)(+0.045)) is obtained at δ(CP)=0. When combining the result with the current best knowledge of oscillation parameters including the world average value of θ(13) from reactor experiments, some values of δ(CP) are disfavored at the 90% C.L.

Mucinous tubular and spindle cell carcinoma of the kidney: A case report and review of the literature

Mucinous tubular and spindle cell carcinoma of the kidney (MTSCC-K) is an unusual renal tumor. It is important to increase the recognition of MTSCC-K and improve the level of clinical diagnosis. The current study presents a case of MTSCC-K with clinical, imaging and pathological examination. A 60-year-old female presented to the First Hospital of Jilin University suffering from lumbodorsalgia on the right side for approximately one month, without gross hematuria and fever. Imaging examination by abdominal computed tomography scan revealed a ~6.5×5.0-cm solid mass in the inferior pole of the right kidney. The patient underwent laparoscopic radical resection of the right kidney. Pathological examination showed that the tumor was composed of small, elongated cords or tubules, in a tightly packed arrangement. Myxoid stroma was shown to be interspersed among the tubular cells, and appeared to exhibit slender tubular spindle cell-like structures. Tumor cells were smaller and cube-shaped or oval, with single small eosinophilic nucleoli and low-grade nuclei. Occasionally, necrosis and foam cell infiltration were observed. Myxoid stroma was stained by acidic mucus. Immunohistochemical markers, including CK7, CK19, EMA, Vimentin and P504S (AMACR) showed positive expression in tumoral cells, but the tumoral cells were CD10-negative. The MTSCC-K is a low-grade polymorphic renal epithelial neoplasm, which may be diagnosed by immunohistochemistry. The patients are likely to have an improved prognosis following surgery compared with patients with other renal cell carcinomas.

Hexavalent chromium reduction under fermentative conditions with lactate stimulated native microbial communities

Microbial reduction of toxic hexavalent chromium (Cr(VI)) in-situ is a plausible bioremediation strategy in electron-acceptor limited environments. However, higher [Cr(VI)] may impose stress on syntrophic communities and impact community structure and function. The study objectives were to understand the impacts of Cr(VI) concentrations on community structure and on the Cr(VI)-reduction potential of groundwater communities at Hanford, WA. Steady state continuous flow bioreactors were used to grow native communities enriched with lactate (30 mM) and continuously amended with Cr(VI) at 0.0 (No-Cr), 0.1 (Low-Cr) and 3.0 (High-Cr) mg/L. Microbial growth, metabolites, Cr(VI), 16S rRNA gene sequences and GeoChip based functional gene composition were monitored for 15 weeks. Temporal trends and differences in growth, metabolite profiles, and community composition were observed, largely between Low-Cr and High-Cr bioreactors. In both High-Cr and Low-Cr bioreactors, Cr(VI) levels were below detection from week 1 until week 15. With lactate enrichment, native bacterial diversity substantially decreased as Pelosinus spp., and Sporotalea spp., became the dominant groups, but did not significantly differ between Cr concentrations. The Archaea diversity also substantially decreased after lactate enrichment from Methanosaeta (35%), Methanosarcina (17%) and others, to mostly Methanosarcina spp. (95%). Methane production was lower in High-Cr reactors suggesting some inhibition of methanogens. Several key functional genes were distinct in Low-Cr bioreactors compared to High-Cr. Among the Cr resistant microbes, Burkholderia vietnamiensis, Comamonas testosterone and Ralstonia pickettii proliferated in Cr amended bioreactors. In-situ fermentative conditions facilitated Cr(VI) reduction, and as a result 3.0 mg/L Cr(VI) did not impact the overall bacterial community structure.

Measurement of neutrino oscillation parameters from muon neutrino disappearance with an off-axis beam

The T2K Collaboration reports a precision measurement of muon neutrino disappearance with an off-axis neutrino beam with a peak energy of 0.6 GeV. Near detector measurements are used to constrain the neutrino flux and cross section parameters. The Super-Kamiokande far detector, which is 295 km downstream of the neutrino production target, collected data corresponding to 3.01×10(20) protons on target. In the absence of neutrino oscillations, 205±17 (syst) events are expected to be detected while only 58 muon neutrino event candidates are observed. A fit to the neutrino rate and energy spectrum, assuming three neutrino flavors and normal mass hierarchy yields a best-fit mixing angle sin2(θ23)=0.514±0.082 and mass splitting |Δm(32)(2)|=2.44(-0.15)(+0.17)×10(-3) eV2/c4. Our result corresponds to the maximal oscillation disappearance probability.

The enhanced effect of surface microstructured porous titanium on adhesion and osteoblastic differentiation of mesenchymal stem cells

Porous titanium with appropriate surface treatments can be osteoinductive. To investigate the effect of surface treatments of porous titanium on the attachment and differentiation of mesenchymal stem cells (MSCs), two kinds of surface microstructured porous titaniums, H₂O₂/TaCl₅ treated one (HTPT), and H₂O₂/TaCl₅ and subsequent simulated body fluid (SBF) treated one (STPT) were fabricated, and non-treated one (NTPT) was used as control. The morphology, specific surface area (SSA), pore distribution and mechanical strength of these materials were characterized respectively, and the results showed that H₂O₂/TaCl₅ treatment led to a significant increase in both SSA and micropores of HTPT, and the further SBF immersion resulted in the formation of a layer of bone-like apatite on the surface of STPT. Although the surface treatments had a little negative impact on the compressive strength and elasticity modulus of porous titanium, the mechanical strength of HTPT or STPT was enough for the bone defect repair of the load-bearing sites. The protein adsorption and cell adhesion experiments confirmed that the microstructured surface notably enhanced porous titanium's protein binding capacity and promoted MSCs adhesion on the surface. More importantly, cell differentiation experiments proved that the microstructured surface evidently elevated the osteoblastic gene expressions of MSCs compared to NTPT. The enhanced biological effect by the surface treatments was more robust on STPT. Therefore, our results suggest that the microstructured surface has great potential for promoting MSCs differentiation towards osteoblasts, giving excellent support for the osteoinduction of porous titanium with appropriate surface treatments.

Microbial biogeochemistry of Boiling Springs Lake: a physically dynamic, oligotrophic, low-pH geothermal ecosystem

Boiling Springs Lake (BSL) in Lassen Volcanic National Park, California, is North America's largest hot spring, but little is known about the physical, chemical, and biological features of the system. Using a remotely operated vessel, we characterized the bathymetry and near-surface temperatures at sub-meter resolution. The majority of the 1.2 ha, pH 2.2 lake is 10 m deep and 50-52 °C, but temperatures reach 93 °C locally. We extracted DNA from water and sediments collected from warm (52 °C) and hot (73-83 °C) sites separated by 180 m. Gene clone libraries and functional gene microarray (GeoChip 3.0) were used to investigate the BSL community, and uptake of radiolabeled carbon sources was used to assess the relative importance of heterotrophic vs. autotrophic production. Microbial assemblages are similar in both sites despite the strong temperature differential, supporting observations of a dynamic, convectively mixed system. Bacteria in the Actinobacteria and Aquificales phyla are abundant in the water column, and Archaea distantly related to known taxa are abundant in sediments. The functional potential appears similar across a 5-year time span, indicating a stable community with little inter-annual variation, despite the documented seasonal temperature cycle. BSL water-derived DNA contains genes for complete C, N, and S cycles, and low hybridization to probes for N and S oxidation suggests that reductive processes dominate. Many of the detected genes for these processes were from uncultivated bacteria, suggesting novel organisms are responsible for key ecosystem services. Selection imposed by low nutrients, low pH, and high temperature appear to result in low diversity and evenness of genes for key functions involved in C, N, and S cycling. Conversely, organic degradation genes appear to be functionally redundant, and the rapid assimilation of radiolabeled organic carbon into BSL cells suggests the importance of allochthonous C fueling heterotrophic production in the BSL C cycle.

The PathoChip, a functional gene array for assessing pathogenic properties of diverse microbial communities

Pathogens present in the environment pose a serious threat to human, plant and animal health as evidenced by recent outbreaks. As many pathogens can survive and proliferate in the environment, it is important to understand their population dynamics and pathogenic potential in the environment. To assess pathogenic potential in diverse habitats, we developed a functional gene array, the PathoChip, constructed with key virulence genes related to major virulence factors, such as adherence, colonization, motility, invasion, toxin, immune evasion and iron uptake. A total of 3715 best probes were selected from 13 virulence factors, covering 7417 coding sequences from 1397 microbial species (2336 strains). The specificity of the PathoChip was computationally verified, and approximately 98% of the probes provided specificity at or below the species level, proving its excellent capability for the detection of target sequences with high discrimination power. We applied this array to community samples from soil, seawater and human saliva to assess the occurrence of virulence genes in natural environments. Both the abundance and diversity of virulence genes increased in stressed conditions compared with their corresponding controls, indicating a possible increase in abundance of pathogenic bacteria under environmental perturbations such as warming or oil spills. Statistical analyses showed that microbial communities harboring virulence genes were responsive to environmental perturbations, which drove changes in abundance and distribution of virulence genes. The PathoChip provides a useful tool to identify virulence genes in microbial populations, examine the dynamics of virulence genes in response to environmental perturbations and determine the pathogenic potential of microbial communities.

Influence of the human MIF promoter polymorphism on hepatocellular carcinoma prognosis

Hepatocellular carcinoma (HCC) is one of the most common worldwide malignancies. A relative complete diagnosis system for primary carcinoma of liver has already been established, but the surgical prognosis for HCC, which depends mainly on postoperative pathological classification and data of recurrence and metastasis, lacks valid experimental indicators. Macrophage migration inhibition factor (MIF) is related to many cancers; hence, the polymorphism of MIF genes may be associated with the surgical prognosis of HCC. The purpose of this study was to investigate the relationship between polymorphisms of MIF gene promoter 794CATT (MIF-794CATT) microsatellite repeats and HCC surgical prognosis and evaluate the contribution of polymorphism to the prognosis of hepatectomy. Sequencing was used to identify the MIF-794CATT of 241 patients who had been submitted to HCC surgery. These patients were classified into 2 groups: one with MIF-794CATT high-repetitive-sequence genotypes (7/x+8/x) and one with low-repetitive-sequence genotypes (5/5+5/6+6/6). Five indictors were analyzed: average survival times were compared using the t-test, and tumor-node-metastasis staging, recurrence and metastasis, differentiation grade, and survival rate were compared using the chi-square test. The (7/x+8/x) CATT group had 139 patients and the (5/5+5/6+6/6) CATT group had 102. Significant differences were found in the 5 factors (P = 0.000, 0.008, 0.002, 0.000, and 0.003, respectively). Patients with MIF-794CATT5-8 low-repetitive-sequence genotypes had better prognosis than those with high-repetitive-sequence genotypes. The polymorphism detection of MIF-794CATT microsatellite repeats is valuable for HCC surgical prognosis.

Icariin: a potential promoting compound for cartilage tissue engineering

OBJECTIVE

To investigate whether icariin, which is a widely used pharmacological constituent in traditional Chinese herbal medicine, can be a potential promoting compound for cartilage tissue engineering.

DESIGN

Icariin was added into cell-hydrogel constructs derived from neonatal rabbit chondrocytes and collagen type I. The chondrogenic gene expressions and the synthesis of cartilage matrix of the seeded cells were detected by quantitative reverse transcription-polymerase chain reaction (qRT-PCR) and Biochemical assay. The effects of icariin-added cell-hydrogel constructs on the restoration of supercritical-sized osteochondral defects of adult rabbit were investigated by histological observation. The cell-hydrogel constructs without Icariin were set for controls.

RESULTS

Icariin obviously up-regulate the expressions included aggrecan, sox9, and collagen type II of seeded chondrocytes from 99.7% to 248%. It increases the synthesis of glycosaminoglycan and collagen type II about fourfold to fivefolds from week 1 to week 4, and accelerates the formation of chondroid tissue in the cell-hydrogel constructs. Even, it improves the restoration efficiency of supercritical-sized osteochondral defects in adult rabbit model, and enhances the integration of new-formed cartilage with subchondral bone.

CONCLUSIONS

Icariin can be a potential promoting compound for cartilage tissue engineering, and it can be a substitute for the use of some growth factors. The long history and extensive cases of safe use in China, Japan and Korea make it more attractive.

Genomic profiling of rice sperm cell transcripts reveals conserved and distinct elements in the flowering plant male germ lineage

Genomic assay of sperm cell RNA provides insight into functional control, modes of regulation, and contributions of male gametes to double fertilization. Sperm cells of rice (Oryza sativa) were isolated from field-grown, disease-free plants and RNA was processed for use with the full-genome Affymetrix microarray. Comparison with Gene Expression Omnibus (GEO) reference arrays confirmed expressionally distinct gene profiles. A total of 10,732 distinct gene sequences were detected in sperm cells, of which 1668 were not expressed in pollen or seedlings. Pathways enriched in male germ cells included ubiquitin-mediated pathways, pathways involved in chromatin modeling including histones, histone modification and nonhistone epigenetic modification, and pathways related to RNAi and gene silencing. Genome-wide expression patterns in angiosperm sperm cells indicate common and divergent themes in the male germline that appear to be largely self-regulating through highly up-regulated chromatin modification pathways. A core of highly conserved genes appear common to all sperm cells, but evidence is still emerging that another class of genes have diverged in expression between monocots and dicots since their divergence. Sperm cell transcripts present at fusion may be transmitted through plasmogamy during double fertilization to effect immediate post-fertilization expression of early embryo and (or) endosperm development.

Molecular cloning, characterization and expression analysis of B cell translocation gene 1 in grass carp Ctenopharyngodon idella

An expressed sequence tag (EST) of B cell translocation gene (BTG) 1 (gcbtg1) was obtained from a grass carp Ctenopharyngodon idellus intestinal complementary (c)DNA library and the full-length cDNA sequence was acquired by rapid amplification of cDNA ends (RACE) technology. The predicted Gcbtg1 protein contains the box A and box B motifs which characterized the BTG and transducer of ERBB2 (TOB) family. Multiple alignment analysis reveals that Gcbtg1 shares an overall identity of 65-94% with Gcbtg1s of other vertebrates. Real-time quantitative PCR analysis reveals that the highest expression level of gcbtg1 was detected in liver and the lowest in muscle. Western blotting analysis indicates that the immunological cross-reactivity occurs between C. idella and human Homo sapiens BTG1 protein. A 1008 bp 5'-flanking region sequence was cloned and analysed.

Characterization of 10 tobacco vein banding mosaic virus isolates from China

The complete RNA genome sequences of 10 tobacco vein banding mosaic virus (TVBMV) isolates from China were determined using five overlapping cDNA clones. TVBMV was divided into three groups for HC-Pro and CP and into two groups for P3 and 6K1. With more isolate sequences analyzed, the phylogenetic results suggest that TVBMV could be divided into four subgroups based on HC-Pro and CP and into three subgroups with P3 and 6K1. Nucleotide sequence diversity analysis showed geographical differentiation among the TVBMV isolates. Three of the 10 isolates were found to have undergone recombination and new recombination sites were identified in the TVBMV genome. All coding genes were under negative selection and the population appeared to have remained stable over a long period. This study also provides preliminary data on the 3´-untranslated region as potentially the best genome sequence for developing transgenic tobacco.

Biochemical markers comparison of dynamic hip screw and Gamma nail implants in the treatment of stable intertrochanteric fracture: a prospective study of 60 patients

This prospective study compared the extent of surgical trauma following dynamic hip screw (DHS) or Gamma nail (GN) implantation in 60 patients (≥ 60 years old) with stable intertrochanteric fracture. Levels of the biochemical markers creatinine kinase (CK) and C-reactive protein (CRP) were measured pre- and postoperatively. CRP levels were statistically significantly lower on postoperative days 1 and 2 in patients in the DHS versus the GN group; no other differences were observed. Surgical procedures for DHS implantation were considered less invasive than those for GN implantation, although the degree of muscle damage was similar in both groups. The degree of bone and bone marrow damage, rather than muscle tissue damage, may be crucial for determining the CRP response during the operative period. It is concluded that DHS implantation may be described as a more 'systemically' minimally invasive procedure than GN implantation.

Analysis of myostatin and its related factors in various porcine tissues

Myostatin is expressed in skeletal muscle tissue where it functions to suppress myoblast proliferation and myofiber hypertrophy. Recently, myostatin was detected in the tendon, mammary gland, and adipose tissue of mice. We sought to determine whether myostatin is expressed in the liver, spleen, lung, and kidney of pigs. Real-time PCR and Western blots demonstrated that myostatin, follistatin, decorin, and activin receptor IIB (ActRIIB) mRNA and proteins were expressed in skeletal muscle, heart muscle, and adipose tissue, and also in liver, spleen, lung, kidney, and cultured fibroblasts. The relative abundance of myostatin was closely related to follistatin and decorin in porcine tissues. Immunohistochemical analysis further demonstrated the presence of myostatin, follistatin, and decorin in the skeletal muscle, adipose tissue, heart muscle, liver, spleen, lung, and kidney of pigs. These results suggest that myostatin could be associated with certain functions of the internal organs, such as energy metabolism or fibrosis. We conclude that myostatin is a factor broadly expressed in the internal organs and muscle tissues of pigs.