Molecular identification of honey entomological origin based on bee mitochondrial 16S rRNA and COI gene sequences

The increasing recognition and production of stingless bee honey has raised the needs to develop rapid, sensitive and accurate methodologies for honey identification through bees' species from the DNA of bees present in honey. Genetic identification of raw honeys produced by different bee species from Malaysia was performed based on mitochondrial DNA sequences and phylogenetic analysis by means of forensically informative nucleotide sequencing (FINS) technique. The 300 bp of mitochondrial large subunit ribosomal RNA (16S rRNA) gene region and mitochondrial cytochrome c oxidase subunit I (COI) gene region were the gene markers used to classify and identify honey produced by Apis honey bees and Trigona stingless bees. The genetic identities of honey origin from Apis dorsata, Apis mellifera, Apis cerana, and Heterotrigona itama were accurately identified. Kelulut honey sourced from the stingless bee was distinguishable from other Apis type of honeys in phylogenetic analyses. This FINS technique is a specific and reliable method for identification of honey origin via its bee source that can be used to overcome the issue of false declaration of honey origin and mislabelling.     

污水厂SBR池DO变化过程及研究

对污水厂SBR池曝气及后搅拌过程中的DO变化情况进行连续监测,取其中5个周期的数据进行分析,并考察曝气时序DO、p H与氮转化的相关性,计算SBR系统的OUR及SOUR值。结果显示曝气过程DO变化可分为3个阶段:第1阶段DO接近1.97 mg/L,波动较大;第2阶段DO稳定上升;第3阶段DO进入平台期。DO与混合液中有机物浓度负相关,有可能通过DO间接表示混合液中有机物浓度。DO和p H可以联合起来指示硝化过程的终点。     

Re‐exploration of the Codon Context Effect on Amber Codon‐Guided Incorporation of Noncanonical Amino Acids in Escherichia coli by the Blue–White Screening Assay

The effect of codon context on amber codon‐guided incorporation of noncanonical amino acids (NAAs) has been previously examined by antibiotic selection. Here, we re‐explored this effect by screening a library in which three nucleotides upstream and downstream of the amber codon were randomised, and inserted within the lacZ‐α gene. Thousands of clones were obtained and distinguished by the depth of blue colour upon exposure to X‐gal. Large‐scale sequencing revealed remarkable preferences in nucleotides downstream of the amber codon, and moderate preferences for upstream nucleotides. Nucleotide preference was quantified by a dual‐luciferase assay, which verified that the optimum context for NAA incorporation, AATTAGACT, was applicable to different proteins. Our work provides a general guide for engineering amber codons into genes of interest in bacteria.     

Heads or Tails: Genotyping of Hepatitis C Virus Concerning the 2k/1b Circulating Recombinant Form

As different hepatitis C virus (HCV) genotypes respond differently to initiated therapy, correct HCV genotyping is essential. A potential risk for misclassification of the intergenotypic HCV circulating recombinant form (CRF) 2k/1b strains exists, depending on the genotyping method used. The aim was to investigate the differences in HCV genotyping methods with regard to CRF 2k/1b and to gain insight in the prevalence of the CRF 2k/1b. Genotyping results by Versant HCV Genotype Assay were compared with nonstructural protein 5B (NS5B) sequencing. In total, from November 2001 until March 2015, 3296 serum samples were analyzed by Versant HCV Genotype Assay. As misclassified CRF is harbored among HCV genotype 2, we further focused our search on 142 (4.3%) samples positive for HCV genotype 2. On 116 (81.7%) retrieved samples, the NS5B sequencing was performed. Twelve out of the 116 retrieved samples (10.3%) were classified as CRF 2k/1b by sequencing of the NS5B region. Ten of these 12 samples were originally misclassified as genotype 2a or 2c, while 2 of them were misclassified as genotype 2. Our results show that the current prevalence of CRF 2k/1b is underestimated. The importance of correct HCV genotyping is emphasized, considering the tailored choice of treatment regimen and overall prognosis.     

化学需氧量和总磷对猪场废水产磷化氢的影响

以猪场原液和沼液作为研究对象,在遮光密闭的环境中,于厌氧序批式反应器(ASBR)内利用钼酸铵分光光度法分别测定单位时间内不同COD和TP浓度下PH3的产生量。结果表明:猪场原液和沼液PH3释放量分别达0.048、0.033 mg/h;COD和TP都能促进磷化氢的产生。     

A Nanochannel Platform for Single DNA Studies: From Crowding,Protein DNA Interaction,to Sequencing of Genomic Information

The study of nanochannel-confined DNA is important from biotechnological and biophysical points of view. We produce nanochannels in elastomer with soft lithography and proton beam writing. Issues concerning DNA confined in such quasi one-dimensional channels are discussed. We describe DNA stretching via the control of channel diameter and buffer conditions and how the extension can be interpreted with theory and computer simulation. We then discuss the conformation of nano-confined DNA crowded by neutral polymers and like-charged proteins. As an example of a protein that has an affinity to DNA, the effect of heat-stable nucleoid-structuring protein, H-NS, on the folding and compaction of DNA is reviewed. Compaction of DNA by eukaryotic protamine and unpacking of pre-compacted DNA through an increase in salt concentration are discussed. We review results obtained with a novel, cross-channel device that allows the monitoring of the dynamic, conformational response of DNA after exposure to a ligand or protein and/or a change in buffer conditions in situ. As a biotechnological application, linearization of DNA by bottlebrush coating with a polypeptide copolymer is discussed. It is demonstrated that large-scale genomic organization can be sequenced using single DNA molecules on an array of elastomeric nanochannels. Overall, our results show that the effects of ligands and proteins on the conformation, folding, and condensation of DNA are not only related to classical controlling factors, such as osmotic pressure, charge, and binding, but that the interplay with confinement in a nanospace is of paramount importance.     

Laboratory silo type and inoculation effects on nutritional composition,fermentation, and bacterial and fungal communities of oat silage

The objectives were to evaluate (1) the use of 2 types of experimental silos (S) to characterize whole-crop oat (Avena sativa L.) silage with or without addition of an inoculant (I), and (2) the effect of inoculation on the microbial community structure of oats ensiled using only plastic bucket silos (BKT). From each of 6 sections in a field, oats were harvested, treated (INO) or not (CON) with inoculant, packed into 19-L BKT or vacuum bags (BG), and ensiled for 217 d. The inoculant added contained Lactobacillus buchneri and Pediococcus pentosaceus (4 × 10⁵ and 1 × 10⁵ cfu/g of fresh oats, respectively). The experimental design was a complete randomized design replicated 6 times. Treatment design was the factorial combination of 2 S × 2 I. Some differences existed between BG versus BKT at silo opening (217 d), including a decreased CP (7.73 vs. 7.04 ± 0.247% of DM) and ethanol (1.93 vs. 1.55 ± 0.155) and increased lactic acid (4.28 vs. 3.65 ± 0.241), respectively. Also, WSC and mold counts were reduced in BG versus BKT for CON (1.78 vs. 2.70 ± 0.162% of DM and 0.8 vs. 2.82 ± 0.409 log cfu/fresh g) but not for INO (～1.53 and 1.55), respectively. Application of INO increased DM recovery (96.1 vs. 92.9 ± 0.63%), aerobic stability (565 vs. 133 ± 29.2 h), acetic acid (2.38 vs. 1.22 ± 0.116% of DM), and reduced NDF (65.0 vs. 67.0 ± 0.57), ADF (36.7 vs. 38.1 ± 0.60), ethanol (0.63 vs. 2.85 ± 0.155), and yeast counts (1.10 vs. 4.13 ± 0.484 log cfu/fresh g) in INO versus CON, respectively. At d 0, no differences were found for S and I on the nutritional composition and background microbial counts. Leuconostocaceae (82.9 ± 4.27%) and Enterobacteriaceae (15.2 ± 3.52) were the predominant bacterial families and unidentified sequences were predominant for fungi. A higher relative abundance of the Davidiellaceae fungal family (34.3 vs. 19.6 ± 4.47) was observed in INO versus CON. At opening (217 d), INO had a lower relative abundance of Leuconostocaceae (42.3 vs. 95.8 ± 4.64) and higher Lactobacillaceae (57.4 vs. 3.9 ± 4.65) versus CON. Despite several differences were found between BKT and BG, both techniques can be comparable for characterizing effects of INO on the most basic measures used in silage evaluation. The use of inoculant improved oat silage quality partially by a shift in the bacterial community composition during ensiling, which mainly consisted of an increased relative abundance of Lactobacillaceae and reduction of Leuconostocaceae relative to CON.