Genetic diversity and paternal origin of domestic donkeys

Numerous studies have been conducted to investigate genetic diversity, origins and domestication of donkey using autosomal microsatellites and the mitochondrial genome, whereas the male-specific region of the Y chromosome of modern donkeys is largely uncharacterized. In the current study, 14 published equine Y chromosome-specific microsatellites (Y-STR) were investigated in 395 male donkey samples from China, Egypt, Spain and Peru using fluorescent labeled microsatellite markers. The results showed that seven Y-STRs-EcaYP9, EcaYM2, EcaYE2, EcaYE3, EcaYNO1, EcaYNO2 and EcaYNO4-were male specific and polymorphic, showing two to eight alleles in the donkeys studied. A total of 21 haplotypes corresponding to three haplogroups were identified, indicating three independent patrilines in domestic donkey. These markers are useful for the study the Y-chromosome diversity and population genetics of donkeys in Africa, Europe, South America and China.

Effects of ginsenoside Rg1 on glucose metabolism and liver injury in streptozotocin-induced type 2 diabetic rats

Type 2 diabetes mellitus (T2-DM) is a chronic metabolic disorder characterized by high blood glucose levels. T2-DM patients suffer from many complications, such as diabetic fatty liver and diabetic nephropathy. The liver, the pivotal organ involved in both glucose and lipid metabolism, is primarily damaged in T2-DM patients, especially in those with high levels of blood lipid. In this study, the hepatoprotective activity of ginsenoside Rg1 was investigated in a T2-DM rat model. The results revealed a potent hepatoprotective effect of ginsenoside Rg1. This effect was primarily mediated by the antiapoptotic effect, inhibition of JNK activity, and suppression of inflammation after ginsenoside Rg1 treatment. Ginsenoside Rg1 also lowered the blood glucose level and insulin resistance index in T2-DM rats. Moreover, the blood lipid profile (total cholesterol, triglycerides, and low-density lipoprotein cholesterol levels) and liver function (aspartate transaminase and alanine transaminase levels) improved after ginsenoside Rg1 treatment. The aforementioned hepatoprotective effects of ginsenoside Rg1 in the T2-DM rat model suggests its clinical potential as an adjuvant drug for T2-DM therapy, especially for T2-DM patients with fatty liver disease.

Abstract P2-04-22: Porous silicon microparticle potentiates anti-tumor immunity

This abstract was not presented at the symposium.

Exploring the Mutational Robustness of Nucleic Acids by Searching Genotype Neighborhoods in Sequence Space

To assess the mutational robustness of nucleic acids, many genome- and protein-level studies have been performed, where nucleic acids are treated as genetic information carriers and transferrers. However, the molecular mechanisms through which mutations alter the structural, dynamic, and functional properties of nucleic acids are poorly understood. Here we performed a SELEX in silico study to investigate the fitness distribution of the l-Arm-binding aptamer genotype neighborhoods. Two novel functional genotype neighborhoods were isolated and experimentally verified to have comparable fitness as the wild-type. The experimental aptamer fitness landscape suggests the mutational robustness is strongly influenced by the local base environment and ligand-binding mode, whereas bases distant from the binding pocket provide potential evolutionary pathways to approach the global fitness maximum. Our work provides an example of successful application of SELEX in silico to optimize an aptamer and demonstrates the strong sensitivity of mutational robustness to the site of genetic variation.

[Application of COⅠ Gene Mini-barcoding in Species Identification of Hair]

OBJECTIVES

To identify the species of mammalian hair using COⅠ gene mini-barcoding technology.

METHODS

A pair of universal primers for mammalian COⅠ gene mini-barcoding were designed. The hair DNA samples of experimental animals from 11 species in 5 orders, mammalia was amplified by PCR technology with universal primers, and the PCR products were sequenced by bi-directional DNA and after the sequences splicing the results were deposited into the BOLD database to perform the homology comparison.

RESULTS

The DNA of hair from all experiment animal species could be totally amplified by the mini-barcoding universal primers designed in this study. The length of amplified fragment was 147 bp. The result of homology comparison in the database showed that the closest matching species were consistent with the experiment animal species. In addition to the matching degree of Panthera leo （98.99%）, all homology matching degree of the other experiment animals were 100%, and the intraspecific genetic distance of Panthera leo was 1%. The interspecific genetic distance was ten times more than the intraspecific genetic distance which could be used for species identification.

CONCLUSIONS

The COⅠ gene mini-barcode technology is established and can provide fast and accurate species identification for hair of mammals.

Precision Measurement of the Boron to Carbon Flux Ratio in Cosmic Rays from 1.9 GV to 2.6 TV with the Alpha Magnetic Spectrometer on the International Space Station

Knowledge of the rigidity dependence of the boron to carbon flux ratio (B/C) is important in understanding the propagation of cosmic rays. The precise measurement of the B/C ratio from 1.9 GV to 2.6 TV, based on 2.3 million boron and 8.3 million carbon nuclei collected by AMS during the first 5 years of operation, is presented. The detailed variation with rigidity of the B/C spectral index is reported for the first time. The B/C ratio does not show any significant structures in contrast to many cosmic ray models that require such structures at high rigidities. Remarkably, above 65 GV, the B/C ratio is well described by a single power law R^{Δ} with index Δ=-0.333±0.014(fit)±0.005(syst), in good agreement with the Kolmogorov theory of turbulence which predicts Δ=-1/3 asymptotically.

Inactivation of Cronobacter sakazakii in reconstituted infant formula by combination of thymoquinone and mild heat

AIMS

The objective of this study was to determine the combined effect of thymoquinone (TQ) and mild heat on Cronobacter sakazakii in reconstituted infant formula.

METHODS AND RESULTS

Reconstituted infant formula samples inoculated with a mixture of four C. sakazakii strains (approx. 6·5 log CFU ml(-1) ) were prepared with various concentrations of TQ (0, 5, 10, 20 and 30 mmol l(-1) ) and were heated to 45, 50 and 55°C for 0, 10, 20, 30, 60 and 120 min, and the surviving populations of C. sakazakii at each sampling time were enumerated. To elucidate the mode of action of TQ, membrane integrity and changes in cell morphology were examined by LIVE/DEAD(®) BacLight(™) bacterial viability kit and field emission scanning electron microscope respectively. TQ at 30 mmol l(-1) reduced the pathogen to undetectable level in between 60 and 120 min at 45°C, 60 min at 50°C and 10 min at 55°C respectively.

CONCLUSIONS

Our results demonstrated that the combined treatments significantly reduced (P < 0·05) the population of C. sakazakii, compared to the control. Cronobacter sakazakii numbers were reduced much more rapidly with higher temperatures and increased concentrations of TQ. And combined treatment inactivated pathogen partly by causing cell membrane disruption.

SIGNIFICANCE AND IMPACT OF THE STUDY

These findings suggested that TQ, together with mild heat, may have potential application in infant formula to control C. sakazakii before consumption and therefore is a possible way to prevent infections associated with C. sakazakii in infant formula.

Insights into the Biogenic Amine Metabolic Landscape during Industrial Semidry Chinese Rice Wine Fermentation

Inspired by concerns about food safety, the metabolic landscape of biogenic amines (BAs) was elucidated during industrial semidry Chinese rice wine fermentation. The main fermentation process represented the largest contribution to BA formation, which corresponded to 69.1% (54.3 mg/L). Principal component analysis revealed that total acid and ethanol were strongly correlated with BAs, indicating that BA formation favored acidic and stressful conditions. Other than putrescine (PUT), spermidine (SPD), and spermine (SPM), 5 BAs exhibited strong relationships with the precursor amino acids (R² > 0.85). PUT was mainly decarboxylated from arginine (89.6%) whereas SPD (100%) and SPM (83.1%) were obtained from ornithine. Interestingly, some SPD could convert back to PUT (24.3%). All 8 BAs showed good relationships with lactic acid bacteria (LAB) (R² around 0.75). Moreover, among the five main LAB genera, Lactobacillus had a positive correlation with BA formation.

Antiproton Flux, Antiproton-to-Proton Flux Ratio, and Properties of Elementary Particle Fluxes in Primary Cosmic Rays Measured with the Alpha Magnetic Spectrometer on the International Space Station

A precision measurement by AMS of the antiproton flux and the antiproton-to-proton flux ratio in primary cosmic rays in the absolute rigidity range from 1 to 450 GV is presented based on 3.49×10^{5} antiproton events and 2.42×10^{9} proton events. The fluxes and flux ratios of charged elementary particles in cosmic rays are also presented. In the absolute rigidity range ∼60 to ∼500  GV, the antiproton p[over ¯], proton p, and positron e^{+} fluxes are found to have nearly identical rigidity dependence and the electron e^{-} flux exhibits a different rigidity dependence. Below 60 GV, the (p[over ¯]/p), (p[over ¯]/e^{+}), and (p/e^{+}) flux ratios each reaches a maximum. From ∼60 to ∼500  GV, the (p[over ¯]/p), (p[over ¯]/e^{+}), and (p/e^{+}) flux ratios show no rigidity dependence. These are new observations of the properties of elementary particles in the cosmos.

Prevalence of genital human papillomavirus among rural and urban populations in southern Yunnan province, China

This study was designed to investigate and compare the HPV prevalence, genotypes distribution and associated risk factors in rural and urban women living in Xishuang Banna district, in the province of Yunnan. A total of 177 and 190 women from rural and urban areas were engaged, respectively. HPV DNA was amplified using the L1 consensus primers system (MY09/11 and GP5/6) and HPV GenoArray test was conducted for genotyping. Proportions were compared by chi-square test, and logistic regression was used to evaluate risk factors. A total of 54 women were positive for HPV DNA. Among rural women, 23 women were positive for HPV infection, of which 21 showed a single infection and 2 had a multiple infection. HPV-16 (10/23) was the most prevalent genotype followed by HPV-52 (5/23), and HPV-58 (5/23). Urban women had a higher infection rate for overall HPV (31/54) and for multiple genotype infection (8/31). HPV-52 (9/31) was the most prevalent genotype followed by HPV-39 (7/31) and HPV-68 (5/31). The age-specific HPV prevalence was also different between rural and urban women. In urban area, women with age <35 years had the highest HPV prevalence, which declined thereafter as age advanced. However, in rural women the highest HPV prevalence was observed in an older age group (>56 years). Ethnicity, smoking and parity were significantly associated with HPV infection among urban women. Our study demonstrates that HPV prevalence and genotype distribution varies among women from rural and urban areas in the south of Yunnan.

Measurement of the Reactor Antineutrino Flux and Spectrum at Daya Bay

This Letter reports a measurement of the flux and energy spectrum of electron antineutrinos from six 2.9 GWth nuclear reactors with six detectors deployed in two near (effective baselines 512 and 561 m) and one far (1579 m) underground experimental halls in the Daya Bay experiment. Using 217 days of data, 296 721 and 41 589 inverse β decay (IBD) candidates were detected in the near and far halls, respectively. The measured IBD yield is (1.55±0.04) ×10(-18)  cm(2) GW(-1) day(-1) or (5.92±0.14) ×10(-43)  cm(2) fission(-1). This flux measurement is consistent with previous short-baseline reactor antineutrino experiments and is 0.946±0.022 (0.991±0.023) relative to the flux predicted with the Huber-Mueller (ILL-Vogel) fissile antineutrino model. The measured IBD positron energy spectrum deviates from both spectral predictions by more than 2σ over the full energy range with a local significance of up to ∼4σ between 4-6 MeV. A reactor antineutrino spectrum of IBD reactions is extracted from the measured positron energy spectrum for model-independent predictions.

Serum uric acid predicts cardiovascular mortality in male peritoneal dialysis patients with diabetes

BACKGROUND AND AIMS

Serum uric acid may predict mortality in diabetic patients and dialysis patients. However, the relationship between serum uric acid and prognosis in diabetic peritoneal dialysis (PD) patients is unclear.

METHODS AND RESULTS

We conducted a cohort study of 1278 incident PD patients, (mean age 47.6 years), of which 328 (25.7%) had diabetes and 289 (22.6%) had diabetic nephropathy. During a median follow-up period of 30.7 months, 231 deaths occurred, of which 126 were ascribed to cardiovascular events. Mean serum uric acid was lower for diabetic patients than non-diabetic patients (6.8 ± 1.3 vs. 7.4 ± 1.4 mg/dL, respectively; P < 0.001). Cox regression models were adjusted for glycated hemoglobin, dialysis-related factors, traditional risk factors, and treatments. After adjustments, the highest sex-specific tertile of uric acid was associated with an increased risk of cardiovascular mortality (HR, 2.26; 95% CI, 1.14-4.48) compared to the lowest tertile in diabetic patients. Adjusted HRs per 1 mg/dL higher uric acid for all-cause and cardiovascular mortality were 1.09 (95% CI, 0.91-1.32) and 1.42 (95% CI, 1.13-1.79) for diabetic men and 1.06 (95% CI, 0.83-1.35) and 1.12 (95% CI, 0.78-1.61) for diabetic women, respectively. Elevated serum uric acid predicted a higher risk of all-cause and cardiovascular mortality in non-diabetic men but not in non-diabetic women.

CONCLUSIONS

Elevated serum uric acid is an independent predictor of cardiovascular mortality in diabetic male PD patients.

Precision Measurement of the Helium Flux in Primary Cosmic Rays of Rigidities 1.9 GV to 3 TV with the Alpha Magnetic Spectrometer on the International Space Station

Knowledge of the precise rigidity dependence of the helium flux is important in understanding the origin, acceleration, and propagation of cosmic rays. A precise measurement of the helium flux in primary cosmic rays with rigidity (momentum/charge) from 1.9 GV to 3 TV based on 50 million events is presented and compared to the proton flux. The detailed variation with rigidity of the helium flux spectral index is presented for the first time. The spectral index progressively hardens at rigidities larger than 100 GV. The rigidity dependence of the helium flux spectral index is similar to that of the proton spectral index though the magnitudes are different. Remarkably, the spectral index of the proton to helium flux ratio increases with rigidity up to 45 GV and then becomes constant; the flux ratio above 45 GV is well described by a single power law.

Searching the Sequence Space for Potent Aptamers Using SELEX in Silico

To isolate functional nucleic acids that bind to defined targets with high affinity and specificity, which are known as aptamers, the systematic evolution of ligands by exponential enrichment (SELEX) methodology has emerged as the preferred approach. Here, we propose a computational approach, SELEX in silico, that allows the sequence space to be more thoroughly explored regarding binding of a certain target. Our approach consists of two steps: (i) secondary structure-based sequence screening, which aims to collect the sequences that can form a desired RNA motif as an enhanced initial library, followed by (ii) sequence enrichment regarding target binding by molecular dynamics simulation-based virtual screening. Our SELEX in silico method provided a practical computational solution to three key problems in aptamer sequence searching: design of nucleic acid libraries, knowledge of sequence enrichment, and identification of potent aptamers. Six potent theophylline-binding aptamers, which were isolated by SELEX in silico from a sequence space containing 4(13) sequences, were experimentally verified to bind theophylline with high affinity: Kd ranging from 0.16 to 0.52 μM, compared with the dissociation constant of the original aptamer-theophylline, 0.32 μM. These results demonstrate the significant potential of SELEX in silico as a new method for aptamer discovery and optimization.

New measurement of antineutrino oscillation with the full detector configuration at Daya Bay

We report a new measurement of electron antineutrino disappearance using the fully constructed Daya Bay Reactor Neutrino Experiment. The final two of eight antineutrino detectors were installed in the summer of 2012. Including the 404 days of data collected from October 2012 to November 2013 resulted in a total exposure of 6.9×10^{5} GW_{th}  ton days, a 3.6 times increase over our previous results. Improvements in energy calibration limited variations between detectors to 0.2%. Removal of six ^{241}Am-^{13}C radioactive calibration sources reduced the background by a factor of 2 for the detectors in the experimental hall furthest from the reactors. Direct prediction of the antineutrino signal in the far detectors based on the measurements in the near detectors explicitly minimized the dependence of the measurement on models of reactor antineutrino emission. The uncertainties in our estimates of sin^{2}2θ_{13} and |Δm_{ee}^{2}| were halved as a result of these improvements. An analysis of the relative antineutrino rates and energy spectra between detectors gave sin^{2}2θ_{13}=0.084±0.005 and |Δm_{ee}^{2}|=(2.42±0.11)×10^{-3}  eV^{2} in the three-neutrino framework.