GENETIC ANALYSIS OF TROPODITHIETIC ACID BIOSYNTHESIS IN MARINE BACTERIA

Members of the Roseobacter clade of alphaproteobacteria are among the most abundant and ecologically relevant marine bacteria. The antibiotic tropodithietic acid (TDA) produced by roseobacters is hypothesized to be a critical component of the roseobacter-phytoplankton symbiosis. TDA production is influenced by environmental conditions. Specifically, in the lab, TDA activity is highest when bacteria are cultured in standing liquid nutrient broth, whereas cells produce negligible TDA in nutrient broth with shaking. Random mutagenesis was used to construct loss-of-function mutants defective in TDA activity (Tda-). Twelve genes were identified as required for Tda activity. Six tda genes, tdaA-F, are physically linked and are carried on pSTM3, a ca. 130-kb plasmid, while the remaining 6 genes are located on the sequenced genome. Genetic and molecular biological evidence demonstrates that tdaA and tdaB form a bicistronic message, tdaCDE are part of a separate operon, and tdaF is likely a part of a third operon. The expression of tdaAB is constitutive, whereas tdaCDE and tdaF mRNA are regulated, showing significantly increased levels when cells are grown in standing liquid broth compared to shaking liquid culturing. Expression of tdaCDE is lost in Tda- strains, but could be restored- tdaA and tdaH failed to respond - by placing wild-type Tda+ strains in close proximity or by adding exogenous TDA to the mutant. These results indicate that TDA acts as an autoinducer of its own synthesis and suggest that roseobacters may use TDA as a quorum signal. Next, I focused attention on the only known regulatory protein, TdaA, involved in tda expression. Disruption of tdaA results in loss of tdaCDE expression, and expression of tdaA in an Escherichia coli background is sufficient to transcribe tdaCDE. Transcriptional activation of the tdaC promoter by TdaA is supported by data from electrophoretic mobility shift assays (EMSA) showing that purified TdaA protein binds specifically to a fragment of DNA containing the tdaC promoter. These results support a hypothesis that TdaA is a positive transcriptional regulator of tdaCDE gene expression whose function requires binding to the tdaC promoter region. One of the mechanisms used by TM1040 to regulate TDA biosynthesis is therefore through TdaA regulator

Quantify single nucleotide polymorphism (SNP) ratio in pooled DNA based on normalized fluorescence real-time PCR

BACKGROUND: Conventional real-time PCR to quantify the allele ratio in pooled DNA mainly depends on PCR amplification efficiency determination and Ct value, which is defined as the PCR cycle number at which the fluorescence emission exceeds the fixed threshold. Because of the nature of exponential calculation, slight errors are multiplied and the variations of the results seem too large. We have developed a new PCR data point analysis strategy for allele ratio quantification based on normalized fluorescence ratio. RESULTS: In our method, initial reaction background fluorescence was determined based upon fitting of raw fluorescence data to four-parametric sigmoid function. After that, each fluorescence data point was first subtracted by respective background fluorescence and then each subtracted fluorescence data point was divided by the specific background fluorescence to get normalized fluorescence. By relating the normalized fluorescence ratio to the premixed known allele ratio of two alleles in standard samples, standard linear regression equation was generated, from which unknown specimens allele ratios were extrapolated using the measured normalized fluorescence ratio. In this article, we have compared the results of the proposed method with those of baseline subtracted fluorescence ratio method and conventional Ct method. CONCLUSION: Results demonstrated that the proposed method could improve the reliability, precision, and repeatability for quantifying allele ratios. At the same time, it has the potential of fully automatic allelic ratio quantification

Causal association of circulating cholesterol levels with dementia: a mendelian randomization meta-analysis

Prospective studies have shown that abnormally circulating cholesterol is associated with the risk of dementia. However, whether the association is causal or not remains unclear. We attempt to infer the causal association in a MR meta-analysis by using ApoE gene polymorphisms as instrument variables. Studies with dementia risk (27 studies) or circulating lipid levels (7 studies) were included, with totally 3136 dementia patients and 3103 healthy controls. The analyses showed that carriers of ε2 allele significantly were of decreased risk of AD (OR = 0.70; 95% CI: 0.58–0.84; P \u3c 0.01), whereas carriers of ε4 allele were of increased risk of AD (OR = 3.62; 95% CI: 3.03–4.32; P \u3c 0.05), compared to these of ε3 allele. Circulating TC was significantly reduced in carriers of ε2 allele (WMD = − 0.29 mmol/L; 95% CI: −0.54 to −0.03; P \u3c 0.05) and increased in carriers of ε4 allele (WMD = 0.42 mmol/l; 95% CI: 0.001–0.84; P \u3c 0.05). In addition, carriers of ε4 allele had reduction in circulating HDL-C (WMD = − 0.04 mmol/L; 95% CI: − 0.07 to −0.001; P \u3c 0.05). In comparing allele ε2 with ε3, the predicted OR of having AD for 1 mg/dL increment in circulating TC was 0.97 (95% CI: 0.86–0.98; P \u3c 0.05). Comparing allele ε4 with ε3, the predicted OR for a 1 mg/dL increment in TC was 1.08 (95% CI: 1.05–17.58; P \u3c 0.05), and reduction in HDL-C was 2.30 (95% CI: 1.51–43.99; P \u3c 0.05). Our findings demonstrate that high circulating TC and reduced HDL-C levels might be potential risk factors of the development of AD

Predictive values of clinical data,molecular biomarkers, and echocardiographic measurements in preterm infants with bronchopulmonary dysplasia

ObjectiveWe aimed to use molecular biomarkers and clinical data and echocardiograms that were collected during admission to predict bronchopulmonary dysplasia (BPD) in preterm infants with gestational age ≤32 weeks.MethodsEighty-two patients (40 with BPD, BPD group and 42 healthy as controls, non-BPD group) admitted to the Department of Neonatology of the Children's Hospital of Soochow University between October 1, 2018, and February 29, 2020, were enrolled in this study at the tertiary hospital. Basic clinical data on the perinatal period, echocardiographic measurements, and molecular biomarkers (N-terminal-pro-B-brain natriuretic peptide, NT-proBNP) were collected. We used multiple logistic regression analysis to establish an early predictive model for detecting BPD development in preterm infants of gestational age ≤32 weeks. We also used a receiver operating characteristic curve to assess the sensitivity and specificity of the model.ResultsNo significant differences were found between the BPD and non-BPD groups in terms of sex, birth weight, gestational age, incidence of asphyxia, maternal age, gravidity, parity, mode of delivery, premature rupture of membranes >18 h, use of prenatal hormones, placental abruption, gestational diabetes mellitus, amniotic fluid contamination, prenatal infections, and maternal diseases. The use of caffeine, albumin, gamma globulin; ventilation; days of FiO2 ≥ 40%; oxygen inhalation time; red blood cell suspension infusion volume (ml/kg); and proportion of infants who received total enteral nutrition (120 kcal/kg.d) ≥24 d after birth were higher in the BPD group than in the non-BPD group. The levels of hemoglobin, hematocrit, and albumin in the BPD group were significantly lower than those in the non-BPD group. The total calorie intake was significantly lower in the BPD group on the 3rd, 7th, and 14th day after birth than in the non-BPD group (P < 0.05). The incidence rates of patent ductus arteriosus (PDA), pulmonary hypertension, and tricuspid regurgitation were significantly higher in the BPD group than in the non-BPD group (P < 0.05). The serum level of NT-proBNP 24 h after birth was significantly higher in the BPD group than in the non-BPD group (P < 0.05). Serum NT-proBNP levels were significantly higher in infants with severe BPD than in those with mild or moderate BPD (P < 0.05).ConclusionAs there were various risk factors for BPD, a combining clinical data, molecular biomarkers, and echocardiogram measurements can be valuable in predicting the BPD. The tricuspid regurgitation flow rate (m/s), NT-proBNP (pg/ml), ventilator-associated pneumonia, days of FiO2 ≥ 40% (d), red blood cell suspension infusion volume (ml/kg), and proportion of infants who received total enteral nutrition (120 kcal/kg.d) ≥24 d after birth were the most practical factors considered for designing an appropriate model for predicting the risk of BPD

An agile laser with ultra-low frequency noise and high sweep linearity

We report on a fiber-stabilized agile laser with ultra-low frequency noise. The frequency noise power spectral density is comparable to that of an ultra-stable cavity stabilized laser at Fourier frequencies higher than 30 Hz. When it is chirped at a constant rate of ~ 40 MHz/s, the max non-linearity frequency error is about 50 Hz peak-to-peak over more than 600 MHz tuning range. The Rayleigh backscattering is found to be a significant frequency noise source dependent on fiber length, chirping rate and the power imbalance of the interferometer arms. We analyze this effect both theoretically and experimentally and put forward techniques to reduce this noise contribution.Comment: 14 pages, 11 figures, accepted by Optics Expres

Unveiling the origin of catalytic sites of Pt nanoparticles decorated on oxygen-deficient vanadium-doped cobalt hydroxide nanosheet for hybrid sodium-air batteries

Highly active bifunctional electrocatalysts are crucial for improving the performance of rechargeable metal-air batteries. However, most reported bifunctional electrocatalysts feature poor electrocatalytic activity and stability toward oxygen reduction reaction (ORR) and oxygen evolution reaction (OER). Here, we have reported the first-ever study of an effective one-step reduction-assisted exfoliation method to exfoliate bulk vanadium-doped cobalt hydroxide (V-doped Co(OH)2, denoted as V-Co(OH)2) into ultrathin nanosheets with abundant oxygen vacancies (V-Co(OH)2-Ov) and simultaneously anchor them with highly dispersed ultrafine Pt nanoparticles (NPs) with a nominal size of 0.8-2.4 nm (denoted as Pt/V-Co(OH)2-Ov). The Pt/V-Co(OH)2-Ov catalyst exhibits improved catalytic performance in ORR/OER. X-ray absorption spectroscopy analysis and theoretical calculations reveal the strong interfacial electronic interactions between Pt NPs and V-Co(OH)2-Ov, which synergistically improves oxygen intermediates' adsorption/desorption, enhancing the ORR and OER performance. Using Pt/V-Co(OH)2-Ov as a catalyst in the air cathode, a hybrid sodium-air battery displays a record value of an ultralow charging-discharging voltage gap of 0.07 V at a current density of 0.01 mA cm-2 with remarkable stability of up to 1000 cycles. This reduction-assisted exfoliation approach provides a new strategy to generate oxygen vacancies in metal hydroxides, which act as anchoring sites for deposition of sub-nanometal NPs via a strong interfacial effect

Moiré beatings in graphene on Ru(0001)

The moiré superstructure of a single layer of carbon on ruthenium, where 25×25 graphene honeycombs sit on 23×23 substrate unit cells, is determined from first principles. The density functional theory (DFT) calculations predict two kinds of structural units, Ω and Y, in the supercell, which are identified as moiré beatings or moirons. The related topographic bucklings, or "hills," have distinct carbon conformations and a height of 1.16 Å. The different moirons are observed with scanning tunneling microscopy (STM), and surface x-ray diffraction (SXRD) also discriminates the two. This connects ab initio DFT calculations with STM and SXRD experiments in unit cells containing more than 4000 atoms

Theoretical calculation of cesium deposition and co-deposition with electronegative elements on the plasma grid in negative ion sources

We studied the work function of cesium deposition and co-deposition with the electronegative element on the plasma grid (PG) using the first-principles calculations. The impurity particles may exist in the background plasma and vacuum chamber wall, and the work function of the PG will be affected. The results indicate that the minimum work functions of pure cesium deposition on Mo (110), W (110), and Mo (112) are reached at a partial monolayer. They are 1.66 eV (σ = 0.56 θ), 1.69 eV (σ = 0.75 θ), and 1.75 eV (σ = 0.88 θ), respectively. An appropriate co-deposition model consisting of cesium with electronegative elements can further decrease the work function. The coverage of cesium and electronegative elements are both 0.34 θ in all the co-deposition models. The F-Cs co-deposition model where the Cs atom and F atom are aligned along the surface normal obtains the lowest work function. They are 1.31 eV for F-Cs on Mo (110), and 1.23 eV for F-Cs on W (110), respectively. The change in work function is linearly related to the change in dipole moment density with a slope of −167.03 VÅ. For pure cesium deposition, two factors control the change in dipole-moment density, one is the electron transfer between adsorbates and the substrate, and another one is the restructuring of surface atoms. There are two additional factors for the co-deposition model. One is the intrinsic dipole moment of the double layer, the other is the angle between the intrinsic dipole moment and the surface. The latter two factors play important roles in increasing the total dipole moment