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1.  Elucidation of the RamA Regulon in Klebsiella pneumoniae Reveals a Role in LPS Regulation 
PLoS Pathogens  2015;11(1):e1004627.
Klebsiella pneumoniae is a significant human pathogen, in part due to high rates of multidrug resistance. RamA is an intrinsic regulator in K. pneumoniae established to be important for the bacterial response to antimicrobial challenge; however, little is known about its possible wider regulatory role in this organism during infection. In this work, we demonstrate that RamA is a global transcriptional regulator that significantly perturbs the transcriptional landscape of K. pneumoniae, resulting in altered microbe-drug or microbe-host response. This is largely due to the direct regulation of 68 genes associated with a myriad of cellular functions. Importantly, RamA directly binds and activates the lpxC, lpxL-2 and lpxO genes associated with lipid A biosynthesis, thus resulting in modifications within the lipid A moiety of the lipopolysaccharide. RamA-mediated alterations decrease susceptibility to colistin E, polymyxin B and human cationic antimicrobial peptide LL-37. Increased RamA levels reduce K. pneumoniae adhesion and uptake into macrophages, which is supported by in vivo infection studies, that demonstrate increased systemic dissemination of ramA overexpressing K. pneumoniae. These data establish that RamA-mediated regulation directly perturbs microbial surface properties, including lipid A biosynthesis, which facilitate evasion from the innate host response. This highlights RamA as a global regulator that confers pathoadaptive phenotypes with implications for our understanding of the pathogenesis of Enterobacter, Salmonella and Citrobacter spp. that express orthologous RamA proteins.
Author Summary
Bacteria can rapidly evolve under antibiotic pressure to develop resistance, which occurs when target genes mutate, or when resistance-encoding genes are transferred. Alternatively, microbes can simply alter the levels of intrinsic proteins that allow the organism to “buy” time to resist antibiotic pressure. Klebsiella pneumoniae is a pathogen that causes significant blood stream or respiratory infections, but more importantly is a bacterium that is increasingly being reported as multidrug resistant. Our data demonstrate that RamA can trigger changes on the bacterial surface that allow Klebsiella to survive both antibiotic challenge, degradation by host immune peptides and resist phagocytosis. We demonstrate that the molecular basis of increased survival of ramA overexpressing K. pneumoniae, against host-derived factors is associated with RamA-driven alterations of the lipid A moiety of Klebsiella LPS. This modification is likely to be linked to Klebsiella’s ability to resist the host response so that it remains undetected by the immune system. The relevance of our work extends beyond RamA in Klebsiella as other pathogens such as Enterobacter spp and Salmonella spp. also produce this protein. Thus our overarching conclusion is that the intrinsic regulator, RamA perturbs host-microbe and microbe-drug interactions.
PMCID: PMC4310594  PMID: 25633080
2.  Antibiotic resistance in Prevotella species isolated from patients with cystic fibrosis 
Journal of Antimicrobial Chemotherapy  2013;68(10):2369-2374.
To compare the antimicrobial susceptibility of Prevotella spp. isolated from cystic fibrosis (CF) and non-CF patients and analyse the impact of antibiotic prescribing in the preceding year on resistance amongst CF isolates.
The susceptibility of 80 CF Prevotella isolates to 12 antibiotics was compared with that of 50 Prevotella isolates from invasive infections in people who did not have CF and 27 Prevotella isolates from healthy controls.
All isolates were susceptible to chloramphenicol, meropenem and piperacillin/tazobactam, with only four isolates resistant to metronidazole. However, resistance to amoxicillin, ceftazidime and tetracycline was apparent in all groups. Significant differences in clindamycin resistance (UK CF, 56%; UK invasive, 10%) and co-amoxiclav non-susceptibility (UK CF, 32%; UK invasive, 12%) were observed between UK CF and UK invasive isolates. The likelihood of non-susceptibility to clindamycin and co-amoxiclav in UK CF isolates was 5.5-fold and 2.5-fold higher relative to that in UK invasive isolates, respectively. Azithromycin MICs were also significantly higher for CF isolates (P < 0.001), which was associated with current prescription of azithromycin. More than 50% of clinical isolates tested in this study were β-lactamase positive.
This study profiles antibiotic susceptibility in Prevotella spp. in CF and demonstrates that meropenem, piperacillin/tazobactam, chloramphenicol and metronidazole are likely to be the most effective antibiotics if treatment is indicated.
PMCID: PMC3772740  PMID: 23696621
anaerobic bacteria; antimicrobial susceptibility; β-lactamase production
3.  Severity of Injury Predicts Subsequent Function in Surgically Treated Displaced Intraarticular Calcaneal Fractures 
The treatment of displaced, intraarticular calcaneal fractures (DIACFs) remains challenging and the best treatment choices remain controversial. The majority of patients will have some lasting functional restrictions. However, it is unclear which patient- or surgeon-related factors predict long-term function.
We determined (1) the impact of patient- and surgeon-related factors on function of patients after internal fixation of DIACFs and (2) whether severity of injury correlated with subsequent function.
We retrospectively reviewed all 210 patients operatively treated for 242 DIACFs between 2000 and 2003; of these, 127 patients (60%) with 149 fractures were available for followup at a minimum of 69 months (average, 95 months; range, 69–122 months). Severity of injury was quantified by the classifications of Sanders and Zwipp Function was quantified using the American Orthopaedic Foot and Ankle Society (AOFAS) Ankle-Hindfoot score, an adjusted Zwipp score, the Foot Function Index (FFI), and the SF-36 physical and mental component summary (PCS and MCS) scores.
At latest followup, the median AOFAS score was 77, the median Zwipp score was 60, the median FFI was 27, and the median SF-36 PCS and MCS scores were 44 and 55, respectively. The foot-related scores and the SF-36 PCS negatively correlated with the severity of injury, work-related injuries, and bilateral fractures.
We found the severity of a DIACF related to subsequent foot function and quality of life. Both fracture severity classifications predicted function. Anatomic reconstruction of the shape and articular surfaces of the calcaneus leads to predictable function in the medium to long term.
Level of Evidence
Level IV, prognostic study. See Instructions for Authors for a complete description of levels of evidence.
PMCID: PMC3734437  PMID: 23690151
4.  Fosfomycin and Tobramycin in Combination Downregulate Nitrate Reductase Genes narG and narH, Resulting in Increased Activity against Pseudomonas aeruginosa under Anaerobic Conditions 
Antimicrobial Agents and Chemotherapy  2013;57(11):5406-5414.
The activity of aminoglycosides, which are used to treat Pseudomonas aeruginosa respiratory infection in cystic fibrosis (CF) patients, is reduced under the anaerobic conditions that reflect the CF lung in vivo. In contrast, a 4:1 (wt/wt) combination of fosfomycin and tobramycin (F:T), which is under investigation for use in the treatment of CF lung infection, has increased activity against P. aeruginosa under anaerobic conditions. The aim of this study was to elucidate the mechanisms underlying the increased activity of F:T under anaerobic conditions. Microarray analysis was used to identify the transcriptional basis of increased F:T activity under anaerobic conditions, and key findings were confirmed by microbiological tests, including nitrate utilization assays, growth curves, and susceptibility testing. Notably, growth in subinhibitory concentrations of F:T, but not tobramycin or fosfomycin alone, significantly downregulated (P < 0.05) nitrate reductase genes narG and narH, which are essential for normal anaerobic growth of P. aeruginosa. Under anaerobic conditions, F:T significantly decreased (P < 0.001) nitrate utilization in P. aeruginosa strains PAO1, PA14, and PA14 lasR::Gm, a mutant known to exhibit increased nitrate utilization. A similar effect was observed with two clinical P. aeruginosa isolates. Growth curves indicate that nitrate reductase transposon mutants had reduced growth under anaerobic conditions, with these mutants also having increased susceptibility to F:T compared to the wild type under similar conditions. The results of this study suggest that downregulation of nitrate reductase genes resulting in reduced nitrate utilization is the mechanism underlying the increased activity of F:T under anaerobic conditions.
PMCID: PMC3811241  PMID: 23959314
5.  Comprehensive histological evaluation of bone implants 
Biomatter  2014;4:e27993.
To investigate and assess bone regeneration in sheep in combination with new implant materials classical histological staining methods as well as immunohistochemistry may provide additional information to standard radiographs or computer tomography. Available published data of bone defect regenerations in sheep often present none or sparely labeled histological images. Repeatedly, the exact location of the sample remains unclear, detail enlargements are missing and the labeling of different tissues or cells is absent. The aim of this article is to present an overview of sample preparation, staining methods and their benefits as well as a detailed histological description of bone regeneration in the sheep tibia. General histological staining methods like hematoxylin and eosin, Masson-Goldner trichrome, Movat’s pentachrome and alcian blue were used to define new bone formation within a sheep tibia critical size defect containing a polycaprolactone-co-lactide (PCL) scaffold implanted for 3 months (n = 4). Special attention was drawn to describe the bone healing patterns down to cell level. Additionally one histological quantification method and immunohistochemical staining methods are described.
PMCID: PMC3979890  PMID: 24504113
bone implants; polycaprolactone-co-lactide scaffold; sheep; histology
6.  Feasibility of visual instrumented movement feedback therapy in individuals with motor incomplete spinal cord injury walking on a treadmill 
Background: Incomplete spinal cord injury (iSCI) leads to motor and sensory deficits. Even in ambulatory persons with good motor function an impaired proprioception may result in an insecure gait. Limited internal afferent feedback (FB) can be compensated by provision of external FB by therapists or technical systems. Progress in computational power of motion analysis systems allows for implementation of instrumented real-time FB. The aim of this study was to test if individuals with iSCI can normalize their gait kinematics during FB and more importantly maintain an improvement after therapy.
Methods: Individuals with chronic iSCI had to complete 6 days (1 day per week) of treadmill-based FB training with a 2 weeks pause after 3 days of training. Each day consists of an initial gait analysis followed by 2 blocks with FB/no-FB. During FB the deviation of the mean knee angle during swing from a speed matched reference (norm distance, ND) is visualized as a number. The task consists of lowering the ND, which was updated after every stride. Prior to the tests in patients the in-house developed FB implementation was tested in healthy subjects with an artificial movement task.
Results: Four of five study participants benefited from FB in the short and medium term. Decrease of mean ND was highest during the first 3 sessions (from 3.93 ± 1.54 to 2.18 ± 1.04). After the pause mean ND stayed in the same range than before. In the last 3 sessions the mean ND decreased slower (2.40 ± 1.18 to 2.20 ± 0.90). Direct influences of FB ranged from 60 to 15% of reduction in mean ND compared to initial gait analysis and from 20 to 1% compared to no-FB sessions.
Conclusions: Instrumented kinematic real-time FB may serve as an effective adjunct to established gait therapies in normalizing the gait pattern after incomplete spinal cord injury. Further studies with larger patient groups need to prove long term learning and the successful transfer of newly acquired skills to activities of daily living.
PMCID: PMC4060051  PMID: 24987344
spinal cord injury; visual realtime feedback; proprioception; gait rehabilitation; treadmill; motion analysis; motor learning
7.  Elucidating the Regulon of Multidrug Resistance Regulator RarA in Klebsiella pneumoniae 
RarA is an AraC-type regulator in Klebsiella pneumoniae, which, when overexpressed, confers a low-level multidrug-resistant (MDR) phenotype linked to the upregulation of both the acrAB and oqxAB efflux genes. Increased rarA expression has also been shown to be integral in the development of tigecycline resistance in the absence of ramA in K. pneumoniae. Given its phenotypic role in MDR, microarray analyses were performed to determine the RarA regulon. Transcriptome analysis was undertaken using strains Ecl8ΔrarA/pACrarA-2 (rarA-expressing construct) and Ecl8ΔrarA/pACYC184 (vector-only control) using bespoke microarray slides consisting of probes derived from the genomic sequences of K. pneumoniae MGH 78578 (NC_009648.1) and Kp342 (NC_011283.1). Our results show that rarA overexpression resulted in the differential expression of 66 genes (42 upregulated and 24 downregulated). Under the COG (clusters of orthologous groups) functional classification, the majority of affected genes belonged to the category of cell envelope biogenesis and posttranslational modification, along with genes encoding the previously uncharacterized transport proteins (e.g., KPN_03141, sdaCB, and leuE) and the porin OmpF. However, genes associated with energy production and conversion and amino acid transport/metabolism (e.g., nuoA, narJ, and proWX) were found to be downregulated. Biolog phenotype analyses demonstrated that rarA overexpression confers enhanced growth of the overexpresser in the presence of several antibiotic classes (i.e., beta-lactams and fluoroquinolones), the antifungal/antiprotozoal compound clioquinol, disinfectants (8-hydroxyquinoline), protein synthesis inhibitors (i.e., minocycline and puromycin), membrane biogenesis agents (polymyxin B and amitriptyline), DNA synthesis (furaltadone), and the cytokinesis inhibitor (sanguinarine). Both our transcriptome and phenotypic microarray data support and extend the role of RarA in the MDR phenotype of K. pneumoniae.
PMCID: PMC3623357  PMID: 23318802
8.  Implementation phase of a multicentre prehospital telemedicine system to support paramedics: feasibility and possible limitations 
Legal regulations often limit the medical care that paramedics can provide. Telemedical solutions could overcome these limitations by remotely providing expert support. Therefore, a mobile telemedicine system to support paramedics was developed. During the implementation phase of this system in four German emergency medical services (EMS), the feasibility and possible limitations of this system were evaluated.
After obtaining ethical approval and providing a structured training program for all medical professionals, the system was implemented on three paramedic-staffed ambulances on August 1st, 2012. Two more ambulances were included subsequently during this month. The paramedics could initiate a consultation with EMS physicians at a teleconsultation centre. Telemedical functionalities included audio communication, real-time vital data transmission, 12-lead electrocardiogram, picture transmission on demand, and video streaming from a camera embedded into the ceiling of each ambulance. After each consultation, telephone-based debriefings were conducted. Data were retrieved from the documentation protocols of the teleconsultation centre and the EMS.
During a one month period, teleconsultations were conducted during 35 (11.8%) of 296 emergency missions with a mean duration of 24.9 min (SD 12.5). Trauma, acute coronary syndromes, and circulatory emergencies represented 20 (57%) of the consultation cases. Diagnostic support was provided in 34 (97%) cases, and the administration of 50 individual medications, including opioids, was delegated by the teleconsultation centre to the paramedics in 21 (60%) missions (range: 1–7 per mission). No medical complications or negative interpersonal effects were reported. All applications functioned as expected except in one case in which the connection failed due to the lack of a viable mobile network.
The feasibility of the telemedical approach was demonstrated. Teleconsultation enabled early initiation of treatments by paramedics operating under the real-time medical direction. Teleconsultation can be used to provide advanced care until the patient is under a physician’s care; moreover, it can be used to support the paramedics who work alone to provide treatment in non-life-threatening cases. Non-availability of mobile networks may be a relevant limitation. A larger prospective controlled trial is needed to evaluate the rate of complications and outcome effects.
PMCID: PMC3710491  PMID: 23844941
Telemedicine; Teleconsultation; Telepresence; Emergency medical service; Analgesia
9.  Genome Sequence of Klebsiella pneumoniae Ecl8, a Reference Strain for Targeted Genetic Manipulation 
Genome Announcements  2013;1(1):e00027-12.
We report the genome sequence of Klebsiella pneumoniae subsp. pneumoniae Ecl8, a spontaneous streptomycin-resistant mutant of strain ECL4, derived from NCIB 418. K. pneumoniae Ecl8 has been shown to be genetically tractable for targeted gene deletion strategies and so provides a platform for in-depth analyses of this species.
PMCID: PMC3569361  PMID: 23405357
10.  Tigecycline challenge triggers sRNA production in Salmonella enterica serovar Typhimurium 
BMC Microbiology  2012;12:195.
Bacteria employ complex transcriptional networks involving multiple genes in response to stress, which is not limited to gene and protein networks but now includes small RNAs (sRNAs). These regulatory RNA molecules are increasingly shown to be able to initiate regulatory cascades and modulate the expression of multiple genes that are involved in or required for survival under environmental challenge. Despite mounting evidence for the importance of sRNAs in stress response, their role upon antibiotic exposure remains unknown. In this study, we sought to determine firstly, whether differential expression of sRNAs occurs upon antibiotic exposure and secondly, whether these sRNAs could be attributed to microbial tolerance to antibiotics.
A small scale sRNA cloning strategy of Salmonella enterica serovar Typhimurium SL1344 challenged with half the minimal inhibitory concentration of tigecycline identified four sRNAs (sYJ5, sYJ20, sYJ75 and sYJ118) which were reproducibly upregulated in the presence of either tigecycline or tetracycline. The coding sequences of the four sRNAs were found to be conserved across a number of species. Genome analysis found that sYJ5 and sYJ118 mapped between the 16S and 23S rRNA encoding genes. sYJ20 (also known as SroA) is encoded upstream of the tbpAyabKyabJ operon and is classed as a riboswitch, whilst its role in antibiotic stress-response appears independent of its riboswitch function. sYJ75 is encoded between genes that are involved in enterobactin transport and metabolism. Additionally we find that the genetic deletion of sYJ20 rendered a reduced viability phenotype in the presence of tigecycline, which was recovered when complemented. The upregulation of some of these sRNAs were also observed when S. Typhimurium was challenged by ampicillin (sYJ5, 75 and 118); or when Klebsiella pneumoniae was challenged by tigecycline (sYJ20 and 118).
Small RNAs are overexpressed as a result of antibiotic exposure in S. Typhimurium where the same molecules are upregulated in a related species or after exposure to different antibiotics. sYJ20, a riboswitch, appears to possess a trans-regulatory sRNA role in antibiotic tolerance. These findings imply that the sRNA mediated response is a component of the bacterial response to antibiotic challenge.
PMCID: PMC3511261  PMID: 22958399
11.  Tigecycline Resistance Can Occur Independently of the ramA Gene in Klebsiella pneumoniae 
Tigecycline resistance in Klebsiella pneumoniae results from ramA upregulation that causes the overexpression of the efflux pump, AcrAB-TolC. Tigecycline mutants, derived from Ecl8ΔramA, can exhibit a multidrug resistance phenotype due to increased transcription of the marA, rarA, acrAB, and oqxAB genes. These findings support the idea that tigecycline or multidrug resistance in K. pneumoniae, first, is not solely dependent on the ramA gene, and second, can arise via alternative regulatory pathways in K. pneumoniae.
PMCID: PMC3421586  PMID: 22644034
12.  Characterization of RarA, a Novel AraC Family Multidrug Resistance Regulator in Klebsiella pneumoniae 
Transcriptional regulators, such as SoxS, RamA, MarA, and Rob, which upregulate the AcrAB efflux pump, have been shown to be associated with multidrug resistance in clinically relevant Gram-negative bacteria. In addition to the multidrug resistance phenotype, these regulators have also been shown to play a role in the cellular metabolism and possibly the virulence potential of microbial cells. As such, the increased expression of these proteins is likely to cause pleiotropic phenotypes. Klebsiella pneumoniae is a major nosocomial pathogen which can express the SoxS, MarA, Rob, and RamA proteins, and the accompanying paper shows that the increased transcription of ramA is associated with tigecycline resistance (M. Veleba and T. Schneiders, Antimicrob. Agents Chemother. 56:4466–4467, 2012). Bioinformatic analyses of the available Klebsiella genome sequences show that an additional AraC-type regulator is encoded chromosomally. In this work, we characterize this novel AraC-type regulator, hereby called RarA (Regulator of antibiotic resistance A), which is encoded in K. pneumoniae, Enterobacter sp. 638, Serratia proteamaculans 568, and Enterobacter cloacae. We show that the overexpression of rarA results in a multidrug resistance phenotype which requires a functional AcrAB efflux pump but is independent of the other AraC regulators. Quantitative real-time PCR experiments show that rarA (MGH 78578 KPN_02968) and its neighboring efflux pump operon oqxAB (KPN_02969_02970) are consistently upregulated in clinical isolates collected from various geographical locations (Chile, Turkey, and Germany). Our results suggest that rarA overexpression upregulates the oqxAB efflux pump. Additionally, it appears that oqxR, encoding a GntR-type regulator adjacent to the oqxAB operon, is able to downregulate the expression of the oqxAB efflux pump, where OqxR complementation resulted in reductions to olaquindox MICs.
PMCID: PMC3421627  PMID: 22644028
13.  Surface modification of implants in long bone 
Biomatter  2012;2(3):149-157.
Coatings of orthopedic implants are investigated to improve the osteoinductive and osteoconductive properties of the implant surfaces and thus to enhance periimplant bone formation. By applying coatings that mimic the extracellular matrix a favorable environment for osteoblasts, osteoclasts and their progenitor cells is provided to promote early and strong fixation of implants. It is known that the early bone ongrowth increases primary implant fixation and reduces the risk of implant failure. This review presents an overview of coating titanium and hydroxyapatite implants with components of the extracellular matrix like collagen type I, chondroitin sulfate and RGD peptide in different small and large animal models. The influence of these components on cells, the inflammation process, new bone formation and bone/implant contact is summarized.
PMCID: PMC3549868  PMID: 23507866
RGD peptide; bone healing; chondroitin sulfate; collagen type I; hyaluronic acid; hydroxyapatite; implants; titanium
14.  Embroidered and surface coated polycaprolactone-co-lactide scaffolds 
Biomatter  2012;2(3):158-165.
Tissue engineering and regenerative techniques targeting bone include a broad range of strategies and approaches to repair, augment, replace or regenerate bone tissue. Investigations that are aimed at optimization of these strategies until clinical translation require control of systemic factors as well as modification of a broad range of key parameters.
This article reviews a possible strategy using a tissue engineering approach and systematically describes a series of experiments evaluating the properties of an embroidered and surface coated polycaprolactone-co-lactide scaffold being considered as bone graft substitute for large bone defects. The scaffold design and fabrication, the scaffolds properties, as well as its surface modification and their influence in vitro are evaluated, followed by in vivo analysis of the scaffolds using orthotopic implantation models in small and large animals.
PMCID: PMC3549869  PMID: 23507867
bone substitute; tissue engineering; scaffold; polycaprolactone-co-lactide; collagen type I; chondroitin sulfate; critical size defect; nude rat; sheep
16.  The impact of auditory working memory training on the fronto-parietal working memory network 
Working memory training has been widely used to investigate working memory processes. We have shown previously that visual working memory benefits only from intra-modal visual but not from across-modal auditory working memory training. In the present functional magnetic resonance imaging study we examined whether auditory working memory processes can also be trained specifically and which training-induced activation changes accompany theses effects. It was investigated whether working memory training with strongly distinct auditory materials transfers exclusively to an auditory (intra-modal) working memory task or whether it generalizes to a (across-modal) visual working memory task. We used adaptive n-back training with tonal sequences and a passive control condition. The memory training led to a reliable training gain. Transfer effects were found for the (intra-modal) auditory but not for the (across-modal) visual transfer task. Training-induced activation decreases in the auditory transfer task were found in two regions in the right inferior frontal gyrus. These effects confirm our previous findings in the visual modality and extents intra-modal effects in the prefrontal cortex to the auditory modality. As the right inferior frontal gyrus is frequently found in maintaining modality-specific auditory information, these results might reflect increased neural efficiency in auditory working memory processes. Furthermore, task-unspecific (amodal) activation decreases in the visual and auditory transfer task were found in the right inferior parietal lobule and the superior portion of the right middle frontal gyrus reflecting less demand on general attentional control processes. These data are in good agreement with amodal activation decreases within the same brain regions on a visual transfer task reported previously.
PMCID: PMC3373207  PMID: 22701418
auditory; n-back task; training; visual; working memory; plasticity; fMRI
17.  Genetic regulation of the ramA locus and its expression in clinical isolates of Klebsiella pneumoniae 
Tigecycline resistance has been attributed to ramA overexpression and subsequent acrA upregulation. The ramA locus, originally identified in Klebsiella pneumoniae, has homologues in Enterobacter and Salmonella spp. In this study, we identify in silico that the ramR binding site is also present in Citrobacter spp. and that Enterobacter, Citrobacter and Klebsiella spp. share key regulatory elements in the control of the romA–ramA locus. RACE (rapid amplification of cDNA ends) mapping indicated that there are two promoters from which romA–ramA expression can be regulated in K. pneumoniae. Correspondingly, electrophoretic binding studies clearly showed that purified RamA and RamR proteins bind to both of these promoters. Hence, there appear to be two RamR binding sites within the Klebsiella romA–ramA locus. Like MarA, RamA binds the promoter region, implying that it might be subject to autoregulation. We have identified changes within ramR in geographically distinct clinical isolates of K. pneumoniae. Intriguingly, levels of romA and ramA expression were not uniformly affected by changes within the ramR gene, thereby supporting the dual promoter finding. Furthermore, a subset of strains sustained no changes within the ramR gene but which still overexpressed the romA–ramA genes, strongly suggesting that a secondary regulator may control ramA expression.
PMCID: PMC3117140  PMID: 21514798
Klebsiella pneumoniae; romA; ramA; ramR; acrA; Tigecycline
18.  In Vivo Selection of a Missense Mutation in adeR and Conversion of the Novel blaOXA-164 Gene into blaOXA-58 in Carbapenem-Resistant Acinetobacter baumannii Isolates from a Hospitalized Patient▿  
Antimicrobial Agents and Chemotherapy  2010;54(12):5021-5027.
The mechanism of stepwise acquired multidrug resistance in Acinetobacter baumannii isolates from a hospitalized patient was investigated. Thirteen consecutive multidrug-resistant isolates were recovered from the same patient over a 2-month period. The Vitek 2 system identified the isolates as meropenem-sensitive Acinetobacter lwoffii; however, molecular identification showed that the isolates were A. baumannii. Etest revealed that the isolates were meropenem resistant. The presence of oxacillinase (OXA)-type enzymes were investigated by sequencing. The clonal relatedness of isolates was assessed by pulsed-field gel electrophoresis (PFGE). Expression of the genes encoding the efflux pumps AdeB and AdeJ was performed by semiquantitative real-time reverse transcription-PCR (qRT-PCR). The adeRS two-component system was sequenced. All isolates had identical PFGE fingerprints, suggesting clonal identity. The first six isolates were positive for the novel blaOXA-164 gene. The following seven isolates, recovered after treatment with a combination of meropenem, amikacin, ciprofloxacin, and co-trimoxazole showed an increase of >7-fold in adeB mRNA transcripts and a missense mutation in blaOXA-164, converting it to blaOXA-58. Sequencing revealed a novel mutation in adeR. These data illustrate how A. baumannii can adapt during antimicrobial therapy, leading to increased antimicrobial resistance.
PMCID: PMC2981280  PMID: 20921306
The Functional Movement ScreenTM (FMSTM) is a screening instrument which evaluates selective fundamental movement patterns to determine potential injury risk. However, despite its global use, there are currently no normative values available for the FMSTM.
To establish normative values for the FMSTM in a population of active, healthy individuals. Secondary aims were to investigate whether performance differed between males and females, between those with and without a previous history of injury, and to establish real-time inter-rater reliability of the FMSTM.
Two hundred and nine (108 females and 101 males) physically active individuals, aged between 18 and 40 years, with no recent (<6 weeks) history of musculoskeletal injury were recruited. All participants performed the FMSTM and were scored using the previously established standardized FMSTM criteria. A representative sub-group participant sample (28%) determined inter rater reliability.
The mean composite FMSTM score was 15.7 with a 95% confidence interval between 15.4 and 15.9 out of a possible total of 21. There was no statistically significant difference in scores between females and males (t207 = .979, p = .329), or those who reported a previous injury and those who did not (t207 = .688, p= .492). Inter-rater reliability (ICC3,1) for the composite FMSTM score was .971, demonstrating excellent reliability. Inter-rater reliability (Kappa) for individual test components of the FMSTM demonstrated substantial to excellent agreement (0.70 — 1.0).
Discussion and Conclusion:
This cross-sectional study provides FMSTM reference values for young, active individuals, which will assist in the interpretation of individual scores when screening athletes for musculoskeletal injury and performance factors.
PMCID: PMC3109893  PMID: 21713227
Pre-participation screening; Functional Movement ScreenTM; injury risk; athletic performance
20.  Compromized geranylgeranylation of RhoA and Rac1 in mevalonate kinase deficiency 
Mevalonate kinase deficiency (MKD) is an autoinflammatory disorder caused by mutations in the MVK gene resulting in decreased activity of the enzyme mevalonate kinase (MK). Although MK is required for biosynthesis of all isoprenoids, in MKD, in particular, the timely synthesis of geranylgeranyl pyrophosphate appears to be compromised. Because small guanosine triphosphatases (GTPases) depend on geranylgeranylation for their proper signaling function, we studied the effect of MK deficiency on geranylgeranylation and activation of the two small GTPases, RhoA and Rac1. We demonstrate that both geranylgeranylation and activation of the two GTPases are more easily disturbed in MKD cells than in control cells when the flux though the isoprenoid biosynthesis pathway is suppressed by low concentrations of simvastatin. The limited capacity of geranylgeranylation in MKD cells readily leads to markedly increased levels of nonisoprenylated and activated GTPases, which will affect proper signaling by these GTPases.
PMCID: PMC2946549  PMID: 20814828
21.  Association of ground hardness with injuries in rugby union 
Ground hardness is considered one of the possible risk factors associated with rugby injuries.
To examine the contribution of ground hardness, rainfall and evapotranspiration to the incidence of injury, and to investigate seasonal injury bias throughout one full season of rugby union.
A prospective epidemiological study of rugby injuries was performed on 271 players from rugby union teams involved in the premier grade rugby competition in Dunedin, New Zealand. Ground hardness was measured before each match over 20 rounds with an industrial penetrometer, and local weather information was collected through the National Institute of Weather and Atmospheric Research and the Otago Regional Council. Poisson mixed models were used to describe injury incidence as a function of ground hardness throughout the season.
The overall injury incidence during the season was 52 injuries per 1000 match player‐hours (95% CI 42 to 65). Although injury incidence decreased gradually by round with a rate ratio of 0.98 (95% CI 0.96 to 0.99) (p = 0.036), and the hardness of match grounds decreased significantly over the season (0.16 MPa/round, 95% CI 0.12 to 0.21, p<0.001), a non‐significant association was demonstrated between injury incidence and ground hardness. Injury incidence was not associated with a combination of ground hardness, rainfall and evapotranspiration on the day of the match or cumulative rainfall and evapotranspiration before each match.
Seasonal change in ground hardness and an early‐season bias of injuries was demonstrated. Although the contribution of ground hardness to injury incidence was not statistically significant, match round and injury incidence were highly correlated, confirming a seasonal bias, which may confound the relationship of injury to ground condition.
PMCID: PMC2465405  PMID: 17504786
rugby injuries; injury incidence; ground hardness; rainfall; evapotranspiration
22.  High-Throughput Detection of Induced Mutations and Natural Variation Using KeyPoint™ Technology 
PLoS ONE  2009;4(3):e4761.
Reverse genetics approaches rely on the detection of sequence alterations in target genes to identify allelic variants among mutant or natural populations. Current (pre-) screening methods such as TILLING and EcoTILLING are based on the detection of single base mismatches in heteroduplexes using endonucleases such as CEL 1. However, there are drawbacks in the use of endonucleases due to their relatively poor cleavage efficiency and exonuclease activity. Moreover, pre-screening methods do not reveal information about the nature of sequence changes and their possible impact on gene function. We present KeyPoint™ technology, a high-throughput mutation/polymorphism discovery technique based on massive parallel sequencing of target genes amplified from mutant or natural populations. KeyPoint combines multi-dimensional pooling of large numbers of individual DNA samples and the use of sample identification tags (“sample barcoding”) with next-generation sequencing technology. We show the power of KeyPoint by identifying two mutants in the tomato eIF4E gene based on screening more than 3000 M2 families in a single GS FLX sequencing run, and discovery of six haplotypes of tomato eIF4E gene by re-sequencing three amplicons in a subset of 92 tomato lines from the EU-SOL core collection. We propose KeyPoint technology as a broadly applicable amplicon sequencing approach to screen mutant populations or germplasm collections for identification of (novel) allelic variation in a high-throughput fashion.
PMCID: PMC2654077  PMID: 19283079
24.  Poly[ethano­lbis(μ3-2-thio­xo-1,2-dihydro­pyridin-1-olato)dilithium(I)] 
The title compound, [Li2(C5H4NOS)2(C2H6O)]n, having two formula units in the asymmetric unit, forms infinite chains of Li2O2 rhombi along b, consisting of four independent Li and O atoms. Metal binding to 2-thio­oxo-1,2-dihydro­pyridin-1-olate occurs in a bidentate fashion via O and S, and in a monodentate manner via the N-oxide O atom. π–π Inter­actions between polymeric chains are evident from centroid-to-centroid distances of pyridine­thione fragments of 3.461 (6)–3.607 (6) Å. The N—O and C—S bond lengths are distinctively different from those in hitherto investigated NiII, ZnII and (H3C)2TlIII complexes of 2-thio­oxo-1,2-dihydro­pyridin-1-olate, but correlate with those reported for 1-hydr­oxy- and 1-alkoxy­pyridine-2(1H)-thio­nes in the solid state.
PMCID: PMC2960834  PMID: 21201855
25.  Complexity Reduction of Polymorphic Sequences (CRoPS™): A Novel Approach for Large-Scale Polymorphism Discovery in Complex Genomes 
PLoS ONE  2007;2(11):e1172.
Application of single nucleotide polymorphisms (SNPs) is revolutionizing human bio-medical research. However, discovery of polymorphisms in low polymorphic species is still a challenging and costly endeavor, despite widespread availability of Sanger sequencing technology. We present CRoPS™ as a novel approach for polymorphism discovery by combining the power of reproducible genome complexity reduction of AFLP® with Genome Sequencer (GS) 20/GS FLX next-generation sequencing technology. With CRoPS, hundreds-of-thousands of sequence reads derived from complexity-reduced genome sequences of two or more samples are processed and mined for SNPs using a fully-automated bioinformatics pipeline. We show that over 75% of putative maize SNPs discovered using CRoPS are successfully converted to SNPWave® assays, confirming them to be true SNPs derived from unique (single-copy) genome sequences. By using CRoPS, polymorphism discovery will become affordable in organisms with high levels of repetitive DNA in the genome and/or low levels of polymorphism in the (breeding) germplasm without the need for prior sequence information.
PMCID: PMC2048665  PMID: 18000544

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