Complicated expansion trajectories of insertion sequences and potential association with horizontal transfer of Wolbachia DNA

DEAR EDITOR,Insertion sequences(ISs) are the simplest structural transposable elements(TEs) in prokaryotes, consisting only of a transposase coding sequence and its bilateral short terminal inverted repeats. Due to their gradually streamlined genomic construction, TEs rarely exist in the genomes of obligate endosymbionts. However, TE content, especially ISs.

A new insertion sequence for incremental Delaunay triangulation

Incremental algorithm is one of the most popular procedures for constructing Delaunay triangulations （DTs）. However, the point insertion sequence has a great impact on the amount of work needed for the construction of DTs. It affects the time for both point location and structure update, and hence the overall computational time of the triangulation algorithm. In this paper, a simple deterministic insertion sequence is proposed based on the breadth-first-search on a Kd-tree with some minor modifications for better performance. Using parent nodes as search-hints, the proposed insertion sequence proves to be faster and more stable than the Hilbert curve order and biased randomized insertion order （BRIO）, especially for non-uniform point distributions over a wide range of benchmark examples.

The Performance of Double Bootstrap Method for Large Sampling Sequence

Studies on the iteration procedure in double bootstrap method have given a great impact on confidence interval performance. However, the procedure was claimed to be complicated and demand intensive computer processor. Considering this problem, an alternative procedure was proposed in this research. Despite of using small sampling sequence, this research was aimed to increase the accuracy estimation using a second replication number which resulted in a large sampling sequence of double bootstrap. In this paper, the alternative double bootstrap method was hybrid onto an example model and its performance was based on Studentised interval. The performance was examined in simulation study and real sample data of sukuk Ijarah. The result showed that hybrid double bootstrap model gave more accurate estimation in terms of its shorter length when dealing with various parameter values and has shown to improve the single bootstrap estimation.

Optimization of Process Parameters for Cracking Prevention of UHSS in Hot Stamping Based on Hammersley Sequence Sampling and Back Propagation Neural Network-Genetic Algorithm Mixed Methods

In order to prevent cracking appeared in the work-piece during the hot stamping operation,this paper proposes a hybrid optimization method based on Hammersley sequence sampling( HSS),finite analysis,backpropagation( BP) neural network and genetic algorithm( GA). The mechanical properties of high strength boron steel are characterized on the basis of uniaxial tensile test at elevated temperatures. The samples of process parameters are chosen via the HSS that encourages the exploration throughout the design space and hence achieves better discovery of possible global optimum in the solution space. Meanwhile, numerical simulation is carried out to predict the forming quality for the optimized design. A BP neural network model is developed to obtain the mathematical relationship between optimization goal and design variables,and genetic algorithm is used to optimize the process parameters. Finally,the results of numerical simulation are compared with those of production experiment to demonstrate that the optimization strategy proposed in the paper is feasible.

Extended role for insertion sequence elements in the antibiotic resistance of Bacteroides

The Bacteroides species are important micro-organisms, both in the normal physiology of the intestines and as frequent opportunistic anaerobic pathogens, with a deeply-rooted phylogenetic origin endowing them with some interesting biological features. Their prevalence in anaerobic clinical specimens is around 60%-80%, and they display the most numerous and highest rates of antibiotic resistance among all pathogenic anaerobes. In these antibiotic resistance mechanisms there is a noteworthy role for the insertion sequence(IS) elements, which are usually regarded as representatives of ‘selfish' genes; the IS elements of Bacteroides are usually capable of up-regulating the antibiotic resistance genes. These include the cep A(penicillin and cephalosporin), cfx A(cephamycin), cfi A(carbapenem), nim(metronidazole) and erm F(clindamycin) resistance genes. This is achieved by outwardoriented promoter sequences on the ISs. Although some representatives are well characterized, e.g., the resistance gene-IS element pairs in certain resistant strains, open questions remain in this field concerning a better understanding of the molecular biology of theantibiotic resistance mechanisms of Bacteroides, which will have clinical implications.

Insertion Sequence-Dependent <i>OmpK</i>36 Mutation Associated Ertapenem Resistance in Clinical <i>Klebsiella pneumoniae</i>

Extended-spectrum β-lactamases (ESBLs) and/or AmpC enzymes combined with deficiency of porins OmpK35 and OmpK36 are important for the development of carbapenem-resistant Klebsiella pneumoniae. We characterized the clinical K. pneumoniae human isolates and investigated the effect of meropenem induction on the ompK35 and ompK36 mutation to develop carbapenem resistance from six carbapenem-susceptible ESBL-producing K. pneumoniae strains. 163 clinical K. pneumoniae isolates were grouped mostly into the ESBL + AmpC (44.2%) and ESBL (42.9%) phenotypes. The resistance rate differed between cephalosporins (52.1% for cefepime - 97.5% for cefotaxime) and carbapenems (16% for meropenem - 28.2% for imipenem) (P blaTEM, blaSHV, blaCTX-M-3-like, and blaCTX-M-14-like of AmpA β-lactamase genes and blaDHA and blaCMY of AmpC β-lactamase genes. Compared to all 163 clinical isolates, the 56 carbapenem-resistant isolates carried less frequently of blaTEM, blaCTXM-14-like, and blaCTXM-3-like and more frequently of blaDHA-1 and blaCMY-2. The carbapenem-resistant isolates differed in prevalence against imipenem, ertapenem, and meropenem and lacked OmpK35 more frequently than OmpK36, but abnormal PCR amplicons were detected fewer in the Omp K35-deficient group than in the OmpK36-deficient group (32.5% vs. 68.4%, respectively). The carbapenem-resistant isolate mostly carried blaDHA (91.1%) and three isolates carried blaKPC-2. Following induction with meropenem insertion sequences in ompK36, not ompK36, were identified as IS5 for KP08, IS1 for KP15, and IS903 for KP16 isolates. OmpK36 deficiency increased resistance to ertapenem, but not imipenem and meropenem. Clinical isolates belonged mainly to ESBL + AmpC group and ESBL group with difference in resistance to cephalosporins and carbapenems, the bla genes. Carbapenem resistant isolates lacked OmpK35 expression, than the OmpK36 expression, Meropenem induction developed the carbapenem resistant isolates with insertion of different insertion sequences in ompK36, not ompK35.

STACKING SEQUENCE OPTIMIZA-TION OF LAMINATED COMPOSITE CYLINDER SHELL FOR MAXIMAL BUCKLING LOAD

A new optimization method for the optimization of stacking of composite glass fiber laminates is developed. The fiber orientation and angle of the layers of the cylindrical shells are sought considering the buckling load. The proposed optimization algorithm applies both finite element analysis and the mode-pursuing sampling （MPS）method. The algorithms suggest the optimal stacking sequence for achieving the maximal buckling load. The procedure is implemented by integrating ANSYS and MATLAB. The stacking sequence designing for the symmetric angle-ply three-layered and five-layered composite cylinder shells is presented to illustrate the optimization process, respectively. Compared with the genetic algorithms, the proposed optimization method is much faster and efficient for composite staking sequence plan.

Insertion sequence transposition activates antimycobacteriophage immunity through an Isr2-silenced lipid metabolism gene island

Insertion sequences(ISs)exist widely in bacterial genomes,but their roles in the evolution of bacterial antiphage defense remain to be clarified.Here,we report that,under the pressure of phage infection,the IS1o96 transposition of Mycobacterium smegmatis into the Isr2 gene can occur at high frequencies,which endows the mutant mycobacterium with a broad-spectrum antiphage ability.Lsr2 functions as a negative regulator and directly silences expression of a gene island composed of 11 lipid metabolism-related genes.The complete or partial loss of the gene island leads to a significant decrease of bacteriophage adsorption to the mycobacterium,thus defending against phage infection.Strikingly,a phage that has evolved mutations in two tail-filament genes can re-escape from the Isr2 inactivation-triggered host defense.This study uncovered a new signaling pathway for activating antimycobacteriophage immunity by Is transposition and provided insight into the natural evolution of bacterial antiphage defense.

High Performance Compressed Sampling for OFDM-UWB Systems

In order to solve the problem of high-speed sampling in OFDM based ultra wide band(UWB) systems, this paper first gives analysis on the applicability of existing compressed sampling methods. Then, on the basis of an established segmented observation model, it presents an optimized parallel segmented compressed sampling(OPSCS) scheme based on Hadamard matrix. The orthogonal Hadamard matrix is adopted to construct the segmented measurement matrix with any dimensions, thus orthogonal or quasi-orthogonal multiplex observation sequences are obtained, and the restricted isometry property is improved. The optimized orthogonal matching pursuit algorithm is also used for the known sparsity avoiding iterative operation. Researches show that the proposed method can effectively reduce the sampling rate in OFDM-UWB systems, and also has a good ability of noise resisting that it achieves a high system performance better than the existing schemes of compressed sampling and even Nyquist rate sampling.

General space-efficient sampling algorithm for suboptimal alignment

Suboptimal alignments always reveal additional interesting biological features and have been successfully used to informally estimate the significance of an optimal alignment. Besides, traditional dynamic programming algorithms for sequence comparison require quadratic space, and hence are infeasible for long protein or DNA sequences. In this paper, a space-efficient sampling algorithm for computing suboptimal alignments is described. The algorithm uses a general gap model, where the cost associated with gaps is given by an affine score, and randomly selects an alignment according to the distribution of weights of all potential alignments. If x and y are two sequences with lengths n and m, respectively, then the space requirement of this algorithm is linear to the sum of n and m. Finally, an example illustrates the utility of the algorithm.

Scientific Drilling-to Construct the Telescopes that Inserting to the Earth Interior

Mankind live in the earth for countless years, but until now;people do not really understand the connotation of the Earth. We know that the earth composition including the lithosphere, the asthenosphere, mantle and core. Of course, the lithosphere supports all the life on Earth. For a long time, geoscientists trying to use all kind of methods such as geological, geophysical and geochemical methods to detect and study the earth, but the knowledge about earth are mostly indirect. Through the direct observation to the lithosphere, people can understand and recognize the plate movement of ocean and the mainland, crustal stress, earthquakes, volcanic processes, deep resources, the origins of life, global climate change and biodiversity. They are all the basis of a series of geosciences problems(Su and Yang, 2010). Geological specimens, especially the true samples from deep of the Earth, are the most directly study subjects for geologists. But the only way to access the true samples from deep of the earth is drilling. The most directly relevant evidence always originated from the deep of the earth, such as core, cuttings, fluid samples and other physical samples. Continental scientific drilling has been demonstrated which is an efficient technique for directly obtaining information from the Earth’s surface to the deep crust, and is acknowledged as ―to build a telescope inserting to the interior of the Earth‖, as well as ―a key for opening the door of the Earth‖. Over the last four decades, continental scientific drilling has achieved great success in enhancing our knowledge of the Earth, and in providing information on mineral resources, large engineering projects and global change. SinoProbe-05 is a new scientific drilling venture,which builds on the success of the Chinese Continental Scientific Drilling Project(CCSD), and is similar to the current major scientific drilling project on the Wenchuan earthquake fault. SinoProbe-05 will focus on 6 critical tectonic and mineral resource regions, including the Jinchuan Cu-Ni sulphide deposits in Gansu, the Luobusa chromite deposits in Tibet, the Tengchong volcano-thermal tectonic zone in Yunnan, the Yudu-Ganxian polymetallic deposits in South China, the Tongling polymetallic deposit and the Luzong volcanic basin and mineral deposit district in Anhui. As of the end of 2013, all of these pilot holes have been completed, all of them have achieved the desired scientific objectives. The construction of another ICDP project, Songke No.2 well, has come to an end. Current well depth is 5929 m. Drilling throughout the Cretaceous strata is just around the corner(The design well depth is 6400 m.). This will be the first complete Cretaceous stratigraphic profile in the world. The deep exploration project which will be stared soon will build a large number of different depths of scientific drilling holes. The deepest hole depth will reach to 13000 m. We believe that the construction of these scientific coring drilling holes will provide geologists with a lot of real core samples. These cores can meet the needs for different geoscience research areas. No doubt, the research results based on these cores will promote China’s geological science research to a new height, of course;will also contribute to the progress of the world’s earth science. This is also a good opportunity to promote China’s drilling technology. So, we know that no advanced drilling technology, no enough high quality samples from the deep of the Earth, the in-depth studies for geosciences will be restricted of course(Zhang et al., 2013).

Assembling a physical map of the genome by marker sequences

Molecular genetic maps were commonly constructed by analyzing the segregation of restriction fragment length polymorphisms (RFLPs). Here we described methodology-marker sequences in a new mapping based on recent documents. With the methods they were unique sequences detected by the polymerase chain reaction (PCR). Each of the methods had its Iimitations and the current trend was to integrate the maps produced by the different methods. Marker sequences contained mainly expressed sequence tags (ESTs),polymorphie sequence-tagged sites (STSs), randomly amplified polymorphic DNA (RAPDs), cIeaved amplified polymorphic sequences (CAPS), amplified fragment Iength pofymorphism (AFLPs), genorne sequence sampling (GSS) and sequence-tagged connectors (STCs) in this paper.

Efficacy of EGFR-TKI sequential therapy in patients with EGFR exon 19 insertion-positive non-small-cell lung cancer:A case report

BACKGROUND Insertions in exon 19 in the epidermal growth factor receptor gene(EGFR)is a rarely seen mutation in non-small cell lung cancer.These patients have been effectively treated with sequential EGFR tyrosine kinase inhibitors(TKIs).CASE SUMMARY Here,we presented a case of non-small cell lung cancer,stage IIIB,with EGFR exon 19 insertion mutation as detected in the right lower lobe by next-generation sequencing.The patient was sequentially treated with first,second,and thirdgeneration EGFR TKIs after the surgical operation.The overall survival of the patient was 21.3 mo.There was no dynamic analysis of drug resistance mechanisms in targeted therapy.CONCLUSION This case emphasized the importance of following the guidelines.In patients with EGFR mutations,repeated and dynamic next-generation sequencing monitoring is necessary to prescribe a personalized treatment plan.

Identification of selenocyst-eine insertion sequence(SECIS) element in eukaryotic selenoproteins by RNA Draw program

The computer program RNA Draw was used to identify the secondary structures in the 3’untranslated regions (3’UTRs) of the mRNAs from 46 eukaryotic seleno-proteins among 7 species. The program found one or two possible SECIS elements in these selenoproteins. The SECIS element consists of a stem-loop or hairpin structure with three conserved sequences of AUGA-(A)AA-GA. SECIS element was not found by the RNA Draw program in randomly selected non-selenoproteins. The results showed that SECIS element is the unique character of the genes ofeukaryotic selenoproteins. Thus it is possible to use RNA Draw to search the SECIS elements in gene bank for potential new selenoproteins.

Construction of Mutant Populations by T-DNA Insertion for Functional Genomic Study in Cotton

The use of transfer DNA(T-DNA)as amutagen has been developed for tagging genes inmany crops,and results showed that T-DNAinsertion is a random event,and that theinserted genes are stable through multiplegenerations.Through sequencing PCR-amplifiedfragments adjacent to the inserted elements,wecan construct the T-DNA flanking database,which would be useful for cloning the genestagged by T-DNA.

Identification of transgene insertions in two genetically modified soybeans using high throughput next generation sequencing

Genetically modified(GM) organisms are widely adopted. However, their safety assessments and control are still of special concern to the public. Identifying and localizing transgene insertion is an essentially prerequisite step. In this study, 2 independent transgene soybean lines were selected(LB4-AtDCGS-1-20-5-2 and CGS-ZG11) as typical cases. Both lines contained expression cassette of At-DCGS that encoding a feedback-insensitive cystathionine gamma-synthase to produce higher level methionine(Met). LB4-AtDCGS-1-20-5-2 was whole genome sequenced with one paired-end 500 bp library and two mate-paired 1 kb and 2 kb libraries using Illumina HiSeq sequencing platform. CGS-ZG11 was sequenced with only one paired-end 500 bp library. Both genomes were assembled,and 2 scaffold sequences(1 for each line) were screened out by aligning with transgene.Then the transgene insertion and its flanking regions in soybean genome were further identified and confirmed by PCR cloning and Sanger sequencing. Results showed that these 2 transgene lines had single copy of inserted transgene. Their transgene insertion contents were identified, which facilitates further safety assessment. These results indicated that genome assembly using high throughput sequencing is a powerful tool for identifying transgene insertions, even with limited knowledge.

Enhancing whole yeast genome rearrangements through multiple LoxPsym sequences

Genomic rearrangements play a significant role in disease,evolution,and tumorigenesis(Mani and Chinnaiyan,2010).While single nucleotide polymorphisms(SNPs)and small insertions/deletions contribute substantially to genetic variation,discerning the independent impact of structural variations poses a challenge.

Visual abstraction of dynamic network via improved multi-class blue noise sampling

Massive sequence view (MSV) is a classic timeline-based dynamic network visualization approach. However, it is vulnerable to visual clutter caused by overlapping edges, thereby leading to unexpected misunderstanding of time-varying trends of network communications. This study presents a new edge sampling algorithm called edge-based multi-class blue noise (E-MCBN) to reduce visual clutter in MSV. Our main idea is inspired by the multi-class blue noise (MCBN) sampling algorithm, commonly used in multi-class scatterplot decluttering. First, we take a node pair as an edge class, which can be regarded as an analogy to classes in multi-class scatterplots. Second, we propose two indicators, namely, class overlap and inter-class conflict degrees, to measure the overlapping degree and mutual exclusion, respectively, between edge classes. These indicators help construct the foundation of migrating the MCBN sampling from multi-class scatterplots to dynamic network samplings. Finally, we propose three strategies to accelerate MCBN sampling and a partitioning strategy to preserve local high-density edges in the MSV. The result shows that our approach can effectively reduce visual clutters and improve the readability of MSV. Moreover, our approach can also overcome the disadvantages of the MCBN sampling (i.e., long-running and failure to preserve local high-density communication areas in MSV). This study is the first that introduces MCBN sampling into a dynamic network sampling.

Subsampling bias and the best-discrepancy systematic cross validation

Statistical machine learning models should be evaluated and validated before putting to work.Conventional k-fold Monte Carlo cross-validation(MCCV)procedure uses a pseudo-random sequence to partition instances into k subsets,which usually causes subsampling bias,inflates generalization errors and jeopardizes the reliability and effectiveness of cross-validation.Based on ordered systematic sampling theory in statistics and low-discrepancy sequence theory in number theory,we propose a new k-fold cross-validation procedure by replacing a pseudo-random sequence with a best-discrepancy sequence,which ensures low subsampling bias and leads to more precise expected-prediction-error(EPE)estimates.Experiments with 156 benchmark datasets and three classifiers(logistic regression,decision tree and na?ve bayes)show that in general,our cross-validation procedure can extrude subsampling bias in the MCCV by lowering the EPE around 7.18%and the variances around 26.73%.In comparison,the stratified MCCV can reduce the EPE and variances of the MCCV around 1.58%and 11.85%,respectively.The leave-one-out(LOO)can lower the EPE around 2.50%but its variances are much higher than the any other cross-validation(CV)procedure.The computational time of our cross-validation procedure is just 8.64%of the MCCV,8.67%of the stratified MCCV and 16.72%of the LOO.Experiments also show that our approach is more beneficial for datasets characterized by relatively small size and large aspect ratio.This makes our approach particularly pertinent when solving bioscience classification problems.Our proposed systematic subsampling technique could be generalized to other machine learning algorithms that involve random subsampling mechanism.

Prime editing-mediated precise knockin of protein tag sequences in the rice genome

Dear Editor,Accurately labeling proteins in living plant cells has long been a challenge and can be addressed by targeted insertion of tag sequences in a given locus.Recent optimized plant prime editors(PEs)enable efficient programmable installation of small insertions or deletions,including insertions of short sequences(Li et al.,2022a,2022b;Jiang et al.,2022;Xu et al.,2022;Zong et al.,2022;Zou et al.,2022).To investigate whether prime editing can be used to tag endogenous proteins in rice,we made use of the enpPE2 system described in our previous report(Li et al.,2022b).