A comparative study of genomes in angiosperms

Angiosperms investigated by DNA/DNA reassociation studies were classified and tested for a taxonomic class- and subclass-specifity in a biometrical fashion. Monocotyledons and Dicotyledons differ significantly from each other with respect to a genomic parameter (U/R-ratio;U single copy DNA fraction;R = 1-U fraction of repetitive DNA). This difference is discussed from an evolutionary and molecular point of view.—Intercorrelations between the fraction of fast repeats, slow repeats, and single copy DNA can be detected. The amount of DNA organized in a short period pattern of interspersion is found to depend on the fraction of repetitive and single copy DNA. The number of DNA segments tandemly arranged in a short period pattern is linearly correlated withR/U-values. This correlation allows for a formula suitable for the estimation of the number of active genes in angiosperms. The analytical complexities of repetitive and single copy DNA are linearly correlated with the genome size of higher plants. The ratioU/R depends on the genome size of angiosperms in a hyperbolic fashion.     

Conforming to the status flow: The influence of altered habitat on fish body-shape characteristics

1. Anthropogenic stream impoundments often result in altered flow regimes and reservoir formations. Functional fish characteristics may change in response to altered flow conditions, and understanding the underlying mechanisms at work (e.g. natural selection and phenotypic plasticity) is of great importance in both evolutionary and conservation contexts. Cyprinella lutrensis is a widely distributed minnow native to stream systems in Missouri, U.S.A. Following impoundment of the Osage River, C. lutrensis currently occurs in the resultant Truman Reservoir and surrounding tributaries. To examine the impacts of this habitat alteration on functional fish characteristics, we hypothesised that C. lutrensis populations in altered systems with no-flow would show an overall less streamlined body shape as compared to those in flowing systems, assuming body streamlining is beneficial for locomotion in flowing environments.
2. We conducted field and laboratory studies to test effects of flow and no-flow on C. lutrensis body shape. Geometric morphometric techniques were used to quantify body shape in field and laboratory individuals, and non-structural lipid extractions were conducted to assess whether fat storage contributes to body shape under flow and no-flow treatments.
3. Morphological comparisons between C. lutrensis from Truman Reservoir and surrounding streams yielded significant differences in body shape, with greater body streamlining in stream populations. A laboratory experiment using artificial stream units revealed similar significant differences in body streamlining between flow and no-flow treatments within a single generation. In addition, individuals under no-flow treatment had significantly higher levels of non-structural lipids compared to flow treatment individuals.
4. Our results indicate that changes in flow regime can alter the evolutionary trajectories (i.e. related to morphology) of fish populations. We suggest that body shape alterations are likely to occur within and across generations in a cumulative manner, therefore, it is plausible that both natural selection and plastic response mechanisms play roles in defining minnow body shape following flow alteration.

     

Demography and genome divergence of lake and stream populations of an East African cichlid fish

Disentangling the processes and mechanisms underlying adaptive diversification is facilitated by the comparative study of replicate population pairs that have diverged along a similar environmental gradient. Such a setting is realized in a cichlid fish from southern Lake Tanganyika, Astatotilapia burtoni, which occurs within the lake proper as well as in various affluent rivers. Previously, we demonstrated that independent lake and stream populations show similar adaptations to the two habitat regimes. However, little is known about the evolutionary and demographic history of the A. burtoni populations in question and the patterns of genome divergence among them. Here, we apply restriction site‐associated DNA sequencing (RADseq) to examine the evolutionary history, the population structure and genomic differentiation of lake and stream populations in A. burtoni. A phylogenetic reconstruction based on genome‐wide molecular data largely resolved the evolutionary relationships among populations, allowing us to re‐evaluate the independence of replicate lake–stream population clusters. Further, we detected a strong pattern of isolation by distance, with baseline genomic divergence increasing with geographic distance and decreasing with the level of gene flow between lake and stream populations. Genome divergence patterns were heterogeneous and inconsistent among lake‐stream population clusters, which is explained by differences in divergence times, levels of gene flow and local selection regimes. In line with the latter, we only detected consistent outlier loci when the most divergent lake–stream population pair was excluded. Several of the thus identified candidate genes have inferred functions in immune and neuronal systems and show differences in gene expression between lake and stream populations.     

Pna Array Technology in Molecular Diagnostics

Abstract

A comparative study using immobilised DNA and PNA oligomers demonstrates the suitability of PNA molecules as sequence specific capture probes in the detection of single point mutations in a DNA analyte and in the analysis of complex analyte mixtures.     

DNA Intercalation and Photoinduced Cleavage by 4-Nitro(N-Hexylamine)1,8-Naphthalimide

Abstract

A novel intercalator, 4-nitro(N-hexylamine)1,8-naphthalimide, was synthesised and its DNA binding and photoinduced DNA cleavage properties were studied. The DNA unwinding results show that it binds through intercalation. Absorption and fluorescence spectroscopy reveal the preference for A/T base pairs as compared to G/C base pairs for the binding. The intercalator produces photoinduced single strand scissions in double helical DNA.     

A Fluorescence Detection and Selection Device for Dna-Molecules Bound to Microspheres

Abstract

A device for the detection and selection of DNA-molecules bound to microspheres has been realized. It is based on a quartz chip with a capillary flowsystem, and confocal fluorescence detection of DNA. The device is to be used to identify and isolate single DNA-molecules for sequencing experiments.     

IV型限制酶ScoMcrA中SRA结构域介导的二聚体化对硫结合结构域功能的影响机制

[背景] 部分细菌的DNA骨架会发生磷硫酰化修饰,硫结合结构域（Sulfur Binding Domain,SBD）可以特异性识别这种生理修饰。与绝大多数SBD-HNH双结构域核酸酶不同,ScoMcrA的SBD和HNH结构域中间插入了一个特异性识别5-甲基胞嘧啶（5mC）修饰DNA的SET and RING-Associated （SRA）结构域。晶体结构显示,单独的SBD是单体,而SBD-SRA是双体。[目的] 探究ScoMcrA中SRA结构域的存在对SBD识别硫修饰DNA的影响及影响方式。[方法] 凝胶迁移实验（Electrophoresis Mobility Shift Assay,EMSA）比较SBD、SBD-SRA对硫修饰DNA结合力的差异;对参与SBD-SRA二聚体化的关键氨基酸残基突变,并检测点突变对SBD-SRA蛋白二聚体化及结合硫修饰DNA的影响。[结果] 相较于SBD结构域,SBD-SRA双结构域对磷硫酰化修饰DNA的结合能力明显增强。对SBD-SRA双体互作界面进行单点突变基本不影响其对硫修饰DNA的结合,当二聚体化界面连续的L₂₆₁LGET₂₆₅突变成A₂₆₁AAAA₂₆₅时,突变体对硫修饰DNA的结合力下降到与SBD相似的水平。[结论] 根据EMSA实验结果可以初步判断,SRA结构域介导的SBD-SRA双体化能增强SBD对硫修饰DNA的结合力;L₂₆₁LGET₂₆₅是SRA结构域上影响SBD对硫修饰DNA结合力的关键氨基酸位点。     

一种制备新生隐球菌单细胞的方法

【目的】建立流式细胞仪分选新生隐球菌单细胞的方法,确定新生隐球菌单细胞恢复生长的条件和能力。【方法】利用Moflo XDP流式细胞分析分选仪,体外测定不同条件下新生隐球菌恢复生长的比率。【结果】建立了流式细胞仪新生隐球菌单细胞分选流程。确定流式细胞仪分选得到的新生隐球菌单细胞具有恢复生长的能力,恢复生长的能力受营养条件和菌株差异的影响。在营养丰富的条件下,新生隐球菌JEC21和H99单细胞恢复生长比率分别为74%和89%。在寡营养条件下,JEC21和H99单细胞恢复生长比率分别为37%和80%。JEC21生长比率随细胞数的增加而升高,细胞数为100个时,生长比率为55%;细胞数为1000个时,生长比率为97%。【结论】流式细胞仪分选得到新生隐球菌单细胞具有恢复生长的能力,生长能力受营养条件、菌株差异的影响。     

基于Golden Gate技术的齐整小核菌转录单元高效组装系统

【目的】为齐整小核菌代谢工程研究建立高效的转录单元组装系统。【方法】通过应用Golden Gate技术,以mobius assembly为基础,分别设计并构建DNA元件标准化接口改造、单转录单元组装、应用质粒(多转录单元)组装等功能的载体,从而形成一套完整的多转录单元组装系统。【结果】构建了2个用于DNA元件标准化接口改造的Level 0载体,4个用于单转录单元组装的Level 1载体,4个用于应用质粒组装的Level 2载体和13个应用质粒组装的辅助质粒。然后应用此系统为齐整小核菌组装了若干经过标准化接口改造的DNA元件质粒、单转录单元质粒和硬葡聚糖相关基因的功能分析质粒。所构建的最终应用质粒可以同时适用于齐整小核菌的根癌农杆菌介导转化法、电穿孔转化法和原生质体转化法。【结论】此质粒系统具有强大的DNA设计、组装和容纳能力,为未来齐整小核菌代谢工程和功能基因组学研究提供了高效的质粒构建技术平台。     

Differential structural status of the RNA counterpart of an undecamer quasi-palindromic DNA sequence present in LCR of human β-globin gene cluster

Our previous work on structural polymorphism shown at a single nucleotide polymorphism (SNP) (A→G) site located on HS4 region of locus control region (LCR) of β-globin gene has established a hairpin→duplex equilibrium corresponding to A→B like DNA transition (Kaushik M, Kukreti, R., Grover, D., Brahmachari, S.K. and Kukreti S. Nucleic Acids Res. 2003; Kaushik M, Kukreti S. Nucleic Acids Res. 2006). The G-allele of A→G SNP has been shown to be significantly associated with the occurrence of β-thalassemia. Considering the significance of this 11-nt long quasi-palindromic sequence [5′-TGGGG(G/A)CCCCA; HP(G/A)11] of β-globin gene LCR, we further explored the differential behavior of the same DNA sequence with its RNA counterpart, using various biophysical and biochemical techniques. In contrast to its DNA counterpart exhibiting a A→B structural transition and an equilibrium between duplex and hairpin forms, the studied RNA oligonucleotide sequence [5′-UGGGG(G/A)CCCCA; RHP(G/A)11] existed only in duplex form (A-conformation) and did not form hairpin. The single residue difference from A to G led to the unusual thermal stability of the RNA structure formed by the studied sequence. Since, naturally occurring mutations and various SNP sites may stabilize or destabilize the local DNA/RNA secondary structures, these structural transitions may affect the gene expression by a change in the protein–DNA recognition patterns.     

eIF3a‐PPP2R5A‐mediated ATM/ATR dephosphorylation is essential for irinotecan‐induced DNA damage response

ObjectivesThe individual differences and pervasive resistance seriously hinder the optimization of irinotecan‐based therapeutic effectiveness. Eukaryotic translation initiation factor 3a (eIF3a) plays a key role in tumour occurrence, prognosis and therapeutic response. This study focused on the role of eIF3a in irinotecan‐induced DNA damage response.Materials and MethodsThe cck8 cell viability and clone survival analyses were used to test the regulatory role of eIF3a on irinotecan sensitivity in HT29 and CACO2 cell lines in vitro. This regulatory role was also verified in vivo by conducting subcutaneous xenograft model. Irinotecan‐induced DNA damage, cell cycle arrest and apoptosis were tested by flow cytometry analysis, TUNEL staining, western blot and comet assays. The immunofluorescence, co‐IP, luciferase reporter assay, RIP and flow cytometric analyses were carried out to investigate the underline mechanism.ResultsWe demonstrated that eIF3a continuously activates ATM/ATR signal by translationally inhibiting PPP2R5A, a phosphatase that directly dephosphorylates and inactivates ATM/ATR after DNA repair complete. Suppression of PPP2R5A resulted in chronic ATM/ATR phosphorylation and activation, impairing DNA repair and enhancing irinotecan sensitivity.ConclusionsOur study suggested eIF3a with a high potential to influence phenotypic functions, which may contribute substantially to the early identification of susceptible individuals and the provision of personalized medication to irinotecan‐treated patients.     

Influence of base flow stream bank seepage on riparian zone nitrogen biogeochemistry

We examined the effect of sustained stream bank seepage during base flow conditions on the pore water nitrogen biogeochemistry of two riparian zones in lowland agricultural areas in southern Ontario, Canada. Nitrate, ammonium and dissolved oxygen concentrations in riparian subsurface water over a two-year period showed well-organized spatial patterns along stream bank seepage flow paths that extended seasonally up to 25 m inland. High levels of dissolved oxygen and NO₃⁻ in stream inflow were depleted rapidly at the stream bank interface suggesting the occurrence of aerobic microbial respiration followed by denitrification. A zone of NH₄⁺ accumulation persisted in more anaerobic sediments inland from the bank margin, although the magnitude and intensity of the pattern varied seasonally. A bromide tracer and NO₃⁻ co-injection at the stream bank interface indicated that bank seepage occurred along preferential flow paths in a poorly sorted gravel layer in the two riparian zones. Depletion of NO₃⁻ in relation to co-injected bromide confirmed that the bank margin was a hot spot of biogeochemical activity within the riparian zone. Conceptual models of humid temperate riparian zones have focused on nitrogen biogeochemistry in relation to hillslope to stream hydrologic flow paths. However, our results suggest that sustained stream bank inflow during low flow conditions can exert a dominant control on riparian nitrogen cycling in lowland landscapes where level riparian zones bounded by perennial streams receive limited subsurface inflows from adjacent slopes.     

Molecular dynamics simulations of valveless pumping in a closed microfluidic tube-system

In this paper, we study the flow which is generated by a valveless pumping mechanism in a closed micro-fluidic tube-system consisting of two tubes with different radii. This system has been investigated by Ottesen [J. T. Ottesen, J. Math. Biol. 46, 309, (2003)] at a macroscopic level. We find that the results from the microscopic simulations qualitatively agree with the macroscopic results. Especially, it is shown that the direction of the flow changes with changing pumping frequency and the location of the pumping device. We study the local flow generated in the system and show that the stream velocities away from the pumping area can be modeled by a superposition of a plug flow and a zero-mean oscillatory flow.     

Synthesis of a Carboxamide Linked UBr∗UBr Dimer–Duplex and Triplex Stabilities of the Corresponding Oligodeoxynucleotides

Abstract

A U^Br?U^Br dimer was synthesized by connecting the appropiate nucleoside monomers through a 5-atom carboxamide linkage. The dimer was incorporated in oligodeoxynucleotides and investigated for hybridization properties toward single and double stranded DNA.     

基于流式细胞仪高通量分选的深海微生物单细胞培养

【目的】建立适用于海洋微生物的流式细胞分选与高通量单细胞培养的方法,通过该方法从印度洋深海样品中分离微生物纯培养菌株。【方法】利用流式细胞仪单细胞分选功能,以前向角(FSC)和侧向角(SSC)散射光信号代替荧光信号作为分选逻辑,对深海水体和沉积物样品中微生物进行单细胞高通量分选和培养。【结果】确定了流式细胞分选的区域和条件,发现所建立方法适于分离海洋水体微生物,而不是沉积物微生物。从印度洋深海水体样品中获得61个潜在新菌株,分属于6个新属种,占分离菌株总数的26.29%,其16S rRNA基因序列与已培养的模式菌株相似性为89.79%–95.37%。【结论】本研究所建立的方法有助于提高发现海洋微生物新物种的效率,获得更多新的海洋微生物资源。     

Negatively Charged,Dye Labeled-Dideoxynucleotides for “Direct-Load” DNA Sequencing

Abstract

A four-color set of negatively charged, single dye as well as energy transfer dye labeled-ddNTPs were synthesized and evaluated in combination with a novel polymerase in a “direct-load” DNA sequencing, obviating the laborious and time consuming post-reaction work-up.     

Population Genetic Structure of Astyanax scabripinnis (Teleostei, Characidae) from an Urban Stream

Despite the great anthropogenic interference on urban streams, information is still scarce about the genetic variability and structure of native fish populations inhabiting such streams. In the present study, random amplified polymorphic DNA (RAPD) markers were used to analyze genetic variability and structure of populations assigned to the Neotropical fish species Astyanax scabripinnis from an urban stream located in Londrina, Paraná State, southern Brazil. Thirty individuals of this species were collected from three sites throughout the upper Cambé stream. A total of 10 primers amplified 159 loci, of which 128 (80.5%) were polymorphic. Each of the three populations showed very similar proportions of polymorphic loci, which ranged from 63.5 to 64.8%. Unbiased genetic distances varied from 0.0612 to 0.0646. Theta_p-test values indicated moderate to high genetic differentiation among individuals from different localities. The number of migrants varied from 1.34 to 1.46, suggesting a low gene flow between populations. The genetic similarity among all individuals studied ranged from 0.424 to 0.848. The results suggest that populations of A. scabripinnis in Cambé stream are undergoing genetic differentiation.     

A Rapid Protocol For Site-directed Mutagenesis and Gene Synthesis Using Synthetic Oligonucleotides

Abstract

DNA segments of 100 to 150 nucleotides in length have been assembled by overlapping synthetic oligonucleotides and cloned directly into the single stranded vector M13 without purification of the synthetic DNA segments prior to cloning.     

钙敏感受体(CaSR)基因986、990多态性与尿石症的相关性研究

目的:探讨钙敏感受体(Ca SR)基因单核昔酸多态性与泌尿系结石的关系。方法:选取90例黑龙江地区的泌尿系结石患者及90例健康对照者外周血标本中的基因组DNA,采用PCR(聚合酶链反应)结合DNA测序,检测并分析Ca SR基因的单核苷酸多态性位点的分布。结果:泌尿系结石组和对照组Ca SR基因第986位、990位频率分布符合Hardy-Weinberg定律,其基因型分布频率在泌尿系结石患者和健康对照者中差异无统计学意义(P0.05),但在泌尿系结石患者组内Ca SR第990位GG纯合子和RG杂合子出现频率明显偏高,差异有统计学意义(P0.05)。结论:Ca SR基因第7外显子第986、990多态性位点与泌尿系结石的形成无直接相关性,但第7外显子第990位A/G单核苷酸多态性可能与泌尿系结石的形成密切相关。     

TARGETING OF A701G NUCLEOTIDE AT THE HUMAN ATP1A1 LOCUS USING A RNA/DNA CHIMERA

ABSTRACT

The single base substitution mediated by chimeric RNA/DNA oligonucleotide is a new promising approach of gene therapy for single base mutation diseases. We exploited this approach to render HeLa cells resistant to ouabain by introducing a single base substitution in the alpha 1 subunit of the NA⁺/K⁺ ATPase human gene. The chimeric oligonucleotide was administered to HeLa cells by electroporation and the frequency of ouabain resistant cells determined. The results showed that the chimeric RNA/DNA oligonucleotide failed to enhance the frequency of ouabain resistant cells supporting the controversy about the conflicting results of the technique.