In addition to exhibiting swimming and twitching motility, Pseudomonas aeruginosa is able to swarm on semisolid (viscous) surfaces. Recent studies have indicated that swarming is a more complex type of motility influenced by a large number of different genes. To investigate the adaptation process involved in swarming motility, gene expression profiles were analyzed by performing microarrays on bacteria from the leading edge of a swarm zone compared to bacteria growing in identical medium under swimming conditions. Major shifts in gene expression patterns were observed under swarming conditions, including, among others, the overexpression of a large number of virulence-related genes such as those encoding the type III secretion system and its effectors, those encoding extracellular proteases, and those associated with iron transport. In addition, swarming cells exhibited adaptive antibiotic resistance against polymyxin B, gentamicin, and ciprofloxacin compared to what was seen for their planktonic (swimming) counterparts. By analyzing a large subset of up-regulated genes, we were able to show that two virulence genes, lasB and pvdQ, were required for swarming motility. These results clearly favored the conclusion that swarming of P. aeruginosa is a complex adaptation process in response to a viscous environment resulting in a substantial change in virulence gene expression and antibiotic resistance.Swarming motility is a multicellular phenomenon involving the coordinated and rapid movement of a bacterial population across a semisolid surface (14). It is widespread among flagellated bacteria, including Salmonella, Vibrio, Yersinia, Serratia, and Proteus (9,18). Swarming is highly dependent on bacterial cell density, nutrient growth medium, and surface condition moistness (53). In addition to physical changes such as an increase in the number of flagella or cell elongation, swarmer cell differentiation results in substantial alterations in metabolic bias and gene expression, indicating that swarming represents a complex lifestyle adaptation in response to particular medium conditions rather than merely a form of locomotion (18,45).Swarming of Pseudomonas aeruginosa is often typified by a dendritic colonial appearance. This gram-negative bacterium is a major cause of hospital-acquired bacterial infections and the most significant pulmonary pathogen in cystic fibrosis patients (17,20,44). It is one of the most difficult infections to treat due to its high natural (intrinsic) antibiotic resistance. It possesses three types of movement depending on medium viscosity, namely, swimming in aqueous environments, twitching on solid surfaces or interfaces, and swarming on semisolid, viscous media, such as those containing 0.4 to 0.7% (wt/vol) agar. It has been previously shown that swarming of P. aeruginosa is dependent on both flagella and type IV pili, which mediate actual movement, as well as on rhamnolipids, which are proposed to enable swarming cells to overcome the strong surface tension of the water surrounding swarmi...

. Only a modest subset of the Mg 2؉ -regulated genes were regulated through either PhoP or PmrA. To determine which genes were directly regulated, a bioinformatic search for conserved binding motifs was combined with confirmatory reverse transcriptase PCR and gel shift promoter binding assays, and the results indicated that very few genes were directly regulated by these response regulators. It was found that in addition to the previously known oprH-phoP-phoQ operon and the pmrHFIJKLM-ugd operon, the PA0921 and PA1343 genes, encoding small basic proteins, were regulated by Mg 2؉ in a PhoP-dependent manner. The number of known PmrAregulated genes was expanded to include the PA1559-PA1560, PA4782-PA4781, and feoAB operons, in addition to the previously known PA4773-PA4775-pmrAB and pmrHFIJKLM-ugd operons.Pseudomonas aeruginosa is an important opportunistic pathogen that is capable of infecting a large number of hosts, including nematodes, insects, plants, animals, and especially humans. It is the third-leading cause of nosocomial infections and is also the leading cause of morbidity and mortality in cystic fibrosis (CF) patients (33). P. aeruginosa is also noted for its metabolic diversity, which allows it to colonize a large number of environmental habitats. The versatility of this organism is believed to be related to the large number of regulatory proteins found in its genome (469 of 5,570 open reading frames) (43).The two-component response regulators constitute one of the larger families of regulatory proteins in P. aeruginosa (43). These systems typically contain a sensor protein that responds to some chemical or physical stimulus, which leads to phosphorylation of the sensor protein at a conserved histidine residue, thus altering the conformation of the sensor and promoting phosphotransfer to a cognate response regulator protein (9). The phosphorylated response regulator then recognizes and binds to a specific DNA sequence, leading to modulation of transcription from that promoter. Although this is often the mechanism, regulation may also occur through phosphatase activity of the sensor kinase with the response regulator (37) or through integration into the signaling cascade of multiple signals from other proteins (32). In P. aeruginosa, there are 64 response regulators and 63 histidine kinases, as well as 16 atypical kinases (36). The functions of the majority of these regulatory proteins have not been established yet.In P. aeruginosa, two separate two-component regulatory systems, PmrA-PmrB (26) and PhoP-PhoQ (21), are known to respond to the presence of limiting concentrations of Mg 2ϩ and to separately regulate certain operons. The PhoPQ system autoregulates the oprH-phoP-phoQ operon (21) under Mg 2ϩ -limiting growth conditions and is also involved in resistance to cationic antimicrobial peptides and polymyxin B and in virulence, as phoQ mutants exhibit increased resistance to cationic antimicrobial peptides and polymyxin B and have reduced virulence (20). Similarly, the PmrAB system regulates resistanc...

With few novel antimicrobials in development, resistance to the current selection of antibiotics increasingly encroaches on our ability to control microbial infections. One limitation in our understanding of the basis of the constraints on current therapies is our poor understanding of antibiotic interactions with bacteria on a global scale. Custom DNA microarrays were used to characterize the response of Pseudomonas aeruginosa to ciprofloxacin, a fluoroquinolone commonly used in therapy against chronic infections by this intrinsically resistant bacterium.

Bioinformatics is now intrinsic to life science research, but the past decade has witnessed a continuing deficiency in this essential expertise. Basic data stewardship is still taught relatively rarely in life science education programmes, creating a chasm between theory and practice, and fuelling demand for bioinformatics training across all educational levels and career roles. Concerned by this, surveys have been conducted in recent years to monitor bioinformatics and computational training needs worldwide. This article briefly reviews the principal findings of a number of these studies. We see that there is still a strong appetite for short courses to improve expertise and confidence in data analysis and interpretation; strikingly, however, the most urgent appeal is for bioinformatics to be woven into the fabric of life science degree programmes. Satisfying the relentless training needs of current and future generations of life scientists will require a concerted response from stakeholders across the globe, who need to deliver sustainable solutions capable of both transforming education curricula and cultivating a new cadre of trainer scientists.

Bioinformatics is recognized as part of the essential knowledge base of numerous career paths in biomedical research and healthcare. However, there is little agreement in the field over what that knowledge entails or how best to provide it. These disagreements are compounded by the wide range of populations in need of bioinformatics training, with divergent prior backgrounds and intended application areas. The Curriculum Task Force of the International Society of Computational Biology (ISCB) Education Committee has sought to provide a framework for training needs and curricula in terms of a set of bioinformatics core competencies that cut across many user personas and training programs. The initial competencies developed based on surveys of employers and training programs have since been refined through a multiyear process of community engagement. This report describes the current status of the competencies and presents a series of use cases illustrating how they are being applied in diverse training contexts. These use cases are intended to demonstrate how others can make use of the competencies and engage in the process of their continuing refinement and application. The report concludes with a consideration of remaining challenges and future plans.