Prediction of human mRNA donor and acceptor sites from the DNA sequence

Artificial neural networks have been applied to the prediction of splice site location in human pre-mRNA. A joint prediction scheme where prediction of transition regions between introns and exons regulates a cutoff level for splice site assignment was able to predict splice site locations with confidence levels far better than previously reported in the literature. The problem of predicting donor and acceptor sites in human genes is hampered by the presence of numerous amounts of false positives: here, the distribution of these false splice sites is examined and linked to a possible scenario for the splicing mechanism in vivo. When the presented method detects 95% of the true donor and acceptor sites, it makes less than 0.1% false donor site assignments and less than 0.4% false acceptor site assignments. For the large data set used in this study, this means that on average there are one and a half false donor sites per true donor site and six false acceptor sites per true acceptor site. With the joint assignment method, more than a fifth of the true donor sites and around one fourth of the true acceptor sites could be detected without accompaniment of any false positive predictions. Highly confident splice sites could not be isolated with a widely used weight matrix method or by separate splice site networks. A complementary relation between the confidence levels of the coding/non-coding and the separate splice site networks was observed, with many weak splice sites having sharp transitions in the coding/non-coding signal and many stronger splice sites having more ill-defined transitions between coding and non-coding.     

基于RNA-Seq数据识别果蝇剪接位点和可变剪接事件

完整基因结构的预测是当前生命科学研究的一个重要基础课题,其中一个关键环节是剪接位点和各种可变剪接事件的精确识别.基于转录组测序（RNA-seq）数据,识别剪接位点和可变剪接事件是近几年随着新一代测序技术发展起来的新技术策略和方法.本工作基于黑腹果蝇睾丸RNA-seq数据,使用TopHat软件成功识别出39718个果蝇剪接位点,其中有10584个新剪接位点.同时,基于剪接位点的不同组合,针对各类型可变剪接特征开发出计算识别算法,成功识别了8477个可变剪接事件（其中新识别的可变剪接事件3922个）,包括可变供体位点、可变受体位点、内含子保留和外显子缺失4种类型.RT-PCR实验验证了2个果蝇基因上新识别的可变剪接事件,发现了全新的剪接异构体.进一步表明,RNA-seq数据可有效应用于识别剪接位点和可变剪接事件,为深入揭示剪接机制及可变剪接生物学功能提供新思路和新手段.     

基于贝叶斯网络的DNA序列剪接位点预测

采用基于贝叶斯网络的建模方法,预测真核生物DNA序列中的剪接位点．分别建立了供体位点和受体位点模型,并根据两种位点的生物学特性,对模型的拓扑结构和上下游节点的选择进行了优化．通过贝叶斯网络的最大似然学习算法求出模型参数后,利用10分组交互验证方法对测试数据进行剪接位点预测。结果显示,受体位点的平均预测准确率为92．5％,伪受体位点的平均预测准确率为94．0％,供体位点的平均预测准确率为92．3％,伪供体位点的平均预测准确率为93．5％,整体效果要好于基于使用独立和条件概率矩阵、以及隐Markov模型的预测方法．表明利用贝叶斯网络对剪接位点建模是预测剪接位点的一种有效手段．     

组织工程复合皮肤应用于皮肤缺损创面的临床疗效观察

目的:临床观察组织工程复合皮肤对烧伤整形后需植皮患者的供皮区缺损创面的有效性及安全性。方法:试验选取不同临床中心烧伤整形后需植皮患者,在供皮区部分创面作为试验区应用组织工程复合皮肤覆盖,邻近创面采用盐水纱布替代作为对照区,应用后按常规方法包扎固定。临床试验时间为6个月,治疗期间观察统计患者的创面反应,愈合时间及愈合情况;对组织工程复合皮肤改善创面愈合质量及安全性进行临床评估。根据创面试验组和对照组的创面愈合时间,应用SPSS统计软件对数据进行方差齐性检验,根据检验结果分别进行独立样本t或t’检验。结果:试验共收集有效病例19例。临床观察显示应用后试验区创面无明显免疫排斥及炎性反应,患者自述疼痛明显减轻,试验区创面愈合时间与对照区相比缩短8d,统计学分析有显著性差异。愈后随访部分患者试验区愈合质量好于对照区,应用后患者疼痛、瘢痕形成等不良反应明显减少。结论:结果表明组织工程复合皮肤作为活型皮肤替代物用于医源性皮肤缺损的修复,这为促进供皮区的创面愈合提供了切实可行的方法。     

Genetic Evidence against Intramolecular Rejoining of the Donor DNA Molecule following Is10 Transposition

Tn10 and IS10 transpose by a nonreplicative mechanism in which the transposon is excised from the donor molecule and integrated into a target DNA site, leaving behind a break at the original donor site. The fate of this broken donor DNA molecule is not known. We describe here two experiments that address this issue. One experiment demonstrates that a polar IS10 element gives rise to polarity-relief revertants at less than 1% the frequency of transposition of the same element in the same culture. In a second experiment, transpositions of an IS10 element from one site in the bacterial genome to another are selected and the resulting isolates examined for alterations at the donor site; none of 1088 such isolates exhibited a detectable change at the donor locus. These results are compatible with two possible fates of the transposon donor molecule: degradation (``donor suicide'), or restoration of the original information at the donor site by a recombinational repair mechanism analogous to double-strand break repair. These results argue against the possibility that the donor molecule gap is simply resealed by intramolecular rejoining.     

The cosmetic split-thickness skin graft donor site

Any split-thickness skin graft donor site is obvious to some degree because of pigment alterations and, at the worst, it can develop hypertrophic scarring. A predictably superior aesthetic result is possible if this site is converted to a full-thickness defect followed by primary closure, because a linear scar is the only residuum. Using a modified tumescent technique, the groin can also be readily used as a split-thickness donor site if a thin graft is preferred; it captures the attributes of an ideal donor site in which pain is diminished, healing rapid, and the scar inconspicuous, just as when it is used as a full-thickness skin graft donor site.     

用支持向量机预测人类基因5’／3’选择性剪切位点

选择性剪切是调解基因表达的重要机制.识别选择性剪切位点是后基因组时代的一个重要工作.本文从最新的EBI人类基因选择性剪切数据库中,选取5＇/3＇选择性剪切位点作为正集,选取在剪切位点附近的假剪切位点作为负集,并把所有的选择性剪切位点和假剪切位点随机分成训练集和测试集.本文选用的预测选择性剪切位点的方法是基于位置权重矩阵和离散增量的支持向量机方法.此方法仅基于训练集,以不同位点的单碱基概率和序列片断的三联体频数作为信息参数,利用位置权重矩阵和离散增量算法结合支持向量机,得到了选择性供体位点和受体位点的分类器,并用此分类器对测试集中的选择性供体位点和受体位点进行预测.对独立测试集中的选择性供体位点和选择性受体位点的预测成功率分别为88.74%和90.86%,特异性分别为85.62%和81.19%.本文预测选择性剪切位点的方法成功率高于其它选择性剪切位点预测方法预测成功率,此预测方法进一步提高了对选择性剪切位点的理论预测能力.     

Mons pubis as a donor site for split-thickness skin grafts

It is extremely important that a donor graft site be selected with attention to the type of graft needed as well as the specific patient's needs and lifestyle. While it is inevitable that any donor site heals with altered pigmentation and texture, we feel that by using a combination of several time-honored techniques in this well-concealed donor site, we have achieved long-term aesthetic results of the transfer of skin grafts from a hair-bearing area.     

Reverse anterior tibial artery flap for reconstruction of foot donor site

The foot offers numerous useful options for hand reconstruction. Hallux transfer, dorsalis pedis flap, second toe transfers, and toe joint transfers offer good functional results in reconstructed hands. However, when the donor site is repaired with skin grafts, delayed wound healing, scarring, and contractures often result. Poor cosmesis of the donor site and altered gait are the main drawbacks of the procedures. The authors propose a new concept of primary reconstruction of the donor foot using a reverse-flow anterior tibial flap from the same leg. Two flaps are raised from the same anterior tibial vessel system in continuity as a distal free flap for hand reconstruction and as a proximal reverse-flow pedicled flap to resurface the donor defect. This technique allows good flap reconstruction of the foot donor site, reducing morbidity and limiting the operation to the same limb. The authors report their experience of 33 cases. There were no failures. Primary wound healing was achieved in the foot donor site, with acceptable cosmesis and satisfactory function.     

Effect of cytidine-5'-monophosphate on peptidyl transferase activity.

The transfer reaction with pA-fMet as a donor substrate is strongly stimulated by CMP, whereas the transfer reaction with CpApCpCpA-acLeu as a donor substrate is inhibited by CMP. These results indicate that the donor site of peptidyl transferase contains specific binding sites for the terminal adenosine and for the cytidylic acid residue in the terminal sequence CpCpA of tRNA and that an attachment of proper nucleotides to the donor site induces a conformational change in peptidyl transferase.     

Epstein–Barr Virus Plasmid Model System for Analyzing Recombination in Human Cells

Homologous recombination stimulated by a double-strand break at a desired target site offers a method to achieve site-specific integration useful for gene therapy and other genetic engineering. To test parameters needed for this strategy, we developed an Epstein-Barr virus shuttle vector model system as a genetic tool. This extrachromosomal plasmid assay system has several advantages over a chromosomal assay. The system detects all classes of recombination events without selection and allows rapid analysis of the frequency and nature of recombination events. We found that a double-strand break at the target site stimulated a large increase in recombination frequency. The resulting recombinants included one-sided insertion events, as well as two-sided or gene conversion events. A circular donor substrate was more effective in recombination than linearized donor DNA.     

Toward a more natural breast: the interpolated thoracoepigastric pedicle in breast reconstruction

A method of reconstructing the breast mound after mastectomy using a superiorly based thoracoepigastric pedicle is presented. The advantages of the method are its relative simplicity and its definition of the inframammary fold. It often obviates the need for inflatable expanders. The prime disadvantage is the scar left on the abdominal donor site.     

Predicting internal exons by oligonucleotide composition and discriminant analysis of spliceable open reading frames.

A new method which predicts internal exon sequences in human DNA has been developed. The method is based on a splice site prediction algorithm that uses the linear discriminant function to combine information about significant triplet frequencies of various functional parts of splice site regions and preferences of oligonucleotides in protein coding and intron regions. The accuracy of our splice site recognition function is 97% for donor splice sites and 96% for acceptor splice sites. For exon prediction, we combine in a discriminant function the characteristics describing the 5'-intron region, donor splice site, coding region, acceptor splice site and 3'-intron region for each open reading frame flanked by GT and AG base pairs. The accuracy of precise internal exon recognition on a test set of 451 exon and 246693 pseudoexon sequences is 77% with a specificity of 79%. The recognition quality computed at the level of individual nucleotides is 89% for exon sequences and 98% for intron sequences. This corresponds to a correlation coefficient for exon prediction of 0.87. The precision of this approach is better than other methods and has been tested on a larger data set. We have also developed a means for predicting exon-exon junctions in cDNA sequences, which can be useful for selecting optimal PCR primers.     

Re-creating Semi-natural Communities: Vacuum Harvesting and Hand Collection of Seed on Calcareous Grassland

Agricultural set-aside and compensation land provide restoration ecologists with opportunities to re-create semi-natural habitats. Restoration sites often have high soil fertility and inadequate seed banks of desirable species. Sowing additional seed is a proven method for establishing chalk grassland vegetation. If seed of local provenance is required, it may be collected by hand or by using specialized machines. Ultimately, the mix collected must provide seed suitable for recreating vegetation similar to that of the donor site. We examine the ability of a vacuum machine to meet this requirement by comparison with hand collection, and we discuss possible effects on invertebrates. Microscope analysis and glasshouse and field trials were used to compare the abundance of seed of different species in harvested mixes with the vegetation composition of the donor site. Seed heads of individual species were examined to determine the number of viable seeds per head and attack rates by phytophagous insects. The mix contained seed of over half the species recorded on the donor site. The seed of taller, more common species was overrepresented in the mix, at the expense of some smaller, mat-forming plants. After one season, however, the vegetation of the field trial plots was of the same type as that of the donor site, although the proportions of the constituent species differed slightly and certain species were absent. Mechanical collection is more efficient than hand collection. Endophagous invertebrates are unlikely to be affected by the machine. Seed collection requires a combination of methods, precise timing, and careful planning to provide a full range of species and to minimize impacts on plant and invertebrate populations.     

Peptidyltransferase center of ribosomes: On the mechanism of action of alkaloid lycorine

The molecular mechanism of action of the alkaloid lycorine has been revised. According to our results, lycorine inhibits the binding of CACCA-Leu←Ac to the donor site of the peptidyltranferase center of wheat-germ ribosomes, whereas the transpeptidation reaction in the system with the minimal model donor is not inhibited. The equilibrium constant of CACCA-Leu←Ac to the donor site of 80 S ribosomes is measured.     

The effects of macrophage-mediated inflammatory response to the donor site on long-term retention of a fat graft in the recipient site in a mice model

Inflammatory responses mediated by macrophages play a role in tissue repair. However, it is unclear whether the repair in the donor site after liposuction would have any effects on fat graft retention in the recipient site. This study is designed to evaluate the effects of a macrophage-mediated inflammatory response in donor sites on long-term retention of fat grafting. In this study, mice were randomly divided into two groups. One underwent simulated liposuction, called the fat procurement plus grafting (Pro-Grafting) group, and the other underwent sham surgery, called the fat grafting only (Grafting Only) group. The prepared fat (0.3 ml each) was engrafted and cellular events over a 90-day period were assessed. We found macrophages were infiltrated into adipose tissue at the recipient site in the Grafting Only group within 7 days and the repair essentially completed within 30 days. By contrast, few macrophages infiltrated the recipient site in the Pro-Grafting group within 7 days and the entire remodeling process took 30 days longer in the Pro-Grafting than the Grafting Only group. Moreover, C-reactive protein levels were immediately upregulated after surgery, and the inflammatory factors' expression was higher at the donor rather than the recipient site. However, the repair processes and the long-term retention rate became normal when the adipose tissue was grafted after the donor site did not require macrophages for repair. Therefore, we suggest higher inflammatory factors promote macrophage infiltration and the adipose tissue regeneration process at the donor site. This process is delayed at the recipient site, which may affect long-term retention of fat grafts.     

The vastus lateralis myocutaneous flap

Four case reports of decubiti treated with vastus lateralis myocutaneous flaps are presented. The operative technique is described in detail. This method, closing the donor site primarily over Hemovac drains and eliminating the use of skin grafts, can be used to cover defects in a variety of locations.