Screening of Polyvalent Phage-Resistant Escherichia coli Strains Based on Phage Receptor Analysis

Bacteria-based biotechnology processes are constantly under threat from bacteriophage infection, with phage contamination being a non-neglectable problem for microbial fermentation. The essence of this problem is the complex co-evolutionary relationship between phages and bacteria. The development of phage control strategies requires further knowledge about phage-host interactions, while the widespread use of Escherichia coli strain BL21 (DE3) in biotechnological processes makes the study of phage receptors in this strain particularly important. Here, eight phages infecting E. coli BL21 (DE3) via different receptors were isolated and subsequently identified as members of the genera T4virus, Js98virus, Felix01virus, T1virus, and Rtpvirus. Phage receptors were identified by whole-genome sequencing of phage-resistant E. coli strains and sequence comparison with wild-type BL21 (DE3). Results showed that the receptors for the isolated phages, designated vB_EcoS_IME18, vB_EcoS_IME253, vB_EcoM_IME281, vB_EcoM_IME338, vB_EcoM_IME339, vB_EcoM_IME340, vB_EcoM_IME341, and vB_EcoS_IME347 were FhuA, FepA, OmpF, lipopolysaccharide, Tsx, OmpA, FadL, and YncD, respectively. A polyvalent phage-resistant BL21 (DE3)-derived strain, designated PR8, was then identified by screening with a phage cocktail consisting of the eight phages. Strain PR8 is resistant to 23 of 32 tested phages including Myoviridae and Siphoviridae phages. Strains BL21 (DE3) and PR8 showed similar expression levels of enhanced green fluorescent protein. Thus, PR8 may be used as a phage resistant strain for fermentation processes. The findings of this study contribute significantly to our knowledge of phage-host interactions and may help prevent phage contamination in fermentation

Seismic behavior of steel-reinforced high-strength concrete composite beams with bonded tendons

To study the seismic behavior of steel-reinforced high-strength concrete composite beams with bonded tendons (PSRHSCBs) under low cyclic loading, 13 PSRHSCBs were designed with the main parameters of the span-to-height ratio of beams (L/H), the cubic strength of concrete (fcu), the eccentricity of H-shaped steel (eH), the volume stirrup ratio (pv), the longitudinal reinforcement ratio (p), and the tension control stress of tendons(σcon). Using the simplified bilinear constitutive model of steel and the nonlinear constitutive model of high-strength concrete, and introducing plastic damage of concrete, fine finite element models were established with ABAQUS software. 11 similar test specimens were conducted by above modeling method, by comparing existing test curves and numerical simulation curves, both of them match well, which verified the validity of the modeling method. Subsequently, parameter analysis for 13 PSRHSCB specimens was performed, and the influence regularity of different parameters on the seismic behavior of this kind of composite beams was obtained. The results show that hysteretic curves of this kind of composite beams are full, and the failure mode is manifested as bending failure. The ultimate load, the energy dissipation capacity and the ductility coefficient of specimens can be improved significantly by increasing pv, on the contrary, the energy dissipation capacity and the ductility coefficient decrease gradually by increasing fcu. The stiffness degradation of specimens significantly slows down with the increasing of L/H and σcon, and the decreasing of eH. Finally, the trilinear skeleton curve model and the restoring force model are established by statistical regression, and the corresponding seismic design suggestions are given, and these can provide theoretical support for the seismic design of such composite beams in actual engineering

Discovery of DNA Viruses in Wild-Caught Mosquitoes Using Small RNA High throughput Sequencing

BACKGROUND: Mosquito-borne infectious diseases pose a severe threat to public health in many areas of the world. Current methods for pathogen detection and surveillance are usually dependent on prior knowledge of the etiologic agents involved. Hence, efficient approaches are required for screening wild mosquito populations to detect known and unknown pathogens. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we explored the use of Next Generation Sequencing to identify viral agents in wild-caught mosquitoes. We extracted total RNA from different mosquito species from South China. Small 18-30 bp length RNA molecules were purified, reverse-transcribed into cDNA and sequenced using Illumina GAIIx instrumentation. Bioinformatic analyses to identify putative viral agents were conducted and the results confirmed by PCR. We identified a non-enveloped single-stranded DNA densovirus in the wild-caught Culex pipiens molestus mosquitoes. The majority of the viral transcripts (.>80% of the region) were covered by the small viral RNAs, with a few peaks of very high coverage obtained. The +/- strand sequence ratio of the small RNAs was approximately 7∶1, indicating that the molecules were mainly derived from the viral RNA transcripts. The small viral RNAs overlapped, enabling contig assembly of the viral genome sequence. We identified some small RNAs in the reverse repeat regions of the viral 5'- and 3' -untranslated regions where no transcripts were expected. CONCLUSIONS/SIGNIFICANCE: Our results demonstrate for the first time that high throughput sequencing of small RNA is feasible for identifying viral agents in wild-caught mosquitoes. Our results show that it is possible to detect DNA viruses by sequencing the small RNAs obtained from insects, although the underlying mechanism of small viral RNA biogenesis is unclear. Our data and those of other researchers show that high throughput small RNA sequencing can be used for pathogen surveillance in wild mosquito vectors

High quality source rocks in trough facies of Upper Permian Dalong Formation, Sichuan Basin

Source rocks in trough facies of the Upper Permian Dalong Formation of the Sichuan Basin were assessed by field observations and measurements in outcrop areas as well as from logging and core/cutting analysis from drilling sites. The results show that in the Dalong Formation, the black shale and sapropelite facies have an average TOC of 5.86%, with the maximum value up to 24.31%, making them high quality hydrocarbon source rocks. Dark cryptite, with a TOC of 0.77% (on average) is also a good hydrocarbon source rock. A dark silicate, with TOC of only 0.13% on average, has no potential to generate hydrocarbons. Since the source rocks are much evolved, the content of chloroform bitumen “A” extracts tend not to be high. The (S1+S2) value of source rocks in the Dalong Formation are low, with only 4.36 mg/g on average. The major macerals of Kerogen of the Dalong Formation are sapropels, averaging 71.5%. Kerogen is mainly Type II1, and a little belongs to II2. The flourishing of pelagic organisms during deposition of the Late Permian Changxing Formation, slow deposition rate of the Dalong Formation and an anoxic and calm deep water depositional environment are the key controlling factors for accumulation, preservation and generation of organic matter in this part of the basin. 摘要: ： 通过四川盆地上二叠统海槽相大隆组露头区野外观察测量和钻井区测井及岩心、岩屑分析，对大隆组烃源岩进行评价。研究表明，大隆组黑色泥质岩、腐泥岩TOC平均值为5.86%，最高可达24.31%，是一套优质烃源岩；大隆组暗色泥晶灰岩TOC平均值可达0.77%，也是很好的烃源岩；大隆组暗色硅质岩TOC平均值仅为0.13%，不具备生烃能力。由于烃源岩演化程度较高，氯仿沥青“A”含量总体不高。大隆组烃源岩（S1＋S2）值总体也比较低，平均值仅4.36 mg/g。烃源岩干酪根显微组分以腐泥组为主，干酪根主要为Ⅱ1型，少量为Ⅱ2型。晚二叠世长兴组沉积期浮游类生物繁盛、大隆组沉积速率缓慢以及缺氧、安静的深水沉积环境是有机质富集、保存、形成优质烃源岩的主要控制因素。图6表2参12 Key words: trough facies, source rock, Upper Permian, Dalong Formation, sapropelite, Sichuan Basi

Isolation, Characterization, and Genome Sequence Analysis of a Novel Lytic Phage, Xoo-sp15 Infecting Xanthomonas oryzae pv. oryzae

Xanthomonas oryzae pv. oryzae (X. oryzae) is a bacterial pathovar of rice diseases all over the world. Owing to emerging antibacterial resistance, phage therapies have gained significant attention to treat various bacterial infections. Nevertheless, comprehensive research is needed for their use as a safe biocontrol agent. In this study, isolation and characterization of a novel phage Xoo-sp15, that infects X. oryzae was ascertained through experimental and bioinformatics analyses to determine its virulent potency and reliability. High throughput sequencing demonstrated that Xoo-sp15 has a dsDNA genome with a total size of 157,091 bp and 39.9% GC content lower than its host (63.6%). Morphological and phylogenetic analyses characterized it as a new member of the Bastille-like group within the family Herelleviridae. In silico analysis revealed that it contains 229 open reading frames and 16 tRNAs. Additionally, this novel phage does not contain any resistant determinants and can infect nine X. oryzae strains. Therefore, Xoo-sp15 has the potential to serve as a novel candidate for phage therapy.publishe

Dual‐scale weighted structural local sparse appearance model for object tracking

It is a great challenge to develop an effective appearance model for robust visual tracking due to various interfering factors, such as pose change, occlusion, background clutter etc. More and more visual tracking methods tend to exploit the local appearance model to deal with the above challenges. In this study, the authors present a simple yet effective weighted structural local sparse appearance model, which can better describe the target appearance information through patch‐based generative weight. To further improve the robustness of tracking, they implement this appearance model on two‐scale patches. The two derived appearance models are then combined to form a collaborative model to play their advantages. Extensive experiments on the tracking benchmark dataset show that the proposed method performs favourably against several state‐of‐the‐art methods