Influence of magnesium ions on biofilm formation by Pseudomonas fluorescens

Mg²⁺ can potentially influence bacterial adhesion directly through effects on electrostatic interactions and indirectly by affecting physiology-dependent attachment processes. However, the effects of Mg²⁺ on biofilm structure are largely unknown. In this study, Pseudomonas fluorescens was used to investigate the influence of Mg²⁺ concentration (0, 0.1 and 1.0 mM MgCl₂) on biofilm growth. Planktonic and attached cells were enumerated (based on DAPI staining) while biofilm structures were examined via confocal laser scanning microscopy and three-dimensional structures were reconstructed. Mg²⁺ concentration had no influence on growth of planktonic cells but, during biofilm formation, Mg²⁺ increased the abundance of attached cells. For attached cells, the influence of Mg²⁺ concentration changed over time, suggesting that the role of Mg²⁺ in bacterial attachment is complex and dynamic. Biofilm structures were heterogeneous and surface colonization and depth increased with increasing Mg²⁺ concentrations. Overall, for P. fluorescens, Mg²⁺ increased initial attachment and altered subsequent biofilm formation and structure.     

Prevalence and genetic diversity of coronaviruses in bats from China

Coronaviruses can infect a variety of animals including poultry, livestock, and humans and are currently classified into three groups. The interspecies transmissions of coronaviruses between different hosts form a complex ecosystem of which little is known. The outbreak of severe acute respiratory syndrome (SARS) and the recent identification of new coronaviruses have highlighted the necessity for further investigation of coronavirus ecology, in particular the role of bats and other wild animals. In this study, we sampled bat populations in 15 provinces of China and reveal that approximately 6.5% of the bats, from diverse species distributed throughout the region, harbor coronaviruses. Full genomes of four coronavirues from bats were sequenced and analyzed. Phylogenetic analyses of the spike, envelope, membrane, and nucleoprotein structural proteins and the two conserved replicase domains, putative RNA-dependent RNA polymerase and RNA helicase, revealed that bat coronaviruses cluster in three different groups: group 1, another group that includes all SARS and SARS-like coronaviruses (putative group 4), and an independent bat coronavirus group (putative group 5). Further genetic analyses showed that different species of bats maintain coronaviruses from different groups and that a single bat species from different geographic locations supports similar coronaviruses. Thus, the findings of this study suggest that bats may play an integral role in the ecology and evolution of coronaviruses.     

BioJazz: in silico evolution of cellular networks with unbounded complexity using rule-based modeling

Systems biologists aim to decipher the structure and dynamics of signaling and regulatory networks underpinning cellular responses; synthetic biologists can use this insight to alter existing networks or engineer de novo ones. Both tasks will benefit from an understanding of which structural and dynamic features of networks can emerge from evolutionary processes, through which intermediary steps these arise, and whether they embody general design principles. As natural evolution at the level of network dynamics is difficult to study, in silico evolution of network models can provide important insights. However, current tools used for in silico evolution of network dynamics are limited to ad hoc computer simulations and models. Here we introduce BioJazz, an extendable, user-friendly tool for simulating the evolution of dynamic biochemical networks. Unlike previous tools for in silico evolution, BioJazz allows for the evolution of cellular networks with unbounded complexity by combining rule-based modeling with an encoding of networks that is akin to a genome. We show that BioJazz can be used to implement biologically realistic selective pressures and allows exploration of the space of network architectures and dynamics that implement prescribed physiological functions. BioJazz is provided as an open-source tool to facilitate its further development and use. Source code and user manuals are available at: http://oss-lab.github.io/biojazz and http://osslab.lifesci.warwick.ac.uk/BioJazz.aspx.     

Differentially Expressed Genes in EEC and LMS Syndromes

Objectives

Ectrodactyly ectodermal dysplasia cleft lip/palate (EEC) syndrome and limb-mammary syndrome (LMS) share a similar phenotype and the same pathogenic gene, which complicates the ability to distinguish between these diagnoses. The current study aims to identify a potential and practical clinical biomarker to distinguish EEC from LMS.

Methods

Two EEC pedigrees and one LMS pedigree that have been previously reported were reanalyzed. After confirmation of the causative mutations for these new patients, whole-genome expression microarray analysis was performed to assess the molecular genetic changes in these families.

Results

Five new patients with classic symptoms were reported, and these individuals exhibited the same mutation as their relatives (c.812 G>C; c.611G>A; and c.680G>A). According to the whole genome expression results, the EEC patients exhibited different gene expression characteristics compared with the LMS patients. More than 5,000 genes were differentially expressed (changes >2 or <0.5-fold) among the EEC patients, LMS patients and healthy individuals. The top three altered pathways have been implicated in apoptosis, the hematopoietic cell lineage and the Toll-like receptor signaling pathway.

Conclusion

Our results provide additional clinical and molecular information regarding EEC and LMS and suggest that peripheral blood cytokines may represent a promising clinical biomarker for the diagnosis of these syndromes.     

Evaluating the Learning Curve for Percutaneous Nephrolithotomy under Total Ultrasound Guidance

Objectives

To investigate the learning curve of percutaneous nephrolithotomy under total ultrasound guidance.

Methods

One hundred and twenty consecutive PCNL operations under total ultrasound guidance performed by a novice surgeon in a tertiary referral center were studied. Operations were analyzed in cohorts of 15 to determine when a plateau was reached for the variables such as operation duration, ultrasound screening time, tract dilation time, stone-free rate and complication rate. Comparison was made with the results of a surgeon who had performed more than 1000 PCNLs. Fluoroscopy was not used at all during procedure.

Results

The mean operation time dropped from 82.5 min for the first 15 patients to a mean of 64.7 min for cases 46 through 60(P = 0.047). The ultrasound screening time was a peak of 6.4 min in the first 15 cases, whereas it dropped to a mean of 3.9 min for cases 46 through 60(P = 0.01). The tract dilation time dropped from 4.9 min for the first 15 patients to a mean of 3.8 min for cases 46 through 60(P = 0.036). The senior surgeon had a mean operating time, screening time and tract dilation time equivalent to those of the novice surgeon after 60 cases. There was no significant difference in stone free rate and complication rate.

Conclusions

The competence of ultrasound guided PCNL is reached after 60 cases with good stone free rate and without major complications.     

苦瓜离体培养过程中内源激素含量的变化

针对苦瓜(Momordica charantia)离体培养中外植体易于产生愈伤组织而难以再生不定芽的问题,本文采用酶联免疫吸附法, 研究了苦瓜组织培养过程中不同发育阶段各外植体内源激素含量的变化, 以探讨不定芽分化与激素水平变化之间的关系, 以及苦瓜难以再生不定芽的内在制约因素。结果表明: (1)苦瓜外植体中IAA含量较高, 而iPAs含量过低, 是苦瓜易于产生愈伤组织而不定芽再生困难的主要原因;(2)不定芽的分化与IAA/iPAs的变化有密切的关系; (3)在离体培养过程中, 保持外源细胞分裂素类物质(如ZT)的适当浓度并及时继代, 有利于苦瓜不定芽的分化。     

微菌落观察法快速检测和鉴别结核杆菌培养物的研究

将取自肺结核患者的219例痰标本接种匡氏琼脂平板,共分离到112例结核菌生长物。其中培养法104例(92.8％)阳性,微菌落观察法108例(96.4％)阳性,微菌落法阳性率稍高。培养法和微菌落法阳性标本首次检出时间分别为18.6d和11d,微菌落检出时间更短(P<0.01)。常规菌型鉴别方法与微菌落法对结核杆菌菌型鉴别的符合率为99％。