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.

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.

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.

Secure Transmission of Compressed Medical Image Sequences on Communication Networks Using Motion Vector Watermarking

Medical imaging plays a key role within modern hospital management systems for diagnostic purposes.Compression methodologies are extensively employed to mitigate storage demands and enhance transmission speed,all while upholding image quality.Moreover,an increasing number of hospitals are embracing cloud computing for patient data storage,necessitating meticulous scrutiny of server security and privacy protocols.Nevertheless,considering the widespread availability of multimedia tools,the preservation of digital data integrity surpasses the significance of compression alone.In response to this concern,we propose a secure storage and transmission solution for compressed medical image sequences,such as ultrasound images,utilizing a motion vector watermarking scheme.The watermark is generated employing an error-correcting code known as Bose-Chaudhuri-Hocquenghem(BCH)and is subsequently embedded into the compressed sequence via block-based motion vectors.In the process of watermark embedding,motion vectors are selected based on their magnitude and phase angle.When embedding watermarks,no specific spatial area,such as a region of interest(ROI),is used in the images.The embedding of watermark bits is dependent on motion vectors.Although reversible watermarking allows the restoration of the original image sequences,we use the irreversible watermarking method.The reason for this is that the use of reversible watermarks may impede the claims of ownership and legal rights.The restoration of original data or images may call into question ownership or other legal claims.The peak signal-to-noise ratio(PSNR)and structural similarity index(SSIM)serve as metrics for evaluating the watermarked image quality.Across all images,the PSNR value exceeds 46 dB,and the SSIM value exceeds 0.92.Experimental results substantiate the efficacy of the proposed technique in preserving data integrity.

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.

A Novel Method of Deinterleaving Radar Pulse Sequences Based on a Modified DBSCAN Algorithm

A modified DBSCAN algorithm is presented for deinterleaving of radar pulses in modern EW environments.A main characteristic of the proposed method is that using only time of arrival of pulses,the method can sort the pulses efficiently.Other PDW information such as rise time,carrier frequency,pulse width,modulation on pulse,fall time and direction of arrival are not required.To identify the valid PRIs in a set of interleaved pulses,an innovative modification of the DBSCAN algorithm is introduced which is accurate and easy to implement.The proposed method determines valid PRIs more accurately and neglects the spurious ones more efficiently as compared to the classical histogram based algorithms such as SDIF.Furthermore,without specifying any input parameter,the proposed method can deinterleave radar pulses while up to 30%jitter is present in the associated PRI.The accuracy and efficiency of the proposed method are verified by computer simulations and real data results.Experimental simulations are based on different real and operational scenarios where the presence of missing and spurious pulses are also considered.So,the simulation results can be of practical significance.

Leachate Lithium Characteristics of Loess-paleosol Sequences on the Chinese Loess Plateau and their Paleoclimatic Significance

The geochemical components of the leachate from loess-paleosol deposits can provide information about climaterelated post-depositional processes.For example,leachate lithium([Li]_(leachate))is a potential paleoclimate proxy because lithium is a typical lithophile element that is readily adsorbed by clay minerals during weathering and pedogenesis,and thus stratigraphic variations in[Li]leachatecan reflect these processes.We investigated the[Li]leachatevalues of two loess-paleosols profiles(the Luochuan and Weinan sections),on a north-south climatic gradient on the Chinese Loess Plateau.Independent paleoclimate information was provided by measurements of magnetic susceptibility,grain size,Rb/Sr ratios,and clay mineral content.During the last glacial-interglacial period,[Li]leachateincreased from 0.39 to 1.97μg/g at Luochuan and from 0.67 to 2.45μg/g at Weinan,mainly due to increasing pedogenesis.Based on these results we developed a conceptual model to explain the variations in[Li]leachate,Li^(+)within loess layers is mainly derived from dust input and the decomposition of primary minerals,influenced by the East Asian winter monsoon,while in paleosol layers Li is mainly derived from clay mineral adsorption during pedogenic processes,influenced by the East Asian summer monsoon.

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.

The asymptotic relation between the first crossing point and the last exit time of Gaussian order statistics sequences

In this paper,we study the asymptotic relation between the first crossing point and the last exit time for Gaussian order statistics which are generated by stationary weakly and strongly dependent Gaussian sequences.It is shown that the first crossing point and the last exit time are asymptotically independent and dependent for weakly and strongly dependent cases,respectively.The asymptotic relations between the first crossing point and the last exit time for stationary weakly and strongly dependent Gaussian sequences are also obtained.

Identification of clade-wide putative cis-regulatory elements from conserved non-coding sequences in Cucurbitaceae genomes

Cis-regulatory elements regulate gene expression and play an essential role in the development and physiology of organisms.Many conserved non-coding sequences(CNSs)function as cis-regulatory elements.They control the development of various lineages.How-ever,predicting clade-wide cis-regulatory elements across several closely related species remains challenging.Based on the relationship between CNSs and cis-regulatory elements,we present a computational approach that predicts the clade-wide putative cis-regulatory elements in 12 Cucurbitaceae genomes.Using 12-way whole-genome alignment,we first obtained 632112 CNSs in Cucurbitaceae.Next,we identified 16552 Cucurbitaceae-wide cis-regulatory elements based on collinearity among all 12 Cucurbitaceae plants.Furthermore,we predicted 3271 potential regulatory pairs in the cucumber genome,of which 98 were verified using integrative RNA sequencing and ChIP sequencing datasets from samples collected during various fruit development stages.The CNSs,Cucurbitaceae-wide cis-regulatory elements,and their target genes are accessible at http://cmb.bnu.edu.cn/cisRCNEs_cucurbit/.These elements are valuable resources for functionally annotating CNSs and their regulatory roles in Cucurbitaceae genomes.

改进灰狼算法优化GBDT在PM_(2.5)预测中的应用

针对灰狼算法易陷入局部最优解和全局搜索能力不足的问题,通过霍尔顿序列(Halton Sequence)搜索算法初始化狼群位置,避免灰狼算法陷入局部最优解和重复运算;引入莱维飞行和随机游动策略对灰狼算法的寻优过程进行优化,以增加算法的全局搜索能力;利用粒子群算法模拟灰狼种群得出的最佳适应度以用于惩罚项改进灰狼算法中的头狼更新策略。使用改进算法优化的梯度提升树(Gradient Boosting Decision Trees,GBDT)模型对北京市大气污染物监测数据中PM_(2.5)质量浓度进行预测,采用3种评估函数对各模型以及混合模型预测效果得分进行评估。结果显示,本文改进的灰狼算法对梯度提升树的优化效果优于其他算法,均方根误差E RMS为6.65μg/m^(3),平均绝对值误差E MA为3.20μg/m^(3),拟合优度(R^(2))为99%,比传统灰狼算法优化结果的均方根误差减少了19.19μg/m^(3),平均绝对值误差降低了10.03μg/m^(3),拟合优度增加了9百分点;与霍尔顿序列和莱维飞行改进的(Levy Flight-Halton Sequence,LHGWO)相比,改进的灰狼算法预测得分的均方根误差降低了10.39μg/m^(3),平均绝对值误差减小了6.71μg/m^(3),拟合优度提高了5百分点。研究表明了预测模型优化的有效性,为未来城市改善空气质量提供了科学依据和技术支持。

About Upper and Lower Strong Fractional Weighted Mean Convergence by Moduli for Triple Sequences

In article, I present a study on upper and lower statistical convergence, and upper and lower strong fractional weighted mean convergence by moduli for triple sequences. One of the generalizations of the discrete operator Cesàro, was weighted mean operators, which are linear operators, too. Given a modulus function f, I established that a triple sequence that is f-upper or lower strong fractional weighted mean convergent, in some supplementary conditions, is also f-lower or upper statistically convergent. The results of this paper adapt the results obtained in [1] and [2] to upper and lower strong fractional weighted mean convergence and to triple sequence concept. Furthermore, new concepts can be applied to the approximation theory, topology, Fourier analysis, analysis interdisciplinary with applications electrical engineering, robotics and other domains.

全基因组测序分析生畜肉中沙门氏菌血清型、耐药性与毒力因子

了解市售生畜肉中沙门氏菌(Salmonella)血清型、序列型(sequence typing,ST)分布、耐药性和毒力因子特征,探讨ST与耐药性和毒力的关系。收集2020—2023年从生畜肉中分离的68株沙门氏菌,用血清凝集法鉴定其血清型,微量肉汤稀释法进行药物敏感检测;全基因组测序分析多位点序列分型、耐药基因与毒力因子,并结合系统发育树分析其相关性。结果表明:68株沙门氏菌可分为14种血清型,以鼠伤寒沙门氏菌和肠炎沙门氏菌为主,ST以ST19、ST34和ST11为主;多重耐药菌株占比69.12%(47/68),对氨苄西林(76.47%)、四环素(55.88%)和萘啶酸(52.94%)耐药率较高;68株沙门氏菌均携带菌毛吸附相关因子、镁离子转运相关因子、非菌毛类吸附相关因子、调控相关因子和分泌系统相关因子;生畜肉中污染的沙门氏菌血清型种类多样,耐药性严重且携带多种毒力因子,需要加强畜类养殖和生产销售的管理。

高通量测序技术在低频突变检测中的应用

体细胞突变的累积与衰老、肿瘤及多种疾病的发生密切相关。在正常组织细胞中,基因组中自发突变和诱发突变的变异等位基因频率极低,对这类低频突变的检测一直面临挑战。第二代和第三代高通量测序(next-generation sequencing,NGS)技术的出现,可以实现任意物种全基因组上变异的直接检测,克服传统突变检测技术的诸多局限性。但是常规NGS由于测序错误率较高从而限制了其在低频突变检测上的应用,基于分子一致性测序策略进行错误矫正的高准确性NGS测序技术作为有效的低频突变检测工具,有望在环境诱变剂的评价与研究、细胞与基因治疗药物风险评估、人群健康风险监测和生命科学基础研究领域发挥重要作用。本文对比经典突变检测方法,对基于NGS的低频突变检测技术研究进展进行综述,并对应用前景进行展望,以期为该技术的进一步开发、研究和在相关领域的应用提供参考。

ASE-ERNIE:一种基于ERNIE的中文指令动作序列生成方法

中文结构灵活多样,同样的语义有多种表达方式,在中文指令过长或存在多组动作的情况下,家庭服务机器人很难正确理解并做出响应。此外,家庭环境的中文指令解析研究在数据方面仍然稀缺。现有的方法不能准确提取出指令中包含的全部动作序列。由此提出一种基于ERNIE方法的动作序列提取(ASE-ERNIE)模型来提取中文指令中的可执行动作序列,该模型通过动作类型和参数之间的关系提取指令信息,将动作序列的提取工作转化为序列标注任务。在指令中存在多组动作并且存在多个参数的情况下,依然能够提取出全部动作序列。通过实验验证了所提方法的有效性,动作序列提取任务的F 1值达到了80.37%。

马瑟兰葡萄果实生长发育和品质变化的转录组分析

【目的】探究酿酒葡萄品种马瑟兰果实生长发育过程中的品质变化,挖掘关键的生长发育及果实品质调控基因,为马瑟兰葡萄栽培措施的精准制定和果实品质提高提供理论依据。【方法】以贺兰山东麓马瑟兰葡萄为试验材料,采集花后20 d、花后45 d、花后75 d及花后100 d不同发育阶段的葡萄果实,测量果粒横径和纵径,测定果实可溶性固形物、总糖、可滴定酸和总酚含量,并进行转录组测序分析。【结果】随着马瑟兰葡萄果实生长发育,果实色泽加深、果粒体积增大,果实可溶性固形物和总糖含量逐渐上升,可滴定酸含量逐渐下降,总酚含量在花后20 d至花后75 d期间逐渐下降而在花后75 d至花后100 d期间略有上升。从不同发育阶段葡萄果实间共筛选到33517个DEGs,花后45 d与花后20 d比较组、花后75 d与花后45 d比较组、花后100 d与花后75 d比较组共有的DEGs为3976个。GO功能注释分析结果表明,各比较组DEGs主要注释到细胞器、细胞膜、含蛋白复合物、细胞过程和代谢过程等功能条目。KEGG信号通路富集分析结果表明,氨基酸的生物合成、糖酵解/糖异生及类黄酮生物合成等是马瑟兰葡萄果实发育过程中的重要信号通路。从富集在类黄酮生物合成信号通路的DEGs中,发现查耳酮合成酶基因(CHS)和黄烷酮-3-羟化酶基因(F3H)均在花后45 d至75 d期间上调表达,F3H在花后75 d至花后100 d期间下调表达,表明CHS与F3H基因在马瑟兰葡萄果皮着色中起重要调控作用。【结论】马瑟兰葡萄生长发育过程中伴随着果实色泽加深、果粒体积增大和生化成分的动态变化。类黄酮生物合成信号通路在葡萄转色过程中起重要作用,CHS和F3H基因影响马瑟兰葡萄果实着色及品质形成。

无创产前检测:迈向下一个十年

无创产前基因检测(NIPT)是过去10余年来产前筛查领域的重大突破,是围产医学领域的引领技术。通过低深度全基因组测序分析孕妇外周血胎儿游离DNA(cffDNA),实现了高效的唐氏综合征产前筛查,同时可扩展应用于其他染色体非整倍体、拷贝数变异等常见胎儿基因组问题的筛查,实现胎儿疾病的早期无创检测。但是,NIPT依然需要更多循证医学证据支持,以迈向更为广阔的应用空间。文章从NIPT适应证选择、NIPT异常结果分析、NIPT结果报道与解读中的伦理学问题、NIPT在胎儿基因变异筛查中的应用以及非cffDNA来源NIPT技术开发等角度,探讨了NIPT目前面临的问题与未来的发展趋势。

抗虫转基因水稻及其杂交水稻对土壤微生物群落多样性与组成的影响

微生物是土壤物质循环与肥力演变的驱动者,其群落组成关系到土壤微生态系统的稳定与可持续性。对抗虫转基因水稻土壤微生物群落变化的研究是其环境安全性评价的重要内容。本研究基于细菌16S rRNA基因和真菌ITS基因的高通量测序,分析了田间试验中抗虫转基因水稻‘MFB’及其转基因杂交水稻‘闽丰A/MFB’‘天丰A/MFB’和‘谷丰A/MFB’与非转基因常规水稻‘闽恢3301’及杂交水稻‘天优华占’的土壤微生物群落多样性与组成的差异,并得出以下结果。首先,与两个非转基因水稻品种相比,抗虫转基因水稻及转基因杂交水稻均能显著增产(P<0.05)。同时,高通量测序结果表明,除水稻成熟期的土壤真菌群落外,与‘闽恢3301’相比‘MFB’的土壤细菌或真菌群落的α-多样性指数Chao1、Observed_species和Shannon均有所提高,且分别在水稻成熟期或分蘖期达到显著性水平(P<0.05);水稻齐穗期转基因杂交水稻‘闽丰A/MFB’‘天丰A/MFB’和‘谷丰A/MFB’的土壤细菌及真菌群落的多样性指数Shannon均介于‘MFB’与‘天优华占’之间;微生物群落β-多样性分析结果表明,本田间试验中不同品种水稻土壤细菌或真菌的群落组成均没有显著差异。但与‘闽恢3301’相比,稻田土壤细菌中丰度最高的变形菌门的相对丰度在‘MFB’土壤中明显增加,且在水稻分蘖期及成熟期达显著水平(P<0.05),而土壤真菌中丰度最高的子囊菌门的相对丰度在‘MFB’土壤中明显减少,且在水稻分蘖期及齐穗期差异显著(P<0.05);水稻齐穗期‘闽丰A/MFB’‘天丰A/MFB’和‘谷丰A/MFB’的土壤变形菌门或子囊菌门的相对丰度也均介于‘MFB’与‘天优华占’之间。此外,通过对微生物群落的功能组成预测可见,随水稻生长,‘MFB’与‘闽恢3301’的土壤细菌群落功能组成间差异存在增大的趋势。综上所述,本研究田间试验中,抗虫转基因水稻及其转基因杂交水稻在增产的同时提高了稻田土壤细菌或真菌群落的多样性,改变了主要细菌或真菌种类的相对丰度,但对细菌或真菌的群落及功能组成的影响不显著。

蒙古扁桃叶绿体遗传特征分析

以古老孑遗植物蒙古扁桃为试材,基于Illumina HiSeq X^(Ten)平台测序,采用生物信息学分析方法,研究了蒙古扁桃叶绿体基因组特征和系统发育情况,以期为蒙古扁桃和近缘种物种鉴定、系统发育地位以及早春观赏植物和西北荒漠草地植物的育种培育提供参考依据。结果表明:蒙古扁桃叶绿体基因组为四分体式结构。其蛋白编码基因共编码26428个密码子,有29种是偏好密码子。密码子UUU数目最多,达1034个;密码子GCG数目最少,为137个。编码亮氨酸的密码子数目最多(2637个),占总量的9.98%;编码色氨酸的密码子数目最少(531个)仅占到1.94%。根据设置参数,发现蒙古扁桃叶绿体基因组中串联重复有16个,SSR位点有31个。SSR大多位于基因间区IGS和LSC区域。SSR中未检测到三核苷酸重复。基于叶绿体全基因组序列数据发现蒙古扁桃与桃亚属的桃和甘肃桃亲缘关系较近。

基于高通量测序技术分析不同窖龄窖泥真菌群落多样性与空间异质性

利用Illumina NovaSeq高通量测序、冗余分析和FUNGuild等方法对甘肃金徽酒10a和50a窖龄窖池及其不同空间位置窖泥的真菌群落结构、真菌菌群与理化因子之间的关系以及真菌功能预测等进行研究。结果表明,随着窖池深度的增加,10 a窖池窖泥的多样性和丰富度呈现降低趋势,50 a窖池窖泥的多样性整体呈现升高趋势,而丰富度则呈现先降低后升高趋势,其中10a窖池窖壁上层的多样性和丰富度均显著高于其他位置(P<0.05),而50a窖池窖底层的多样性和丰富度均显著高于其他位置(P<0.05)。10a窖池窖壁层的多样性和丰富度显著高于50a窖池(P<0.05),而50a窖底层的多样性和丰富度明显高于10a窖池(P<0.05)。所有窖泥样品共检测到21个真菌门和520个真菌属,其中子囊菌门(Ascomycota)、担子菌门(Basidiomycota)、被孢霉门(Mortierellomycota)和罗兹菌门(Rozellomycota)4个优势真菌门以及曲霉属(Aspergillus)和哈萨克斯坦酵母属(Kazachstania)等多数优势真菌属的相对丰度随窖池窖龄和空间位置的变化差异显著(P<0.05)。镰刀霉属(Fusarium)、Aspergillus、Kazachstania和红曲霉属(Monascus)与水分、腐殖质、K^(+)和Ca^(2+)含量呈正相关,枝孢菌属(Cladosporium)、维希尼克氏酵母属(Vishniacozyma)与pH值呈正相关。窖泥真菌营养类型主要有腐生营养型和病理-腐生-共生营养型等7种,功能类群包括4个单一功能群和7个混合功能群。通过系统分析不同窖龄窖池和空间位置的窖泥真菌群落多样性,为明确甘肃金徽酒窖泥的真菌群落结构及空间分布规律奠定了理论基础。