Intragenic spatial patterns of codon usage bias in prokaryotic and eukaryotic genomes

To study the roles of translational accuracy, translational efficiency, and the Hill-Robertson effect in codon usage bias, we studied the intragenic spatial distribution of synonymous codon usage bias in four prokaryotic (Escherichia coli, Bacillus subtilis, Sulfolobus tokodaii, and Thermotoga maritima) and two eukaryotic (Saccharomyces cerevisiae and Drosophila melanogaster) genomes. We generated supersequences at each codon position across genes in a genome and computed the overall bias at each codon position. By quantitatively evaluating the trend of spatial patterns using isotonic regression, we show that in yeast and prokaryotic genomes, codon usage bias increases along translational direction, which is consistent with purifying selection against nonsense errors. Fruit fly genes show a nearly symmetric M-shaped spatial pattern of codon usage bias, with less bias in the middle and both ends. The low codon usage bias in the middle region is best explained by interference (the Hill-Robertson effect) between selections at different codon positions. In both yeast and fruit fly, spatial patterns of codon usage bias are characteristically different from patterns of GC-content variations. Effect of expression level on the strength of codon usage bias is more conspicuous than its effect on the shape of the spatial distribution.     

里氏木霉RutC30常温常压等离子体（ARTP）诱变筛选pyr4基因缺陷型菌株及转化系统的建立

以里氏木霉Trichoderma reesei重要工业生产菌RutC30为出发菌株,通过等离子体（ARTP）诱变筛选,以5-氟乳清酸（5-FOA）和尿苷（Uridine）进行筛选,获得一株pyr4基因缺陷株RutC30ΔU3。用含有野生型里氏木霉pyr4基因的互补质粒转化突变株,可回复野生性状。经测序发现其pyr4基因在核酸序列多个位点发生突变,其中包括两个错义突变和一个移码突变,从而导致乳清酸核苷-5′-磷酸脱羧酶失活。经遗传稳定性研究分析,传代5次后仍保持良好的尿苷依赖性、去葡萄糖阻遏以及高产纤维素酶特性。经实验筛选获得了pyr4基因缺陷菌株可作为基因表达系统的受体菌株,建立了以尿苷营养缺陷为筛选标记的木霉转化系统。     

Preliminary results on nematicidal activity from culture filtrates of Basidiomycetes against the pine wood nematode,Bursaphelenchus xylophilus (Aphelenchoididae)

One hundred and eighty one fungal species that were isolated from the fresh fruiting bodies collected in the Mountains of Pu Er County of Yunnan Province, China were tested on the pine wood nematode,Bursaphelenchus xylophilus in vitro. Each fungal species was grown in Czapek broth and potato dextrose broth (PDB). Fifteen filtrates fromAmauroderma austrosinense, Amauroderma macer, Filoboletus sp.,Laccaria tortilis, Lactarius gerardii, Lentinula edodes, Oudemansiella longipes, Oudemansiella mucida, Peziza sp.,Pleurotus sp.,Sinotermitomyces carnosus (two strains),Strobilomyces floccopus, Termitomyces albuminosus, Tylopilus striatulus grown on PDB were found to be pathogenic to the tested nematodes. Eleven filtrates fromAmanita junguillea, Amanita sp.,Daedalea sepiaria, Fistulina hepatica, Omphalotus olearius, Oudemansiella mucida, Peziza sp.,Pleurotus pulmatus, Ramaria sp.,Tricholoma conglobatum, Tylopilus striatulus grown on Czapek broth were also pathogenic to the nematodes. When screening for nematicidal potential of fungi, it is important to study the growth medium conditions necessary to obtain the optimal nematicidal effect as fungal filtrates growing on different liquid media showed a very inconsistent toxicity towards nematodes.     

外源基因表达造成的群体感应细菌生存压力的建模分析

外源基因的表达及其对细菌种群的影响对于群体感应系统和合成生物学产业的研究具有重要意义。然而,人们对于表达外源蛋白的细菌本身的行为模式仍然知之甚少。为了研究菌落生长和外源基因表达的过程究竟受到哪些因素的影响,文中测量了受Lux类受体调控的外源基因在N-酰基高丝氨酸内酯 (N-acyl homoserine lactone,N-AHL) 信号分子诱导下的表达,并模拟了其对细菌种群动态的影响。文中建立了一个假设性的数学模型,对信号分子诱导表达下细菌种群生长受影响的现象进行了分析。先前的研究通常将细菌种群生长受群体感应系统影响的现象归咎于合成群体感应信号分子的消耗与N-AHL信号分子的毒性,文中提供了对于这种生存压力的另一种可能的解释。     

Complete genome sequence of the bacterium Ketogulonicigenium vulgare Y25

Ketogulonicigenium vulgare is characterized by the efficient production of 2KGA from L-sorbose. Ketogulonicigenium vulgare Y25 is known as a 2-keto-L-gulonic acid-producing strain in the vitamin C industry. Here we report the finished, annotated genome sequence of Ketogulonicigenium vulgare Y25.     

Tenascin-R distinct domains modulate migration of neural stem/progenitor cells in vitro

Extracellular matrix (ECM) molecules constitute a "niche" that modulates the migration, proliferation, and differentiation of neural stem/progenitor cells (NSPCs). The glycoprotein Tenascin-R (TN-R) is an ECM molecule, comprising multiple domains. Either the whole TN-R molecule or its distinct domains has been demonstrated to play a very important role in the developing central nervous system. However, little is known about the effect of the TN-R domain on NSPCs, especially NSPC migration. In the present study, we first show that both TN-R domains epidermal growth factor-like repeat (EGFL) and fibronectin type III (FN)6-8 can inhibit the NSPCs migration from neurospheres in vitro. Furthermore, both the EGFL and FN6-8 domains affect the distribution of neurons generated from neurospheres, indicating that EGFL and FN6-8 domains inhibit the motility of neurons generated from neurospheres. These results suggest that TN-R has an inhibitory effect on NSPCs migration.     

沙枣花蜜腺的发育解剖学研究

沙枣的花蜜腺位于花柱基部的筒状花盘上,属花盘蜜腺,其蜜腺位于花盘外方,由分履表皮和产蜜组织组成。分泌表皮具有角质层和变态的气孔器。产蜜组织在发育过程中,其液泡和淀粉粒都随着蜜腺的发育呈现一定的消长规律,最后形成的蜜汁由盘状蜜腺表面的气孔泌出。     

新生儿抚触的研究进展

新生儿抚触作为儿科护理的新理念,是一种对新生儿健康十分有益的自然健康医疗技术。开展新生儿抚触对新生儿有特别重要的意义。抚触可以促进婴儿体格和智能的发育、增进睡眠、稳定情绪;抚触可以增强免疫力、促进食物的消化和吸收;抚触可以促进早产儿生长发育、新生儿缺氧缺血性脑病患儿的康复;抚触可以降低新生儿黄疸、避免发生胆红素脑病;抚触可促进母婴之间情感交流;抚触可利于产后妈妈的恢复。总之,无论是对家庭、社会、医院、还是对新生儿自身来讲,抚触都是非常有意义、重要且必要的,作为家长及医院工作人员都应该了解并掌握新生儿抚触的方法以及注意事项,因此,在临床工作和家庭中都应该积极主动的广泛开展新生儿抚触,目前各国都在研究并开展新生儿抚触这种护理技术,未来新生儿抚触将会被越来越多的家庭所认识并在医院中和家庭中广泛开展。     

江苏沿江生态防护林树种评价体系的建立与树种的初步筛选

采用层次分析法(AHP),以生长适应性、生态防护能力、景观价值和经济价值为Ⅰ级指标,以耐水湿性、抗污染性、生长速率、树冠特征、枝条特征和根系特征以及叶、花、果、树干和树形的观赏价值及材用、药用、食用和工业价值为Ⅱ级指标,确定各评价指标的权重值和赋值,建立了江苏沿江生态防护林树种综合评价体系.将江苏沿江生态防护林划分为水源涵养和水土保持林、景观防护林、污染隔离林和农林复合防护林4种类型,以耐水湿性、抗污染性、抗风性、水土保持能力、景观价值、经济价值和生长速率为评价指标,并设置各指标的权重值,建立了江苏沿江生态防护林树种分类评价体系.利用综合评价体系对223个树种进行评价,分别筛选出适用于江苏沿江生态防护林建设的综合得分前20位的落叶乔木、常绿乔木和灌木种类,其中,落叶乔木包括中山杉(Taxodium distichum 'Zhongshansha' )、池杉(T. ascendens Brongn. )、落羽杉[T. distichum (L. ) Rich. ]、墨西哥落羽杉(T. mucronatum Tenore)和水杉(Metasequoia glyptostroboides Hu et Cheng)等,常绿乔木包括樟树[Cinnamomum camphora (L. ) Presl]、北美红杉[Sequoia sempervirens (Lamb. ) Lindl. ]、浙江樟(C. chekiangensis Nakai)和青冈[Cyclobalanopsis glauca (Thunb. ) Oerst. ]等,灌木种类包括杞柳(Salix suchowensis Cheng)、木芙蓉(Hibiscus mutabilis L. )、夹竹桃(Nerium oleander L. )和栀子(Gardenia jasminoides Ellis)等.分类评价结果显示,在223个树种中有许多树种都可在4种类型的防护林中通用,这些通用树种包括中山杉、水杉、落羽杉、池杉、墨西哥落羽杉、樟树、杞柳、木芙蓉和栀子等;另外,从生活型角度,针对不同的防护林类型筛选出了一些适宜的树种.研究结果显示,该评价体系在江苏沿江生态防护林建设中具有一定的实用价值.