Genomic analysis reveals key aspects of prokaryotic symbiosis in the phototrophic consortium “Chlorochromatium aggregatum”

Background

‘Chlorochromatium aggregatum’ is a phototrophic consortium, a symbiosis that may represent the highest degree of mutual interdependence between two unrelated bacteria not associated with a eukaryotic host. ‘Chlorochromatium aggregatum’ is a motile, barrel-shaped aggregate formed from a single cell of ‘Candidatus Symbiobacter mobilis”, a polarly flagellated, non-pigmented, heterotrophic bacterium, which is surrounded by approximately 15 epibiont cells of Chlorobium chlorochromatii, a non-motile photolithoautotrophic green sulfur bacterium.

Results

We analyzed the complete genome sequences of both organisms to understand the basis for this symbiosis. Chl. chlorochromatii has acquired relatively few symbiosis-specific genes; most acquired genes are predicted to modify the cell wall or function in cell-cell adhesion. In striking contrast, ‘Ca. S. mobilis’ appears to have undergone massive gene loss, is probably no longer capable of independent growth, and thus may only reproduce when consortia divide. A detailed model for the energetic and metabolic bases of the dependency of ‘Ca. S. mobilis’ on Chl. chlorochromatii is described.

Conclusions

Genomic analyses suggest that three types of interactions lead to a highly sophisticated relationship between these two organisms. Firstly, extensive metabolic exchange, involving carbon, nitrogen, and sulfur sources as well as vitamins, occurs from the epibiont to the central bacterium. Secondly, ‘Ca. S. mobilis’ can sense and move towards light and sulfide, resources that only directly benefit the epibiont. Thirdly, electron cycling mechanisms, particularly those mediated by quinones and potentially involving shared protonmotive force, could provide an important basis for energy exchange in this and other symbiotic relationships.     

早期液体复苏对感染性休克患者血流动力学的影响

目的：早期液体复苏对感染性休克患者血流动力学的影响。方法：选取2012年2月-2013年2月我院ICU收治的26例感染性休克患者作为研究对象,随机分为对照组和试验组,各13例。两组患者均采用PICCO监测,并根据早期复苏目标导向（Earlygoaldirectedtherapy,EGDT）进行早期液体复苏治疗。对照组和试验组复苏液分别为林格液和6％羟乙基淀粉130／0．4氯化钠溶液。分别于复苏开始时（Oh）、8h和24h收集患者的血流动力学参数。结果：两组患者CO及PAWP水平均随着时间的延长下降,而CI、CVP及SVR水平均随着时间的增加上升。除对照组CI外,与开始复苏（oh）相比较试验组和对照组的C0、CI、CVP、SVR及PAWP与开始复苏（O小时）相比较均有显著差异（P值均〈0．05）。经重复测量资料的．方差分析进行比较发现,与对照组相比较,试验组CVP和SVR上升水平及PAWP下降水平明显,差异具有统计学意义（P值均〈0．05）。结论：感染性休克患者使用6％羟乙基淀粉130／0．4氯化钠溶液进行复苏,能更好的改善患者的血流动力学指标。     

Picornavirus internal ribosome entry site elements can stimulate translation of upstream genes

Certain viral and cellular mRNAs initiate translation cap-independently at internal ribosome entry site (IRES) elements. Picornavirus IRES elements are widely used in dicistronic or multicistronic vectors in gene therapy, virus replicon systems, and analysis of IRES function. In such vectors, expression of the upstream gene often serves as internal control to standardize the readings of IRES-driven downstream reporter activity. Picornaviral IRES elements translate optimally at up to 120 mM K(+) concentration, whereas genes used as upstream reporters usually have lower salt optima when present in monocistronic mRNAs. However, here we show that such reporter genes are efficiently translated at higher K(+) concentrations when placed upstream of a functional picornavirus IRES. This translation enhancement occurs in cis, is independent of the nature of the first reporter and of second reporter translation, and is conferred by the IRESs of picornaviruses but not of hepatitis C virus. A defective picornavirus IRES with a deletion killing IRES activity but leaving the binding site for initiation factor eIF4G intact retains translation enhancement activity. Translation enhancement on a capped mRNA is disabled by m(7)GDP. In addition, the C-terminal fragment of eIF4G can confer translation enhancement also on uncapped mRNA. We conclude that whenever eIF4F has been captured to a dicistronic mRNA by binding to a picornavirus IRES via its eIF4G moiety, it can be provided in cis to the 5'-end of the RNA and there stimulate translation initiation, either by binding to the cap nucleotide using its eIF4E moiety or by binding to the RNA cap-independently using its eIF4G moiety.     

Investigation on the precaecal and faecal digestibility of lactulose and inulin and their influence on nutrient digestibility and microbial characteristics

This study was conducted to determine the pre-caecal and faecal digestibility of lactulose and inulin and the influence of these substances on nutrient digestibility and microbial characteristics. In metabolic trials three of six male growing pigs (German Landrace x Pietrain) were fitted with an ileo-rectal anastomosis (IRA) in end-to-end technique with preserved ileo-caeco-colic valve. The metabolic trials were conducted from day 21-63 after surgery. The remaining pigs were used as intact partners (IN) for the IRA pigs. The experimental diets, based on corn, wheat, barley and soybean meal, were supplemented with either 1.5% lactulose or 2% inulin in replacement of diatomaceous earth (control). Pre-caecal digestibility of lactulose and inulin was assessed to be 79 and 98%, respectively. faecal digestibility was determined as 100%. The supplementation of lactulose and inulin had only minor effects on the pre-caecal and faecal digestibility of nutrients. Significant differences in nutrient digestibility were obvious between IRA and IN pigs, whereas the IRA pigs showed lower digestibility values with the exception of ether extracts (EE). Bacterial population in the digesta of IRA and IN pigs were not affected by the experimental diets except the concentration of gram-negative anaerobes, which inclined when the IRA pigs received the lactulose diet. The pH of chyme was significantly lower than the pH of faeces, however the pH was unaffected by the different supplemented diets. The concentration of volatile fatty acids (VFA) in pre-caecal chyme decreased significantly when IRA pigs received the lactulose supplemented diet whereas VFA in faeces were unaffected by the supplementation. IRA pigs administered with lactulose excreted more N via the urine, but the nitrogen balance remained unaffected. From the present investigation it can be concluded that lactulose and inulin did only partly or scarcely fulfill the expectation of acting as prebiotics in pigs.     

A data management system for structural genomics

Background  

Structural genomics (SG) projects aim to determine thousands of protein structures by the development of high-throughput techniques for all steps of the experimental structure determination pipeline. Crucial to the success of such endeavours is the careful tracking and archiving of experimental and external data on protein targets.     

Detection of aflatoxin-contaminated grain by three granivorous bird species

Supplemental feeding of game species and the use of backyard feeders to attract avian wildlife are common practices throughout the United States. However, these activities may expose wildlife to aflatoxins. We tested the hypothesis that wild birds would avoid consuming aflatoxin-contaminated feed. Individual northern bobwhites (Colinus virginianus), white-winged doves (Zenaida asiatica), and green jays (Cyanocorax yncas) were presented with feeders that had four compartments, which contained milo that was contaminated with aflatoxin levels of 0, 100, 500, and 1,000 microg/kg, respectively. Feed remaining was weighed at 6, 12, 18, 24, 36, 48, 60, and 72 hr after the initiation of the trial. White-winged doves and northern bobwhites did not avoid contaminated feed. However, green jays selected against aflatoxin-tainted grain. Because white-winged doves and northern bobwhites did not avoid contaminated feed, the risk of exposure to this potentially hazardous toxin exists for these species.     

The RTP site shared by the HIV-1 Tat protein and the 11S regulator subunit alpha is crucial for their effects on proteasome function including antigen processing

Nuclease A (NucA) from Anabaena sp. is a non-specific endonuclease able to degrade single and double-stranded DNA and RNA. The endonucleolytic activity is inhibited by the nuclease A inhibitor (NuiA), which binds to NucA with 1:1 stoichiometry and picomolar affinity. In order to better understand the mechanism of inhibition, the solution structure of NuiA was determined by NMR methods. The fold of NuiA is an alpha-beta-alpha sandwich but standard database searches by DALI and TOP revealed no structural homologies. A visual inspection of alpha-beta-alpha folds in the CATH database revealed similarities to the PR-1-like fold (SCOP nomenclature). The similarities include the ordering of secondary structural elements, a single helix on one face of the alpha-beta-alpha sandwich, and three helices on the other face. However, a major difference is in the IV helix, which in the PR-1 fold is short and perpendicular to the I and III helices, but in NuiA is long and parallel to the I and III helices. Additionally, a strand insertion in the beta-sheet makes the NuiA beta-sheet completely antiparallel in organization. The fast time-scale motions of NuiA, characterized by enhanced flexibility of the extended loop between helices III and IV, also show similarities to P14a, which is a PR-1 fold. We propose that the purpose of the PR-1 fold is to form a stable scaffold to present this extended structure for biological interactions with other proteins. This hypothesis is supported by data that show that when NuiA is bound to NucA significant changes in chemical shift occur in the extended loop between helices III and IV.     

An AFM determination of the effects on surface roughness caused by cleaning of fused silica and glass substrates in the process of optical biosensor preparation

The covalent attachment of organic films and of biological molecules to fused silica and glass substrates is important for many applications. For applications such as biosensor development, it is desired that the immobilised molecules be assembled in a uniform layer on the surface so as to provide for reproducibility and speed of surface interactions. For optimal derivatisation the surface must be appropriately cleaned to remove contamination, to create surface attachment sites such as hydroxyl groups, and to control surface roughness. The irregularity of the surface can be significant in defining the integrity and density of immobilised films. Numerous cleaning methods exist for fused silica and glass substrates and these include gas plasmas, and combinations of acids, bases and organic solvents that are allowed to react at varying temperatures. For many years, we have used a well established method based on a combination of washing with basic peroxide followed by acidic peroxide to clean and hydroxylate the surface of fused silica and glass substrates before oligonucleotide immobilisation. Atomic force microscopy (AFM) has been used to evaluate the effect of cleaning on surface roughness for various fused silica and glass samples. The results indicate that surface roughness remains substantial after use of this common cleaning routine, and can provide a surface area that is more than 10% but less than 30% larger than anticipated from geometric considerations of a planar surface.