Retroviral Oligonucleotide Distributions Correlate with Biased Nucleotide Compositions of Retrovirus Sequences,Suggesting a Duplicative Stepwise Molecular Evolution

A computer-assisted analysis was made of 24 complete nucleotide sequences selected from the vertebrate retroviruses to represent the ten viral groups. The conclusions of this analysis extend and strengthen the previously made hypothesis on the Moloney murine leukemia virus: The evolution of the nucleotide sequence appears to have occurred mainly through at least three overlapping levels of duplication: (1) The distributions of overrepresented (3–6)-mers are consistent with the universal rule of a trend toward TG/CT excess and with the persistence of a certain degree of symmetry between the two strands of DNA. This suggests one or several original tandemly repeated sequences and some inverted duplications. (2) The existence of two general core consensuses at the level of these (3–6)-mers supports the hypothesis of a common evolutionary origin of vertebrate retroviruses. Consensuses more specific to certain sequences are compatible with phylogenetic trees established independently. The consensuses could correspond to intermediary evolutionary stages. (3) Most of the (3–6)-mers with a significantly higher than average frequency appear to be internally repeated (with monomeric or oligomeric internal iterations) and seem to be at least partly the cause of the bias observed by other researchers at the level of retroviral nucleotide composition. They suggest a third evolutionary stage by slippage-like stepwise local duplications. Received: 3 January 1996 / Accepted: 27 March 1996     

不同方法修复Pilon骨折的临床疗效比较

目的:比较不同方法修复Pilon骨折的临床疗效。方法:选取我院收治的Pilon骨折患者156例为研究对象,根据手术方法不同,将患者分成研究组和对照组,每组78例。研究组给予分步延期切开复位内固定手术治疗,对照组给予有限内固定结合外固定的手术治疗。观察并比较两组患者的踝关节功能、术中出血量、骨折愈合时间、住院时间以及术后不良反应的发生情况等。结果:与术前比较,两组患者术后踝关节功能均获得改善,且研究组踝关节功能优秀率高于对照组,差异具有统计学意义(P0.05);研究组患者术中出血量、骨折愈合时间、住院时间均明显低于对照组,差异具有统计学意义(P0.05);研究组不良反应发生率低于对照组,差异具有统计学意义(P0.05)。结论:分步延期切开复位内固定手术治疗pilon骨折的临床效果显著,是临床治疗pilon骨折的理想方案。但在临床实践中,应根据患者病情选择合适的治疗方案。     

Microsatellites: consensus and controversy

Microsatellite DNA loci have recently been adopted for many biological applications. Comparative studies across a wide range of species has revealed many details of their mutational properties and evolutionary life cycles. Experience shows that a full understanding of these processes is essential to ensure the effective use of microsatellites as analytical tools. In this article, we review the controversies that have arisen as biologists have taken up this new technology and the emerging consensus that has resulted from their debates. We point to the need for comparative DNA sequencing studies to produce input data for a new generation of theoretical models of microsatellite behaviour. We conclude by presenting our own conceptual model, ‘Snakes and Ladders’, as an aid to theory development.     

A Statistical Evaluation of Sediment Quality Triad Benthic Community Measurements in PAH-Impacted Sediments at a Manufactured Gas Plant Site along the Hudson River

The sediment quality triad (SQT) assumes that three measurements (sediment chemistry, laboratory bioassay, and benthic macroinvertebrate counts) comprise an independent assessment of impact, which when integrated using a weight-of-evidence approach provides a comprehensive assessment of risk. An SQT assessment was conducted on 41 sediment samples collected adjacent to a manufactured gas plant site on the freshwater reach of the Hudson River in New York State. The assessment shows that the benthic macroinvertebrate data did not correlate with either sediment or pore water polycyclic aromatic hydrocarbon (PAH) concentrations, nor did these data show consistent relationships to the results of laboratory bioassay testing (Hyalella azteca 28-day survival or biomass). The benthic community across the site and reference areas was comprised of few taxa, all of which were pollution-tolerant organisms with tolerance values greater than or equal to five. Only in significantly impacted sediment samples with PAH concentrations in the thousands of milligrams per kilogram, pore water concentrations above 100 toxic units, and visible non-aqueous phase liquid present in the sample did the benthic macroinvertebrate data show a response. In contrast, sediment and pore water PAH measurements and H. azteca toxicity testing provided consistent interpretation of impact. These results illustrate that benthic macroinvertebrate data may contain less information value and be a more challenging line of evidence to interpret in triad studies conducted in certain ecological settings; in this case, a large-order river with a relatively depauperate benthic community dominated by species tolerant of PAHs.     

Convenient synthesis of sulfated oligofucosides

Two types of sulfated octyl tetra- to octaoligofucosides with different sulfation patterns were synthesized employing a combination of stepwise elongation and convergent strategies in which trichloroacetimidates and thioglycosides were selected as the glycosyl donors.     

Solving dynamical inverse problems by means of Metabolic P systems

MP (Metabolic P) systems are a class of P systems introduced for modelling metabolic processes. We refer to the dynamical inverse problem as the problem of identifying (discrete) mathematical models exhibiting an observed dynamics. In this paper, we complete the definition of the algorithm LGSS (Log-gain Stoichiometric Stepwise regression) introduced in Manca and Marchetti (2011) for solving a general class of dynamical inverse problems. To this aim, we develop a reformulation of the classical stepwise regression in the context of MP systems. We conclude with a short review of two applications of LGSS for discovering the internal regulation logic of two phenomena relevant in systems biology.     

Record performances at the Boston Marathon: Biometeorological factors

Air temperature and relative humidity have long been suspected of affecting the performance of marathon runners. Though these factors are important in their extremes, we show that other factors are even more indicative of race performances. Performances of the top 3 finishers in the last 30 Boston Marathons were correlated with hourly meteorological data for each race day. These 90 individual performances were classified as: record breaking performances (31), average performances (35), and unusually slow performances (24). The factors that help predict record breaking and unusually slow performances are: (i) wet bulb temperature, (ii) percent sky cover, and (iii) presence or absence of a light precipitation. Record breaking performances are characterized by a wet bulb temperature of <7.8°C, and 100% sky cover. A light drizzle is also conducive to better performances. On the other hand, unusually low performances are accompanied by a wet bulb temperature of >7.8°C, and a sky cover of 50% or less. No light, precipitation was recorded on any of the unusually slow race days. A graphic analysis clearly shows these relationships to exist. In addition, a multiple regression analysis confirms the importance of these variables. The authors advise that these are reliable predictors; however, when considering marathon races held in various geographical regions and differing climatic regimes, the exact numerical thresholds used here may not apply.     

Possible multiple origins of replication in primate mitochondria: Alternative role of tRNA sequences

DNA replication in vertebrate mitochondria is usually directional, leaving different portions of the genome single-stranded for different periods of time. During this time, mutations resulting from deaminations of cytosines to thymines and adenines to guanines accumulate on the heavy strand. Therefore, T/C and G/A ratios increase along mitochondrial genomes, proportionally to the time spent single-stranded during replication. Such trends exist at third codon positions for base ratios averaged across genes in individual genomes as well as for gene-specific and site-specific substitution frequencies estimated using phylogenetic methods. We use multiple regressions to test for the potential functioning of all 12 tRNA clusters in 19 primate mitochondrial genomes as alternative origins of light strand replication (OL). We provide a general algorithm for calculating time spent single stranded by a given site for any possible locations of the site and OL. For codon positions 1, 2, and 3, respectively, 23%, 9% and 35% of tRNA gene clusters have significant (p < 0.05) deamination gradients originating from them. The strength of the deamination gradient originating from tRNA gene clusters varies among species, and for five clusters, correlates with the tendency of tRNA genes in each of these clusters to form secondary structures that resemble the OL's structure. This is notably true for all codon positions for tRNA-Lys, which in absence of nuclear regulation, forms secondary structures resembling the hairpin structure of OL. For two tRNA gene clusters, correlations were statistically significant, but opposite to the direction expected by the known unidirectional replication, putatively compatible with bi-directional replication. Few substitutions in tRNA sequences can be neutral at the level of cloverleaf structure and function, yet significantly alter capacities to form OL-like structures, causing sudden evolution of genome-wide nucleotide contents.     

玉米幼苗抗氧化酶活性、脯氨酸含量变化及与其耐寒性的关系

研究了黄C（耐寒型）和Mo17（低温敏感型）两种耐寒性不同的玉米自交系幼苗在低温逆境（5 ℃,3 d）下,根、中胚轴和胚芽鞘3个部位过氧化氢酶（CAT）、过氧化物酶（POD）活性和脯氨酸（Pro）含量变化及与其耐寒性的关系.结果表明,低温期间,黄C的中胚轴、胚芽鞘相对生长率显著高于Mo17;黄C的根、中胚轴、胚芽鞘3个部位的CAT、POD活性和Pro含量变化率（其中,中胚轴分别为39.02%、-31.35%和86.86%）均高于Mo17（中胚轴变化率分别为1.86%、-48.67%和12.01%）;黄C 3个部位的质膜透性（中胚轴为22.05%）均低于Mo17（中胚轴为29.11%）.逐步回归分析表明黄C低温期间积累的干物质主要与Pro含量有关,而Mo17主要与POD活性有关,玉米幼苗中胚轴对低温反应最敏感,中胚轴Pro含量变化率与玉米耐寒性关系最密切.