结缕草(Zoysia japonica Steud.)种子打破休眠方法的比较

结缕草 (ＺｏｙｓｉａｊａｐｏｎｉｃａＳｔｅｕｄ .)为禾本科多年生草本植物 ,广泛分布于我国东部沿海地区 ,集中分布在我国的辽宁和山东境内 ,在胶东和辽东半岛有大面积的野生种群 ,是我国结缕草种子的主要产地。结缕草具有极其发达的根茎和匍匐茎 ,是适于放牧的优良牧草 ,也是抗逆性强、低矮密集型的优质草坪植物。然而 ,结缕草种子具有深休眠特性 ,在自然条件下发芽率低、发芽速度慢 ,从而给它的开发和利用带来了阻碍。近年来国内外已有一些学者对其深休眠的原因进行了研究。韩建国等认为该种子休眠为综合型休眠 ,颖苞对水分和空气的进…     

Universal method for SNP identification

A new approach to the identification of point mutations by allele-specific PCR was proposed. The mutation R408W of the human phenylalanine hydroxylase gene was used as a model. A high specificity of the approach was achieved by the use of primers partially complementary to the genomic DNA. Polyethylene glycol covalently attached to one of the allele-specific primers provides for the differential identification of the PCR products due to a change in electrophoretic mobility.__________Translated from Bioorganicheskaya Khimiya, Vol. 31, No. 2, 2005, pp. 213–215.Original Russian Text Copyright © 2005 by Brenner, Ivanova, Pyshnyi, Morozov.     

The signature of seeds in resurrection plants: a molecular and physiological comparison of desiccation tolerance in seeds and vegetative tissues

Desiccation-tolerance in vegetative tissues of angiosperms hasa polyphyletic origin and could be due to 1) appropriation ofthe seed-specific program of gene expression that protects orthodoxseeds against desiccation, and/or 2) a sustainable version ofthe abiotic stress response. We tested these hypotheses by comparingmolecular and physiological data from the development of orthodoxseeds, the response of desiccation-sensitive plants to abioticstress, and the response of desiccation-tolerant plants to extremewater loss. Analysis of publicly-available gene expression dataof 35 LEA proteins and 68 anti-oxidant enzymes in the desiccation-sensitiveArabidopsis thaliana identified 13 LEAs and 4 anti-oxidantsexclusively expressed in seeds. Two (a LEA6 and 1-cys-peroxiredoxin)are not expressed in vegetative tissues in A. thaliana, buthave orthologues that are specifically activated in desiccatingleaves of Xerophyta humilis. A comparison of antioxidant enzymeactivity in two desiccation-sensitive species of Eragrostiswith the desiccation-tolerant E. nindensis showed equivalentresponses upon initial dehydration, but activity was retainedat low water content in E. nindensis only. We propose that theseantioxidants are housekeeping enzymes and that they are protectedfrom damage in the desiccation-tolerant species. Sucrose isconsidered an important protectant against desiccation in orthodoxseeds, and we show that sucrose accumulates in drying leavesof E. nindensis, but not in the desiccation-sensitive Eragrostisspecies. The activation of "seed-specific" desiccation protectionmechanisms (sucrose accumulation and expression of LEA6 and1-cys-peroxiredoxin genes) in the vegetative tissues of desiccation-tolerantplants points towards acquisition of desiccation tolerance fromseeds.     

A comparison of Brussels sprout seedling establishment from ungerminated and low-moisture-content germinated seeds

The moisture content of newly-germinated Brussels sprout seeds (radicles 1 ± 0·5 mm long) was reduced to 16% without loss of viability when compared with untreated newly-germinated seeds. Seedling emergence and growth from these low-moisture-content germinated (LMCG) seeds and ungerminated seeds were compared in cellular trays and seedbeds. A greater number of seedlings emerged more uniformly and more rapidly from LMCG seeds than from ungerminated dry seeds, leading to larger, more uniform seedlings for subsequent transplanting. Post-germination separation in sucrose solutions before drying resulted in a seed batch with 98% of germinated seeds. As there was a positive relationship between the rate of germination and subsequent seedling growth, it is suggested that germinated-seed separation techniques could be used to select the most vigorous seedlings.     

Indel seeds for homology search

We are interested in detecting homologous genomic DNA sequences with the goal of locating approximate inverted, interspersed, and tandem repeats. Standard search techniques start by detecting small matching parts, called seeds, between a query sequence and database sequences. Contiguous seed models have existed for many years. Recently, spaced seeds were shown to be more sensitive than contiguous seeds without increasing the random hit rate. To determine the superiority of one seed model over another, a model of homologous sequence alignment must be chosen. Previous studies evaluating spaced and contiguous seeds have assumed that matches and mismatches occur within these alignments, but not insertions and deletions (indels). This is perhaps appropriate when searching for protein coding sequences (<5% of the human genome), but is inappropriate when looking for repeats in the majority of genomic sequence where indels are common. In this paper, we assume a model of homologous sequence alignment which includes indels and we describe a new seed model, called indel seeds, which explicitly allows indels. We present a waiting time formula for computing the sensitivity of an indel seed and show that indel seeds significantly outperform contiguous and spaced seeds when homologies include indels. We discuss the practical aspect of using indel seeds and finally we present results from a search for inverted repeats in the dog genome using both indel and spaced seeds.     

Universal inheritable barcodes for identifying organisms

The needs for recognition of novel conventional or transgenic organisms include protection of patented or Identity Preserved lines, detecting transgenics and tracing dispersal. We propose simple ‘Biobarcodes™’ using universal PCR primers to recognize the universal ‘nonsense’ recognition site of all biobarcodes, followed by a variable nonsense sequence. The proposed sequences are long enough to allow recognition in spite of mutations, have stop codons to prevent coding, and will not self anneal. Sequences of PCR-amplified biobarcodes can be compared to a universal database.     

Universal Count Correction for High-Throughput Sequencing

We show that existing RNA-seq, DNase-seq, and ChIP-seq data exhibit overdispersed per-base read count distributions that are not matched to existing computational method assumptions. To compensate for this overdispersion we introduce a nonparametric and universal method for processing per-base sequencing read count data called Fixseq. We demonstrate that Fixseq substantially improves the performance of existing RNA-seq, DNase-seq, and ChIP-seq analysis tools when compared with existing alternatives.     

The relationship between beta-mannosidase and endo-beta-mannanase activities in tomato seeds during and following germination: a comparison of seed populations and individual seeds

beta-Mannosidase and endo-beta-mannanase are involved in the mobilization of the mannan-containing cell walls of the tomato seed endosperm. The activities of both enzymes increase in a similar temporal manner in the micropylar and lateral endosperm during and following germination. This increase in enzyme activities in the micropylar endosperm is not markedly reduced in seeds imbibed in abscisic acid although, in the lateral endosperm, endo-beta-mannanase activity is more suppressed by this inhibitor than is the activity of beta-mannosidase. Gibberellin-deficient (gib-1) mutants of tomato do not germinate unless imbibed in gibberellin; low beta-mannosidase activity, and no endo-beta-mannanase activity is present in seeds imbibed in water, but both enzymes increase strongly in activity in the seeds imbibed in the growth regulator. For production of full activity of both beta-mannosidase and endo-beta-mannanase in the endosperm, this tissue must be in contact with the embryo for at least the first 6 h of imbibition, which is indicative of a stimulus diffusing from the embryo to the endosperm during this time. These results suggest some correlation between the activities of beta-mannosidase and endo-beta-mannanase, particularly in the micropylar endosperm, in populations of tomato seeds imbibed in water, abscisic acid and gibberellin. However, when individual micropylar endosperm parts are used to examine the effect of the growth regulators and of imbibition in water on the production of the two enzymes, it is apparent that within these individual seed parts there may be large differences in the amount of enzyme activity present. Micropylar endosperms with high endo-beta-mannanase activity do not necessarily have high beta-mannosidase activity, and vice versa, which is indicative of a lack of co-ordination of the activities of these two enzymes within individuals of a population.     

Loose versus stranded seeds in permanent prostate brachytherapy: Dosimetric comparison of intraoperative plans

PurposeTo compare target volume coverage and critical organ dosimetry of intraoperative treatment plans for loose seed (LS) and stranded seed (SS) ¹²⁵I permanent implants for low and intermediate risk prostate cancer.MethodsTwo hundred and five patients who underwent permanent seed brachytherapy were included in the study. For prostate dosimetry V90, V100, V150, V200, D90 and COIN were used. The dose to urethra and rectum was determined by the maximal dose and relative doses that cover specified volumes. Means and standard deviations were calculated and statistically compared.ResultsOn average, 54 (range, 30–78) and 48 (range, 31–67) seeds were implanted in the prostate with individual median activities of 0.62 U (range, 0.52–0.70 U) and 0.71 U (range, 0.65–0.71 U) for LS and SS technique, respectively. The target coverage was slightly better with SS (V100: 98% vs. 96%, p < 0.05; D90: 172 Gy vs. 166 Gy, p < 0.05), but more conformal dose distributions were observed with LS (COIN: 0.70 vs. 0.63, p < 0.05). The dose homogeneity did not differ significantly between the two groups. Regarding the dose to urethra and rectum all dose parameters were significantly lower with LS.ConclusionsLS resulted in less dose to the urethra and rectum compared to SS in intraoperative dosimetry. A slightly better target volume coverage with decreased conformity of dose distribution is reported with SS. More studies are necessary to determine how these results will affect postoperative dosimetry, and ultimately, clinical outcome.     

Good spaced seeds for homology search

MOTIVATION: Filtration is an important technique used to speed up local alignment as exemplified in the BLAST programs. Recently, Ma et al. discovered that better filtering can be achieved by spacing out the matching positions according to a certain pattern, instead of contiguous positions to trigger a local alignment in their PatternHunter program. Such a match pattern is called a spaced seed. RESULTS: Our numerical computation shows that the ranks of spaced seeds (based on sensitivity) change with the sequences similarity. Since homologous sequences may have diverse similarity, we assess the sensitivity of spaced seeds over a range of similarity levels and present a list of good spaced seeds for facilitating homology search in DNA genomic sequences. We validate that the listed spaced seeds are indeed more sensitive using three arbitrarily chosen pairs of DNA genomic sequences.     

Treatment of cotton seeds for germination

Summary Effects of H₂SO₄, H₂O₂, C₂H₅OH and of acetone on germination of cotton seeds and on the growth of seedling root were studied under laboratory conditions. H₂SO₄ or H₂O₂ hastened germination but decreased the ultimate number of seeds germinated. Higher temperature (27°C) hastened germination and increased the number of seeds germinated. Root length remained unaffected by treatments at room temperature while H₂SO₄ or H₂SO₄/H₂O₂ substantially decreased it at 27°C.     

Universal method for single nucleotide substitution identification

A new approach to the identification of point mutations by allele-specific PCR was proposed. The mutation R408W of the human phenylalanine hydroxylase gene was used as a model. A high specificity of the approach was achieved by the use of primers partially complementary to the genomic DNA. Polyethylene glycol covalently attached to one of the allele-specific primers provides for the differential identification of the PCR products due to a change in electrophoretic mobility.     

A Universal Glass Support for Oligonucleotide Synthesis

Abstract

A single type of controlled pore glass derivatized with 3-anisoyl-2′(3′)-O-benzoyluridine 5′-O-succinyl residues can be used as the support in solid phase syntheses of either oligoribo- or oligodeoxyribonucleotides.     

Universal primer cocktails for fish DNA barcoding

Reliable recovery of the 5′ region of the cytochrome c oxidase 1 (COI) gene is critical for the ongoing effort to gather DNA barcodes for all fish species. In this study, we develop and test primer cocktails with a view towards increasing the efficiency of barcode recovery. Specifically, we evaluate the success of polymerase chain reaction amplification and the quality of resultant sequences using three primer cocktails on DNA extracts from representatives of 94 fish families. Our results show that M13‐tailed primer cocktails are more effective than conventional degenerate primers, allowing barcode work on taxonomically diverse samples to be carried out in a high‐throughput fashion.     

Novel Photocleavable Universal Support for Oligonucleotide Synthesis

Abstract

A novel photocleavable universal support for the automated solid phase synthesis of oligonucleotides is described. The linker between the growing oligonucleotide chain and CPG support contains a nucleophilic amine protected with a photocleavable group. On exposure to UV light, this group is detached and the free amine affords cleavage of the oligonucleotide from the support. The use of long wavelength UV light avoids damage to the DNA.     

Universal similarity measure for comparing protein structures

We introduce a new variant of the root mean square distance (RMSD) for comparing protein structures whose range of values is independent of protein size. This new dimensionless measure (relative RMSD, or RRMSD) is zero between identical structures and one between structures that are as globally dissimilar as an average pair of random polypeptides of respective sizes. The RRMSD probability distribution between random polypeptides converges to a universal curve as the chain length increases. The correlation coefficients between aligned random structures are computed as a function of polypeptide size showing two characteristic lengths of 4.7 and 37 residues. These lengths mark the separation between phases of different structural order between native protein fragments. The implications for threading are discussed.