绒山羊源大肠杆菌噬菌体φPTK的分子生物学特性及对小鼠大肠杆菌感染的防治效果

【背景】抗生素耐药问题是影响人类及养殖业健康的重要因素,噬菌体能特异性裂解细菌,成为抗生素替代品研究热点,是解决抗生素耐药难题、促进养殖业健康发展的新途径。【目的】通过研究绒山羊源大肠杆菌烈性噬菌体φPTK (phage target of K1)的分子生物学特性,同时利用小鼠感染模型研究φPTK对小鼠大肠杆菌感染的防治效果,为绒山羊大肠杆菌病的防控提供新策略。【方法】用聚乙二醇-氯化钠(PEG 8000-NaCl)浓缩φPTK后,采用透射电子显微镜观察其超微形态结构;运用苯酚-氯仿法提取φPTK核酸后通过Illumina HiSeq高通量测序分析其全基因组结构,使用Mauve比较基因组学分析,通过MEGA绘制噬菌体进化树;通过构建小鼠感染模型分析φPTK对小鼠感染大肠杆菌的防治效果。【结果】透射电镜显示φPTK头部为正多面体形,直径90 nm,有长约112 nm、直径约18 nm的可收缩长尾;φPTK基因组全长169 688 bp,GC含量37.72%,有264个开放阅读框,含穿孔素-裂解酶(holin-lysin)裂解系统,有抗穿孔素蛋白和裂解抑制辅助蛋白,未发现抗生素耐药基因和毒力基因;比较基因组分析表明,φPTK为一株新的绒山羊源大肠杆菌烈性噬菌体;小鼠大肠杆菌感染前和感染后分别使用φPTK进行预防和治疗的试验表明,未使用φPTK的阳性对照组小鼠全部死亡,预防组和治疗组小鼠存活率分别为80%和60%。【结论】噬菌体φPTK是一株能够在小鼠大肠杆菌感染中具有较好预防效果的有尾噬菌体目(Caudovirales)肌尾噬菌体科(Myoviridae)绒山羊源大肠杆菌烈性噬菌体,本研究为绒山羊噬菌体生物制剂的创制奠定了基础。     

Development of genomic resources for Wenchengia alternifolia (Lamiaceae) based on genome skimming data

Wenchengia alternifolia (Lamiaceae), the sole species of the genus Wenchengia is extremely rare and is currently listed as Critically Endangered (CR) on the IUCN Red List. The species had long been considered endemic to Hainan Island, China and was once believed to be extinct until a small remnant population was rediscovered at the type locality in 2010. Four more populations were later found on Hainan and in Vietnam. In order to develop genomic resources for further studies on population genetics and conservation biology of this rare species, we identified infraspecific molecular markers in the present study, using genome skimming data of five individuals collected from two populations on Hainan Island and three populations in Vietnam respectively. The length of plastome of the five individuals varied from 152,961 bp to 150,204 bp, and exhibited a typical angiosperm quadripartite structure. Six plastid hotspot regions with the Pi > 0.01 (trnH-psbA, psbA-trnK, rpl22, ndhE, ndhG-ndhI and rps15-ycf1), 1621 polymorphic gSSRs, as well as 1657 candidate SNPs in 237 variant nuclear genes were identified, thereby providing important information for further genetic studies.     

Proteomic analysis of early‐response to mechanical stress in neonatal rat mandibular condylar chondrocytes

The objectives of this study were to investigate the early response to mechanical stress in neonatal rat mandibular chondrocytes by proteomic analysis. To evaluate its molecular mechanism, chondrocytes were isolated and cultured in vitro, then loaded mechanical stress by four‐point bending system on different patterns. Morphological observation, flow cytometric analysis, and MTT assays indicated that 4,000 µstrain loading for 60 min was an appropriate mechanical stimulus for the following proteome analysis, which produced a transient but obvious inhibitory effect on the cell cycle. Therefore, we took a proteomic approach to identify significantly differential expression proteins in chondrocytes under this mechanical stress. Using 2‐DE and MALDI‐TOF, we identified seven differentially expressed proteins including the MAPK pathway inhibitor RKIP, cytoskeleton proteins, actin and vimentin, and other selected proteins. Some differentially expressed proteins were validated by both Western blot analysis and fluorescent staining of cytoskeleton at different loading times. The vimentin and RKIP responsive expression were also proven in vivo in oral orthopedic treatment rats, which was in line with the result in vitro. The histological changes in cartilage also showed the inhibition effect. Furthermore, the expressional level of phosphorylated ERK was increased, which demonstrates the changes in MAPK activity. Taken together, these data indicate that mechanical stress resulted in vimentin expression changes first and then led to the subsequent changes in actin expression, MAPK pathway regulated by RKIP and heat shock protein GRP75. All those changes contributed to the cytoskeleton remolding and cell cycle inhibition, finally led to condylar remodeling. J. Cell. Physiol. 223:610–622, 2010. © 2010 Wiley‐Liss, Inc.     

Discovery of multiple IGS haplotypes within genotypes of Puccinia striiformis

In a search for specific molecular markers for population analysis of Puccinia striiformis f. sp. tritici, the ribosomal DNA (rDNA) intergenic spacer (IGS) 1 region (rDNA-IGS1, between the 28S and the 5S rDNA genes) was amplified, cloned, and sequenced. It was found to exhibit multiple bands and length polymorphism. Surprisingly, single isolates were found to possess between three to five different IGS1 haplotypes. Bands were cloned and sequenced, and two highly variable regions (α and β) were found between conserved regions, with repeat units interspersed in both types of regions. There were 14 different repeat units, and these were sometimes grouped further into four combinations of repeat units, with a few individual nucleotides (A or C) inserted between the repeats. Among three geographically dispersed isolates, the variable region α was divided into eight types, and the variable region β was divided into two types based on repeat units. Most of the 14 repeat units were shared by the variable and the conserved regions. Among the three isolates, there were a total of 12 IGS1 haplotypes, but some of these were shared between isolates such that there were only eight unique haplotypes. The occurrence of multiple haplotypes within single isolates may be useful for analyzing the population structure, tracking the origin of annual epidemics and providing insights into evolutionary biology of this pathogen.     

Fossil fishes from china provide first evidence of dermal pelvic girdles in osteichthyans

Background

The pectoral and pelvic girdles support paired fins and limbs, and have transformed significantly in the diversification of gnathostomes or jawed vertebrates (including osteichthyans, chondrichthyans, acanthodians and placoderms). For instance, changes in the pectoral and pelvic girdles accompanied the transition of fins to limbs as some osteichthyans (a clade that contains the vast majority of vertebrates – bony fishes and tetrapods) ventured from aquatic to terrestrial environments. The fossil record shows that the pectoral girdles of early osteichthyans (e.g., Lophosteus, Andreolepis, Psarolepis and Guiyu) retained part of the primitive gnathostome pectoral girdle condition with spines and/or other dermal components. However, very little is known about the condition of the pelvic girdle in the earliest osteichthyans. Living osteichthyans, like chondrichthyans (cartilaginous fishes), have exclusively endoskeletal pelvic girdles, while dermal pelvic girdle components (plates and/or spines) have so far been found only in some extinct placoderms and acanthodians. Consequently, whether the pectoral and pelvic girdles are primitively similar in osteichthyans cannot be adequately evaluated, and phylogeny-based inferences regarding the primitive pelvic girdle condition in osteichthyans cannot be tested against available fossil evidence.

Methodology/Principal Findings

Here we report the first discovery of spine-bearing dermal pelvic girdles in early osteichthyans, based on a new articulated specimen of Guiyu oneiros from the Late Ludlow (Silurian) Kuanti Formation, Yunnan, as well as a re-examination of the previously described holotype. We also describe disarticulated pelvic girdles of Psarolepis romeri from the Lochkovian (Early Devonian) Xitun Formation, Yunnan, which resemble the previously reported pectoral girdles in having integrated dermal and endoskeletal components with polybasal fin articulation.

Conclusions/Significance

The new findings reveal hitherto unknown similarity in pectoral and pelvic girdles among early osteichthyans, and provide critical information for studying the evolution of pelvic girdles in osteichthyans and other gnathostomes.     

The action of Cu2+ on Bacillus thuringiensis growth investigated by microcalorimetry

By using an LKB-2277 Bioactivity Monitor, ampoule mode, the heat output of Bacillus thuringiensis growth metabolism has been determined at 28 degrees C and effect of Cu2+ on B. thuringiensis growth was studied. Copper has been regarded as an essential trace element for life. Its deficiency may be the cause of diseases. Cu2+ of different concentration have different effects on B. thuringiensis growth metabolism, Cu2+ of low concentration (0-30 micrograms/ml) can promote the growth of B. thuringiensis, and Cu2+ of high concentration (40-120 micrograms/ml) is able to inhibit its growth and B. thuringiensis can't grow at all when the concentration of Cu2+ is up to 130 micrograms/ml.     

Response of Soil Bacterial Community Structure to Permafrost Degradation in the Upstream Regions of the Shule River Basin,Qinghai–Tibet Plateau

Permafrost degradation affects soil properties and vegetation, but little is known about its consequent effects on the soil bacterial community. In this study, we analyzed the bacterial community structure of 12 permafrost-affected soil samples from four principal permafrost types, sub-stable permafrost (SSP), transition permafrost (TP), unstable permafrost (UP) and extremely unstable permafrost (EUP), to investigate the effects of vegetation characteristics and soil properties on bacterial community structure during the process of permafrost degradation. Proteobacteria, Acidobacteria, Actinobacteria and Bacteroidetes were the predominant phyla in all four permafrost soil types. The relative abundance of Proteobacteria decreased in the order SSP > TP> UP > EUP, whereas the abundance of Actinobacteria increased in the order SSP < TP < UP < EUP. Moreover, the Actinobacteria/Proteobacteria ratio increased significantly in the order SSP < TP < UP < EUP along with permafrost degradation, which may be useful as a sign of permafrost degradation. Redundancy analysis (RDA) showed that bacterial communities could be clustered by permafrost types. Analysis of single factors revealed that soil moisture (SM) was the most important factor affecting the bacterial community structure and diversity, followed by soil total nitrogen (STN) and vegetation cover (VC). Partial RDA analysis showed that the soil properties and vegetation characteristics jointly shaped the bacterial community structure. Hence, we can conclude that permafrost degradation, caused by global warming, affects vegetation and soil properties and consequently drives changes in the soil bacterial community structure.