added generic NER plans

BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-19339076.txt

+Bile resistance in Lactococcus lactis strains varies with cellular fatty acid composition: analysis by using different growth media.
+Bile resistance is one of the basic characteristics of probiotic bacteria. The aim of this study was to investigate the characteristics of bile resistance in lactococci by studying the relationship between bile resistance and cellular fatty acid composition in lactococcci grown on different media. We determined the bile resistance of 14 strains in lactose-free M17 medium supplemented with either glucose only (GM17) or lactose only (LM17). Gas chromatographic analyses of free lipids extracted from the tested strains were used for determining their fatty acid composition. A correlation analysis of all strains grown in both media revealed significant positive correlations between bile resistance and relative contents of hexadecanoic acid and octadecenoic acid, and negative correlations between bile resistance and relative contents of hexadecenoic acid and C-19 cyclopropane fatty acid. It is also a fact that the fatty acids associated with bile resistance depended on species, strain, and/or growth medium. In L. lactis subsp. cremoris strains grown in GM17 medium, the bile-resistant strains had significantly more octadecenoic acid than the bile-sensitive strains. In LM17 medium, bile-resistant strains had significantly more octadecenoic acid and significantly less C-19 cyclopropane fatty acid than the bile-sensitive strains. In L. lactis subsp. lactis strains, bile resistances of some of the tested strains were altered by growth medium. Some strains were resistant to bile in GM17 medium but sensitive to bile in LM17 medium. Some strains were resistant in both media tested. The strains grown in GM17 medium had significantly more hexadecanoic acid and octadecenoic acid, and significantly less tetradecanoic acid, octadecadienoic acid and C-19 cyclopropane fatty acid than the strains grown in LM17 medium. In conclusion, the fatty acid compositions of the bile-resistant lactococci differed from those of the bile-sensitive ones. More importantly, our data suggest that altering their fatty acid composition (i.e. increased hexadecanoic acid and octadecenoic acid and decreased hexadecenoic acid and C-19 cyclopropane fatty acid) by changing growth conditions may be a useful way to enhance their bile resistance in lactococci.

BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-19396518.txt

+Rapid detection of eight causative pathogens for the diagnosis of bacterial meningitis by real-time PCR.
+We aimed to detect causative pathogens in cerebrospinal fluid (CSF) collected from patients diagnosed with bacterial meningitis by real-time polymerase chain reaction (PCR). In addition to Streptococcus pneumoniae, Haemophilus influenzae, and Mycoplasma pneumoniae described previously, five other pathogens, Neisseria meningitidis, Escherichia coli, Streptococcus agalactiae, Staphylococcus aureus, and Listeria monocytogenes, were targeted, based on a large-scale surveillance in Japan. Results in CSF from neonates and children (n=150), and from adults (n=18) analyzed by real-time PCR with molecular beacon probes were compared with those of conventional culturing. The total time from DNA extraction from CSF to PCR analysis was 1.5 h. The limit of detection for these pathogens ranged from 5 copies to 28 copies per tube. Nonspecific positive reactions were not recognized for 37 microorganisms in clinical isolates as a negative control. The pathogens were detected in 72.0% of the samples by real-time PCR, but in only 48.2% by culture, although the microorganisms were completely concordant. With the real-time PCR, the detection rate of H. influenzae from CSF was high, at 45.2%, followed by S. pneumoniae (21.4%), S. agalactiae (2.4%), E. coli (1.8%), L. monocytogenes (0.6%), and M. pneumoniae (0.6%). The detection rate with PCR was significantly better than that with cultures in patients with antibiotic administration (chi2=18.3182; P=0.0000). In conclusion, detection with real-time PCR is useful for rapidly identifying the causative pathogens of meningitis and for examining the clinical course of chemotherapy.

BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-19494280.txt

+Involvement of CD252 (CD134L) and IL-2 in the expression of cytotoxic proteins in bacterial- or viral-activated human T cells.
+Regulation of cytotoxic effector molecule expression in human CTLs after viral or bacterial activation is poorly understood. By using human autologous dendritic cells (DCs) to prime T lymphocytes, we found perforin only highly up-regulated in virus- (HSV-1, vaccinia virus) but not in intracellular bacteria- (Listeria innocua, Listeria monocytogenes, Mycobacterium tuberculosis, Chlamydophila pneumoniae) activated CTLs. In contrast, larger quantities of IFN-gamma and TNF-alpha were produced in Listeria-stimulated cultures. Granzyme B and granulysin were similarly up-regulated by all tested viruses and intracellular bacteria. DCs infected with HSV-1 showed enhanced surface expression of the costimulatory molecule CD252 (CD134L) compared with Listeria-infected DC and induced enhanced secretion of IL-2. Adding blocking CD134 or neutralizing IL-2 Abs during T cell activation reduced the HSV-dependent up-regulation of perforin. These data indicate a distinct CTL effector function in response to intracellular pathogens triggered via differing endogenous IL-2 production upon costimulation through CD252.

BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-19501788.txt

+Construction of an attenuated Pseudomonas fluorescens strain and evaluation of its potential as a cross-protective vaccine.
+Ferric uptake regulator (Fur) is a global transcription regulator that is ubiquitous to Gram-negative bacteria and regulates diverse biological processes, including iron uptake, cellular metabolism, stress response, and production of virulence determinants. As a result, for many pathogenic bacteria, Fur plays a crucial role in the course of infection and disease development. In this study, the fur gene was cloned from a pathogenic Pseudomonas fluorescens strain, TSS, isolated from diseased Japanese flounder cultured in a local farm. TSS Fur can partially complement the defective phenotype of an Escherichia coli fur mutant. A TSS fur null mutant, TFM, was constructed. Compared to TSS, TFM exhibits reduced growth ability, aberrant production of outer membrane proteins, decreased resistance against host serum bactericidal activity, impaired ability to disseminate in host blood and tissues, and drastic attenuation in overall bacterial virulence in a Japanese flounder infection model. When used as a live vaccine administered via the injection, immersion, and oral routes, TFM affords high levels of protection upon Japanese flounder against not only P. fluorescens infection but also Aeromonas hydrophila infection. Furthermore, a plasmid, pJAQ, was constructed, which expresses the coding element of the Vibrio harveyi antigen AgaV-DegQ. TFM harboring pJAQ can secret AgaV-DegQ into the extracellular milieu. Vaccination of Japanese flounder with live TFM/pJAQ elicited strong immunoprotection against both V. harveyi and A. hydrophila infections.

BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-19552770.txt

+Prevalence of thermotolerant Campylobacter in partridges (Perdix perdix).
+To estimate the prevalence of thermotolerant Campylobacter spp. in commercially reared partridges (Perdix perdix) in southern Italy.
+Cloacal swabs of partridges (n = 240), equally distributed between male and female birds, from a game bird farm located in the Southern Italy were examined for the prevalence of thermotolerant Campylobacter spp. The samples were processed in order to detect thermotolerant Campylobacter spp. by culture methods. The positive samples were then confirmed by multiplex polymerase chain reaction. Thermotolerant Campylobacter spp. were isolated from 118 (49.2%) of the 240 cloacal swabs examined. As proved by PCR, 100% of the strains were identified as Campylobacter coli (118/118), and 15 (12.7%) out of the 118 positive samples were also positive for Campylobacter jejuni. In contrast, Campylobacter lari was not identified. Adult partridges showed a significantly higher prevalence (P < 0.05) than younger ones.
+These results reinforce the assumption that game birds may be considered as potential carriers of Campylobacter spp. for human being and other animal species.
+Although an earlier 1986 publication described the prevalence of Campylobacter coli in commercially reared partridges, this is the first report to confirm the species of Campylobacter using a PCR test.

BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-19621381.txt

+A general strategy for the bacterial expression of amyloidogenic peptides using BCL-XL-1/2 fusions.
+Biophysical studies on amyloidogenic and aggregation-prone peptides often require large quantities of material. However, solid-phase synthesis, handling, and purification of peptides often present challenges on these scales. Recombinant expression is an attractive alternative because of its low cost, the ability to isotopically label the peptides, and access to sequences exceeding approximately 50 residues. However, expression systems that seek to solubilize amyloidogenic peptides suffer from low yields, difficult optimizations, and isolation challenges. We present a general strategy for expressing and isolating amyloidogenic peptides in Escherichia coli by fusion to a polypeptide that drives the expression of attached peptides into bacterial inclusion bodies. This scheme minimizes toxicity during bacterial growth and enables the processing and handling of the peptides in denaturing solutions. Immobilized metal affinity chromatography, reverse phase HPLC, and cyanogen bromide cleavage are used to isolate the peptide, followed by further reverse phase HPLC, which yields milligram quantities of the purified peptide. We demonstrate that driving the peptides into inclusion bodies using fusion to BCL-XL-1/2 is a general strategy for their expression and isolation, as exemplified by the production of 11 peptides species.

BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-19622846.txt

+Detection of Staphylococcus aureus including MRSA on environmental surfaces in a jail setting.
+We examined jail environmental surfaces to explore whether they might serve as reservoirs of viable methicillin-resistant Staphylococcus aureus (MRSA). We swabbed 132 surfaces, inoculated primary and secondary mannitol salts and oxacillin-resistant screening agar, and used API tests to identify S. aureus and E-tests to determine methicillin/oxacillin resistance. We recovered S. aureus from 10 (7.6%) surfaces; eight (6.1%) isolates were MRSA. We ran pulsed-field gel electrophoresis on six resistant isolates and observed three patterns, one of which was identical to that identified in a previous study of inmates' nasal specimens. Finding MRSA-contaminated surfaces on a variety of environmental surfaces in the absence of an overt outbreak emphasizes that correctional facilities should have protocols for environmental cleaning as a component of MRSA prevention.

BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-19656787.txt

+Protection of Salmonella by ampicillin-resistant Escherichia coli in the presence of otherwise lethal drug concentrations.
+Microbial systems have become the preferred testing grounds for experimental work on the evolution of traits that benefit other group members. This work, based on conceptual and theoretical models of frequency-dependent selection within populations, has proven fruitful in terms of understanding the dynamics of group beneficial or 'public goods' traits within species. Here, we expand the scope of microbial work on the evolution of group-beneficial traits to the case of multi-species communities, particularly those that affect human health. We examined whether beta-lactamase-producing Escherichia coli could protect ampicillin-sensitive cohorts of other species, particularly species that could cause human disease. Both beta-lactamase-secreting E. coli and, surprisingly, those engineered to retain it, allowed for survival of a large number of ampicillin-sensitive cohorts of Salmonella enterica serovar Typhimurium, including both laboratory and clinical isolates. The Salmonella survivors, however, remained sensitive to ampicillin when re-plated onto solid medium and there was no evidence of gene transfer. Salmonella survival did not even require direct physical contact with the resistant E. coli. The observed phenomenon appears to involve increased release of beta-lactamase from the E. coli when present with S. enterica. Significantly, these findings imply that resistant E. coli, that are not themselves pathogenic, may be exploited, even when they are normally selfish with respect to other E. coli. Thus, Salmonella can gain protection against antibiotics from E. coli without gene transfer, a phenomenon not previously known. As a consequence, antibiotic-resistant E. coli can play a decisive role in the survival of a species that causes disease and may thereby interfere with successful treatment.

BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-20005916.txt

+Usage of signaling in neurodegeneration and regeneration of peripheral nerves by leprosy bacteria.
+Multiple signaling pathways play key regulatory roles during the development of peripheral nervous system (PNS) and also in neuroregeneration process following nerve degeneration. Schwann cells, the glial cells of the PNS, by interacting with neuronal (axonal) ligands, mainly neuregulins via receptor tyrosine kinase (RTK) complex, ErbB2/ErbB3, initiate intracellular signaling pathways to drive proliferation and differentiation of Schwann cells, both during development and the process of regeneration and re-myelination after nerve injury. One of the major signaling kinases, extracellular signal-regulated kinase-1/2 (ERK1/2), that is also a downstream signaling pathway of neuregulin-ErbB2/ErbB3 activation, has been identified as a key regulator of Schwann cell proliferation, differentiation, demyelination and nerve regeneration. Recent studies have provided evidence that the bacterium that causes human leprosy, Mycobacterium leprae that has a unique capacity to invade Schwann cells of the adult PNS, utilizes the neuregulin-ErbB2/ErbB3 associated signaling network to the bacterial advantage. M. leprae directly bind to ErbB2 on myelinated Schwann cells and activate the RTK by a novel route that bypasses the classical neuregulin/growth factor-induced ErbB2-ErbB3 heterodimerization, and subsequently induce downstream the canonical Erk1/2 signaling, leading to myelin breakdown and subsequent axonal damage. This initial injury provides a survival advantage for M. leprae as it induces de-differentiation and generates myelin-free cells, which are highly susceptible to M. leprae invasion and promote bacterial survival. Once invaded M. leprae activate Erk1/2 via a non-canonical pathway and subsequently increase the cell proliferation and maintain the infected cells in de-differentiated state, thereby preventing remyelination. Therefore, by subverting major RTKs and signaling pathways in adult Schwann cells M. leprae appear to propagate the bacterial niche and maintain survival within the PNS. These studies may also provide new insights into our understanding of signaling mechanisms involve in both neurodegeneration and neuroregeneration.

BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-20073421.txt

+The effect of interferon-gamma and lipopolysaccharide on the growth of Francisella tularensis LVS in murine macrophage-like cell line J774.
+Francisella tularensis, a causative agent of human tularemia, displaying the ability to proliferate inside the human cells.
+To evaluate the growth potential of F. tularensis LVS strain in macrophage-like cell line J774 modulated by recombinant interferon gamma and E. coli derived lipopolysaccharide.
+Stimulation of J774 cells either by interferon-gamma or lipopolysaccharide alone, or especially in combination before infection F. tularensis, revealed protective effects. Higher concentrations of stimulating agents were needed to inhibit ongoing F. tularensis infection.
+Stimulation of J774 cell line by combination of interferon-gamma with lipopolysaccharide inhibits the intracellular growth of F. tularensis.

BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-20148898.txt

+The presence of professional phagocytes dictates the number of host cells targeted for Yop translocation during infection.
+Type III secretion systems deliver effector proteins from Gram-negative bacterial pathogens into host cells, where they disarm host defences, allowing the pathogens to establish infection. Although Yersinia pseudotuberculosis delivers its effector proteins, called Yops, into numerous cell types grown in culture, we show that during infection Y. pseudotuberculosis selectively targets Yops to professional phagocytes in Peyer's patches, mesenteric lymph nodes and spleen, although it colocalizes with B and T cells as well as professional phagocytes. Strikingly, in the absence of neutrophils, the number of cells with translocated Yops was significantly reduced although the bacterial loads were similar, indicating that Y. pseudotuberculosis did not arbitrarily deliver Yops to the available cells. Using isolated splenocytes, selective binding and selective targeting to professional phagocytes when bacteria were limiting was also observed, indicating that tissue architecture was not required for the tropism for professional phagocytes. In isolated splenocytes, YadA and Invasin increased the number of all cells types with translocated Yops, but professional phagocytes were still preferentially translocated with Yops in the absence of these adhesins. Together these results indicate that Y. pseudotuberculosis discriminates among cells it encounters during infection and selectively delivers Yops to phagocytes while refraining from translocation to other cell types.

BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-20174624.txt

+Neutrophils are resistant to Yersinia YopJ/P-induced apoptosis and are protected from ROS-mediated cell death by the type III secretion system.
+The human innate immune system relies on the coordinated activity of macrophages and polymorphonuclear leukocytes (neutrophils or PMNs) for defense against bacterial pathogens. Yersinia spp. subvert the innate immune response to cause disease in humans. In particular, the Yersinia outer protein YopJ (Y. pestis and Y. pseudotuberculosis) and YopP (Y. enterocolitica) rapidly induce apoptosis in murine macrophages and dendritic cells. However, the effects of Yersinia Yop J/P on neutrophil fate are not clearly defined.
+In this study, we utilized wild-type and mutant strains of Yersinia to test the contribution of YopJ and YopP on induction of apoptosis in human monocyte-derived macrophages (HMDM) and neutrophils. Whereas YopJ and YopP similarly induced apoptosis in HMDMs, interaction of human neutrophils with virulence plasmid-containing Yersinia did not result in PMN caspase activation, release of LDH, or loss of membrane integrity greater than PMN controls. In contrast, interaction of human PMNs with the virulence plasmid-deficient Y. pestis strain KIM6 resulted in increased surface exposure of phosphatidylserine (PS) and cell death. PMN reactive oxygen species (ROS) production was inhibited in a virulence plasmid-dependent but YopJ/YopP-independent manner. Following phagocytic interaction with Y. pestis strain KIM6, inhibition of PMN ROS production with diphenyleneiodonium chloride resulted in a reduction of PMN cell death similar to that induced by the virulence plasmid-containing strain Y. pestis KIM5.
+Our findings showed that Yersinia YopJ and/or YopP did not induce pronounced apoptosis in human neutrophils. Furthermore, robust PMN ROS production in response to virulence plasmid-deficient Yersinia was associated with increased PMN cell death, suggesting that Yersinia inhibition of PMN ROS production plays a role in evasion of the human innate immune response in part by limiting PMN apoptosis.

BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-20400104.txt

+Microbiota in pediatric inflammatory bowel disease.
+To test the hypothesis that compared with controls, children with inflammatory bowel disease (IBD) exhibit differences in the relationships between gut microbiota and disease activity.
+Children and adolescents (n = 69; median age, 14 years) with IBD and 25 healthy controls (median age, 14 years) were recruited for the study. The disease activity was determined according to the Pediatric Ulcerative Colitis Activity Index or the Pediatric Crohn Disease Activity Index. Cell counts of 9 bacterial groups and species in the fecal microbiota were monitored by real-time polymerase chain reaction analysis.
+Although no major changes were observed in patients with ulcerative colitis, except for a decrease in bifidobacteria in the active state of IBD, children with active and inactive Crohn's disease (CD) had lower numbers of Faecalibacterium prausnitzii and bifidobacteria (P <.05), and patients with active CD had higher numbers of Escherichia coli (P <.05).
+The microbiota in children with CD is characterized by decreased numbers of F praunsitzii and increased numbers of E coli.

BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-20580604.txt

+Effects of a probiotic fermented milk beverage containing Lactobacillus casei strain Shirota on defecation frequency, intestinal microbiota, and the intestinal environment of healthy individuals with soft stools.
+The effects of drinking a fermented milk beverage that contains Lactobacillus casei strain Shirota (LcS) at 40 billion bacterial cells/bottle for 4 weeks (probiotics, 1 bottle/day) on defecation frequency, intestinal microbiota and the intestinal environment of healthy individuals with soft stools were evaluated. Thirty-four healthy adults who had soft stools were randomised into 2 groups, and the effects of a regular 4-week intake of probiotics were evaluated by a placebo-controlled, double-blind, parallel-group comparative design. Defecation frequency significantly decreased after the 4-week intake period compared with before the probiotic treatment. The stool quality significantly improved (hardened) compared to the placebo. Also, the water content of the stools was lower in the probiotic group than in the placebo group. Live LcS was recovered at 6.9 ± 1.3 and 7.2 ± 0.8 log(10) CFU per 1g of stool after 2 and 4 weeks, respectively, of probiotic treatment. The number of bifidobacteria in the stools also increased significantly compared with the level before starting the probiotics. The organic acid levels (total, acetic acid, propionic acid, and butyric acid) significantly increased compared with the level before intake in both the probiotic and placebo groups, but they returned to the original levels after the end of the intake period. These results suggest that probiotic fermented milk beverage has an intestine-conditioning effect by improving the frequency of defecation and stool quality and increasing the intrinsic bifidobacteria in healthy individuals with soft stool.

BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-20672296.txt

+An 18-month study of the safety and efficacy of repeated courses of inhaled aztreonam lysine in cystic fibrosis.
+Chronic airway infection with Pseudomonas aeruginosa (PA) causes morbidity and mortality in patients with cystic fibrosis (CF). Additional anti-PA therapies are needed to improve health status and health-related quality of life. AIR-CF3 was an international 18-month, open-label study to evaluate the safety and efficacy of repeated courses of aztreonam for inhalation solution (AZLI, now marketed as Cayston®) in patients aged ≥ 6 years with CF and PA infection who previously participated in one of two Phase 3 studies: AIR-CF1 or AIR-CF2. Patients received up to nine courses (28 days on/28 days off) of 75 mg AZLI two (BID) or three times daily (TID) based on randomization in the previous trials. 274 patients, mean age 28.5 years (range: 8-74 years), participated. Mean treatment adherence was high (92.0% BID group, 88.0% TID group). Hospitalization rates were low and adverse events were consistent with CF. With each course of AZLI, FEV(1) and scores on the Cystic Fibrosis Questionnaire-Revised Respiratory Symptom scale improved and bacterial density in sputum was reduced. Benefits waned in the 28 days off therapy, but weight gain was sustained over the 18 months. There were no sustained decreases in PA susceptibility. A dose response was observed; AZLI TID-treated patients demonstrated greater improvements in lung function and respiratory symptoms over 18 months. Repeated intermittent 28-day courses of AZLI treatment were well tolerated. Clinical benefits in pulmonary function, health-related quality of life, and weight were observed with each course of therapy. AZLI is a safe and effective new therapy in patients with CF and PA airway infection.

BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-21148810.txt

+TLR2-dependent pathway of heterologous down-modulation for the CC chemokine receptors 1, 2, and 5 in human blood monocytes.
+During innate immune responses, the inflammatory CC chemokine receptors CCR1, CCR2, and CCR5 mediate the recruitment of blood monocytes to infected tissues by promoting cell migration in response to chemokines CCL2-5. Toll-like receptors also play an essential role, allowing pathogen recognition by the recruited monocytes. Here, we demonstrate that Toll-like receptor 2 (TLR2) stimulation by lipoteichoic acid (LTA) from Staphylococcus aureus leads to gradual down-modulation of CCR1, CCR2, and CCR5 from the plasma membrane of human blood-isolated monocytes and inhibits chemotaxis. Interestingly, LTA does not promote rapid desensitization of chemokine-mediated calcium responses. We found that the TLR2 crosstalk with chemokine receptors is not dependent on the Toll/interleukin-1 receptor domain-containing adaptor protein, but instead involves phospholipase C, the small G protein Rac1, and is phorbol ester sensitive. Activation of this pathway by LTA lead to β-arrestin-mediated endocytosis of Ser349-phosphorylated CCR5 into recycling endosomes, as does CCL5 treatment. However, LTA-induced internalization of CCR5 is a slower process associated with phospholipase C-mediated and phorbol ester-sensitive phosphorylation. Overall, our data indicate that TLR2 negatively regulates CCR1, CCR2, and CCR5 on human blood monocytes by activating the machinery used to support chemokine-dependent down-modulation and provide a molecular mechanism for inhibiting monocyte migration after pathogen recognition.

BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-21270066.txt

+Lymphogranuloma venereum presenting as perianal ulceration: an emerging clinical presentation?
+An outbreak of lymphogranuloma venereum (LGV) infection has been recognised in the UK since 2004, predominantly affecting HIV-positive men who have sex with men (MSM). Patients typically present with proctitis symptoms. The prevalence of rectal LGV in MSM attending sexually transmitted infection clinics in London is estimated at 1%. Health Protection Agency surveillance has shown a decrease in anorectal manifestations despite little demographic change. Two cases of HIV-infected patients presenting with isolated perianal ulcer disease are reported here. Both cases were confirmed to have rectal Chlamydia trachomatis-specific DNA of an LGV associated serovar. As presentations of LGV diversify, further education and surveillance are needed in order to reduce transmission and prevent long-term complications. A strong argument already exists for the incorporation of chlamydia nucleic acid amplification tests in the management of MSM with proctitis; this paper provides evidence that this should be extended to MSM with perianal ulcer disease.

BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-21476570.txt

+Absorption linear dichroism measured directly on a single light-harvesting system: the role of disorder in chlorosomes of green photosynthetic bacteria.
+Chlorosomes are light-harvesting antennae of photosynthetic bacteria containing large numbers of self-aggregated bacteriochlorophyll (BChl) molecules. They have developed unique photophysical properties that enable them to absorb light and transfer the excitation energy with very high efficiency. However, the molecular-level organization, that produces the photophysical properties of BChl molecules in the aggregates, is still not fully understood. One of the reasons is heterogeneity in the chlorosome structure which gives rise to a hierarchy of structural and energy disorder. In this report, we for the first time directly measure absorption linear dichroism (LD) on individual, isolated chlorosomes. Together with fluorescence-detected three-dimensional LD, these experiments reveal a large amount of disorder on the single-chlorosome level in the form of distributions of LD observables in chlorosomes from wild-type bacterium Chlorobaculum tepidum . Fluorescence spectral parameters, such as peak wavelength and bandwidth, are measures of the aggregate excitonic properties. These parameters obtained on individual chlorosomes are uncorrelated with the observed LD distributions and indicate that the observed disorder is due to inner structural disorder along the chlorosome long axis. The excitonic disorder that is also present is not manifested in the LD distributions. Limiting values of the LD parameter distributions, which are relatively free of the effect of structural disorder, define a range of angles at which the excitonic dipole moment is oriented with respect to the surface of the two-dimensional aggregate of BChl molecules. Experiments on chlorosomes of a triple mutant of Chlorobaculum tepidum show that the mutant chlorosomes have significantly less inner structural disorder and higher symmetry, compatible with a model of well-ordered concentric cylinders. Different values of the transition dipole moment orientations are consistent with a different molecular level organization of BChl's in the mutant and wild-type chlorosomes.

BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-21498521.txt

+The lipid A from Vibrio fischeri lipopolysaccharide: a unique structure bearing a phosphoglycerol moiety.
+Vibrio fischeri, a bioluminescent marine bacterium, exists in an exclusive symbiotic relationship with the Hawaiian bobtail squid, Euprymna scolopes, whose light organ it colonizes. Previously, it has been shown that the lipopolysaccharide (LPS) or free lipid A of V. fischeri can trigger morphological changes in the juvenile squid's light organ that occur upon colonization. To investigate the structural features that might be responsible for this phenomenon, the lipid A from V. fischeri ES114 LPS was isolated and characterized by multistage mass spectrometry (MS(n)). A microheterogeneous mixture of mono- and diphosphorylated diglucosamine disaccharides was observed with variable states of acylation ranging from tetra- to octaacylated forms. All lipid A species, however, contained a set of conserved primary acyl chains consisting of an N-linked C14:0(3-OH) at the 2-position, an unusual N-linked C14:1(3-OH) at the 2'-position, and two O-linked C12:0(3-OH) fatty acids at the 3- and 3'-positions. The fatty acids found in secondary acylation were considerably more variable, with either a C12:0 or C16:1 at the 2-position, C14:0 or C14:0(3-OH) at the 2'-position, and C12:0 or no substituent at the 3'-position. Most surprising was the presence of an unusual set of modifications at the secondary acylation site of the 3-position consisting of phosphoglycerol (GroP), lysophosphatidic acid (GroP bearing C12:0, C16:0, or C16:1), or phosphatidic acid (GroP bearing either C16:0 + C12:0 or C16:0 + C16:1). Given their unusual nature, it is possible that these features of the V. fischeri lipid A may underlie the ability of E. scolopes to recognize its symbiotic partner.

BioNLP-ST-2016_BB-cat+ner/BB-cat+ner-21511409.txt

+Molecular epidemiology of Pasteurella multocida in dairy and beef calves.
+The molecular epidemiology of Pasteurella multocida has rarely been studied at the farm level in cattle. The aim of this study was to determine whether single or multiple strains of P. multocida tend to exist within farms. Molecular characterisation was carried out on isolates obtained from nasal swabs from 105 calves from 32 randomly selected beef and dairy farms located throughout Scotland, and from 131 calves from 20 farms in the Mayenne region of France, where sampling occurred in response to respiratory disease outbreaks. P. multocida isolates were characterised by random-amplified polymorphic DNA (RAPD) typing and pulsed-field gel electrophoresis (PFGE) using restriction enzyme ApaI. In addition, isolates representative of each farm/RAPD profile combination were typed by multilocus sequence typing (MLST). Among 105 Scottish isolates, 15 RAPD profiles were distinguished. The majority of farms (27/32) had indistinguishable profiles in all positive animals. Five farms had two profiles. Among 140 French isolates, 23 RAPD profiles were distinguished. More within-farm heterogeneity was observed although 10/20 farms had just one profile (E4) in sampled calves. Profile E4 accounted for 60% (84/140) of French isolates. PFGE was more discriminatory than RAPD but confirmed results with respect to within farm homogeneity or heterogeneity of strains, whereas MLST was not discriminatory enough for farm level epidemiology. As in other host species, either several strains or one dominant strain of P. multocida may exist within farms, with evidence for a role of management factors such as movements onto the farm in the number of strains detected.