[5, 7, 8] Although direct comparisons of available anti-TNF agents in randomized controlled settings are not available, improvements in symptom control appear to be similar across agents.[5, 7, 8] Patients

with RA are known to be at high risk of infection[9] and lymphoma.[10] It is likely that this results from multiple factors, including the disease itself (through altered immunologic function), as well as due to comorbidities and pharmacotherapy.[9, 11] Although it is hypothesized that RA itself is a risk factor for increased infection, it is currently unknown how much RA may increase infection risk independent of related factors, such as treatment with DMARDs. learn more One study by Smitten et al.[12] adjusted for confounders including comorbid conditions and prescription medication use and found an elevated hazard ratio for infection requiring hospitalization among patients with RA (2.03; 95% CI: 1.93–2.13). Both the tDMARDs and anti-TNF bDMARDs interrupt RA pathophysiology by targeting the inflammatory process.[13] Anti-TNF www.selleckchem.com/products/ipilimumab.html agents target TNF, a key proinflammatory cytokine, by direct interference with receptor binding.[1] However, TNF has a beneficial role in the immune system and in tumor surveillance.[6] Therefore, interruption of the inflammatory cascade with anti-TNFs may also suppress immunologic response. Following the 1998 Carbohydrate introduction of two anti-TNF

agents (infliximab and etanercept), reports from the US Food and Drug Administration’s Adverse Event Reporting System suggested

a higher incidence of tuberculosis (TB)[14] and lymphoma[10] in patients treated with these drugs. The close proximity of these events to anti-TNF therapy initiation, and the known immunosuppressive actions of anti-TNF agents, suggested a potential causal link. However, available data were limited and inadequate to make a clear association. The development of registries in several countries for patients treated with biologic agents, as well as the publication of a number of claims-based studies, has provided a larger database and longer timeframe from which to evaluate these safety endpoints. Despite differences in methodology, registry and health claims database studies conducted in the US and Western Europe have found a significantly higher risk for serious bacterial infection (SBI) with bDMARDs compared with tDMARDs.[6, 15-17] Estimates of risk have been highly variable, ranging from a 20% to a 400% increase, and appear to be greatest during the first 6 months of treatment.[6, 15, 16] Compared with patients who have not received anti-TNF treatment, a higher incidence of TB has also been reported with anti-TNF agents in Korea, Spain, Sweden and the US.[18-21] The potential for negative safety endpoints among anti-TNF agents has also been explored.

, 2005; Fig. 1). The VTA was further subdivided along its rostrocaudal

extent because of previous reports of functional specificity in rats and mice (Olson et al., 2005; Ikemoto, 2007) and a relative lack of region-specific analysis in the hamster. Rostral sections were defined as having TH cells adjacent to the fasciculus retroflexus prior to the onset of the interpeduncular nucleus; caudal sections were defined as having interpeduncular nucleus present prior to the medial lemniscus merging with the cerebral peduncle; tail sections were defined as having a rounded interpeduncular nucleus prior to the oral part of the pontine nuclei (Fig. 1). Upon completion of microscopic inspection and analysis, similar effects of age and swab exposure

were found in Obeticholic Acid the rostral and caudal portions of each VTA subregion; therefore, data from rostral and caudal IF, PN and PBP sections were combined within subregion for statistical analysis and presentation here. Anatomically matched tissue sections throughout the extent of each region of interest (2–5 sections per subregion, depending on size) were selected at see more 4× magnification. In the Acb, Me and VMH, subregion contours were manually traced bilaterally according to the atlas and cytoarchitecture in Nissl-stained sections and then overlaid Afatinib onto corresponding immunohistochemically treated tissue sections for cell counting. In the mPFC, 600 × 600 μm boxes were placed in the mPFC relative to the medial brain edge and corpus callosum. In the hypothalamus, boxes were drawn to surround all orexin-ir cells medial or lateral to the lateral edge of the fornix in immunohistochemically treated tissue sections. In the VTA, contours were drawn unilaterally in immunohistochemically treated tissue sections. Cell counts were made within a contour by a single experimenter blind to hamster treatment with an UPlanSApo 40 ×  (0.9NA)

objective on an Olympus BX51 microscope under brightfield illumination using Neurolucida (version 7; Microbrightfield, Williston, VT, USA). All quantification was performed on double-labeled immunohistochemically treated tissue; cells were considered Fos-ir if they had a distinct nucleus with visible puncta stained dark red-brown and TH- or orexin-ir if the cytoplasm was stained gray-blue. In all regions, single-labeled Fos-ir cells were counted; the number of Fos-ir cells within each subregion contour was divided by the area of that contour to create a measure of cell density within a section. These density data control for any change in subregion area with age, and generally detect similar effects of treatment as do cell count data.

3C. To discern the most stable pattern of cluster assignment across subjects, we applied the spectral clustering algorithm to the consensus matrices and computed the modified silhouette. Figure 3F plots the modified silhouette values, and suggests that, across subjects, the most stable pattern of cluster assignment is for K = 4. Qualitatively, the surface maps for the solutions computed on the basis of the consensus matrix are highly Selleckchem CHIR99021 similar to those computed on the basis of the group-average η2 matrix (Fig. 4), and the VI metric demonstrates that

the best similarity between the clustering solutions is for K = 2 : 4 (Fig. 3G). On the basis of the clustering analyses, we concluded that K = 4 represented the most favorable solution (see Fig. 4). Qualitatively, the four clusters were located in the superior part of the inferior frontal gyrus, bordering the inferior

frontal sulcus (Cluster 1), the lateral pars opercularis PCI-32765 molecular weight and pars triangularis (Cluster 2), inferior precentral cortex (Cluster 3) and a fourth region extending medially within the Sylvian fissure from the inferior-most tip of the ventral premotor cortex and the pars opercularis towards the anterior insula (Cluster 4). To verify these clusters as functionally distinct regions of ventrolateral frontal cortex, we examined the RSFC associated with four spherical seed ROIs of 4-mm radius, centered on the centers-of-mass of each of the clusters of the group-average

K = 4 spectral clustering solution. Figure 5 shows the group-level (Z > 2.3; cluster significance P < 0.05, corrected) RSFC for each of the four G protein-coupled receptor kinase clusters, as well as direct comparisons between clusters. The pattern of RSFC observed for Cluster 2, which includes the central parts of the pars opercularis and pars triangularis, is very similar to those observed for ROIs based in BAs 44 and 45 (compare Cluster 2 in Fig. 5 with BA 44 and 45 in Fig. 1). Similarly, the pattern of RSFC for Cluster 3, which includes the inferior part of the precentral gyrus, is consistent with that for the ROI based in BA 6 (compare Cluster 3 in Fig. 5 with BA 6 in Fig. 1). The voxels in Cluster 1 probably separate from the rest of the large ventrolateral frontal region of interest that was defined for the clustering analysis by virtue of the fact that they are located along the inferior frontal sulcus on the border with the middle frontal gyrus, which would include voxels of areas 8 and 9/46v in the upper bank of the inferior frontal sulcus and adjacent middle frontal gyrus. Specifically, Cluster 1 exhibited RSFC with almost all of the inferior frontal gyrus, anterior to and including the inferior precentral sulcus, dorsal BA 6 and BA 8 in the middle frontal gyrus, the intraparietal sulcus, and the caudal middle and inferior temporal cortex. The comparison Cluster 1 > Cluster 2 (Fig.

The spectrum of microbial agents causing RTI had been previously described and include numerous viruses (eg, influenza, parainfluenza, respiratory syncitial virus, metapneumovirus, adenovirus, rhinovirus, and coronavirus) as well as some bacteria (eg, Streptococcus sp., M. pneumoniae, L. pneumophila).18 In the subset of our 99 patients evaluated with RT-PCR and a throat Selleckchem EPZ015666 swab, an infectious agent was found in 65.6%. This is much higher than that observed in many other studies

performed in travelers or during influenza season. In a series of 500 Hajj pilgrims presenting with upper RTI, 54 (10%) had a positive viral throat culture.19 Of these 54 positive cultures, 27 (50%) were due to influenza B, 7 (12%) due to RSV, 4 (7%) due to parainfluenza, and 3 (5%) due to influenza A.19 In another study of 255 Iranian pilgrims with RTI, 83 (32%) had a viral pathogen isolated by throat culture.20 Of these 83 positive throat cultures, influenza was diagnosed in 25 (9.8%), followed by parainfluenza in 19 (7.4%), rhinovirus in 15 (5.9%), adenovirus in 14 (5.4%), enterovirus in 5 (2%), and RSV in 4 (1.6%); coinfection with two viruses was observed in one patient (0.4%).20 Of 67

German travelers that fulfilled the WHO case definition of suspected or probable severe acute respiratory syndrome (SARS) during the 2003 outbreak, influenza and PIVs Ruxolitinib nmr accounted for 14.2 and 15.5% of the viral etiologies by RT-PCR, whereas 56.8% of the cases remain unexplained.21 Therefore, the viruses isolated in travelers include viruses other than InfA and InfB. In a study performed at San Francisco University Medical Center during the influenza season, a viral agent was identified (through shell vial assay and PCR) in 103 (39%) of the patients with RTI.22 Lastly, among 420 patients with ILI recruited over 3 years in

Sao Paulo (Brazil), RT-PCR were performed on nasal washes and 61.8% were positive for respiratory viruses.23 Therefore, RT-PCR leads to an etiological diagnosis of RTI in about two thirds of the cases. Although this study took place during the early months of the influenza A(H1N1) 2009 outbreak, this strain of influenza virus was isolated only in 18% of the microbiological evaluated cases. We found that ILI was mainly because of influenza (30%) aminophylline but other viruses (37%) such as rhinovirus (22%) were also involved. This supports previous data in Brazil where ILI was reported in 240 of 420 patients (57.1%), with influenza and rhinovirus accounting for 30.9 and 19.6% of the ILI etiologies, respectively.23 Otherwise viruses identified during passed flu epidemics were also diverse as reported in other studies.22,24 We were unable to identify risk factors for infection with influenza virus A(H1N1) in our patients with RTI (data not shown), probably because of the limited number of cases evaluated during the inclusion period (April–July).

Conversely, administration of antioxidants reduces oxidative stress and toxicity induced by HIV

and HCV in vitro [15]. Thus, oxidative injury appears to occur as a direct result of HCV infection of hepatocytes. In addition, the number of mitochondrial DNA copies is reduced in HIV/HCV coinfection compared with either HIV or HCV monoinfection, reflecting the consequences of oxidative stress [16]. Disease progression is attributable, at least in part, to cumulative oxidative stress and antioxidant DNA Damage inhibitor depletion [17] and provides the basis for one of the mechanisms for hepatic disease progression. Infection with HIV is also characterized by increased oxidative stress [11,18–20], and depletion of antioxidant nutrients, including vitamins A and E, zinc and selenium [17,21,22]. Both HIV [11] and HCV monoinfections have been recognized as conditions that elevate oxidative stress, which in turn contributes to liver fibrosis [9,10,13]. However, information on measures of oxidative stress and antioxidant status in HIV/HCV coinfection is limited. The objective of our study PD-166866 mw was to determine oxidative stress and antioxidant status in a cohort of HIV/HCV-coinfected and HIV-monoinfected drug users in Miami in order to provide a basis for potential future adjuvant therapies

for patients with HIV/HCV coinfection. From March 2002 to February 2006, 212 HIV-infected drug users were recruited for this study in Miami. Participants needed to be

older than 18 years of age, confirmed with HIV seropositivity, and active drug users (determined by urine toxicology). This study was approved by the Florida International University Institutional Review Board. Appropriate written informed consent was obtained from all participants and clinical research was conducted in accordance with guidelines for human experimentation as specified by the US Department of Health and Human Services and/or authors’ institutions. After being screened for eligibility, participants underwent an assessment interview that Fenbendazole included demographic, medical, nutritional and recreational drug-related questionnaires. A physical examination was completed and anthropometrics were measured. After overnight fasting, blood samples were obtained to confirm HIV, HCV and hepatitis B virus (HBV) status, and to determine CD4 cell count, HIV viral load, complete blood cell count and blood chemistry, including the plasma concentrations of antioxidant nutrients (vitamins A and E, zinc and selenium) and markers of oxidative stress (plasma MDA and a major antioxidant enzyme, glutathione peroxidase). Lymphocyte phenotype was determined with a four-colour immunophenotyping panel of monoclonal antibodies. Differential counts were determined using a Coulter MaxM (Beckman Coulter Inc., Brea, CA) haematology instrument and corroborated with cytocentrifuge smears.

, 2011). In our study, amino acid sequence analysis revealed the presence of different A. baumannii p38 MAPK apoptosis PilA groups (Fig. 3). The isolates within these PilA groups were clonally related and exhibited the same motility characteristics, e.g. the international clone I isolates shared a highly similar PilA amino acid sequence and all exhibited a twitching phenotype. Interestingly, the PilA sequences from other motile bacterial species clustered with PilA from the motile A. baumannii isolates, e.g. the P. aeruginosa and D. nodosus PilA shared the highest homology levels with PilA from international clone I isolates

and X. fastidiosa PilA with that from ATCC strain 17978. Linking adherence phenotypes to genotypes was also attempted, as multiple adherence mechanisms have been identified. Although Bap (Loehfelm et al., 2008) showed major sequence variation, no direct link between adherence characteristics and sequence homology could be established. The pgaABCD cluster responsible for production of poly-beta-1-6-N-acetylglucosamine (Choi et al., 2009), and ompA (Gaddy et al., 2009) displayed a high level

of conservation between Panobinostat the investigated strains, therefore, sequence differences that may be linked to a phenotype could not be observed. In total, four different type I pili clusters were identified in the six sequenced strains included in this study; AB57_1744-1747, AB57_2565-2570 (csu cluster) (Tomaras et al., 2003), AB57_2420-2423 and AB57_2003-2007. The csu gene cluster was well conserved between the strains investigated; however, csuB of ATCC 17978 contained a single base-pair (bp) insertion, which resulted in a truncation dipyridamole of the open reading frame. Subsequently, the gap between the csuB and csuC open reading frames increased from 5 bp to 96 bp. Although transcription is unlikely to

be influenced by the single bp insertion, the increase between csuB and csuC may affect translation of csuC and other downstream genes in this operon. Interestingly, this strain showed the lowest level of binding to abiotic surfaces of all A. baumannii strains investigated, with the exception of strain RB02c (Fig. 1). The first open reading frame of the AB57_1744-1747 and AB57_2420-2423 polycistronic gene clusters contained homopolymeric tracts of varying lengths, and were therefore reanalysed by Sanger sequencing. Sequence differences were rebutted for AB57_1744_1747 using Sanger sequencing, however, strains ATCC 17978 and ATCC 19606 appeared to have an additional thymine in AB57_2423, which resulted in a frame-shift. However, even with this additional information, no direct correlation could be determined between the presence of type I pili clusters AB57_1744-1747, AB57_2420-2423 or AB57_2003-2007 and adherence to either biotic or abiotic surfaces. The Australian clinical A. baumannii isolates showed a similar clonal distribution to that found in Europe, viz.

“
“Proteorhodopsins (PRs), light-driven proton pumps, constitute the largest family of the microbial rhodopsins. PRs are widely distributed in the oceanic environment and freshwater, but no bacteria with PRs have been isolated from freshwater so far. To facilitate isolation of the bacteria with PR genes, we constructed

INCB024360 solubility dmso a vector system that can be used to clone potential PR genes and render color changes when overexpressed in Escherichia coli. Using this method, we successfully isolated a strain with PR gene from freshwater and identified it as Exiguobacterium sp. JL-3. The full length PR gene was then cloned using the SEFA PCR method. Protein sequence alignment showed that JL-3_PR shares high sequence identity (84–89%) with the PRs from Exiguobacterium strains, but low sequence identity (< 38%) with other PRs. Surprisingly, we could not detect any proton-pumping activity in the native JL-3 cells and protoplasts, but the recombinant JL-3_PR do pump protons when overexpressed in E. coli. Sequence analysis further revealed that the PRs from Exiguobacterium had an unusual lysine as the proton donor instead of the typical acidic residue. These data suggest that JL-3_PR is a sensory PR rather than a proton pump. "
“Pseudomonas aeruginosa

are known to have a wide physiological potential allowing them to constantly populate diverse environments leading to severe infections of humans such as septicemia, leg ulcers, and burn wounds. We set out to probe physiological characteristics of P. aeruginosa isolates from diabetic see more leg ulcers collected from Helsinki metropolitan area. A total of 61 clinical isolates were obtained. Detailed phenotypic (physiological) characteristics [outer membrane (OM) permeability, membrane voltage, and activity of multidrug

resistance pumps] were determined in several growth phases leading to the division of the analyzed set of P. aeruginosa strains into five distinct clusters including Adenosine cells with similar physiological properties. In addition, their antibiotic resistance patterns and genetic heterogeneity were determined. Multiple isolates from the same patient were genetically very closely related and belonged to the same phenotypic cluster. However, genetically close isolates from different patients expressed very different phenotypic properties. The characteristics of infected patients seem to determine the growth environments for microorganisms that adapt by changing their physiological and/or genetic properties. “
“Cysteine synthase A encoded by cysK catalyzes the synthesis of cysteine from O-acetylserine. Expression of cysK in Escherichia coli is under the control of CysB, a LysR family transcription factor. Herein we showed that the expression of cysK is regulated by several genetic and environmental factors in addition to CysB: two genetic factors, OmpR and CysE, and lithium. Based on the findings, we constructed the high-level expression system of cysK.

, 2005). The function of this gene is not known. In other bacterial species that possess more than one chaperonin gene, the differential expression of these genes is generally seen. In particular, in cases where one gene has been shown from genetic analysis to be the essential chaperonin, this gene generally shows the highest level of expression, whereas the other genes that may play additional roles are expressed at lower levels or under more specific conditions (e.g. Fischer et al., 1993; de León et al., 1997; Kovács et al., 2001; Gould et al., 2007; Hu et al., 2008; Sato

et al., 2008). As part of our characterization of the three chaperonin genes and the proteins that they encode in the mycobacterial species M. smegmatis, we have measured their expression under normal growth and in response to various stresses, and www.selleckchem.com/products/wnt-c59-c59.html we report these results here. The bacterial strains are shown in Table 1. All oligonucleotides were synthesized by Alta Biosciences or [for use in quantitative real-time PCR (qRT-PCR)] by Applied Biosystems, and are shown in Table 2. Escherichia coli was grown in Luria–Bertani

(LB) broth. A solid medium was prepared by adding 1.5% agar to the LB broth. Mycobacterium smegmatis was cultured in Difco Middlebrook 7H9 buy Nivolumab broth (BD Biosciences) containing ADC and 0.05% Tween 80, or in Difco Middlebrook 7H10 agar with ADC (BD Biosciences) and 0.05% Tween 80. Antibiotics were used at 100 μg mL−1 (ampicillin) or 50 μg mL−1 (kanamycin) for E. coli, and 20 μg mL−1 (kanamycin) and 150 μg mL−1 (hygromycin) for M. smegmatis. Protein sequences were identified and extracted from GenBank, aligned using clustalw with

default values, and phylogenetic trees were drawn using phylip or neighbourhood joining, using upgma for clustering. A 10 mL mid-log culture of M. smegmatis (grown in 7H9 Pomalidomide solubility dmso and ADC with 0.05% Tween80) was mixed with 4 vol. of 5 M GTC buffer (5 M guanidinium isothiocyanate) lysis solution and mixed rapidly by swirling. Cells were pelleted by centrifugation at 1200 g for 30 min, resuspended in 1 mL of 4 M GTC solution, centrifuged for a minute at 16 000 g and resuspended in 1.2 mL of TRI reagent (Fluka Biochemicals), which was added to 0.5 mL of 0.1 mm ceramic beads in 2-mL screw-capped microcentrifuge tubes. The tubes were spun using a reciprocal shaker (Hybaid Ribolyser) at the maximum speed setting (6.5) for 45 s, and then left at room temperature for 10 min. Chloroform (200 μL) was then added and the tubes were vortexed for 30 s. The tubes were then left at room temperature for 10 min to partition the aqueous and the organic phases and then centrifuged at 16 000 g at 4 °C for 15 min. The lighter aqueous phase was transferred to a fresh tube, mixed with an equal volume of chloroform, vortexed and incubated at room temperature for 10 min before centrifuging at 16 000 g at 4 °C for 15 min. The aqueous phase was transferred to a new tube and 0.8 vol.

In a symbiotic host system, collagen degradation could benefit the bacteria, but would be harmful for the eukaryotic host. Using a polyphasic approach, we investigated the presence of

collagenolytic activity in the bacterial community hosted by the marine sponge Cymbastela concentrica. Functional screening for collagenase activity using metagenomic library clones (227 Mbp) and cultured isolates of sponge’s bacterial community, as well as bioinformatic analysis of metagenomic shotgun-sequencing data (106 679 predicted genes) were used. The results show that the abundant members of the bacterial community contain very few genes encoding for collagenolytic enzymes, while some low-abundance Selleck GSK126 sponge isolates possess collagenolytic activities. These findings indicate that collagen is not a preferred nutrient source for the majority of the members of the bacterial community associated with healthy C. concentrica, and that some low-abundance bacteria have collagenase activities that have the potential to harm the sponge through tissue degradation. Collagen is the major component of extracellular matrices of all metazoan life and represents an important protein conferring integrity and the physical form of eukaryotic organisms

(Harrington, 1996; Exposito et al., 2008). Sponges are among the oldest Metazoa and often contain collagen, which is either dispersed as Selleckchem Trichostatin A thin fibrils or organized as bundles, termed spongin, in the intercellular matrix (Simpson, 1984; Brusca & Brusca, 1990). The expression of collagen is known to be essential for the development and structural integrity of sponges (Garrone et al., 1975; Shimizu & Yochizato, 1993; Krasko et al., 2000). Sponges harbour specific bacterial communities in different

cellular compartments, often for an extended period of time, and hence close associations between the microorganisms and the sponge host have been established (Taylor et al., 2007). Collagen is an essential and abundant part of the internal mesohyl structure of most sponges Pyruvate dehydrogenase lipoamide kinase isozyme 1 (and in particular the Demospongia), where many microorganisms reside. As a rich source of nitrogen and carbon, collagen could provide nutrients for the sponge-associated microorganisms, and this may potentially have implications for the structural integrity of the host. A few cases of sponge diseases have been attributed to the presence of bacterial pathogens (Gaino & Pronzato, 1989; Webster et al., 2002; Mukherjee et al., 2009) and collagenolytic enzymes have been speculated to lead to tissue necrosis in sponges. Generally, bacterial collagenases, including the well-characterized enzymes from Clostridium sp. (Matsushita et al., 1994) and Vibrio sp. (Yu & Lee, 1999; Vaitkevicius et al., 2008), have been linked to pathogenicity and are regarded as virulence factors in human disease.

, 2008). Chitin degradation via released chitinases has been well described for marine bacteria of the genera Vibrio and Pseudoalteromonas (Keyhani & Roseman, 1999; Baty et al., 2000; Meibom et al., 2004) and for freshwater bacteria of the genus Aeromonas (Janda, 1985; von Graevenitz, 1987; Lan et al., 2008). On the contrary, chitin degradation via cell-associated chitinases is largely unexplored. It has been described that many chitinolytic bacteria of the Cytophaga/Flavobacterium group of check details the Bacteroidetes, which are abundant inhabitants of marine and freshwater environments and contribute significantly to polymer

degradation in the open water (Cottrell & Kirchman, 2000; Kirchman, 2002; Lemarchand et al., 2006; Alonso et al., 2007; Beier & Bertilsson, 2011), do not release chitinases (Sundarraj & Bhat, 1972; Gooday, 1990). Recent genome analyses of several Bacteroidetes such as Flavobacterium johnsoniae suggest that chitin degradation in this group of bacteria proceeds via surface-bound chitinolytic enzymes that are very similar Ribociclib price to the well-described starch utilization system (sus) of Bacteroides thetaiotaomicron (Bauer et al., 2006; Xie et al., 2007; Martens et al., 2009; McBride et al., 2009).

The goal of our study was to investigate the interactions of bacteria with contrasting mechanisms for chitin degradation to identify the strategies they apply for overcoming their respective disadvantages. As this is difficult to study within natural communities, we set up a reductionistic laboratory model system with a defined co-culture

of aquatic bacteria, Aeromonas hydrophila strain AH-1N and Flavobacterium sp. strain 4D9. Previously, we reported that strains of Aeromonas and of the Cytophaga/Flavobacterium group were dominant in the same enrichment cultures, in which the microbial communities of the littoral zone of the oligotrophic Cepharanthine Lake Constance had been supplied with artificial organic particles as substrate (Styp von Rekowski et al., 2008). Thus, members of these bacterial groups coexist in the same environment. As described above for polymers in general, naturally occurring chitin is usually linked to other organic components such as proteins or glucans (Gooday, 1990). To account for this in our study, we embedded chitin into agarose beads. Aeromonas hydrophila strain AH-1N (Lynch et al., 2002) and Flavobacterium sp. strain 4D9, a Lake Constance isolate formerly called Cytophaga sp. strain 4D9 (Styp von Rekowski et al., 2008; GenBank accession number EF395377), were cultivated in the mineral medium B (Jagmann et al., 2010). When acetate (5 mM) and tryptone (0.1%) were used as carbon and energy sources, 5 mM NH4Cl was present in the medium. When suspended chitin [0.5% (w/v)], embedded chitin (two chitin-containing agarose beads per test tube), or GlcNAc (5 mM) served as carbon, energy, and nitrogen source, ammonium was omitted from the medium. Both strains were maintained on solid (1.