Our system could be developed as a potential model for studying the effects of HIV and highly active antiretroviral therapy (HAART) in vitro. “
“The emergence of HIV drug resistance is a crucial issue in Africa, where second-line antiretroviral therapy

(ART) is limited, expensive and complex. We assessed the association between adherence patterns and resistance emergence over time, using an adherence measure that distinguishes low adherence from treatment interruptions, in rural Cameroon. We performed a cohort study among patients receiving nonnucleoside reverse transcriptase inhibitor (NNRTI)-based ART in nine district hospitals, using data from the Stratall trial MEK inhibitor (2006−2010). Genotypic mutations associated with antiretroviral drug resistance were assessed when 6-monthly HIV viral loads were > 5000

HIV-1 RNA copies/mL. ART adherence AZD2281 ic50 data were collected using face-to-face questionnaires. Combined indicators of early (1−3 months) and late (6 months to t − 1; t is the time point when the resistance had been detected) adherence were constructed. Multivariate logistic regression and Cox models were used to assess the association between adherence patterns and early (at 6 months) and late (after 6 months) resistance emergence, respectively. Among 456 participants (71% women; median age 37 years), 45 developed HIV drug resistance (18 early and 27 late). Early low adherence (< 80%) and treatment interruptions (> 2 days) were associated with early resistance [adjusted odds ratio (95% confidence interval) 8.51 (1.30–55.61) and 5.25 (1.45–18.95), respectively]. Early treatment interruptions were also associated with late resistance [adjusted hazard ratio (95% confidence interval) 3.72 (1.27–10.92)]. The emergence of HIV drug resistance on first-line NNRTI-based regimens was associated with different

patterns of adherence over time. Ensuring optimal early adherence through specific interventions, adequate management of drug stocks, and viral load monitoring before is a clinical and public health priority in Africa. “
“The central goal of the HIV in Europe Initiative is to promote testing and treatment throughout Europe and Central Asia in order to decrease the number of people living with HIV presenting late for care. This article summarizes the results from the HIV in Europe 2009 Conference and the early results of the projects set up by the initiative, and discusses their implications for the future. In November 2009, 100 key stakeholders from 25 countries met in Stockholm at the HIV in Europe Conference. The focus was to address five key issues that contribute to the barriers to testing identified in 2007 at an innovative HIV conference. The conference discussed barriers to testing and other reasons for late presentation and outlined concrete recommendations to address the problem.

, 2003). BtkB may also be involved in the heat-shock response. After reaching the maximum density, btkB mutant began to decrease rapidly. The cellular reversal of M. xanthus gliding is regulated by chemotaxis homologues (Shi et al., 2000). btkB mutant cells reversed

direction selleck inhibitor approximately every 4.2 min on average, which was similar to that of wild-type cells (4.6 min). The wild-type and btkB mutant strains (9 × 109 cells mL−1) were cultured on CF agar. The wild-type cells moved to aggregation centers and then formed mound-shaped fruiting bodies by 48–72 h on CF agar. After 3 days of development, the wild-type strain had produced dark fruiting bodies containing refractile sonication- and heat-resistant spores, while the btkB mutant strain had produced I-BET-762 datasheet only translucent aggregates that were not

filled with refractile spores (Fig. 5a). The btkB mutant cells formed fruiting bodies about 24 h later than the wild-type strain. The viable spore numbers produced by the mutant at 4 and 5 days were approximately 20–30% those of the wild-type strain; however, the final yield of viable spores for btkB mutant at 7 days was similar to that of the wild-type strain (Fig. 5b). Gram-positive type of M. xanthus BY kinase, BtkA, is required for the formation of mature spores (Kimura et al., 2011), while BtkB is not essential to form mature spores. The btkB mutant produced a high level of yellow pigment during fruiting body formation (data not shown). The fruiting bodies of btkB mutant were harvested by gently scraping the surface with a bacteria spreader and were suspended in TM buffer. After centrifugation, the supernatant had a UV absorption maximum of 380 nm. This is in agreement with the major yellow pigment, DKxanthene-534, of M. xanthus DK1622 (λmax = 379 nm),

which is essential for developmental sporulation (Meiser et al., 2006). On the other hand, when vegetative cells were cultured with 0.5 M glycerol in CYE medium, the mutant cells sporulated at the same rate as wild-type cells Glutathione peroxidase (data not shown). EPS is an important component for social behaviors in M. xanthus, including gliding motility and fruiting body formation. EPS is the binding target for type IV pili in S-motility (Li et al., 2003) and forms a scaffold within the fruiting body structure (Shimkets, 1986; Lux et al., 2004). EPS production was analyzed quantitatively by the binding of Congo red and trypan blue. Exponentially growing cells (8 × 108 cells mL−1) in CYE medium were used for the assays, and the percentage of dye bound by cells was determined. btkB mutant cells bound Congo red and trypan blue at lower levels than wild-type cells. The btkB mutant bound 23.8 ± 0.2% and 7.1 ± 1.3% of Congo red and trypan blue, respectively, compared with 40.3 ± 0.1% and 29.8 ± 0.3% for the wild type. We also determined the amount of EPS from broken cell pellets. As shown in Fig.

The rationale for this approach includes avoiding adverse pharmacokinetic and pharmacodynamic interactions between ART and chemotherapy and the theoretical concern that PIs may inhibit

lymphocyte apoptosis and thus contribute to chemoresistance of lymphomas [63]. Although no new HIV mutations were identified, these studies were small and ART was promptly reinstituted after abbreviated chemotherapy. Nevertheless, it took 12–18 months after completing chemotherapy for plasma HIV viraemia to become undetectable in many patients [61]. Importantly, patients with NHL frequently present with CD4 cell counts <200 cells/μL and thus the reduction in CD4 cell count associated with systemic chemotherapy and structured suspension of Androgen Receptor Antagonist datasheet ART is not ideal. We suggest starting

ART in HIV-positive patients with cervical cancer (2C). We recommend starting ART in HIV-positive patients who are commencing radiotherapy or chemotherapy for cervical cancer (1D). There is less clear evidence to support see more starting ART in women diagnosed with invasive cervical cancer, despite its status as an AIDS-defining illness. Co-registration studies have shown that ART has not reduced the incidence of cervical cancer [64-66], moreover the effects of ART on pre-invasive cervical dysplasia have been variable with some studies suggesting that ART causes regression of cervical intraepithelial neoplasia [67-73] and others showing no beneficial effect of ART [74-77]. The effects of ART on outcomes in HIV-positive women with invasive

cervical cancer have not been reported but analogies with anal cancer may be drawn as the malignancies share common pathogenesis and treatment modalities. Combined chemoradiotherapy in anal cancer has been shown to cause Bumetanide significant and prolonged CD4 suppression even when ART is administered concomitantly [78-81]. Similarly the toxicity of chemoradiotherapy for HIV-associated anal cancer appears to be less profound among patients given ART compared to historical controls [79, 80, 82-87]. We suggest starting ART in HIV-positive patients with non-AIDS-defining malignancies (2C). We recommend starting ART in HIV-positive patients who are commencing immunosuppressive radiotherapy or chemotherapy for non-AIDS-defining malignancies (1C). While ART has little effect on the incidence of NADMs [33, 88-95] and there is no evidence that ART alone causes regression of NADMs, the immunosuppressive effects of both chemotherapy [35, 57-59] and radiotherapy [78-81] may justify starting ART in HIV-positive individuals who are commencing systemic anticancer therapy or radiotherapy. We recommend that potential pharmacokinetic interactions between ARVs and systemic anticancer therapy are checked before administration (with tools such as: http://www.hiv-druginteractions.org) (GPP).

However, many amacrine types have not been studied systematically because, in particular, amacrine cells with large dendritic fields, i.e. wide-field amacrine cells, have a low abundance and are therefore difficult to target. Here, we used a transgenic mouse line expressing the coding sequence of enhanced green fluorescent protein under the promoter for choline acetyltransferase (ChAT-EGFP mouse) and characterized a single wide-field amacrine

cell population monostratifying in layer 2/3 of the inner plexiform layer (WA-S2/3 cell). Somata of WA-S2/3 cells are located either in the inner nuclear layer or are displaced to the ganglion cell layer and exhibit a low cell density. Using immunohistochemistry, we show that WA-S2/3 cells are presumably GABAergic but may also release acetylcholine as their somata are weakly positive for ChAT. Two-photon-guided patch-clamp Epigenetic signaling inhibitors recordings from intact retinas revealed WA-S2/3 cells to be ON-OFF cells with a homogenous receptive field even larger than the dendritic field. The large spatial extent of the receptive field is most likely due to the extensive homologous and heterologous coupling among WA-S2/3 cells and to other amacrine cells, respectively, as

indicated by tracer injections. In summary, we have characterized a novel type of GABAergic ON-OFF wide-field amacrine cell which is ideally suited to providing long-range inhibition to ganglion cells due to its strong coupling. “
“Pain in infancy influences pain reactivity in later life, but how and why this occurs is poorly understood. Afatinib Here we review the evidence for developmental plasticity of nociceptive pathways in animal models and discuss the peripheral and central mechanisms that underlie this plasticity. Adults who have experienced neonatal injury display increased pain and injury-induced hyperalgesia in the affected region but mild injury can also induce widespread baseline hyposensitivity across the rest of the body surface, suggesting the involvement of several underlying mechanisms, depending upon the

type of early life experience. Peripheral nerve sprouting and dorsal horn central sensitization, disinhibition and neuroimmune priming are discussed in relation to the increased pain and hyperalgesia, while altered descending pain control Rucaparib ic50 systems driven, in part, by changes in the stress/HPA axis are discussed in relation to the widespread hypoalgesia. Finally, it is proposed that the endocannabinoid system deserves further attention in the search for mechanisms underlying injury-induced changes in pain processing in infants and children. “
“We investigated the sensitivity of visual mismatch negativity (vMMN) to an abstract and non-semantic category, vertical mirror symmetry. Event-related potentials (ERPs) elicited by random and symmetric square patterns, delivered in passive oddball paradigm (participants played a video game), were recorded.

In humans, general wellbeing is closely related to pain perception, which also makes it necessary in rodents to consider modulators as well as readouts of overall wellbeing. Optimizing this website the above parameters in study design and the new developments that are forthcoming to test the affective motivational components of pain hold promise in solving inconsistencies across studies and improving their broad applicability in translational research. In this review, we critically discuss a variety of behavioral tests that have been developed and reported in recent years, attempt to weigh their benefits and potential limitations, and discuss

key requirements and challenges that lie ahead in measuring ongoing pain in rodent models. “
“Ischemic stroke is currently treated with thrombolytic therapy with a drawback to induce hemorrhagic

transformation (HT) if applied beyond its relatively narrow treatment time window. The present study was designed to examine the role of IMM-H004, a derivative of coumarin, in recombinant tissue plasminogen activator (tPA)-induced HT. Rats subjected to 6 h of thromboembolic occlusion or middle cerebral artery occlusion received tPA with or without IMM-H004. Delayed tPA intervention drastically increased the risk of HT and exaggerated the ischemic injury. To assess the effect of IMM-H004 on delayed treatment of tPA-induced toxicity after ischemia and reperfusion, various approaches were used, including a behavior test, TTC-staining, determination of cerebral hemorrhage, Mitomycin C chemical structure laser speckle imaging, Western blot, gelatin zymogram, immunohistochemistry and immunofluorescence staining. Experiments were also conducted in vitro in human brain microvascular endothelial cells (HBMECs) and PC12

cells to explore the mechanism for the role of IMM-H004. Combination therapy of tPA and IMM-H004 prevented the development of HT, and reduced the mortality rate, infarct volume and brain edema. IMM-H004 also exerted a protective role by decreasing matrix metalloproteinases, the co-localization of matrix metalloproteinase-2 with astrocytes and increasing occludin. Experiments in HBMECs and PC12 revealed an elevation in ATP level and a protein kinase A- and PI3K-dependent activation of Akt by IMM-H004 after tPA administration. These results suggest IMM-H004 as a promising Progesterone adjuvant to alleviate the detrimental side effects of tPA in clinical therapy of ischemic stroke, and contribute to better understand the mechanism for the beneficial role of this novel remedy. “
“The serotonin-1A (5-HT1A) receptor functions as a pre-synaptic autoreceptor in serotonin neurons that regulates their activity, and is also widely expressed on non-serotonergic neurons as a post-synaptic heteroreceptor to mediate serotonin action. The 5-HT1A receptor gene is strongly repressed by a dual repressor element (DRE), which is recognized by two proteins: Freud-1/CC2D1A and another unknown protein.

difficile isolated from humans and

animals (Arroyo et al., 2005; Rodriguez-Palacios et al., 2007a; Rupnik, 2007), it is not yet clearly determined whether animals could serve as a significant source for human infection. Therefore, finding the original shedding source of C. difficile remains a pressing clinical quest. Birds are a remarkable biological phenomenon and have been a crucial epizootiological factor for transmission of viable pathogens over long geographic distances. Migratory birds are responsible for the wide geographic distribution of viruses (Eastern equine encephalitis virus, West Nile virus, Influenza A, Newcastle disease virus), bacteria (Anaplasma phagocytophilum, Borrelia burgdorferi, Campylobacter jejuni, Pasteurella multocida, Clostridium botulinum, Mycobacterium avium), as well as protozoa and parasites (Hubálek, 2004). During congregation of birds at their migration destinations, horizontal transmission of pathogens can occur between SGI-1776 mw individuals

and between species. In such instances, the transmission of C. difficile to uninfected populations, including humans, is possible. The aims of the present study were to determine whether wild migrating passerine birds in Europe (1) have Selleckchem PFT�� C. difficile in their feces, and, if so, (2) to determine genotypes of C. difficile colonizing their intestinal system. Ringing and sampling of wild living passerine birds was conducted in August 2009 and 2010 at the bird ringing station near Vrhnika town (45°46′N, 14°18′E) in the central part of Slovenia. All sampled Paclitaxel supplier birds were captured with mist nets. They were placed in net bags/sacks in groups of 1–10 according to species. They were ringed, weighed, measured, and their age was determined. Captured birds were migrating passerines breeding in north and temperate regions of Europe and overwintering in Mediterranean and Africa. All birds (n=465) were sampled with special micro-applicators (Hygroplastic Corp.) to avoid cloacal damage. A total of 98 cloacal swabs were cultured individually; the remaining (n=367) samples were pooled according to the species and cultured in pools of up to 10 samples (Table 1). Cloacal

swabs were stored in an anaerobic environment no more than 3 h after collection and transported to the laboratory within 24 h. The samples were then inoculated into cyloserine–cefoxitin fructose enrichment broth (Oxoid, UK) supplemented with 0.1% sodium taurocholate (Sigma-Aldrich) for 7 days. Subsequently, 1 mL of inoculated broth from each sample/pool was mixed with an equal amount of ethanol and left at room temperature for 30 min. After the alcohol shock, the samples were inoculated onto standard selective medium enriched with cycloserine and cefoxitin (C. difficile agar base and C. difficile selective supplement; Oxoid) and incubated anaerobically at 37 °C for 2 days (Arroyo et al., 2005; Avbersek et al., 2009). Identification of isolates was based on morphological criteria and typical odor.

The database is a depository of complete information on: the chemical structure of peptides; target species; target object of cell; peptide antimicrobial/haemolytic/cytotoxic activities; and experimental conditions BIBF 1120 supplier at which activities were estimated. The dbaasp search page allows the user to search peptides according to their structural characteristics, complexity type (monomer,

dimer and two-peptide), source, synthesis type (ribosomal, nonribosomal and synthetic) and target species. The database prediction algorithm provides a tool for rational design of new antimicrobial peptides. dbaasp is accessible at http://www.biomedicine.org.ge/dbaasp/. “
“There is limited information on whether parasites

act as vectors to transmit bacteria in fish. In this trial, we used Ichthyophthirius multifiliis and fluorescent Edwardsiella ictaluri as a model to study the interaction between parasite, bacterium, and fish. The percentage (23–39%) of theronts fluorescing after exposure to E. ictaluri was significantly higher than control theronts (~ 6%) using flow cytometry. Theronts exposed to E. ictaluri at 4 × 107 CFU mL−1 showed a higher percentage (~ 60%) of fluorescent theronts compared to those (42%) exposed to 4 × 103 CFU mL−1 at 4 h. All tomonts (100%) carried the bacterium after exposure to E. ictaluri. buy Fluorouracil Edwardsiella ictaluri survived and replicated during tomont division. Confocal microscopy demonstrated that E. ictaluri was associated with the tomont surface. Among theronts released from tomonts exposed to E. ictaluri, 31–66% were observed with attached E. ictaluri. Sixty percent of fish exposed to theronts treated with 5 × 107E. ictaluri mL−1 were positive for E. ictaluri at 4 h as determined by qPCR or fluorescent microscopy. Fluorescent E. ictaluri were observed on trophonts in skin and gill wet mounts of dead fish. This study demonstrated that Ich could vector E. ictaluri to channel catfish. In aquaculture systems, fish rarely encounter

a single pathogen. Most often, fish are concomitantly infected by multiple disease agents (Shoemaker et al., 2008). Parasitism has been demonstrated to enhance bacterial invasion where parasitic injuries serve as portals of entry Pregnenolone (Buchmann & Lindenstrøm, 2002; Busch et al., 2003; Bandilla et al., 2006). Ahne (1985) reported that parasites Argulus foliaceus and Piscicola geometra served as mechanical vectors for spring viremia of carp virus (SVCV). Vijayan et al. (2005) reported that polychaete worms acted as vectors of white spot syndrome virus in the transmission of white spot disease to the shrimp Penaeus monodon. Cusack & Cone (1985) detected bacterial colonies on the surface of Gyrodactylus by scanning electron microscopy. However, they did not determine whether the bacteria were pathogenic to fish, and thus, the exact role of the bacteria was not clear.

In their study, young children had higher proportionate morbidity rates.4 Newman-Klee and colleagues stated that the similar incidence of morbidity in children and adults, as well as the mildness of the morbid episodes, challenges the view that it is unwise to travel with small children.5 We initiated a prospective study which aimed at (1) assessing the incidence rate of ailments in children and their parents or caregivers, further referred to as parents, traveling to (sub)tropical destinations, and (2) characterizing the types of ailments occurring and defining risk

factors for traveling children in comparison to their parents. This prospective observational study was conducted at the Travel Clinic check details of the Havenziekenhuis in Rotterdam, the Netherlands, from May to August 2010. Ethical clearance was granted by the ethics committee of the Erasmus Medical Centre, Rotterdam. Participants were included after written informed consent. Families visiting the Travel Clinic for pre-travel health advice and expat families receiving a medical checkup were eligible for inclusion. The inability to read and write in Dutch was considered an exclusion criterion. All participants received a standardized questionnaire, detailing 33 defined ailments.6 The forms were filled out prior to departure and weekly during their stay abroad. A parent filled out the questionnaires

of children with an age below 12 years. Participants who failed to return or complete their questionnaires were considered lost to follow-up. Ailments were graded semi-quantitatively as follows: Grade Celecoxib I (mild): In cases where an ailment did not affect daily routine. The ailment rates were expressed

www.selleckchem.com/products/PF-2341066.html as the number of ailments per personmonth of travel. Given the broad array of destinations, destinations were grouped by continent in Asia, Africa, and South and Central America (S/C America). Turkey was regarded as an Asian country. To evaluate ailments rate in relation to a specific destination, ailments were also grouped in dermatological disorders, respiratory disorders, diarrheal disorders, and systemic febrile illnesses. Statistical analysis was performed with GraphPad Prism software, version 5.03 (GraphPad software, Inc., San Diego, CA, USA). The Log-rank (Mantel–Cox) test was used for comparison of Kaplan–Meier survival curves. Ailment rates between the various age categories were compared with the Kruskal–Wallis (non-parametric ANOVA) test followed by Dunn’s multiple comparisons test. Relative risks were calculated using the Fisher’s exact test using Yate’s continuity correction. Of the 233 children and 104 parents participating, we excluded 12 children and 7 parents who changed their travel plans, traveled to a European country, or traveled after September 2010, leaving 221 children and 97 parents. In total 152 children (69%) and 47 parents (48%) returned their questionnaires. The general characteristics and travel demographics are shown in Table 1.

017) (Table 3). In addition, those making HRIPD visits had a higher likelihood of being seen by a physician (P<0.001). HRIPD visits also received more diagnostic tests (P<0.001), but fewer procedures (P=0.019). Notably, 15.5% of

HRIPD visits received HIV serology testing, which included testing based on clinical suspicion of HIV infection and/or testing based on potential occupational/nonoccupational exposure. HRIPD visits were also prescribed Vorinostat molecular weight more medications in the ED. The most frequently prescribed medications for HRIPD visits were antimicrobials (44.5%), of which 82.0% were antibiotics and 32.1% were antiretrovirals. Approximately one-seventh of HRIPD visits received antiretroviral prescriptions (Table 3). In terms of disposition, HRIPD visits had significantly longer durations of ED stay and a higher likelihood of hospital admission. Further analysis identified age, gender, race, insurance type, US region of ED, fever as RFV, and visits requiring

‘emergent/urgent’ care as also being associated with admission. Multivariate analysis adjusted for these covariates showed that HRIPD visits were 7.67 times more likely Palbociclib chemical structure to lead to hospitalization than non-HRIPD visits (Table 4). Even after excluding those HRIPD visits with HIV serology testing and without antiretroviral therapy being administered (i.e. visits of patients presumed to have been newly identified as HIV infected), HRIPD visits were still significantly more likely to result in hospitalization (OR 7.24). The temporal changes in ED utilization by HRIPD visits in the three study periods are summarized in Table 5. The proportion of HRIPD visits that required ‘emergent/urgent’ care increased significantly

with time (Table 5), as did the proportion of non-HRIPD visits requiring such care (48.5% in 1993–1996, 68.1% in 1997–2000, and 64.1% in 2001–2005; P<0.001). The wait time to be seen by a provider decreased from the second to the third period (P=0.003). The proportions of HRIPD visits seen by attending physicians or by registered nurses (RNs) and/or licensed practical nurses (LPNs) differed over the three periods of observation (P=0.023 and 0.033, respectively). From 1997 to 2005, the number of diagnostic tests that patients CYTH4 with HRIPD received, including complete blood count determinations, increased significantly. From 1993 to 2005, the proportion of HRIPD visits where patients were given intravenous fluids also differed with time. Notably, 12.2% of HRIPD visits only had HIV/AIDS as their ED discharge diagnosis. Among all HRIPD visits, a substantial proportion had infectious diseases (42.2%; 95% CI 33.1–51.2) as co-diagnoses. Of these infectious diseases, pneumonia (25.1%; 95% CI 16.7–33.5) and OIs (16.7%; 95% CI 10.5–22.9) were the most common co-diagnoses. HRIPD visits accounted for approximately half a million ED visits in the USA over the 13 years of observation.

Each growth condition was repeated once. Total RNA was extracted according to the protocol provided by Qiagen (RNeasy Mini Kit). For cell harvest, 2 volumes of RNAprotect Bacteria Reagent (Qiagen) were added to 1 volume bacterial culture and mixed vigorously. The solution was incubated at room temperature for 5 min and immediately centrifuged at 5000 g for 10 min. For cell lysis, the cell pellet was resuspended in a 10% aliquot of the initial

Selleck ICG-001 sample volume containing 1 mg mL−1 lysozyme in 10 mM Tris/HCl, 1 mM EDTA, pH 8.0, and incubated at room temperature for 20 min. Then, 1.8 mL RLT buffer (Qiagen) containing 1% (v/v) β-mercaptoethanol was added and mixed intensively, APO866 research buy followed by the addition of 1.2 mL ethanol.

The RNA solution was purified using the RNeasy Mini Kit, by applying the total volume stepwise to one column. On-column DNase digestion was performed twice for 20 min to ensure the complete removal of genomic DNA. RNA integrity and purity were checked by agarose gel electrophoresis. cDNA synthesis was performed from about 10 μg total RNA with a statistically distributed mixture of hexanucleotides as primers (random priming) using SuperscriptII (Invitrogen) reverse transcriptase according to the manufacturer’s protocols. An aliquot of 25 μg cDNA was sequenced using the Genome Analyzer II at GATC Biotech AG (Konstanz). For this, the cDNA was nebulized to generate fragments <800 bp long. A terminal ‘A’ was then transferred to the 3′ end and cDNA fragments were ligated to adapters, purified and bridge amplified. Thirty-six cycles of sequencing-by-synthesis were performed Cytidine deaminase for each library using the Genome Analyzer GAII SR. illumina genome analyzer pipeline

software (version 0.2) was used to qualify reads (Klockgether et al., 2010). Sequence reads that passed the default signal quality filter and were not aligned by ELAND (Efficient Large-Scale Alignment of Nucleotide Databases) to a reference of the P. putida rRNA genes were used for gene expression analysis. The reads were subsequently aligned to the P. putida genome (NC_002947.3) using the bowtie software package (Langmead et al., 2009). The remaining reads mapped to rRNA were subsequently excluded with a custom PERL script. Four nucleotides were trimmed from the 3′ end of each read and a seed size of 28 bp was used, in which two mismatches were allowed. The quality mismatch sum was 100 and results were transformed into a SAM format (command line: bowtie -t putida -l 28 -e 100 –best –sam -3 4 -n 2 -p 7). A summary table was then generated using the integrative web analysis tool galaxy (Giardine et al., 2005). The functions ‘coverage’ and ‘join’ were used, respectively, to summarize (1) the coverage of each ORF from the P. putida NCBI annotation (version NC_002947.