De novo genome assembly and analysis of non-allelic recombination in pathogenic yeast Candida glabrata

Candida glabrata is an opportunistic pathogen in humans, responsible for approximately 20% of disseminated candidiasis. C. glabrata’s ability to adhere to host tissue is mediated by GPI-anchored cell wall proteins (GPI-CWPs); the corresponding genes contain long tandem repeat regions and form large gene families. These tandem repeats cause mis-assemblies of GPI-CWP genes in C. glabrata genome. Subtelomeres of C. glabrata are particularly rich in GPI-CWP genes, and share homology with each other. Consequently, the subtelomeres are mis-assembled in genome sequences assembled from short sequencing reads. In this thesis, we used the long single-molecule real time (SMRT) reads and performed de novo genome assembly of the C. glabrata genome to establish the correct structure of GPI-CWP genes and the subtelomeres. We assembled the genome of six C. glabrata strains: the type strain, CBS138; our lab strain, BG2; four serial clinical isolates, BG3993-96 to assess genome changes during infection. With high quality sequences in hand, we then assess recombinational exchange between GPI-CWP genes by non-allelic mitotic recombination. This question is difficult to address with normal aligners, and we developed a k-mer based method to identify recombination. Our assembly established the correct subtelomere structure of Candida glabrata, and provides correct structure of the GPI-CWP gene families. Our analysis of the clinical isolates showed a very modest level of genetic change during the period of infection. Two of the four isolates are hyperadherent, and we identified a mutation in the gene encoding the transcription factor Yap6 as a likely candidate resulting in this phenotypic change. Our k-mer based method was applied genome wide to identify non allelic mitotic recombination events including in complex repeat regions. We documented a higher apparent recombination rate between subtelomeric genes and overall between GPI-CWP genes, independent of their location. In addition, we could document mitotic exchange between non-subtelomeric, non-GPI-CWP genes

Increased levels of soluble CD226 in sera accompanied by decreased membrane CD226 expression on peripheral blood mononuclear cells from cancer patients

<p>Abstract</p> <p>Background</p> <p>As a cellular membrane triggering receptor, CD226 is involved in the NK cell- or CTL-mediated lysis of tumor cells of different origin, including freshly isolated tumor cells and tumor cell lines. Here, we evaluated soluble CD226 (sCD226) levels in sera, and membrane CD226 (mCD226) expression on peripheral blood mononuclear cells (PBMC) from cancer patients as well as normal subjects, and demonstrated the possible function and origin of the altered sCD226, which may provide useful information for understanding the mechanisms of tumor escape and for immunodiagnosis and immunotherapy.</p> <p>Results</p> <p>Soluble CD226 levels in serum samples from cancer patients were significantly higher than those in healthy individuals (<it>P </it>< 0.001), while cancer patients exhibited lower PBMC mCD226 expression than healthy individuals (<it>P </it>< 0.001). CD226-Fc fusion protein could significantly inhibit the cytotoxicity of NK cells against K562 cells in a dose-dependent manner. Furthermore, three kinds of protease inhibitors could notably increase mCD226 expression on PMA-stimulated PBMCs and Jurkat cells with a decrease in the sCD226 level in the cell culture supernatant.</p> <p>Conclusion</p> <p>These findings suggest that sCD226 might be shed from cell membranes by certain proteases, and, further, sCD226 may be used as a predictor for monitoring cancer, and more important, a possible immunotherapy target, which may be useful in clinical application.</p

The Genetic Polymorphisms of HLA Are Strongly Correlated with the Disease Severity after Hantaan Virus Infection in the Chinese Han Population

The polymorphism of human leukocyte antigen (HLA), which is a genetic factor that influences the progression of hemorrhagic fever with renal syndrome (HFRS) after Hantaan virus (HTNV) infection, was incompletely understood. In this case-control study, 76 HFRS patients and 370 healthy controls of the Chinese Han population were typed for the HLA-A, -B, and -DRB1 loci. The general variation at the HLA-DRB1 locus was associated with the onset of HFRS (P<0.05). The increasing frequencies of HLA-DRB1*09 and HLA-B*46-DRB1*09 in HFRS patients were observed as reproducing a previous study. Moreover, the HLA-B*51-DRB1*09 was susceptible to HFRS (P=0.037; OR =3.62; 95% CI: 1.00–13.18). The increasing frequencies of HLA-B*46, HLA-B*46-DRB1*09, and HLA-B*51-DRB1*09 were observed almost in severe/critical HFRS patients. The mean level of maximum serum creatinine was higher in HLA-B*46-DRB1*09 (P=0.011), HLA-B*51-DRB1*09 (P=0.041), or HLA-B*46 (P=0.011) positive patients than that in the negative patients. These findings suggest that the allele HLA-B*46 and haplotypes HLA-B*46-DRB1*09 and HLA-B*51-DRB1*09 in patients could contribute to a more severe degree of HFRS and more serious kidney injury, which improve our understanding of the HLA polymorphism for a different outcome of HTNV infection

Manipulating the 3D organization of the largest synthetic yeast chromosome

Whether synthetic genomes can power life has attracted broad interest in the synthetic biology field. Here, we report de novo synthesis of the largest eukaryotic chromosome thus far, synIV, a 1,454,621-bp yeast chromosome resulting from extensive genome streamlining and modification. We developed megachunk assembly combined with a hierarchical integration strategy, which significantly increased the accuracy and flexibility of synthetic chromosome construction. Besides the drastic sequence changes, we further manipulated the 3D structure of synIV to explore spatial gene regulation. Surprisingly, we found few gene expression changes, suggesting that positioning inside the yeast nucleoplasm plays a minor role in gene regulation. Lastly, we tethered synIV to the inner nuclear membrane via its hundreds of loxPsym sites and observed transcriptional repression of the entire chromosome, demonstrating chromosome-wide transcription manipulation without changing the DNA sequences. Our manipulation of the spatial structure of synIV sheds light on higher-order architectural design of the synthetic genomes. </p

Optimal UAV Formation Tracking Control with Dynamic Leading Velocity and Network-Induced Delays

With the rapid development of UAV technology, the research of optimal UAV formation tracking has been extensively studied. However, the high maneuverability and dynamic network topology of UAVs make formation tracking control much more difficult. In this paper, considering the highly dynamic features of uncertain time-varying leader velocity and network-induced delays, the optimal formation control algorithms for both near-equilibrium and general dynamic control cases are developed. First, the discrete-time error dynamics of UAV leader&ndash;follower models are analyzed. Next, a linear quadratic optimization problem is formulated with the objective of minimizing the errors between the desired and actual states consisting of velocity and position information of the follower. The optimal formation tracking problem of near-equilibrium cases is addressed by using a backward recursion method, and then the results are further extended to the general dynamic case where the leader moves at an uncertain time-varying velocity. Additionally, angle deviations are investigated, and it is proved that the similar state dynamics to the general case can be derived and the principle of control strategy design can be maintained. By using actual real-world data, numerical experiments verify the effectiveness of the proposed optimal UAV formation-tracking algorithm in both near-equilibrium and dynamic control cases in the presence of network-induced delays

Enhanced U(VI) bioreduction by alginate-immobilized uranium-reducing bacteria in the presence of carbon nanotubes and anthraquinone-2,6-disulfonate

Uranium-reducing bacteria were immobilized with sodium alginate, anthraquinone-2, 6-disulfonate (AQDS), and carbon nanotubes (CNTs). The effects of different AQDS-CNTs contents, U(IV) concentrations, and metal ions on U(IV) reduction by immobilized beads were examined. Over 97.5% U(VI) (20 mg/L) was removed in 8 hr when the beads were added to 0.7% AQDS-CNTs, which was higher than that without AQDS-CNTs. This result may be attributed to the enhanced electron transfer by AQDS and CNTs. The reduction of U(VI) occurred at initial U(VI) concentrations of 10 to 100 mg/L and increased with increasing AQDS-CNT content from 0.1% to 1%. The presence of Fe(III), Cu(II) and Mn(II) slightly increased U(VI) reduction, whereas Cr(VI), Ni(II), Pb(II), and Zn(II) significantly inhibited U(VI) reduction. After eight successive incubation-washing cycles or 8 hr of retention time (HRT) for 48 hr of continuous operation, the removal efficiency of uranium was above 90% and 92%, respectively. The results indicate that the AQDS-CNT/AL/cell beads are suitable for the treatment of uranium-containing wastewaters. (C) 2015 The Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences. Published by Elsevier B.V.</p

enhanceduvibioreductionbyalginateimmobilizeduraniumreducingbacteriainthepresenceofcarbonnanotubesandanthraquinone26disulfonate

Uranium-reducing bacteria were immobilized with sodium alginate, anthraquinone-2, 6-disulfonate (AQDS), and carbon nanotubes (CNTs). The effects of different AQDS-CNTs contents, U(IV) concentrations, and metal ions on U(IV) reduction by immobilized beads were examined. Over 97.5% U(VI) (20 mg/L) was removed in 8 hr when the beads were added to 0.7% AQDS-CNTs, which was higher than that without AQDS-CNTs. This result may be attributed to the enhanced electron transfer by AQDS and CNTs. The reduction of U(VI) occurred at initial U(VI) concentrations of 10 to 100 mg/L and increased with increasing AQDS-CNT content from 0.1% to 1%. The presence of Fe(III), Cu(II) and Mn(II) slightly increased U(VI) reduction, whereas Cr(VI), Ni(II), Pb(II), and Zn(II) significantly inhibited U(VI) reduction. After eight successive incubation-washing cycles or 8 hr of retention time (HRT) for 48 hr of continuous operation, the removal efficiency of uranium was above 90% and 92%, respectively. The results indicate that the AQDS-CNT/AL/cell beads are suitable for the treatment of uranium-containing wastewaters. (C) 2015 The Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences. Published by Elsevier B.V

Cell wall protein variation, break-induced replication, and subtelomere dynamics in Candida glabrata.

Candida glabrata is an opportunistic pathogen of humans, responsible for up to 30% of disseminated candidiasis. Adherence of C. glabrata to host cells is mediated by adhesin-like proteins (ALPs), about half of which are encoded in the subtelomeres. We performed a de novo assembly of two C. glabrata strains, BG2 and BG3993, using long single-molecule real-time (SMRT) reads, and constructed high-quality telomere-to-telomere assemblies of all 13 chromosomes to assess differences between C. glabrata strains. We documented variation between strains, and in agreement with earlier studies, found high (~0.5%-1%) frequencies of SNVs across the genome, including within subtelomeric regions. We documented changes in ALP gene structure and complement: there are large length differences in ALP genes in different strains, resulting from copy number variation in tandem repeats. We compared strains to characterize chromosome rearrangement events including within the poorly characterized subtelomeric regions. We show that rearrangements within the subtelomere regions all affect ALP-encoding genes, and 14/16 involve just the most terminal ALP gene. We present evidence that these rearrangements are mediated by break-induced replication. This study highlights the constrained nature of subtelomeric changes impacting ALP gene complement and subtelomere structure

A DRL-Driven Intelligent Optimization Strategy for Resource Allocation in Cloud-Edge-End Cooperation Environments

Complex dynamic services and heterogeneous network environments make the asymmetrical control a curial issue to handle on the Internet. With the advent of the Internet of Things (IoT) and the fifth generation (5G), the emerging network applications lead to the explosive growth of mobile traffic while bringing forward more challenging service requirements to future radio access networks. Therefore, how to effectively allocate limited heterogeneous network resources to improve content delivery for massive application services to ensure network quality of service (QoS) becomes particularly urgent in heterogeneous network environments. To cope with the explosive mobile traffic caused by emerging Internet services, this paper designs an intelligent optimization strategy based on deep reinforcement learning (DRL) for resource allocation in heterogeneous cloud-edge-end collaboration environments. Meanwhile, the asymmetrical control problem caused by complex dynamic services and heterogeneous network environments is discussed and overcome by distributed cooperation among cloud-edge-end nodes in the system. Specifically, the multi-layer heterogeneous resource allocation problem is formulated as a maximal traffic offloading model, where content caching and request aggregation mechanisms are utilized. A novel DRL policy is proposed to improve content distribution by making cache replacement and task scheduling for arriving content requests in accordance with the information about users&rsquo; history requests, in-network cache capacity, available link bandwidth and topology structure. The performance of our proposed solution and its similar counterparts are analyzed in different network conditions