Ac/Ds Transposition Activity in Transgenic Rice Population and DNA Flanking Sequence of Ds Insertion Sites

The Agrobacterium mediated transgenic rice ( Oryza saliva L.) population with inserts of maize transposon Activator/Dissociation (Ac/Ds) was investigated. DNA sequences flanking the T-DNA were analyzed with inverse PCR. Results showed that 65.4% of the T-DNA was integrated in different locations of rice genome, and some T-DNA flanking sequences were located on certain chromosomes. A number of T-DNA was found to have inserted into protein coding regions. In order to induce transposition of the inserted Ds elements, 354 crosses of Ac x Ds and Ds x Ac were constructed. The excision frequency of Ds element trans-activated by Ac transposase was 22.7% in the F-2 populations, and the transposition was confirmed with analyses of DNA sequences flanking the Ds elements. In addition to the transposition due to 'cut-paste' mechanism, Ds can replicate itself and integrate into a new locus, and inaccurate excisions were also found. A proportion of DNA segments flanking the Ds elements showed no homologies to sequences published in GenBank, of which two were registered under the accession numbers AF355153 and AF355770. The strategy of using transposon tagging for rice genomics study was discussed.

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.

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.

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.

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.

X-Linked Dominant Congenital Ptosis Cosegregating with an Interstitial Insertion of a Chromosome 1p21.3 Fragment into a Quasipalindromic Sequence in Xq27.1

Blepharoptosis (ptosis) is defined as the abnormal drooping of the upper eyelid and is a feature of many conditions. It can be in isolated or syndromic form, bilateral or unilateral and congenital or acquired. Previously we have carried out linkage analysis on a family with dominantly inherited congenital bilateral isolated ptosis and found the condition to be linked to a region of approximately 20 megabases of chromosome Xq24-Xq27.1 with a cumulative LOD score of 5.89. We now describe further analysis using array comparative genomic hybridisation (array CGH), fluorescence in situ hybridisation (FISH), long range PCR and sequencing. This has enabled us to identify and characterise at the level of DNA sequence an insertional duplication and rearrangement involving chromosomes 1p21.3 and a small quasipalindromic sequence in Xq27.1, disruption of which has been associated with other phenotypes but which is cosegregating with X-linked congenital bilateral isolated ptosis in this family. This work highlights the significance of the small quasipalindromic sequence in genomic rearrangements involving Xq27.1 and the importance of comprehensive molecular and molecular cytogenetic investigations to fully characterise genomic structural complexity.

Mitochondrial targeting sequence of magnetoreceptor MagR:More than just targeting

Iron-sulfur clusters(ISC)are essential cofactors for proteins involved in various biological processes,such as electron transport,biosynthetic reactions,DNA repair,and gene expression regulation.ISC assembly protein IscA1(or MagR)is found within the mitochondria of most eukaryotes.Magnetoreceptor(MagR)is a highly conserved A-type iron and iron-sulfur cluster-binding protein,characterized by two distinct types of iron-sulfur clusters,[2Fe-2S]and[3Fe-4S],each conferring unique magnetic properties.MagR forms a rod-like polymer structure in complex with photoreceptive cryptochrome(Cry)and serves as a putative magnetoreceptor for retrieving geomagnetic information in animal navigation.Although the N-terminal sequences of MagR vary among species,their specific function remains unknown.In the present study,we found that the N-terminal sequences of pigeon MagR,previously thought to serve as a mitochondrial targeting signal(MTS),were not cleaved following mitochondrial entry but instead modulated the efficiency with which iron-sulfur clusters and irons are bound.Moreover,the N-terminal region of MagR was required for the formation of a stable MagR/Cry complex.Thus,the N-terminal sequences in pigeon MagR fulfil more important functional roles than just mitochondrial targeting.These results further extend our understanding of the function of MagR and provide new insights into the origin of magnetoreception from an evolutionary perspective.

A Novel Insertion Solution for the Travelling Salesman Problem

The studypresents theHalfMax InsertionHeuristic (HMIH) as a novel approach to solving theTravelling SalesmanProblem (TSP). The goal is to outperform existing techniques such as the Farthest Insertion Heuristic (FIH) andNearest Neighbour Heuristic (NNH). The paper discusses the limitations of current construction tour heuristics,focusing particularly on the significant margin of error in FIH. It then proposes HMIH as an alternative thatminimizes the increase in tour distance and includes more nodes. HMIH improves tour quality by starting withan initial tour consisting of a ‘minimum’ polygon and iteratively adding nodes using our novel Half Max routine.The paper thoroughly examines and compares HMIH with FIH and NNH via rigorous testing on standard TSPbenchmarks. The results indicate that HMIH consistently delivers superior performance, particularly with respectto tour cost and computational efficiency. HMIH’s tours were sometimes 16% shorter than those generated by FIHand NNH, showcasing its potential and value as a novel benchmark for TSP solutions. The study used statisticalmethods, including Friedman’s Non-parametric Test, to validate the performance of HMIH over FIH and NNH.This guarantees that the identified advantages are statistically significant and consistent in various situations. Thiscomprehensive analysis emphasizes the reliability and efficiency of the heuristic, making a compelling case for itsuse in solving TSP issues. The research shows that, in general, HMIH fared better than FIH in all cases studied,except for a few instances (pr439, eil51, and eil101) where FIH either performed equally or slightly better thanHMIH. HMIH’s efficiency is shown by its improvements in error percentage (δ) and goodness values (g) comparedto FIH and NNH. In the att48 instance, HMIH had an error rate of 6.3%, whereas FIH had 14.6% and NNH had20.9%, indicating that HMIH was closer to the optimal solution. HMIH consistently showed superior performanceacross many benchmarks, with lower percentage error and higher goodness values, suggesting a closer match tothe optimal tour costs. This study substantially contributes to combinatorial optimization by enhancing currentinsertion algorithms and presenting a more efficient solution for the Travelling Salesman Problem. It also createsnew possibilities for progress in heuristic design and optimization methodologies.

The Application of Nicotiana benthamiana as a Transient Expression Host to Clone the Coding Sequences of Plant Genes

Coding sequences (CDS) are commonly used for transient gene expression, in yeast two-hybrid screening, to verify protein interactions and in prokaryotic gene expression studies. CDS are most commonly obtained using complementary DNA (cDNA) derived from messenger RNA (mRNA) extracted from plant tissues and generated by reverse transcription. However, some CDS are difficult to acquire through this process as they are expressed at extremely low levels or have specific spatial and/or temporal expression patterns in vivo. These challenges require the development of alternative CDS cloning technologies. In this study, we found that the genomic intron-containing gene coding sequences (gDNA) from Arabidopsis thaliana, Oryza sativa, Brassica napus, and Glycine max can be correctly transcribed and spliced into mRNA in Nicotiana benthamiana. In contrast, gDNAs from Triticum aestivum and Sorghum bicolor did not function correctly. In transient expression experiments, the target DNA sequence is driven by a constitutive promoter. Theoretically, a sufficient amount of mRNA can be extracted from the N. benthamiana leaves, making it conducive to the cloning of CDS target genes. Our data demonstrate that N. benthamiana can be used as an effective host for the cloning CDS of plant genes.

Production of Light Fraction-Based Pyrolytic Fuel from Spirulina platensis Microalgae Using Various Low-Cost Natural Catalysts and Insertion

The use of catalysts has significantly enhanced the yield and quality of in-situ pyrolysis products.However,there is a lack of understanding regarding pyrolysis approaches that utilize several low-cost natural catalysts(LCC)and their placement within the reactor.Therefore,this study aims to examine the effects of various LCC on the insitu pyrolysis of spirulina platensis microalgae(SPM)and investigate the impact of different types of catalysts.We employed LCCsuch as zeolite,dolomite,kaolin,and activated carbon,with both layered and uniformlymixed LCCSPM placements.Each experiment was conducted at a constant temperature of 500℃for 60 min.The resulting pyrolytic liquids(bio-oil)and syngas were analyzed using a Gas Chromatography Mass Spectrometry(GC-MS)analyzer to determine the distribution of hydrocarbon compounds.The experimental results indicated that the presence of catalysts significantly influenced the mass yield productivity of liquid fuels and syngas.Activated carbon and zeolite were preferred among the four catalysts for producing liquid fuels(22.4 and 18.6 wt%)when layered and uniformly mixed,respectively.Kaolin with a layered mixture with SPM was more suitable for the production of light fractions(C_(5)–C_(12)),achieving approximately 95.7%peak area,while zeolite with a uniform mixture produced the highest light fraction at about 86.3%peak area.All catalysts except kaolin significantly increased the aromatic compounds in the liquid fuels.Although the amount of oxygenated hydrocarbons in the bio-oil remained relatively high,the final hydrocarbon composition was highly comparable to conventional fuels such as gasoline-88,which has a C_(5)–C_(12)hydrocarbon distribution of approximately 88.1%peak area.Regarding the syngas products,all catalysts except activated carbon successfully converted nitromethane compounds into tetranitromethane hydrocarbons,with activated carbon predominantly yielding nitromethane compounds.

Enhancing hydrogen evolution and oxidation kinetics through oxygen insertion into nickel lattice

Nickel-based materials,including metallic Ni and Ni oxide,have been widely studied in the exploration of non-precious-metal hydrogen electrocatalysts,but neither pure Ni nor NiO is ideal for the hydrogen evolution reaction(HER)and hydrogen oxidation reaction(HOR).In this paper,an oxygen insertion strategy was applied on nickel to regulate its hydrogen electrocatalytic performance,and the oxygen-inserted nickel catalyst was successfully obtained with the assistance of tungsten dioxide support(denoted as O-Ni/WO_(2)).The partial insertion of oxygen in Ni maintains the face-centered cubic arrangement of Ni atoms,simultaneously expanding the lattice and increasing the lattice spacing.Consequently,the adsorption strength of^(*)H and^(*)OH on Ni is optimized,thus resulting in superior electrocatalytic performance of0-Ni/WO_(2)in alkaline HER/HOR.The Tafel slope of O-Ni/WO_(2)@NF for HER is 56 mV dec^(-1),and the kinetic current density of O-Ni/WO_(2)for HOR reaches 4.85 mA cm^(-2),which is ahead of most currently reported catalysts.Our proposed strategy of inserting an appropriate amount of anions into the metal lattice could provide more possibilities for the design of high-performance catalysts.

Identification and characterization of FpRco1 in regulating vegetative growth and pathogenicity based on T-DNA insertion in Fusarium pseudograminearum

Fusarium pseudograminearum is a devastating pathogen that causes Fusarium crown rot(FCR)in wheat and poses a significant threat to wheat production in terms of grain yield and quality.However,the mechanism by which F.pseudograminearum infects wheat remains unclear.In this study,we aimed to elucidate these mechanisms by constructing a T-DNA insertion mutant library for the highly virulent strain WZ-8A of F.pseudograminearum.By screening this mutant library,we identified nine independent mutants that displayed impaired pathogenesis in barley leaves.Among these mutants,one possessed a disruption in the gene FpRCO1 that is an ortholog of Saccharomyces cerevisiae RCO1,encoding essential component of the Rpd3S histone deacetylase complex in F.pseudograminearum.To further investigate the role of FpRCO1 in F.pseudograminearum,we employed a split-marker approach to knock out FpRCO1 in F.pseudograminearum WZ-8A.FpRCO1 deletion mutants exhibit reduced vegetative growth,conidium production,and virulence in wheat coleoptiles and barley leaves,whereas the complementary strain restores these phenotypes.Moreover,under stress conditions,the FpRCO1 deletion mutants exhibited increased sensitivity to NaCl,sorbitol,and SDS,but possessed reduced sensitivity to H_(2)O_(2)compared to these characteristics in the wild-type strain.RNA-seq analysis revealed that deletion of FpRCO1 affected gene expression(particularly the downregulation of TRI gene expression),thus resulting in significantly reduced deoxynivalenol(DON)production.In summary,our findings highlight the pivotal role of FpRCO1 in regulating vegetative growth and development,asexual reproduction,DON production,and pathogenicity of F.pseudograminearum.This study provides valuable insights into the molecular mechanisms underlying F.pseudograminearum infection in wheat and may pave the way for the development of novel strategies to combat this devastating disease.

An efficient method for constructing a random insertional mutant library for forward genetics in Nannochloropsis oceanica

Insertional mutation,phenotypic evaluation,and mutated gene cloning are widely used to clone genes from scratch.Exogenous genes can be integrated into the genome during non-homologous end joining(NHEJ)of the double-strand breaks of DNA,causing insertional mutation.The random insertional mutant library constructed using this method has become a method of forward genetics for gene cloning.However,the establishment of a random insertional mutant library requires a high transformation efficiency of exogenous genes.Many microalgal species show a low transformation efficiency,making constructing random insertional mutant libraries difficult.In this study,we established a highly efficient transformation method for constructing a random insertional mutant library of Nannochloropsis oceanica,and tentatively tried to isolate its genes to prove the feasibility of the method.A gene that may control the growth rate and cell size was identified.This method will facilitate the genetic studies of N.oceanica,which should also be a reference for other microalgal species.

Possible effects of selecting different station distributions in the optimal sequence estimation method

Since the inception of the optimal sequence estimation (OSE) method,various research teams have substantiated its efficacy as the optimal stacking technique for handling array data,leading to its successful application in numerous geoscience studies.Nevertheless,concerns persist regarding the potential impact of aliasing resulting from the choice of distinct station distributions on the outcomes derived from OSE.In this investigation,I employ theoretical deduction and experimental analysis to elucidate the reasons behind the immunity of the Y_(l'm')-related common signal obtained through OSE to variations in station distribution selection.The primary objective of OSE is also underscored,i.e.,to restore/strip a Y_(l'm')-related common periodic signal from various stations.Furthermore,I provide additional clarification that the‘Y_(l'm')-related common signal’and the‘Y_(l'm')-related equivalent excitation sequence’are distinct concepts.These analyses will facilitate the utilization of the OSE technique by other researchers in investigating intriguing geophysical phenomena and attaining sound explanations.

Velamentous Cord Insertion: Interest of Antenatal Diagnosis and Review of the Literature

Velamentous insertion of the umbilical cord corresponds to the insertion of the cord directly on amniotic membranes. It is a rare situation whose frequency varies from 0.5% to 1.69% of single pregnancies. It must be diagnosed during the morphological ultrasound of the 2nd trimester, actively looking for the association with a vasa previa, due to the risk of fetal haemorrhagic threat. We report an antenatal diagnosis of velamentous cord insertion and its management with literature review.

Selection and application of wavelet transform in high-frequency sequence stratigraphy analysis of coarse-grained sediment in rift basin

Wavelet transformation is a widely used method in high-frequency sequence stratigraphic analysis.However, the application is problematic since different wavelets always return the same sequence analysis results. To address this issue, we applied five commonly used wavelets to theoretical sequence models to document some application criteria. Five gradual scale-change sequence models were simplified from the glutenite succession deposition by gravity flows to form the fining-upwards cycle sequences(FUCS) and coarsening-upwards cycle sequences(CUCS). After conducting theoretical sequence model tests, the optimal wavelet(sym4) was selected and successfully used with actual data to identify the sequence boundaries. We also proposed a new method to optimize the scale of continuous wavelet transformation(CWT) for sequence boundary determination. We found that the balloon-like marks in scalograms of db4, sym4, and coif4 wavelet determine, respectively, the fourth-order sequence boundary, the thick succession sequence boundaries in FUCS, and the thick succession sequence in FUCS and CUCS. Comparing the sequence identification results shows that the asymmetric wavelets had an advantage in high-frequency sequence boundary determination and sedimentary cycle discrimination through the amplitude trend of the coefficient, in which the sym4 wavelet is the most effective. In conclusion, the asymmetry of wavelets is the first selection principle, of which asymmetric wavelets are more sensitive to sediment deposition by flood flows. The match of the wavelet between the sequence is the second selection principle, in which the correlation of time-frequency impacts the accuracy of sequence surface localization. However, the waveform of the wavelet is a visual and abstract parameter for sequence boundary detection. The appropriate wavelet for lacustrine sequence analysis is the asymmetric wavelet with a weak number of side lobes. The depositional flows, depositional process,and autogenic are three sedimentary factors that influence the sequence analysis results.

Pig pangenome graph reveals functional features of non‑reference sequences

Background The reliance on a solitary linear reference genome has imposed a significant constraint on our compre-hensive understanding of genetic variation in animals.This constraint is particularly pronounced for non-reference sequences(NRSs),which have not been extensively studied.Results In this study,we constructed a pig pangenome graph using 21 pig assemblies and identified 23,831 NRSs with a total length of 105 Mb.Our findings revealed that NRSs were more prevalent in breeds exhibiting greater genetic divergence from the reference genome.Furthermore,we observed that NRSs were rarely found within coding sequences,while NRS insertions were enriched in immune-related Gene Ontology terms.Notably,our investigation also unveiled a close association between novel genes and the immune capacity of pigs.We observed substantial differences in terms of frequencies of NRSs between Eastern and Western pigs,and the heat-resistant pigs exhibited a substantial number of NRS insertions in an 11.6 Mb interval on chromosome X.Additionally,we discovered a 665 bp insertion in the fourth intron of the TNFRSF19 gene that may be associated with the ability of heat tolerance in South-ern Chinese pigs.Conclusions Our findings demonstrate the potential of a graph genome approach to reveal important functional features of NRSs in pig populations.

Phylogenetic, phylogeographic and divergence time analysis of Anopheles subpictus species complex using ITS2 and COI sequences

Objective:To address the phylogenetic and phylogeographic relationship between different lineages of Anopheles(An.)subpictus species complex in most parts of the Asian continent by maximum utilization of Internal Transcriber Spacer 2(ITS2)and cytochrome C oxidase I(COI)sequences deposited at the GenBank.Methods:Seventy-five ITS2,210 COI and 26 concatenated sequences available in the NCBI database were used.Phylogenetic analysis was performed using Bayesian likelihood trees,whereas median-joining haplotype networks and time-scale divergence trees were generated for phylogeographic analysis.Genetic diversity indices and genetic differentiation were also calculated.Results:Two genetically divergent molecular forms of An.subpictus species complex corresponding to sibling species A and B are established.Species A evolved around 37-82 million years ago in Sri Lanka,India,and the Netherlands,and species B evolved around 22-79 million years ago in Sri Lanka,India,and Myanmar.Vietnam,Thailand,and Cambodia have two molecular forms:one is phylogenetically similar to species B.Other forms differ from species A and B and evolved recently in the above mentioned countries,Indonesia and the Philippines.Genetic subdivision among Sri Lanka,India,and the Netherlands is almost absent.A substantial genetic differentiation was obtained for some populations due to isolation by large geographical distances.Genetic diversity indices reveal the presence of a long-established stable mosquito population,at mutation-drift equilibrium,regardless of population fluctuations.Conclusions:An.subpictus species complex consists of more than two genetically divergent molecular forms.Species A is highly divergent from the rest.Sri Lanka and India contain only species A and B.

On power series statistical convergence and new uniform integrability of double sequences

In the present paper,we mostly focus on P_(p)^(2)-statistical convergence.We will look into the uniform integrability via the power series method and its characterizations for double sequences.Also,the notions of P_(p)^(2)-statistically Cauchy sequence,P_(p)^(2)-statistical boundedness and core for double sequences will be described in addition to these findings.

A cloud model target damage effectiveness assessment algorithm based on spatio-temporal sequence finite multilayer fragments dispersion

To solve the problem of target damage assessment when fragments attack target under uncertain projectile and target intersection in an air defense intercept,this paper proposes a method for calculating target damage probability leveraging spatio-temporal finite multilayer fragments distribution and the target damage assessment algorithm based on cloud model theory.Drawing on the spatial dispersion characteristics of fragments of projectile proximity explosion,we divide into a finite number of fragments distribution planes based on the time series in space,set up a fragment layer dispersion model grounded in the time series and intersection criterion for determining the effective penetration of each layer of fragments into the target.Building on the precondition that the multilayer fragments of the time series effectively assail the target,we also establish the damage criterion of the perforation and penetration damage and deduce the damage probability calculation model.Taking the damage probability of the fragment layer in the spatio-temporal sequence to the target as the input state variable,we introduce cloud model theory to research the target damage assessment method.Combining the equivalent simulation experiment,the scientific and rational nature of the proposed method were validated through quantitative calculations and comparative analysis.