Discrimination of Four Marine Biofilm-Forming Bacteria by LC-MS Metabolomics and Influence of Culture Parameters.

PubMed

Favre, Laurie; Ortalo-Magné, Annick; Greff, Stéphane; Pérez, Thierry; Thomas, Olivier P; Martin, Jean-Charles; Culioli, Gérald

2017-05-05

Most marine bacteria can form biofilms, and they are the main components of biofilms observed on marine surfaces. Biofilms constitute a widespread life strategy, as growing in such structures offers many important biological benefits. The molecular compounds expressed in biofilms and, more generally, the metabolomes of marine bacteria remain poorly studied. In this context, a nontargeted LC-MS metabolomics approach of marine biofilm-forming bacterial strains was developed. Four marine bacteria, Persicivirga (Nonlabens) mediterranea TC4 and TC7, Pseudoalteromonas lipolytica TC8, and Shewanella sp. TC11, were used as model organisms. The main objective was to search for some strain-specific bacterial metabolites and to determine how culture parameters (culture medium, growth phase, and mode of culture) may affect the cellular metabolism of each strain and thus the global interstrain metabolic discrimination. LC-MS profiling and statistical partial least-squares discriminant analyses showed that the four strains could be differentiated at the species level whatever the medium, the growth phase, or the mode of culture (planktonic vs biofilm). A MS/MS molecular network was subsequently built and allowed the identification of putative bacterial biomarkers. TC8 was discriminated by a series of ornithine lipids, while the P. mediterranea strains produced hydroxylated ornithine and glycine lipids. Among the P. mediterranea strains, TC7 extracts were distinguished by the occurrence of diamine derivatives, such as putrescine amides.

The antibacterial peptide ABP-CM4: the current state of its production and applications.

PubMed

Li, Jian Feng; Zhang, Jie; Xu, Xing Zhou; Han, Yang Yang; Cui, Xian Wei; Chen, Yu Qing; Zhang, Shuang Quan

2012-06-01

The increasing resistance of bacteria and fungi to currently available antibiotics is a major concern worldwide, leading to enormous efforts to develop new antibiotics with new modes of actions. Antibacterial peptide CM4 (ABP-CM4) is a small cationic peptide with broad-spectrum activities against bacteria, fungi, and tumor cells, which may possibly be used as a promising candidate for a new antibiotic. For pharmaceutical applications, a large quantity of antimicrobial peptides needs to be produced economically. In this communication, the progress in the structural characteristics, heterologous production, and biological evaluation of ABP-CM4 are reviewed.

Prevention, Treatment and Tiagnosis of Pathogenic Infections by Using Pulsed Light Radiation Propagating Through Metamaterials

NASA Astrophysics Data System (ADS)

Enaki, N.; Paslari, T.; Turcan, M.; Bazgan, S.; Ristoscu, C.; Mihailescu, I. N.

2018-06-01

We propose novel optical methods for prevention, treatment and diagnosis of infections by pathogens using metamaterials with various geometries consisting of microspheres (i.e. photonic crystals, photonic molecules) and optical fibers structures. Around the adjacent elements of metamaterials appear the evanescent zones of propagated pulsed light radiation overlapping each other. This effect gives us the possibility to significantly increase the decontamination volume especially in non-transparent media. The parking geometries of microspheres and optical fibers ensure the efficient contact zone between the pulsed light radiation with contaminated materials (gases, liquids, tissues, implant surfaces). The penetration depth of evanescent field in contaminated materials can achieve values comparable with pathogens dimensions. We propose an attractive antimicrobial strategy using combined action of ultrashort pulses with different frequencies and pulse duration to achieve the selective decontamination of microorganisms with minimal effects on the components of human cells and tissues. We take into consideration the intrinsic symmetries of microorganisms protein structures (inclusive virus capsids) and their possible resonant excitation in double frequencies induced Raman scattering. The development of nonlinear models of the excitation of vibration modes of biomolecules of viruses and bacteria are revised taking into consideration the multi-mode aspects of interaction of pulsed light with excited biomolecules of pathogens. This method opens new possibilities in decontamination and diagnosis of the new collective processes, which can take place in viruses, bacteria, or other cellular structures under the action of external light pulses. Exponential distribution of radiation in evanescent zone gives us the possibility to capture and trap the viruses and bacteria along the optical fibers or/and microsphere surfaces.

Elucidating Duramycin’s Bacterial Selectivity and Mode of Action on the Bacterial Cell Envelope

DOE PAGES

Hasim, Sahar; Allison, David P.; Mendez, Berlin; ...

2018-02-14

The use of naturally occurring antimicrobial peptides provides a promising route to selectively target pathogenic agents and to shape microbiome structure. Lantibiotics, such as duramycin, are one class of bacterially produced peptidic natural products that can selectively inhibit the growth of other bacteria. However, despite longstanding characterization efforts, the microbial selectivity and mode of action of duramycin are still obscure. We describe here a suite of biological, chemical, and physical characterizations that shed new light on the selective and mechanistic aspects of duramycin activity. Bacterial screening assays have been performed using duramycin and Populus-derived bacterial isolates to determine species selectivity.more » Lipidomic profiles of selected resistant and sensitive strains show that the sensitivity of Gram-positive bacteria depends on the presence of phosphatidylethanolamine (PE) in the cell membrane. Further the surface and interface morphology were studied by high resolution atomic force microscopy and showed a progression of cellular changes in the cell envelope after treatment with duramycin for the susceptible bacterial strains. Together, these molecular and cellular level analyses provide insight into duramycin’s mode of action and a better understanding of its selectivity.« less

Elucidating Duramycin’s Bacterial Selectivity and Mode of Action on the Bacterial Cell Envelope

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hasim, Sahar; Allison, David P.; Mendez, Berlin

The use of naturally occurring antimicrobial peptides provides a promising route to selectively target pathogenic agents and to shape microbiome structure. Lantibiotics, such as duramycin, are one class of bacterially produced peptidic natural products that can selectively inhibit the growth of other bacteria. However, despite longstanding characterization efforts, the microbial selectivity and mode of action of duramycin are still obscure. We describe here a suite of biological, chemical, and physical characterizations that shed new light on the selective and mechanistic aspects of duramycin activity. Bacterial screening assays have been performed using duramycin and Populus-derived bacterial isolates to determine species selectivity.more » Lipidomic profiles of selected resistant and sensitive strains show that the sensitivity of Gram-positive bacteria depends on the presence of phosphatidylethanolamine (PE) in the cell membrane. Further the surface and interface morphology were studied by high resolution atomic force microscopy and showed a progression of cellular changes in the cell envelope after treatment with duramycin for the susceptible bacterial strains. Together, these molecular and cellular level analyses provide insight into duramycin’s mode of action and a better understanding of its selectivity.« less

How Markovian is exciton dynamics in purple bacteria?

NASA Astrophysics Data System (ADS)

Vaughan, Felix; Linden, Noah; Manby, Frederick R.

2017-03-01

We investigate the extent to which the dynamics of excitons in the light-harvesting complex LH2 of purple bacteria can be described using a Markovian approximation. To analyse the degree of non-Markovianity in these systems, we introduce a measure based on fitting Lindblad dynamics, as well as employing a recently introduced trace-distance measure. We apply these measures to a chromophore-dimer model of exciton dynamics and use the hierarchical equation-of-motion method to take into account the broad, low-frequency phonon bath. With a smooth phonon bath, small amounts of non-Markovianity are present according to the trace-distance measure, but the dynamics is poorly described by a Lindblad master equation unless the excitonic dimer coupling strength is modified. Inclusion of underdamped, high-frequency modes leads to significant deviations from Markovian evolution in both measures. In particular, we find that modes that are nearly resonant with gaps in the excitonic spectrum produce dynamics that deviate most strongly from the Lindblad approximation, despite the trace distance measuring larger amounts of non-Markovianity for higher frequency modes. Overall we find that the detailed structure in the high-frequency region of the spectral density has a significant impact on the nature of the dynamics of excitons.

Identification of gram-negative and gram-positive bacteria by fluorescence studies

NASA Astrophysics Data System (ADS)

Demchak, Jonathan; Calabrese, Joseph; Tzolov, Marian

2011-03-01

Several type strains of bacteria including Vibrio fischeri, Azotobacter vinelandii, Enterobacter cloacae, and Corynebacterium xerosis, were cultured in the laboratory following standard diagnostic protocol based on their individual metabolic strategies. The bacterial cultures were not further treated and they were studied in their pristine state (pure culture - axenic). The fluorescent studies were applied using a continuous wave and a pulsed excitation light sources. Emission and excitation spectra were recorded for the continuous wave excitation and they all show similar spectral features with the exception of the gram positive bacteria showing vibronic structures. The vibrational modes involved in these vibronic bands have energy typical for carbon-carbon vibrations. The fluorescence is quenched in addition of water, even a very thin layer, which confirms that the observed spectral features originate from the outer parts of the bacteria. These results allow to conclude that the fluorescence spectroscopy can be used as a method for studying the membranes of the bacteria and eventually to discriminate between gram positive and gram negative bacteria. The pulsed experiments show that the fluorescence lifetime is in the sub-microsecond range. The results indicate that the observed spectra are superposition of the emission with different lifetimes.

Crystal structure of secretory protein Hcp3 from Pseudomonas aeruginosa.

PubMed

Osipiuk, Jerzy; Xu, Xiaohui; Cui, Hong; Savchenko, Alexei; Edwards, Aled; Joachimiak, Andrzej

2011-03-01

The Type VI secretion pathway transports proteins across the cell envelope of Gram-negative bacteria. Pseudomonas aeruginosa, an opportunistic Gram-negative bacterial pathogen infecting humans, uses the type VI secretion pathway to export specific effector proteins crucial for its pathogenesis. The HSI-I virulence locus encodes for several proteins that has been proposed to participate in protein transport including the Hcp1 protein, which forms hexameric rings that assemble into nanotubes in vitro. Two Hcp1 paralogues have been identified in the P. aeruginosa genome, Hsp2 and Hcp3. Here, we present the structure of the Hcp3 protein from P. aeruginosa. The overall structure of the monomer resembles Hcp1 despite the lack of amino-acid sequence similarity between the two proteins. The monomers assemble into hexamers similar to Hcp1. However, instead of forming nanotubes in head-to-tail mode like Hcp1, Hcp3 stacks its rings in head-to-head mode forming double-ring structures.

[Study on the biological characteristic of Blastocystis hominis: morphology, mode of reproduction and the relation to bacteria].

PubMed

Qiao, Ji-ying; Zhang, Xu; Wei, Zhi-chao; Yang, Jun-hua; Li, Ya-qing; Zhang, Rong

2006-11-01

To observe the reproductive modes of Blastocystis hominis and study the relation between this protozoa and bacteria. Using the Iodine and Haematoxylin staining, the morphology of B. h from patients and RPMI 1640 medium were observed. The B. h positive mucous diarrheal specimens were cultured and identified any possible known pathogenic intestinal bacteria. B. h and colibacillus were co-cultured to observe the interaction between them. Four modes of reproduction for B. h were confirmed: binary fission, endodyogeny, multiple fission and budding. The fact that there was no other intestinal pathogens in half of the B. h positive specimens suggested B. h may cause disease independently. B. h and colibacillus were restrained each other. B. h reproduces in at least four modes. B. h could be a pathogen and its pathogenesis may be related to micro-ecological changes.

Structure and Mode-of-Action of the Two-Peptide (Class-IIb) Bacteriocins.

PubMed

Nissen-Meyer, Jon; Oppegård, Camilla; Rogne, Per; Haugen, Helen Sophie; Kristiansen, Per Eugen

2010-03-01

This review focuses on the structure and mode-of-action of the two-peptide (class-IIb) bacteriocins that consist of two different peptides whose genes are next to each other in the same operon. Optimal antibacterial activity requires the presence of both peptides in about equal amounts. The two peptides are synthesized as preforms that contain a 15-30 residue double-glycine-type N-terminal leader sequence that is cleaved off at the C-terminal side of two glycine residues by a dedicated ABC-transporter that concomitantly transfers the bacteriocin peptides across cell membranes. Two-peptide bacteriocins render the membrane of sensitive bacteria permeable to a selected group of ions, indicating that the bacteriocins form or induce the formation of pores that display specificity with respect to the transport of molecules. Based on structure-function studies, it has been proposed that the two peptides of two-peptide bacteriocins form a membrane-penetrating helix-helix structure involving helix-helix-interacting GxxxG-motifs that are present in all characterized two-peptide bacteriocins. It has also been suggested that the membrane-penetrating helix-helix structure interacts with an integrated membrane protein, thereby triggering a conformational alteration in the protein, which in turn causes membrane-leakage. This proposed mode-of-action is similar to the mode-of-action of the pediocin-like (class-IIa) bacteriocins and lactococcin A (a class-IId bacteriocin), which bind to a membrane-embedded part of the mannose phosphotransferase permease in a manner that causes membrane-leakage and cell death.

Class D β-lactamases do exist in Gram-positive bacteria

DOE PAGES

Toth, Marta; Antunes, Nuno Tiago; Stewart, Nichole K.; ...

2015-11-09

Production of β-lactamases of one of four molecular classes (A, B, C and D) is the major mechanism of bacterial resistance to β-lactams, the largest class of antibiotics, which have saved countless lives since their inception 70 years ago. Although several hundred efficient class D enzymes have been identified in Gram-negative pathogens over the last four decades, none have been reported in Gram-positive bacteria. Here we demonstrate that efficient class D β-lactamases capable of hydrolyzing a wide array of β-lactam substrates are widely disseminated in various species of environmental Gram-positive organisms. Class D enzymes of Gram-positive bacteria have a distinctmore » structural architecture and employ a unique substrate-binding mode that is quite different from that of all currently known class A, C and D β-lactamases. In conclusion, these enzymes thus constitute a previously unknown reservoir of novel antibiotic-resistance enzymes.« less

Class D β-lactamases do exist in Gram-positive bacteria

DOE Office of Scientific and Technical Information (OSTI.GOV)

Toth, Marta; Antunes, Nuno Tiago; Stewart, Nichole K.

Production of β-lactamases of one of four molecular classes (A, B, C and D) is the major mechanism of bacterial resistance to β-lactams, the largest class of antibiotics, which have saved countless lives since their inception 70 years ago. Although several hundred efficient class D enzymes have been identified in Gram-negative pathogens over the last four decades, none have been reported in Gram-positive bacteria. Here we demonstrate that efficient class D β-lactamases capable of hydrolyzing a wide array of β-lactam substrates are widely disseminated in various species of environmental Gram-positive organisms. Class D enzymes of Gram-positive bacteria have a distinctmore » structural architecture and employ a unique substrate-binding mode that is quite different from that of all currently known class A, C and D β-lactamases. In conclusion, these enzymes thus constitute a previously unknown reservoir of novel antibiotic-resistance enzymes.« less

Class D β-lactamases do exist in Gram-positive bacteria

PubMed Central

Toth, Marta; Antunes, Nuno Tiago; Stewart, Nichole K.; Frase, Hilary; Bhattacharya, Monolekha; Smith, Clyde; Vakulenko, Sergei

2015-01-01

Production of β-lactamases of the four molecular classes (A, B, C, and D) is the major mechanism of bacterial resistance to β-lactams, the largest class of antibiotics that have saved countless lives since their inception 70 years ago. Although several hundred efficient class D enzymes have been identified in Gram-negative pathogens over the last four decades, they have not been reported in Gram-positive bacteria. Here we demonstrate that efficient class D β-lactamases capable of hydrolyzing a wide array of β-lactam substrates are widely disseminated in various species of environmental Gram-positive organisms. Class D enzymes of Gram-positive bacteria have a distinct structural architecture and employ a unique substrate binding mode quite different from that of all currently known class A, C, and D β-lactamases. They constitute a novel reservoir of antibiotic resistance enzymes. PMID:26551395

tRNomics: analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features.

PubMed Central

Marck, Christian; Grosjean, Henri

2002-01-01

From 50 genomes of the three domains of life (7 eukarya, 13 archaea, and 30 bacteria), we extracted, analyzed, and compared over 4,000 sequences corresponding to cytoplasmic, nonorganellar tRNAs. For each genome, the complete set of tRNAs required to read the 61 sense codons was identified, which permitted revelation of three major anticodon-sparing strategies. Other features and sequence peculiarities analyzed are the following: (1) fit to the standard cloverleaf structure, (2) characteristic consensus sequences for elongator and initiator tDNAs, (3) frequencies of bases at each sequence position, (4) type and frequencies of conserved 2D and 3D base pairs, (5) anticodon/tDNA usages and anticodon-sparing strategies, (6) identification of the tRNA-Ile with anticodon CAU reading AUA, (7) size of variable arm, (8) occurrence and location of introns, (9) occurrence of 3'-CCA and 5'-extra G encoded at the tDNA level, and (10) distribution of the tRNA genes in genomes and their mode of transcription. Among all tRNA isoacceptors, we found that initiator tDNA-iMet is the most conserved across the three domains, yet domain-specific signatures exist. Also, according to which tRNA feature is considered (5'-extra G encoded in tDNAs-His, AUA codon read by tRNA-Ile with anticodon CAU, presence of intron, absence of "two-out-of-three" reading mode and short V-arm in tDNA-Tyr) Archaea sequester either with Bacteria or Eukarya. No common features between Eukarya and Bacteria not shared with Archaea could be unveiled. Thus, from the tRNomic point of view, Archaea appears as an "intermediate domain" between Eukarya and Bacteria. PMID:12403461

Eradication of Multi-drug Resistant Bacteria by Ni Doped ZnO Nanorods: Structural, Raman and optical characteristics

NASA Astrophysics Data System (ADS)

Jan, Tariq; Iqbal, Javed; Ismail, Muhammad; Mansoor, Qaisar; Mahmood, Arshad; Ahmad, Amaar

2014-07-01

In this paper, ZnO nanorods doped with varying amounts of Ni have been prepared by chemical co-precipitation technique. Structural investigations provide the evidence that Ni is successfully doped into ZnO host matrix without having any secondary phases. Scanning electron microscopy (SEM) images reveal the formation of rodlike structure of undoped ZnO with average length and diameter of 1 μm and 80 nm, respectively. Raman spectroscopy results show that the E1LO phonons mode band shifts to the higher values with Ni doping, which is attributed to large amount of crystal defects. Ni doping is also found to greatly influence the optical properties of ZnO nanorods. The influence of Ni doping on antibacterial characteristics of ZnO nanorods have been studied by measuring the growth curves of Escherichia coli (E. coli), Methicillin-resistant Staphylococcus aureus (S. aureus) and Pseudomonas aeruginosa (P. aeruginosa) bacteria in the presence of prepared nanorods. ZnO nanorods antibacterial potency is found to increase remarkably with Ni doping against S. aureus and P. aeruginosa microbials, which might possibly be due to the increase in reactive oxygen species (ROS) generation. Interestingly, it is observed that Ni doped ZnO nanorods completely eradicates these multi-drug resistant bacteria.

The dynamic bacterial communities of a melting High Arctic glacier snowpack

PubMed Central

Hell, Katherina; Edwards, Arwyn; Zarsky, Jakub; Podmirseg, Sabine M; Girdwood, Susan; Pachebat, Justin A; Insam, Heribert; Sattler, Birgit

2013-01-01

Snow environments can occupy over a third of land surface area, but little is known about the dynamics of snowpack bacteria. The effect of snow melt on bacterial community structure and diversity of surface environments of a Svalbard glacier was examined using analyses of 16S rRNA genes via T-RFLP, qPCR and 454 pyrosequencing. Distinct community structures were found in different habitat types, with changes over 1 week apparent, in particular for the dominant bacterial class present, Betaproteobacteria. The differences observed were consistent with influences from depositional mode (snowfall vs aeolian dusts), contrasting snow with dust-rich snow layers and near-surface ice. Contrary to that, slush as the decompositional product of snow harboured distinct lineages of bacteria, further implying post-depositional changes in community structure. Taxa affiliated to the betaproteobacterial genus Polaromonas were particularly dynamic, and evidence for the presence of betaproteobacterial ammonia-oxidizing bacteria was uncovered, inviting the prospect that the dynamic bacterial communities associated with snowpacks may be active in supraglacial nitrogen cycling and capable of rapid responses to changes induced by snowmelt. Furthermore the potential of supraglacial snowpack ecosystems to respond to transient yet spatially extensive melting episodes such as that observed across most of Greenland's ice sheet in 2012 merits further investigation. PMID:23552623

The dynamic bacterial communities of a melting High Arctic glacier snowpack.

PubMed

Hell, Katherina; Edwards, Arwyn; Zarsky, Jakub; Podmirseg, Sabine M; Girdwood, Susan; Pachebat, Justin A; Insam, Heribert; Sattler, Birgit

2013-09-01

Snow environments can occupy over a third of land surface area, but little is known about the dynamics of snowpack bacteria. The effect of snow melt on bacterial community structure and diversity of surface environments of a Svalbard glacier was examined using analyses of 16S rRNA genes via T-RFLP, qPCR and 454 pyrosequencing. Distinct community structures were found in different habitat types, with changes over 1 week apparent, in particular for the dominant bacterial class present, Betaproteobacteria. The differences observed were consistent with influences from depositional mode (snowfall vs aeolian dusts), contrasting snow with dust-rich snow layers and near-surface ice. Contrary to that, slush as the decompositional product of snow harboured distinct lineages of bacteria, further implying post-depositional changes in community structure. Taxa affiliated to the betaproteobacterial genus Polaromonas were particularly dynamic, and evidence for the presence of betaproteobacterial ammonia-oxidizing bacteria was uncovered, inviting the prospect that the dynamic bacterial communities associated with snowpacks may be active in supraglacial nitrogen cycling and capable of rapid responses to changes induced by snowmelt. Furthermore the potential of supraglacial snowpack ecosystems to respond to transient yet spatially extensive melting episodes such as that observed across most of Greenland's ice sheet in 2012 merits further investigation.

Biosynthesis of silver nanoparticles by Pseudomonas spp. isolated from effluent of an electroplating industry.

PubMed

Punjabi, Kapil; Yedurkar, Snehal; Doshi, Sejal; Deshapnde, Sunita; Vaidya, Shashikant

2017-08-01

The aim of this study was to isolate and screen bacteria from soil and effluent of electroplating industries for the synthesis of silver nanoparticles and characterize the potential isolate. Soil and effluent of electroplating industries from Mumbai were screened for bacteria capable of synthesizing silver nanoparticles. From two soils and eight effluent samples 20 bacterial isolates were obtained, of these, one was found to synthesize silver nanoparticles. Synthesis of silver nanoparticle by bacteria was confirmed by undertaking characterization studies of nanoparticles that involved spectroscopy and electron microscopic techniques. The potential bacteria was found to be Gram-negative short rods with its biochemical test indicating Pseudomonas spp . Molecular characterization of the isolate by 16S r DNA sequencing was carried out which confirmed its relation to Pseudomonas hibiscicola ATCC 19867. Stable nanoparticles synthesized were 50 nm in size and variable shapes as seen in SEM micrographs. The XRD and FTIR confirmed the crystalline structure of nanoparticles and presence of biomolecules mainly proteins as agents for reduction and capping of nanoparticles. The study demonstrates synthesis of nanoparticles by bacteria from effluent of electroplating industry. This can be used for large scale synthesis of nanoparticles by cost effective and environmentally benign mode of synthesis.

Atomic resolution mechanistic studies of ribocil: A highly selective unnatural ligand mimic of the E. coli FMN riboswitch

DOE Office of Scientific and Technical Information (OSTI.GOV)

Howe, John A.; Xiao, Li; Fischmann, Thierry O.

2016-08-02

Bacterial riboswitches are non-coding RNA structural elements that direct gene expression in numerous metabolic pathways. The key regulatory roles of riboswitches, and the urgent need for new classes of antibiotics to treat multi-drug resistant bacteria, has led to efforts to develop small-molecules that mimic natural riboswitch ligands to inhibit metabolic pathways and bacterial growth. Recently, we reported the results of a phenotypic screen targeting the riboflavin biosynthesis pathway in the Gram-negative bacteria Escherichia coli that led to the identification of ribocil, a small molecule inhibitor of the flavin mononucleotide (FMN) riboswitch controlling expression of this biosynthetic pathway. Although ribocil ismore » structurally distinct from FMN, ribocil functions as a potent and highly selective synthetic mimic of the natural ligand to repress riboswitch-mediated ribB gene expression and inhibit bacterial growth both in vitro and in vivo. Herein, we expand our analysis of ribocil; including mode of binding in the FMN binding pocket of the riboswitch, mechanisms of resistance and structure-activity relationship guided efforts to generate more potent analogs.« less

Mode of action and resistance studies unveil new roles for tropodithietic acid as an anticancer agent and the γ-glutamyl cycle as a proton sink.

PubMed

Wilson, Maxwell Z; Wang, Rurun; Gitai, Zemer; Seyedsayamdost, Mohammad R

2016-02-09

While we have come to appreciate the architectural complexity of microbially synthesized secondary metabolites, far less attention has been paid to linking their structural features with possible modes of action. This is certainly the case with tropodithietic acid (TDA), a broad-spectrum antibiotic generated by marine bacteria that engage in dynamic symbioses with microscopic algae. TDA promotes algal health by killing unwanted marine pathogens; however, its mode of action (MoA) and significance for the survival of an algal-bacterial miniecosystem remains unknown. Using cytological profiling, we herein determine the MoA of TDA and surprisingly find that it acts by a mechanism similar to polyether antibiotics, which are structurally highly divergent. We show that like polyether drugs, TDA collapses the proton motive force by a proton antiport mechanism, in which extracellular protons are exchanged for cytoplasmic cations. The α-carboxy-tropone substructure is ideal for this purpose as the proton can be carried on the carboxyl group, whereas the basicity of the tropylium ion facilitates cation export. Based on similarities to polyether anticancer agents we have further examined TDA's cytotoxicity and find it to exhibit potent, broad-spectrum anticancer activities. These results highlight the power of MoA-profiling technologies in repurposing old drugs for new targets. In addition, we identify an operon that confers TDA resistance to the producing marine bacteria. Bioinformatic and biochemical analyses of these genes lead to a previously unknown metabolic link between TDA/acid resistance and the γ-glutamyl cycle. The implications of this resistance mechanism in the context of the algal-bacterial symbiosis are discussed.

Mode of action and resistance studies unveil new roles for tropodithietic acid as an anticancer agent and the γ-glutamyl cycle as a proton sink

PubMed Central

Wilson, Maxwell Z.; Wang, Rurun; Gitai, Zemer; Seyedsayamdost, Mohammad R.

2016-01-01

While we have come to appreciate the architectural complexity of microbially synthesized secondary metabolites, far less attention has been paid to linking their structural features with possible modes of action. This is certainly the case with tropodithietic acid (TDA), a broad-spectrum antibiotic generated by marine bacteria that engage in dynamic symbioses with microscopic algae. TDA promotes algal health by killing unwanted marine pathogens; however, its mode of action (MoA) and significance for the survival of an algal–bacterial miniecosystem remains unknown. Using cytological profiling, we herein determine the MoA of TDA and surprisingly find that it acts by a mechanism similar to polyether antibiotics, which are structurally highly divergent. We show that like polyether drugs, TDA collapses the proton motive force by a proton antiport mechanism, in which extracellular protons are exchanged for cytoplasmic cations. The α-carboxy-tropone substructure is ideal for this purpose as the proton can be carried on the carboxyl group, whereas the basicity of the tropylium ion facilitates cation export. Based on similarities to polyether anticancer agents we have further examined TDA’s cytotoxicity and find it to exhibit potent, broad-spectrum anticancer activities. These results highlight the power of MoA-profiling technologies in repurposing old drugs for new targets. In addition, we identify an operon that confers TDA resistance to the producing marine bacteria. Bioinformatic and biochemical analyses of these genes lead to a previously unknown metabolic link between TDA/acid resistance and the γ-glutamyl cycle. The implications of this resistance mechanism in the context of the algal-bacterial symbiosis are discussed. PMID:26802120

Alteration of the mode of antibacterial action of a defensin by the amino-terminal loop substitution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gao, Bin; Zhu, Shunyi, E-mail: Zhusy@ioz.ac.cn

Highlights: Black-Right-Pointing-Pointer Al-M is an engineered fungal defensin with the n-loop of an insect defensin. Black-Right-Pointing-Pointer Al-M adopts a native defensin-like structure with high antibacterial potency. Black-Right-Pointing-Pointer Al-M kills bacteria through a membrane disruptive mechanism. Black-Right-Pointing-Pointer This work sheds light on the functional evolution of CS{alpha}{beta}-type defensins. -- Abstract: Ancient invertebrate-type and classical insect-type defensins (AITDs and CITDs) are two groups of evolutionarily related antimicrobial peptides (AMPs) that adopt a conserved cysteine-stabilized {alpha}-helical and {beta}-sheet (CS{alpha}{beta}) fold with a different amino-terminal loop (n-loop) size and diverse modes of antibacterial action. Although they both are identified as inhibitors of cell wallmore » biosynthesis, only CITDs evolved membrane disruptive ability by peptide oligomerization to form pores. To understand how this occurred, we modified micasin, a fungus-derived AITDs with a non-membrane disruptive mechanism, by substituting its n-loop with that of an insect-derived CITDs. After air oxidization, the synthetic hybrid defensin (termed Al-M) was structurally identified by circular dichroism (CD) and functionally evaluated by antibacterial and membrane permeability assays and electronic microscopic observation. Results showed that Al-M folded into a native-like defensin structure, as determined by its CD spectrum that is similar to that of micasin. Al-M was highly efficacious against the Gram-positive bacterium Bacillus megaterium with a lethal concentration of 1.76 {mu}M. As expected, in contrast to micasin, Al-M killed the bacteria through a membrane disruptive mechanism of action. The alteration in modes of action supports a key role of the n-loop extension in assembling functional surface of CITDs for membrane disruption. Our work provides mechanical evidence for evolutionary relationship between AITDs and CITDs.« less

Disinfection of indoor air microorganisms in stack room of university library using gaseous chlorine dioxide.

PubMed

Hsu, Ching-Shan; Lu, Ming-Chun; Huang, Da-Ji

2015-02-01

As with all indoor public spaces in Taiwan, the stack rooms in public libraries should meet the air quality guidelines laid down by the Taiwan Environmental Protection Administration. Accordingly, utilizing a university library in Taiwan for experimental purposes, this study investigates the efficiency of gaseous chlorine dioxide (ClO2) as a disinfection agent when applied using three different treatment modes, namely a single-daily disinfection mode (SIM), a twice-daily disinfection mode (TWM), and a triple-daily disinfection mode (TRM). For each treatment mode, the ClO2 is applied using an ultrasonic aerosol device and is performed both under natural lighting conditions and under artificial lighting conditions. The indoor air quality is evaluated before and after each treatment session by measuring the bioaerosol levels of bacteria and fungi. The results show that for all three disinfection modes, the application of ClO2 reduces the indoor bacteria and fungi concentrations to levels lower than those specified by the Taiwan EPA (i.e., bacteria <1500 CFU/m(3), fungi <1000 CFU/m(3)), irrespective of the lighting conditions under which the disinfection process is performed. For each disinfection mode, a better disinfection efficiency is obtained under natural lighting conditions since ClO2 readily decomposes under strong luminance levels. Among the three treatment modes, the disinfection efficiencies of the TWM and TRM modes are very similar under natural lighting conditions and are significantly better than that of the SIM mode. Thus, overall, the results suggest that the TWM treatment protocol represents the most cost-effective and efficient method for meeting the indoor air quality requirements of the Taiwan EPA.

Nanoscale structure-activity relationships, mode of action, and biocompatibility of gold nanoparticle antibiotics.

PubMed

Bresee, Jamee; Bond, Constance M; Worthington, Roberta J; Smith, Candice A; Gifford, Jennifer C; Simpson, Carrie A; Carter, Carly J; Wang, Guankui; Hartman, Jesse; Osbaugh, Niki A; Shoemaker, Richard K; Melander, Christian; Feldheim, Daniel L

2014-04-09

The emergence of resistance to multiple antimicrobial agents by pathogenic bacteria has become a significant global public health threat. Multi-drug-resistant (MDR) Gram-negative bacteria have become particularly problematic, as no new classes of small-molecule antibiotics for Gram-negative bacteria have emerged in over two decades. We have developed a combinatorial screening process for identifying mixed ligand monolayer/gold nanoparticle conjugates (2.4 nm diameter) with antibiotic activity. The method previously led to the discovery of several conjugates with potent activity against the Gram-negative bacterium Escherichia coli. Here we show that these conjugates are also active against MDR E. coli and MDR Klebsiella pneumoniae. Moreover, we have shown that resistance to these nanoparticles develops significantly more slowly than to a commercial small-molecule drug. These results, combined with their relatively low toxicity to mammalian cells and biocompatibility in vivo, suggest that gold nanoparticles may be viable new candidates for the treatment of MDR Gram-negative bacterial infections.

Bacterial community compositions of coking wastewater treatment plants in steel industry revealed by Illumina high-throughput sequencing.

PubMed

Ma, Qiao; Qu, Yuanyuan; Shen, Wenli; Zhang, Zhaojing; Wang, Jingwei; Liu, Ziyan; Li, Duanxing; Li, Huijie; Zhou, Jiti

2015-03-01

In this study, Illumina high-throughput sequencing was used to reveal the community structures of nine coking wastewater treatment plants (CWWTPs) in China for the first time. The sludge systems exhibited a similar community composition at each taxonomic level. Compared to previous studies, some of the core genera in municipal wastewater treatment plants such as Zoogloea, Prosthecobacter and Gp6 were detected as minor species. Thiobacillus (20.83%), Comamonas (6.58%), Thauera (4.02%), Azoarcus (7.78%) and Rhodoplanes (1.42%) were the dominant genera shared by at least six CWWTPs. The percentages of autotrophic ammonia-oxidizing bacteria and nitrite-oxidizing bacteria were unexpectedly low, which were verified by both real-time PCR and fluorescence in situ hybridization analyses. Hierarchical clustering and canonical correspondence analysis indicated that operation mode, flow rate and temperature might be the key factors in community formation. This study provides new insights into our understanding of microbial community compositions and structures of CWWTPs. Copyright © 2014 Elsevier Ltd. All rights reserved.

The Bacteriome of Bat Flies (Nycteribiidae) from the Malagasy Region: a Community Shaped by Host Ecology, Bacterial Transmission Mode, and Host-Vector Specificity.

PubMed

Wilkinson, David A; Duron, Olivier; Cordonin, Colette; Gomard, Yann; Ramasindrazana, Beza; Mavingui, Patrick; Goodman, Steven M; Tortosa, Pablo

2016-01-08

The Nycteribiidae are obligate blood-sucking Diptera (Hippoboscoidea) flies that parasitize bats. Depending on species, these wingless flies exhibit either high specialism or generalism toward their hosts, which may in turn have important consequences in terms of their associated microbial community structure. Bats have been hypothesized to be reservoirs of numerous infectious agents, some of which have recently emerged in human populations. Thus, bat flies may be important in the epidemiology and transmission of some of these bat-borne infectious diseases, acting either directly as arthropod vectors or indirectly by shaping pathogen communities among bat populations. In addition, bat flies commonly have associations with heritable bacterial endosymbionts that inhabit insect cells and depend on maternal transmission through egg cytoplasm to ensure their transmission. Some of these heritable bacteria are likely obligate mutualists required to support bat fly development, but others are facultative symbionts with unknown effects. Here, we present bacterial community profiles that were obtained from seven bat fly species, representing five genera, parasitizing bats from the Malagasy region. The observed bacterial diversity includes Rickettsia, Wolbachia, and several Arsenophonus-like organisms, as well as other members of the Enterobacteriales and a widespread association of Bartonella bacteria from bat flies of all five genera. Using the well-described host specificity of these flies and data on community structure from selected bacterial taxa with either vertical or horizontal transmission, we show that host/vector specificity and transmission mode are important drivers of bacterial community structure. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

The Bacteriome of Bat Flies (Nycteribiidae) from the Malagasy Region: a Community Shaped by Host Ecology, Bacterial Transmission Mode, and Host-Vector Specificity

PubMed Central

Duron, Olivier; Cordonin, Colette; Gomard, Yann; Ramasindrazana, Beza; Mavingui, Patrick; Goodman, Steven M.; Tortosa, Pablo

2016-01-01

The Nycteribiidae are obligate blood-sucking Diptera (Hippoboscoidea) flies that parasitize bats. Depending on species, these wingless flies exhibit either high specialism or generalism toward their hosts, which may in turn have important consequences in terms of their associated microbial community structure. Bats have been hypothesized to be reservoirs of numerous infectious agents, some of which have recently emerged in human populations. Thus, bat flies may be important in the epidemiology and transmission of some of these bat-borne infectious diseases, acting either directly as arthropod vectors or indirectly by shaping pathogen communities among bat populations. In addition, bat flies commonly have associations with heritable bacterial endosymbionts that inhabit insect cells and depend on maternal transmission through egg cytoplasm to ensure their transmission. Some of these heritable bacteria are likely obligate mutualists required to support bat fly development, but others are facultative symbionts with unknown effects. Here, we present bacterial community profiles that were obtained from seven bat fly species, representing five genera, parasitizing bats from the Malagasy region. The observed bacterial diversity includes Rickettsia, Wolbachia, and several Arsenophonus-like organisms, as well as other members of the Enterobacteriales and a widespread association of Bartonella bacteria from bat flies of all five genera. Using the well-described host specificity of these flies and data on community structure from selected bacterial taxa with either vertical or horizontal transmission, we show that host/vector specificity and transmission mode are important drivers of bacterial community structure. PMID:26746715

Current therapies in treatment and prevention of fracture wound biofilms: why a multifaceted approach is essential for resolving persistent infections

PubMed Central

Blanchette, Krystle A.; Wenke, Joseph C.

2018-01-01

Traumatic orthopedic injuries, particularly extremity wounds, are a significant cause of morbidity. Despite prophylactic antibiotic treatment and surgical intervention, persistent infectious complications can and do occur. Persistent bacterial infections are often caused by biofilms, communities of antibiotic tolerant bacteria encased within a matrix. The structural and metabolic differences in this mode of growth make treatment difficult. Herein, we describe both established and novel, experimental treatments targeted at various stages of wound healing that are specifically aimed at reducing and eliminating biofilm bacteria. Importantly, the highly tolerant nature of these bacterial communities suggests that most singular approaches could be circumvented and a multifaceted, combinatorial approach will be the most effective strategy for treating these complicated infections. PMID:29761067

View of the bacterial strains of Escherichia coli M-17 and its interaction with the nanoparticles of zinc oxide by means of atomic force microscopy

NASA Astrophysics Data System (ADS)

Sagitova, A.; Yaminsky, I.; Meshkov, G.

2016-08-01

Visualization of the structure of biological objects plays a key role in medicine, biotechnology, nanotechnology and IT-technology. Atomic force microscopy (AFM) is a promising method of studying of objects’ morphology and structure. In this work, AFM was used to determine the size and shape of the bacterial strains of Escherichia coli M-17 and visualization its interaction with the nanoparticles of zinc oxide. The suspension of E.coli bacteria was applied to natural mica and studied by contact mode using the FemtoScan multifunctional scanning probe microscope.

Diverse Mechanisms of Sulfur Decoration in Bacterial tRNA and Their Cellular Functions

PubMed Central

Zheng, Chenkang; Black, Katherine A.; Dos Santos, Patricia C.

2017-01-01

Sulfur-containing transfer ribonucleic acids (tRNAs) are ubiquitous biomolecules found in all organisms that possess a variety of functions. For decades, their roles in processes such as translation, structural stability, and cellular protection have been elucidated and appreciated. These thionucleosides are found in all types of bacteria; however, their biosynthetic pathways are distinct among different groups of bacteria. Considering that many of the thio-tRNA biosynthetic enzymes are absent in Gram-positive bacteria, recent studies have addressed how sulfur trafficking is regulated in these prokaryotic species. Interestingly, a novel proposal has been given for interplay among thionucleosides and the biosynthesis of other thiocofactors, through participation of shared-enzyme intermediates, the functions of which are impacted by the availability of substrate as well as metabolic demand of thiocofactors. This review describes the occurrence of thio-modifications in bacterial tRNA and current methods for detection of these modifications that have enabled studies on the biosynthesis and functions of S-containing tRNA across bacteria. It provides insight into potential modes of regulation and potential evolutionary events responsible for divergence in sulfur metabolism among prokaryotes. PMID:28327539

Lactoferricin B inhibits bacterial macromolecular synthesis in Escherichia coli and Bacillus subtilis.

PubMed

Ulvatne, Hilde; Samuelsen, Ørjan; Haukland, Hanne H; Krämer, Manuela; Vorland, Lars H

2004-08-15

Most antimicrobial peptides have an amphipathic, cationic structure, and an effect on the cytoplasmic membrane of susceptible bacteria has been postulated as the main mode of action. Other mechanisms have been reported, including inhibition of cellular functions by binding to DNA, RNA and proteins, and the inhibition of DNA and/or protein synthesis. Lactoferricin B (Lfcin B), a cationic peptide derived from bovine lactoferrin, exerts slow inhibitory and bactericidal activity and does not lyse susceptible bacteria, indicating a possible intracellular target. In the present study incorporation of radioactive precursors into DNA, RNA and proteins was used to demonstrate effects of Lfcin B on macromolecular synthesis in bacteria. In Escherichia coli UC 6782, Lfcin B induces an initial increase in protein and RNA synthesis and a decrease in DNA synthesis. After 10 min, the DNA-synthesis increases while protein and RNA-synthesis decreases significantly. In Bacillus subtilis, however, all synthesis of macromolecules is inhibited for at least 20 min. After 20 min RNA-synthesis increases. The results presented here show that Lfcin B at concentrations not sufficient to kill bacterial cells inhibits incorporation of radioactive precursors into macromolecules in both Gram-positive and Gram-negative bacteria.

Ferredoxin:thioredoxin reductase (FTR) links the regulation of oxygenic photosynthesis to deeply rooted bacteria.

PubMed

Balsera, Monica; Uberegui, Estefania; Susanti, Dwi; Schmitz, Ruth A; Mukhopadhyay, Biswarup; Schürmann, Peter; Buchanan, Bob B

2013-02-01

Uncovered in studies on photosynthesis 35 years ago, redox regulation has been extended to all types of living cells. We understand a great deal about the occurrence, function, and mechanism of action of this mode of regulation, but we know little about its origin and its evolution. To help fill this gap, we have taken advantage of available genome sequences that make it possible to trace the phylogenetic roots of members of the system that was originally described for chloroplasts-ferredoxin, ferredoxin:thioredoxin reductase (FTR), and thioredoxin as well as target enzymes. The results suggest that: (1) the catalytic subunit, FTRc, originated in deeply rooted microaerophilic, chemoautotrophic bacteria where it appears to function in regulating CO(2) fixation by the reverse citric acid cycle; (2) FTRc was incorporated into oxygenic photosynthetic organisms without significant structural change except for addition of a variable subunit (FTRv) seemingly to protect the Fe-S cluster against oxygen; (3) new Trxs and target enzymes were systematically added as evolution proceeded from bacteria through the different types of oxygenic photosynthetic organisms; (4) an oxygenic type of regulation preceded classical light-dark regulation in the regulation of enzymes of CO(2) fixation by the Calvin-Benson cycle; (5) FTR is not universally present in oxygenic photosynthetic organisms, and in certain early representatives is seemingly functionally replaced by NADP-thioredoxin reductase; and (6) FTRc underwent structural diversification to meet the ecological needs of a variety of bacteria and archaea.

Higher-order micro-fiber modes for Escherichia coli manipulation using a tapered seven-core fiber

PubMed Central

Rong, Qiangzhou; Zhou, Yi; Yin, Xunli; Shao, Zhihua; Qiao, Xueguang

2017-01-01

Optical manipulation using optical micro- and nano-fibers has shown potential for controlling bacterial activities such as E. coli trapping, propelling, and binding. Most of these manipulations have been performed using the propagation of the fundamental mode through the fiber. However, along the maximum mode-intensity axis, the higher-order modes have longer evanescent field extensions and larger field amplitudes at the fiber waist than the fundamental mode, opening up new possibilities for manipulating E. coli bacteria. In this work, a compact seven-core fiber (SCF)-based micro-fiber/optical tweezers was demonstrated for trapping, propelling, and rotating E. coli bacteria using the excitation of higher-order modes. The diameter of the SCF taper was 4 µm at the taper waist, which was much larger than that of previous nano-fiber tweezers. The laser wavelength was tunable from 1500 nm to 1600 nm, simultaneously causing photophoretic force, gradient force, and scattering force. This work provides a new opportunity for better understanding optical manipulation using higher-order modes at the single-cell level. PMID:28966849

Higher-order micro-fiber modes for Escherichia coli manipulation using a tapered seven-core fiber.

PubMed

Rong, Qiangzhou; Zhou, Yi; Yin, Xunli; Shao, Zhihua; Qiao, Xueguang

2017-09-01

Optical manipulation using optical micro- and nano-fibers has shown potential for controlling bacterial activities such as E. coli trapping, propelling, and binding. Most of these manipulations have been performed using the propagation of the fundamental mode through the fiber. However, along the maximum mode-intensity axis, the higher-order modes have longer evanescent field extensions and larger field amplitudes at the fiber waist than the fundamental mode, opening up new possibilities for manipulating E. coli bacteria. In this work, a compact seven-core fiber (SCF)-based micro-fiber/optical tweezers was demonstrated for trapping, propelling, and rotating E. coli bacteria using the excitation of higher-order modes. The diameter of the SCF taper was 4 µm at the taper waist, which was much larger than that of previous nano-fiber tweezers. The laser wavelength was tunable from 1500 nm to 1600 nm, simultaneously causing photophoretic force, gradient force, and scattering force. This work provides a new opportunity for better understanding optical manipulation using higher-order modes at the single-cell level.

Bacillus thuringiensis: A story of a successful bioinsecticide

PubMed Central

Bravo, Alejandra; Likitvivatanavong, Supaporn; Gill, Sarjeet S.; Soberón, Mario

2013-01-01

Bacillus thuringiensis (Bt) bacteria are insect pathogens that rely on insecticidal pore forming proteins known as Cry and Cyt toxins to kill their insect larval hosts. At least four different non-structurally related families of proteins form the Cry toxin group of toxins. The expression of certain Cry toxins in transgenic crops has contributed to an efficient control of insect pests resulting in a significant reduction in chemical insecticide use. The mode of action of the three domain Cry toxin family involves sequential interaction of these toxins with several insect midgut proteins facilitating the formation of a pre-pore oligomer structure and subsequent membrane insertion that leads to the killing of midgut insect cells by osmotic shock. In this manuscript we review recent progress in understanding the mode of action of this family of proteins in lepidopteran, dipteran and coleopteran insects. Interestingly, similar Cry-binding proteins have been identified in the three insect orders, as cadherin, aminopeptidase-N and alkaline phosphatase suggesting a conserved mode of action. Also, recent data on insect responses to Cry toxin attack is discussed. Finally, we review the different Bt based products, including transgenic crops, that are currently used in agriculture. PMID:21376122

Inactivation of Bacteria in Oil Field Injected Water by a Pulsed Plasma Discharge Process

NASA Astrophysics Data System (ADS)

Xin, Qing; Li, Zhongjian; Lei, Lecheng; Yang, Bin

2016-09-01

Pulsed plasma discharge was employed to inactivate bacteria in the injection water for an oil field. The effects of water conductivity and initial concentration of bacteria on elimination efficiency were investigated in the batch and continuous flow modes. It was demonstrated that Fe2+ contained in injection water could enhance the elimination efficiency greatly. The addition of reducing agent glutathione (GSH) indicated that active radicals generated by pulsed plasma discharges played an important role in the inactivation of bacteria. Moreover, it was found that the microbial inactivation process for both batch and continuous flow mode well fitted the model based on the Weibull's survival function. supported by Zhejiang Province Welfare Technology Applied Research Project of China (No. 2014C31137), National Natural Science Foundation of China (Nos. 21436007 and U1462201), and the Fundamental Research Funds for the Central Universities of China (No. 2015QNA4032)

Establishment of Lactobacillus plantarum strain in honey bee digestive tract monitored using gfp fluorescence.

PubMed

Javorský, P; Fecskeová, L Kolesár; Hrehová, L; Sabo, R; Legáth, J; Pristas, P

2017-04-26

Lactic acid bacteria are symbiotic bacteria that naturally reside in the gastrointestinal tract of honey bees. They serve a multitude of functions and are considered beneficial and completely harmless. In our experiments Lactobacillus plantarum strain B35, isolated from honey bee digestive tract, was modified using pAD43-25 plasmid carrying a functional GFP gene sequence (gfpmut3a) and used as a model for monitoring and optimisation of the mode of application. The establishment of this strain in honey bee digestive tract was monitored using GFP fluorescence. Three different modes of oral application of this strain were tested: water suspension of lyophilised bacteria, aerosol application of these bacteria and consumption of sugar honey paste containing the lyophilised lactobacilli. Two days after administration the L. plantarum B35-gfp was present throughout the honey bee digestive tract with 10 4 -10 5 cfu/bee with highest count observed for aerosol application.

Exploration of multiple Sortase A protein conformations in virtual screening

NASA Astrophysics Data System (ADS)

Gao, Chunxia; Uzelac, Ivana; Gottfries, Johan; Eriksson, Leif A.

2016-02-01

Methicillin resistant Staphylococcus aureus (MRSA) has become a major health concern which has brought about an urgent need for new therapeutic agents. As the S. aureus Sortase A (SrtA) enzyme contributes to the adherence of the bacteria to the host cells, inhibition thereof by small molecules could be employed as potential antivirulence agents, also towards resistant strains. Albeit several virtual docking SrtA campaigns have been reported, no strongly inhibitatory non-covalent binders have as yet emerged therefrom. In order to better understand the binding modes of small molecules, and the effect of different receptor structures employed in the screening, we herein report on an exploratory study employing 10 known binders and 500 decoys on 100 SrtA structures generated from regular or steered molecular dynamics simulations on four different SrtA crystal/NMR structures. The results suggest a correlation between the protein structural flexibility and the virtual screening performance, and confirm the noted immobilization of the β6/β7 loop upon substrate binding. The NMR structures reported appear to perform slightly better than the Xray-crystal structures, but the binding modes fluctuate tremendously, and it might be suspected that the catalytic site is not necessarily the preferred site of binding for some of the reported active compounds.

Exploration of multiple Sortase A protein conformations in virtual screening

PubMed Central

Gao, Chunxia; Uzelac, Ivana; Gottfries, Johan; Eriksson, Leif A.

2016-01-01

Methicillin resistant Staphylococcus aureus (MRSA) has become a major health concern which has brought about an urgent need for new therapeutic agents. As the S. aureus Sortase A (SrtA) enzyme contributes to the adherence of the bacteria to the host cells, inhibition thereof by small molecules could be employed as potential antivirulence agents, also towards resistant strains. Albeit several virtual docking SrtA campaigns have been reported, no strongly inhibitatory non-covalent binders have as yet emerged therefrom. In order to better understand the binding modes of small molecules, and the effect of different receptor structures employed in the screening, we herein report on an exploratory study employing 10 known binders and 500 decoys on 100 SrtA structures generated from regular or steered molecular dynamics simulations on four different SrtA crystal/NMR structures. The results suggest a correlation between the protein structural flexibility and the virtual screening performance, and confirm the noted immobilization of the β6/β7 loop upon substrate binding. The NMR structures reported appear to perform slightly better than the Xray-crystal structures, but the binding modes fluctuate tremendously, and it might be suspected that the catalytic site is not necessarily the preferred site of binding for some of the reported active compounds. PMID:26846342

Engineering monolayer poration for rapid exfoliation of microbial membranes.

PubMed

Pyne, Alice; Pfeil, Marc-Philipp; Bennett, Isabel; Ravi, Jascindra; Iavicoli, Patrizia; Lamarre, Baptiste; Roethke, Anita; Ray, Santanu; Jiang, Haibo; Bella, Angelo; Reisinger, Bernd; Yin, Daniel; Little, Benjamin; Muñoz-García, Juan C; Cerasoli, Eleonora; Judge, Peter J; Faruqui, Nilofar; Calzolai, Luigi; Henrion, Andre; Martyna, Glenn J; Grovenor, Chris R M; Crain, Jason; Hoogenboom, Bart W; Watts, Anthony; Ryadnov, Maxim G

2017-02-01

The spread of bacterial resistance to traditional antibiotics continues to stimulate the search for alternative antimicrobial strategies. All forms of life, from bacteria to humans, are postulated to rely on a fundamental host defense mechanism, which exploits the formation of open pores in microbial phospholipid bilayers. Here we predict that transmembrane poration is not necessary for antimicrobial activity and reveal a distinct poration mechanism that targets the outer leaflet of phospholipid bilayers. Using a combination of molecular-scale and real-time imaging, spectroscopy and spectrometry approaches, we introduce a structural motif with a universal insertion mode in reconstituted membranes and live bacteria. We demonstrate that this motif rapidly assembles into monolayer pits that coalesce during progressive membrane exfoliation, leading to bacterial cell death within minutes. The findings offer a new physical basis for designing effective antibiotics.

Crystal Structure of 4,6-α-Glucanotransferase Supports Diet-Driven Evolution of GH70 Enzymes from α-Amylases in Oral Bacteria.

PubMed

Bai, Yuxiang; Gangoiti, Joana; Dijkstra, Bauke W; Dijkhuizen, Lubbert; Pijning, Tjaard

2017-02-07

Food processing and refining has dramatically changed the human diet, but little is known about whether this affected the evolution of enzymes in human microbiota. We present evidence that glycoside hydrolase family 70 (GH70) glucansucrases from lactobacilli, synthesizing α-glucan-type extracellular polysaccharides from sucrose, likely evolved from GH13 starch-acting α-amylases, via GH70 4,6-α-glucanotransferases. The crystal structure of a 4,6-α-glucanotransferase explains the mode of action and unique product specificity of these enzymes. While the α-amylase substrate-binding scaffold is retained, active-site loops adapted to favor transglycosylation over hydrolysis; the structure also gives clues as to how 4,6-α-glucanotransferases may have evolved further toward sucrose utilization instead of starch. Further supported by genomic, phylogenetic, and in vivo studies, we propose that dietary changes involving starch (and starch derivatives) and sucrose intake were critical factors during the evolution of 4,6-α-GTs and glucansucrases from α-amylases, allowing oral bacteria to produce extracellular polymers that contribute to biofilm formation from different substrates. Copyright © 2017 Elsevier Ltd. All rights reserved.

Nocturnal Production of Endospores in Natural Populations of Epulopiscium-Like Surgeonfish Symbionts

PubMed Central

Flint, Joseph F.; Drzymalski, Dan; Montgomery, W. Linn; Southam, Gordon; Angert, Esther R.

2005-01-01

Prior studies have described a morphologically diverse group of intestinal microorganisms associated with surgeonfish. Despite their diversity of form, 16S rRNA gene surveys and fluorescent in situ hybridizations indicate that these bacteria are low-G+C gram-positive bacteria related to Epulopiscium spp. Many of these bacteria exhibit an unusual mode of reproduction, developing multiple offspring intracellularly. Previous reports have suggested that some Epulopiscium-like symbionts produce dormant or phase-bright intracellular offspring. Close relatives of Epulopiscium, such as Metabacterium polyspora and Clostridium lentocellum, are endospore-forming bacteria, which raises the possibility that the phase-bright offspring are endospores. Structural evidence and the presence of dipicolinic acid demonstrate that phase-bright offspring of Epulopiscium-like bacteria are true endospores. In addition, endospores are formed as part of the normal daily life cycle of these bacteria. In the populations studied, mature endospores were seen only at night and the majority of cells in a given population produced one or two endospores per mother cell. Phylogenetic analyses confirmed the close relationship between the endospore-forming surgeonfish symbionts characterized here and previously described Epulopiscium spp. The broad distribution of endospore formation among the Epulopiscium phylogenetic group raises the possibility that sporulation is a characteristic of the group. We speculate that spore formation in Epulopiscium-like symbionts may be important for dispersal and may also enhance survival in the changing conditions of the fish intestinal tract. PMID:16237029

Small angle X-ray scattering as a high-throughput method to classify antimicrobial modes of action.

PubMed

von Gundlach, A R; Garamus, V M; Gorniak, T; Davies, H A; Reischl, M; Mikut, R; Hilpert, K; Rosenhahn, A

2016-05-01

Multi-drug resistant bacteria are currently undermining our health care system worldwide. While novel antimicrobial drugs, such as antimicrobial peptides, are urgently needed, identification of new modes of action is money and time consuming, and in addition current approaches are not available in a high throughput manner. Here we explore how small angle X-ray scattering (SAXS) as high throughput method can contribute to classify the mode of action for novel antimicrobials and therefore supports fast decision making in drug development. Using data bases for natural occurring antimicrobial peptides or predicting novel artificial peptides, many candidates can be discovered that will kill a selected target bacterium. However, in order to narrow down the selection it is important to know if these peptides follow all the same mode of action. In addition, the mode of action should be different from conventional antibiotics, in consequence peptide candidates can be developed further into drugs against multi-drug resistant bacteria. Here we used one short antimicrobial peptide with unknown mode of action and compared the ultrastructural changes of Escherichia coli cells after treatment with the peptide to cells treated with classic antibiotics. The key finding is that SAXS as a structure sensitive tool provides a rapid feedback on drug induced ultrastructural alterations in whole E. coli cells. We could demonstrate that ultrastructural changes depend on the used antibiotics and their specific mode of action. This is demonstrated using several well characterized antimicrobial compounds and the analysis of resulting SAXS curves by principal component analysis. To understand the result of the PCA analysis, the data is correlated with TEM images. In contrast to real space imaging techniques, SAXS allows to obtain nanoscale information averaged over approximately one million cells. The measurement takes only seconds, while conventional tests to identify a mode of action require days or weeks per single substance. The antimicrobial peptide showed a different mode of action as all tested antibiotics including polymyxin B and is therefore a good candidate for further drug development. We envision SAXS to become a useful tool within the high-throughput screening pipeline of modern drug discovery. This article is part of a Special Issue entitled: Antimicrobial peptides edited by Karl Lohner and Kai Hilpert. Copyright © 2015 Elsevier B.V. All rights reserved.

The Functional Implications of Bottom Up and Top Down Controls on Marine Bacteria in Arthur Harbor, a Highly Productive Coastal Setting on the West Antarctic Peninsula

NASA Astrophysics Data System (ADS)

Bowman, J. S.; Amaral-Zettler, L. A.; Rich, J. J.; Luria, C.; Ducklow, H. W.

2016-02-01

Marine bacteria can be broadly classified into two groups based on their ecology; slow growing oligotrophic specialists and fast growing copiotrophs. These ecological strategies are associated with specific taxonomic and functional groups, making it possible to use 16S rRNA gene amplicon and shotgun metagenomic data to qualitatively, and possibly quantitatively, identify the contribution of each strategy to marine biogeochemical cycles. We leveraged a 5-year (2009 to 2014) time series of 16S rRNA gene amplicon data for Arthur Harbor, located near Palmer Station, Antarctica, to identify trends in the abundance of taxa associated with each ecological strategy. Using emergent self-organizing maps, we identified four recurring "modes" in bacterial community structure based on the relative abundance of the ubiquitous SAR11 clade. A different bacterial genus was dominant in each mode; Pelagibacter, Polaribacter, Roseobacter, and Colwellia. To explore the functional implications of these different modes we applied shotgun metagenomics and functional predictions using the newly available tool PAPRICA, in combination with flow cytometry and estimates of bacterial production. Our annotation and assembly of binned contigs corresponding to the dominant genera illuminate the succession of metabolic functions across the 2013-2014 austral summer and inform the timing of autotrophic and mixotrophic (putatively bacterivorous) phytoplankton blooms. Surprisingly, while the abundance of Pelagibacter 16S rRNA gene reads was negatively correlated with the concentration of chlorophyll a, the ratio of Pelagibacter to Polaribacter and Roseobacter was poorly correlated with the ratio of high nucleic acid (HNA) to low nucleic acid (LNA) bacteria as determined by flow cytometry, and the relative size of the HNA population at times contrasted sharply with chlorophyll a. These findings suggest that the physiological state of bacterial cells and top down controls play a strong role in HNA: LNA dynamics.

The Cyclic Antibacterial Peptide Enterocin AS-48: Isolation, Mode of Action, and Possible Food Applications.

PubMed

Grande Burgos, María José; Pulido, Rubén Pérez; Del Carmen López Aguayo, María; Gálvez, Antonio; Lucas, Rosario

2014-12-08

Enterocin AS-48 is a circular bacteriocin produced by Enterococcus. It contains a 70 amino acid-residue chain circularized by a head-to-tail peptide bond. The conformation of enterocin AS-48 is arranged into five alpha-helices with a compact globular structure. Enterocin AS-48 has a wide inhibitory spectrum on Gram-positive bacteria. Sensitivity of Gram-negative bacteria increases in combination with outer-membrane permeabilizing treatments. Eukaryotic cells are bacteriocin-resistant. This cationic peptide inserts into bacterial membranes and causes membrane permeabilization, leading ultimately to cell death. Microarray analysis revealed sets of up-regulated and down-regulated genes in Bacillus cereus cells treated with sublethal bacteriocin concentration. Enterocin AS-48 can be purified in two steps or prepared as lyophilized powder from cultures in whey-based substrates. The potential applications of enterocin AS-48 as a food biopreservative have been corroborated against foodborne pathogens and/or toxigenic bacteria (Listeria monocytogenes, Bacillus cereus, Staphylococcus aureus, Escherichia coli, Salmonella enterica) and spoilage bacteria (Alicyclobacillus acidoterrestris, Bacillus spp., Paenibacillus spp., Geobacillus stearothermophilus, Brochothrix thermosphacta, Staphylococcus carnosus, Lactobacillus sakei and other spoilage lactic acid bacteria). The efficacy of enterocin AS-48 in food systems increases greatly in combination with chemical preservatives, essential oils, phenolic compounds, and physico-chemical treatments such as sublethal heat, high-intensity pulsed-electric fields or high hydrostatic pressure.

The Cyclic Antibacterial Peptide Enterocin AS-48: Isolation, Mode of Action, and Possible Food Applications

PubMed Central

Grande Burgos, María José; Pérez Pulido, Rubén; López Aguayo, María del Carmen; Gálvez, Antonio; Lucas, Rosario

2014-01-01

Enterocin AS-48 is a circular bacteriocin produced by Enterococcus. It contains a 70 amino acid-residue chain circularized by a head-to-tail peptide bond. The conformation of enterocin AS-48 is arranged into five alpha-helices with a compact globular structure. Enterocin AS-48 has a wide inhibitory spectrum on Gram-positive bacteria. Sensitivity of Gram-negative bacteria increases in combination with outer-membrane permeabilizing treatments. Eukaryotic cells are bacteriocin-resistant. This cationic peptide inserts into bacterial membranes and causes membrane permeabilization, leading ultimately to cell death. Microarray analysis revealed sets of up-regulated and down-regulated genes in Bacillus cereus cells treated with sublethal bacteriocin concentration. Enterocin AS-48 can be purified in two steps or prepared as lyophilized powder from cultures in whey-based substrates. The potential applications of enterocin AS-48 as a food biopreservative have been corroborated against foodborne pathogens and/or toxigenic bacteria (Listeria monocytogenes, Bacillus cereus, Staphylococcus aureus, Escherichia coli, Salmonella enterica) and spoilage bacteria (Alicyclobacillus acidoterrestris, Bacillus spp., Paenibacillus spp., Geobacillus stearothermophilus, Brochothrix thermosphacta, Staphylococcus carnosus, Lactobacillus sakei and other spoilage lactic acid bacteria). The efficacy of enterocin AS-48 in food systems increases greatly in combination with chemical preservatives, essential oils, phenolic compounds, and physico-chemical treatments such as sublethal heat, high-intensity pulsed-electric fields or high hydrostatic pressure. PMID:25493478

Fragmentation modes and the evolution of life cycles.

PubMed

Pichugin, Yuriy; Peña, Jorge; Rainey, Paul B; Traulsen, Arne

2017-11-01

Reproduction is a defining feature of living systems. To reproduce, aggregates of biological units (e.g., multicellular organisms or colonial bacteria) must fragment into smaller parts. Fragmentation modes in nature range from binary fission in bacteria to collective-level fragmentation and the production of unicellular propagules in multicellular organisms. Despite this apparent ubiquity, the adaptive significance of fragmentation modes has received little attention. Here, we develop a model in which groups arise from the division of single cells that do not separate but stay together until the moment of group fragmentation. We allow for all possible fragmentation patterns and calculate the population growth rate of each associated life cycle. Fragmentation modes that maximise growth rate comprise a restrictive set of patterns that include production of unicellular propagules and division into two similar size groups. Life cycles marked by single-cell bottlenecks maximise population growth rate under a wide range of conditions. This surprising result offers a new evolutionary explanation for the widespread occurrence of this mode of reproduction. All in all, our model provides a framework for exploring the adaptive significance of fragmentation modes and their associated life cycles.

Fragmentation modes and the evolution of life cycles

PubMed Central

Rainey, Paul B.

2017-01-01

Reproduction is a defining feature of living systems. To reproduce, aggregates of biological units (e.g., multicellular organisms or colonial bacteria) must fragment into smaller parts. Fragmentation modes in nature range from binary fission in bacteria to collective-level fragmentation and the production of unicellular propagules in multicellular organisms. Despite this apparent ubiquity, the adaptive significance of fragmentation modes has received little attention. Here, we develop a model in which groups arise from the division of single cells that do not separate but stay together until the moment of group fragmentation. We allow for all possible fragmentation patterns and calculate the population growth rate of each associated life cycle. Fragmentation modes that maximise growth rate comprise a restrictive set of patterns that include production of unicellular propagules and division into two similar size groups. Life cycles marked by single-cell bottlenecks maximise population growth rate under a wide range of conditions. This surprising result offers a new evolutionary explanation for the widespread occurrence of this mode of reproduction. All in all, our model provides a framework for exploring the adaptive significance of fragmentation modes and their associated life cycles. PMID:29166656

Living together in biofilms: the microbial cell factory and its biotechnological implications.

PubMed

Berlanga, Mercedes; Guerrero, Ricardo

2016-10-01

In nature, bacteria alternate between two modes of growth: a unicellular life phase, in which the cells are free-swimming (planktonic), and a multicellular life phase, in which the cells are sessile and live in a biofilm, that can be defined as surface-associated microbial heterogeneous structures comprising different populations of microorganisms surrounded by a self-produced matrix that allows their attachment to inert or organic surfaces. While a unicellular life phase allows for bacterial dispersion and the colonization of new environments, biofilms allow sessile cells to live in a coordinated, more permanent manner that favors their proliferation. In this alternating cycle, bacteria accomplish two physiological transitions via differential gene expression: (i) from planktonic cells to sessile cells within a biofilm, and (ii) from sessile to detached, newly planktonic cells. Many of the innate characteristics of biofilm bacteria are of biotechnological interest, such as the synthesis of valuable compounds (e.g., surfactants, ethanol) and the enhancement/processing of certain foods (e.g., table olives). Understanding the ecology of biofilm formation will allow the design of systems that will facilitate making products of interest and improve their yields.

Quantitative fluorescent in-situ hybridization: a hypothesized competition mode between two dominant bacteria groups in hydrogen-producing anaerobic sludge processes.

PubMed

Huang, C-L; Chen, C-C; Lin, C-Y; Liu, W-T

2009-01-01

Two hydrogen-producing continuous flow stirred tank reactors (CSTRs) fed respectively with glucose and sucrose were investigated by polymerase chain reaction-denatured gradient gel electrophoresis (PCR-DGGE) and fluorescent in-situ hybridization (FISH). The substrate was fed in a continuous mode decreased from hydraulic retention time (HRT) 10 hours to 6, 5, 4, 3, and 2 hours. Quantitative fluorescent in-situ hybridization (FISH) observations further demonstrated that two morphotypes of bacteria dominated both microbial communities. One was long rod bacteria which can be targeted either by Chis150 probe designed to hybridize the gram positive low G + C bacteria or the specific oligonucleotide probe Lg10-6. The probe Lg10-6, affiliated with Clostridium pasteurianum, was designed and then checked with other reference organisms. The other type, unknown group, which cannot be detected by Chis150 was curved rod bacteria. Notably, the population ratios of the two predominant groups reflected the different operational performance of the two reactors, such as hydrogen producing rates, substrate turnover rates and metabolites compositions. Therefore, a competition mode of the two dominant bacteria groups was hypothesized. In the study, 16S rRNA-based gene library of hydrogen-producing microbial communities was established. The efficiency of hydrogen yields was correlated with substrates (glucose or sucrose), HRT, metabolites compositions (acetate, propionate, butyrate and ethanol), thermal pre-treatment (seed biomass was heated at 100 degrees C for 45 minutes), and microbial communities in the bioreactor, not sludge sources (municipal sewage sludge, alcohol-processing sludge, or bean-processing sludge). The designed specific oligonucleotide probe Lg10-6 also provides us a useful and fast molecular tool to screen hydrogen-producing microbial communities in the future research.

Antimicrobial Peptides Targeting Gram-Positive Bacteria

PubMed Central

Malanovic, Nermina; Lohner, Karl

2016-01-01

Antimicrobial peptides (AMPs) have remarkably different structures as well as biological activity profiles, whereupon most of these peptides are supposed to kill bacteria via membrane damage. In order to understand their molecular mechanism and target cell specificity for Gram-positive bacteria, it is essential to consider the architecture of their cell envelopes. Before AMPs can interact with the cytoplasmic membrane of Gram-positive bacteria, they have to traverse the cell wall composed of wall- and lipoteichoic acids and peptidoglycan. While interaction of AMPs with peptidoglycan might rather facilitate penetration, interaction with anionic teichoic acids may act as either a trap for AMPs or a ladder for a route to the cytoplasmic membrane. Interaction with the cytoplasmic membrane frequently leads to lipid segregation affecting membrane domain organization, which affects membrane permeability, inhibits cell division processes or leads to delocalization of essential peripheral membrane proteins. Further, precursors of cell wall components, especially the highly conserved lipid II, are directly targeted by AMPs. Thereby, the peptides do not inhibit peptidoglycan synthesis via binding to proteins like common antibiotics, but form a complex with the precursor molecule, which in addition can promote pore formation and membrane disruption. Thus, the multifaceted mode of actions will make AMPs superior to antibiotics that act only on one specific target. PMID:27657092

[Bacterial diversity in sequencing batch biofilm reactor (SBBR) for landfill leachate treatment using PCR-DGGE].

PubMed

Xiao, Yong; Yang, Zhao-hui; Zeng, Guang-ming; Ma, Yan-he; Liu, You-sheng; Wang, Rong-juan; Xu, Zheng-yong

2007-05-01

For studying the bacterial diversity and the mechanism of denitrification in sequencing bath biofilm reactor (SBBR) treating landfill leachate to provide microbial evidence for technique improvements, total microbial DNA was extracted from samples which were collected from natural landfill leachate and biofilm of a SBBR that could efficiently remove NH4+ -N and COD of high concentration. 16S rDNA fragments were amplified from the total DNA successfully using a pair of universal bacterial 16S rDNA primer, GC341F and 907R, and then were used for denaturing gradient gel electrophoresis (DGGE) analysis. The bands in the gel were analyzed by statistical methods and excided from the gel for sequencing, and the sequences were used for homology analysis and then two phylogenetic trees were constructed using DNAStar software. Results indicated that the bacterial diversity of the biofilm in SBBR and the landfill leachate was abundant, and no obvious change of community structure happened during running in the biofilm, in which most bacteria came from the landfill leachate. There may be three different modes of denitrification in the reactor because several different nitrifying bacteria, denitrifying bacteria and anaerobic ammonia oxidation bacteria coexisted in it. The results provided some valuable references for studying microbiological mechanism of denitrification in SBBR.

Physical mode of bacteria and virus coevolution

NASA Astrophysics Data System (ADS)

Han, Pu; Niestemski, Liang; Deem, Michael

2013-03-01

Single-cell hosts such as bacteria or archaea possess an adaptive, heritable immune system that protects them from viral invasion. This system, known as the CRISPR-Cas system, allows the host to recognize and incorporate short foreign DNA or RNA sequences from viruses or plasmids. The sequences form what are called ``spacers'' in the CRISPR. Spacers in the CRISPR loci provide a record of the host and predator coevolution history. We develop a physical model to study the dynamics of this coevolution due to immune pressure. Hosts and viruses reproduce, die, and evolve due to viral infection pressure, host immune pressure, and mutation. We will discuss the differing effects of point mutation and recombination on CRISPR evolution. We will also discuss the effect of different spacer deletion mechanisms. We will describe population structure of hosts and viruses, how spacer diversity depends on position within CRISPR, and match of the CRISPR spacers to the virus population.

Mycobacterium biofilms: factors involved in development, dispersal, and therapeutic strategies against biofilm-relevant pathogens.

PubMed

Xiang, Xiaohong; Deng, Wanyan; Liu, Minqiang; Xie, Jianping

2014-01-01

Many bacteria can develop biofilm (BF), a multicellular structure largely combining bacteria and their extracellular polymeric substances (EPS). The formation of biofilm results in an alternative existence in which microbes ensure their survival in adverse environments. Biofilm-relevant infections are more persistent, resistant to most antibiotics, and more recalcitrant to host immunity. Mycobacterium tuberculosis, the causative agent of tuberculosis, can develop biofilm, though whether M. tuberculosis can form biofilm within tuberculosis patients has yet to be determined. Here, we summarize the factors involved in the development and dispersal of mycobacterial biofilms, as well as underlying regulatory factors and inhibitors against biofilm to deepen our understanding of their development and to elucidate potential novel modes of action for future antibiotics. Key factors in biofilm formation identified as drug targets represent a novel and promising avenue for developing better antibiotics.

Comparative evaluation of antimicrobial effects of Er:YAG, diode, and CO₂ lasers on titanium discs: an experimental study.

PubMed

Tosun, Emre; Tasar, Ferda; Strauss, Robert; Kıvanc, Dolunay Gulmez; Ungor, Cem

2012-05-01

This study examined carbon dioxide (CO(2); 10,600 nm), diode (808 nm), and erbium (Er):yttrium-aluminum-garnet (YAG; 2,940 nm) laser applications on Staphylococcus aureus contaminated, sandblasted, large-grit, acid-etched surface titanium discs and performed a comparative evaluation of the obtained bactericidal effects and the applicability of these effects in clinical practice. This study was carried out in 5 main groups: Er:YAG laser in very short pulse (VSP) emission mode, Er:YAG laser in short pulse (SP) emission mode, diode laser with a 320-nm fiber optic diode laser with an R24-B handpiece, and CO(2) laser. After laser irradiation, dilutions were spread on sheep blood agar plates and, after an incubation period of 24 hours, colony-forming units were counted and compared with the control group, and the bactericidal activity was assessed in relation to the colony counts. The CO(2) laser eliminated 100% of the bacteria at 6 W, 20 Hz, and a 10-ms exposure time/pulse with a 10-second application period (0.8-mm spot size). The continuous-wave diode laser eliminated 97% of the bacteria at 1 W using a 10-second application with a 320-μm optic fiber, 100% of the bacteria were killed with a 1-W, 10-second continuous-wave application with an R14-B handpiece. The Er:YAG laser eliminated 100% of the bacteria at 90 mJ and 10 Hz using a 10-second application in a superpulse mode (300-ms exposure time/pulse). The Er:YAG laser also eliminated 99% to 100% of the bacteria in VSP mode at 90 mJ and 10 Hz with a 10-second application. The results of this study show that a complete, or near complete, elimination of surface bacteria on titanium surfaces can be accomplished in vitro using a CO(2), diode, or Er:YAG laser as long as appropriate parameters are used. Copyright © 2012 American Association of Oral and Maxillofacial Surgeons. All rights reserved.

Effects of Bacteria on Artemia franciscana Cultured in Different Gnotobiotic Environments

PubMed Central

Marques, Antonio; Dinh, Thi; Ioakeimidis, Christos; Huys, Geert; Swings, Jean; Verstraete, Willy; Dhont, Jean; Sorgeloos, Patrick; Bossier, Peter

2005-01-01

The use of probiotics is receiving considerable attention as an alternative approach to control microbiota in aquaculture farms, especially in hatching facilities. However, application with consistent results is hampered by insufficient information on their modes of action. To investigate whether dead bacteria (allowing investigation of their nutritional effect) or live bacteria (allowing evaluation of their probiotic effect) have any beneficial effect towards Artemia franciscana and, subsequently, if live bacteria have probiotic effects beyond the effects observed with dead bacteria, a model system was employed using gnotobiotic Artemia as a test organism. Nauplii were cultured in the presence of 10 bacterial strains combined with four different major axenic live feeds (two strains of Saccharomyces cerevisiae and two strains of Dunaliella tertiolecta) differing in their nutritional values. In combination with poor- and medium-quality live feeds, dead bacteria exerted a strong effect on Artemia survival but a rather weak or no effect on individual length and constituted a maximum of only 5.9% of the total ash-free dry weight supplied. These effects were reduced or even disappeared when medium- to good-quality major feed sources were used, possibly due to improvements in the health status of Artemia. Some probiotic bacteria, such as GR 8 (Cytophaga spp.), improved (not always significantly) the performance of nauplii beyond the effect observed with dead bacteria, independently of the feed supplied. The present approach can be an excellent system to study the exact mode of action of bacteria, especially if combined with challenge tests or other types of analysis (e.g., transcriptome and proteonomic analysis). PMID:16085818

Chitinase producing bacteria with direct algicidal activity on marine diatoms

PubMed Central

Li, Yi; Lei, Xueqian; Zhu, Hong; Zhang, Huajun; Guan, Chengwei; Chen, Zhangran; Zheng, Wei; Fu, Lijun; Zheng, Tianling

2016-01-01

Chitinase producing bacteria can involve extensively in nutrient cycling and energy flow in the aquatic environment through degradation and utilization of chitin. It is well known that diatoms cells are encased by box-like frustules composed of chitin. Thus the chitin containing of diatoms shall be a natural target of chitinase producing bacteria, however, the interaction between these two organismic groups has not been studied thus far. Therefore, in this study, the algicidal mechanism of one chitinase producing bacterium (strain LY03) on Thalassiosira pseudonana was investigated. The algicidal range and algicidal mode of strain LY03 were first studied, and then bacterial viability, chemotactic ability and direct interaction characteristic between bacteria and diatom were also confirmed. Finally, the characteristic of the intracellular algicidal substance was identified and the algicidal mechanism was determined whereby algicidal bacterial cells showed chemotaxis to algal cells, fastened themselves on algal cells with their flagella, and then produced chitinase to degrade algal cell walls, and eventually caused algal lysis and death. It is the first time to investigate the interaction between chitinase producing bacteria and diatoms, and this novel special interaction mode was confirmed in this study, which will be helpful in protection and utilization of diatoms resources. PMID:26902175

Chitinase producing bacteria with direct algicidal activity on marine diatoms.

PubMed

Li, Yi; Lei, Xueqian; Zhu, Hong; Zhang, Huajun; Guan, Chengwei; Chen, Zhangran; Zheng, Wei; Fu, Lijun; Zheng, Tianling

2016-02-23

Chitinase producing bacteria can involve extensively in nutrient cycling and energy flow in the aquatic environment through degradation and utilization of chitin. It is well known that diatoms cells are encased by box-like frustules composed of chitin. Thus the chitin containing of diatoms shall be a natural target of chitinase producing bacteria, however, the interaction between these two organismic groups has not been studied thus far. Therefore, in this study, the algicidal mechanism of one chitinase producing bacterium (strain LY03) on Thalassiosira pseudonana was investigated. The algicidal range and algicidal mode of strain LY03 were first studied, and then bacterial viability, chemotactic ability and direct interaction characteristic between bacteria and diatom were also confirmed. Finally, the characteristic of the intracellular algicidal substance was identified and the algicidal mechanism was determined whereby algicidal bacterial cells showed chemotaxis to algal cells, fastened themselves on algal cells with their flagella, and then produced chitinase to degrade algal cell walls, and eventually caused algal lysis and death. It is the first time to investigate the interaction between chitinase producing bacteria and diatoms, and this novel special interaction mode was confirmed in this study, which will be helpful in protection and utilization of diatoms resources.

Exobiology Robotics Laboratory to Search for Life on Martian Subsurface Water and Permafrost

NASA Astrophysics Data System (ADS)

Gan, D. C.; Kuznetz, L.; Chu, D.; Chang, V.; Yamada, M.; Lee, C.; Lee, R.

2000-07-01

A conceptual design of a robotics laboratory was constructed to search for life forms in Martian subsurface water and permafrost by cultivation of bacteria by using a variety of media to grow bacteria of the Archea group and Eubacteria. Other growth, morphology, motility and mode of reproduction of bacteria and organisms of the Protista will be observed with microscopy. The entire operations is controlled by a computer.

Developing Pantetheinase-Resistant Pantothenamide Antibacterials: Structural Modification Impacts on PanK Interaction and Mode of Action.

PubMed

Barnard, Leanne; Mostert, Konrad J; van Otterlo, Willem A L; Strauss, Erick

2018-05-11

Pantothenamides (PanAms) are analogues of pantothenate, the biosynthetic precursor of coenzyme A (CoA), and show potent antimicrobial activity against several bacteria and the malaria parasite in vitro. However, pantetheinase enzymes that normally degrade pantetheine in human serum also act on the PanAms, thereby reducing their potency. In this study, we designed analogues of the known antibacterial PanAm N-heptylpantothenamide (N7-Pan) to be resistant to pantetheinase by using three complementary structural modification strategies. We show that, while two of these are effective in imparting resistance, the introduced modifications have an impact on the analogues' interaction with pantothenate kinase (PanK, the first CoA biosynthetic enzyme), which acts as a metabolic activator and/or target of the PanAms. This, in turn, directly affects their mode of action. Importantly, we discover that the phosphorylated version of N7-Pan shows pantetheinase resistance and antistaphylococcal activity, providing a lead for future studies in the ongoing search of PanAm analogues that show in vivo efficacy.

A novel rhamno-mannan exopolysaccharide isolated from biofilms of Burkholderia multivorans C1576.

PubMed

Dolfi, Stefania; Sveronis, Aris; Silipo, Alba; Rizzo, Roberto; Cescutti, Paola

2015-06-26

Burkholderia multivorans C1576 is a Gram negative opportunistic pathogen causing serious lung infection in cystic fibrosis patients. Considering that bacteria naturally form biofilms, and exopolysaccharides are recognized as important factors for biofilm architecture set-up, B. multivorans was grown both in biofilm and in non-biofilm mode on two different media in order to compare the exopolysaccharides biosynthesized in these different experimental conditions. The exopolysaccharides produced were purified and their structure was determined resorting mainly to NMR spectroscopy, ESI mass spectrometry and gas chromatography coupled to mass spectrometry. The experimental data showed that both in biofilm and non-biofilm mode B. multivorans C1576 produced a novel exopolysaccharide having the following structure: [Formula: see text]. About 50% of the 2-linked rhamnose residues are substituted on C-3 with a methyl ether group. The high percentage of deoxysugar Rha units, coupled with OMe substitutions, suggest a possible role for polymer domains with marked hydrophobic characteristics able to create exopolysaccharide junction zones favouring the stability of the biofilm matrix. Copyright © 2015 Elsevier Ltd. All rights reserved.

Characterizing the structure-function relationship reveals the mode of action of a novel antimicrobial peptide, P1, from jumper ant Myrmecia pilosula.

PubMed

Tseng, Tien-Sheng; Tsai, Keng-Chang; Chen, Chinpan

2017-06-01

Microbial infections of antibiotic-resistant strains cause serious diseases and have a significant impact on public health worldwide, so novel antimicrobial drugs are urgently needed. Insect venoms, a rich source of bioactive components containing antimicrobial peptides (AMPs), are attractive candidates for new therapeutic agents against microbes. Recently, a novel peptide, P1, identified from the venom of the Australian jumper ant Myrmecia pilosula, showed potent antimicrobial activities against both Gram-negative and Gram-positive bacteria, but its structure-function relationship is unknown. Here, we used biochemical and biophysical techniques coupled with computational simulations to explore the mode of action of P1 interaction with dodecylphosphocholine (DPC) micelles as a model membrane system. Our circular dichroism (CD) and NMR studies revealed an amphipathic α-helical structure for P1 upon interaction with DPC micelles. A paramagnetic relaxation enhancement approach revealed that P1 orients its α-helix segment (F6-G14) into DPC micelles. In addition, the α-helix segment could be essential for membrane permeabilization and antimicrobial activity. Moreover, the arginine residues R8, R11, and R15 significantly contribute to helix formation and membrane-binding affinity. The lysine residue K19 of the C-terminus functionally guides P1 to interact with DPC micelles in the early interaction stage. Our study provides insights into the mode of action of P1, which is valuable in modifying and developing potent AMPs as antibiotic drugs.

Stimulated phase-shift acoustic nanodroplets enhance vancomycin efficacy against methicillin-resistant Staphylococcus aureus biofilms.

PubMed

Guo, Hao; Wang, Ziming; Du, Quanyin; Li, Pan; Wang, Zhigang; Wang, Aimin

2017-01-01

Bacterial biofilms on the surface of prostheses are becoming a rising concern in managing prosthetic joint infections. The inherent resistant features of biofilms render traditional antimicrobial therapy unproductive and revision surgery outcomes uncertain. This situation has prompted the exploration of novel antimicrobial strategies. The synergy of ultrasound microbubbles and vancomycin has been proposed as an efficient alternative for biofilm eradication. The purpose of this study was to evaluate the anti-biofilm effect of stimulated phase-shift acoustic nanodroplets (NDs) combined with vancomycin. We fabricated lipid phase-shift NDs with a core of liquid perfluoropentane. A new phase change mode for NDs incorporating an initial unfocused low-intensity pulsed ultrasound for 5 minutes and a subsequent incubation at 37°C into a 24-hour duration was developed. Methicillin-resistant Staphylococcus aureus (MRSA) biofilms were incubated with vancomycin and NDs under the hybrid stimulation. Biofilm morphology following treatment was determined using confocal laser scanning microscopy and scanning electron microscopy. Resazurin assay was used to quantify bactericidal efficacy against MRSA biofilm bacteria. NDs treated sequentially with ultrasound and heating at 37°C achieved gradual and substantial ND vaporization and cavitation in a successive process. NDs after stimulation were capable of generating stronger destruction on biofilm structure which was best characterized by residual circular arc margins and more dead bacteria. Furthermore, NDs combined with vancomycin contributed to significantly decreasing the metabolic activity of bacteria in MRSA biofilms ( P <0.05). Phase-shift acoustic NDs could exert a significant bactericidal effect against MRSA biofilms through a new stimulation mode. Acoustic NDs present advantages over microbubbles for biofilm damage. This anti-biofilm strategy could be used either alone or as an enhancer of traditional antibiotics in the control of prosthetic joint infections.

Hyperthermia studies using inductive and ultrasound methods on E. coli bacteria and mouse glioma cells

NASA Astrophysics Data System (ADS)

Cabral-Prieto, A.; López-Callejas, R.; Rodríguez-Méndez, B. G.; Santos-Cuevas, C. L.; Celis-Almazán, J.; Olea-Mejía, O.; Gómez-Morales, J. L.; Peña-Eguiluz, R.; Valencia-Alvarado, R.; Mercado-Cabrera, A.; Muñoz-Castro, A. E.; García-Santibañez, F.

2017-11-01

The survival of Escherichia coli bacteria and mouse glioma cells were studied under different temperatures using direct heating in water, ultrasound, and magnetic fluid hyperthermia. The survival of these microorganisms depended on whether the heating mode was continuous or discontinuous, surviving more in the former than in the discontinuous heating mode. Whereas Escherichia coli bacteria did not survive at temperatures ≥50∘C, the mouse glioma cells did not survive at temperatures ≥48∘C. The survival of both these microorganisms was independent of the presence or absence of the magnetic nanoparticles of magnetite, suggesting that these, having mean particle sizes of 9.5, 8.5 and 5, did not show any apparent cytotoxicity effect. Present results also showed that the inductive heating system which used a radiofrequency of 13.56 MHz, providing a maximum magnetic field strength of 160 A/m, the electric rather than magnetic heating predominated.

Interpretation of mutation induction by accelerated heavy ions in bacteria

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kozubek, S.; Ryznar, L.; Horneck, G.

In this report, a quantitative interpretation of mutation induction cross sections by heavy charged particles in bacterial cells is presented. The approach is based on the calculation of the fraction of energy deposited by indirect hits in the sensitive structure. In these events the particle does not pass through the sensitive volume, but this region is hit by {delta} rays. Four track structure models, developed by Katz, Chatterjee et al, Kiefer and Straaten and Kudryashov et al., respectively, were used for the calculations. With the latter two models, very good agreement of the calculations with experimental results on mutagenesis inmore » bacteria was obtained. Depending on the linear energy transfer (LET{infinity}) of the particles, two different modes of mutagenic action of heavy ions are distinguished: {open_quotes}{delta}-ray mutagenesis,{close_quotes} which is related to those radiation qualities that preferentially kill the cells in direct hits (LET{infinity} {ge} 100 keV/{mu}m), and {open_quotes}track core mutagenesis,{close_quotes} which arises from direct hits and is observed for lighter ions or ions with high energy (LET{infinity} {le} 100 keV/{mu}m). 37 refs., 6 figs., 1 tab.« less

[Investigation on the phenomena of bacteria exceeding standards in rural pit water treated by ultrafiltration membrane].

PubMed

Yue, Yinling; Zhang, Lan; Ling, Bo

2011-11-01

To investigate the phenomenon of bacteria exceeding standards in rural pit water, which was intermittently operated by water pump equipped with ultrafiltration membrane, and to explore the solutions. Polyvinyl chloride (PVC) alloy capillary membranes combined with UV, disinfectant, one-way valve, water-seal, high water level-water tank and direct outlet were tested. The operation on water treatment was intermittent, simulating the ways of treating pit water in the rural. The combination modes of ultrafiltration membrane with UV, disinfectant and high water level-water tank are valid in solving the problem of high turbidity and microorganism of pit water stored in cellars, the quality of effluents was consistent with the requirements of the national standards. While the combination modes of ultrafiltration membrane with one-way valve or water-seal were less desirable, more bacteria in treated water than raw water were observed because of bacteria breeding on the membrane component. In order to avoid excessive bacteria in filtered pit water caused by intermittent operation, it is recommended that for the pit water in high water level water tanks, the ultrafiltration membranes should be cleaned with disinfectants on a regular basis. The effluent pit water from underground cellars should be disinfected with UV after ultrafiltration.

Potential of Plant Essential Oils and Their Components in Animal Agriculture - in vitro Studies on Antibacterial Mode of Action.

PubMed

O'Bryan, Corliss A; Pendleton, Sean J; Crandall, Philip G; Ricke, Steven C

2015-01-01

The antimicrobial activity of essential oils and their components has been recognized for several years. Essential oils are produced as secondary metabolites by many plants and can be distilled from all different portions of plants. The recent emergence of bacteria resistant to multiple antibiotics has spurred research into the use of essential oils as alternatives. Recent research has demonstrated that many of these essential oils have beneficial effects for livestock, including reduction of foodborne pathogens in these animals. Numerous studies have been made into the mode of action of essential oils, and the resulting elucidation of bacterial cell targets has contributed to new perspectives on countering antimicrobial resistance and pathogenicity of these bacteria. In this review, an overview of the current knowledge about the antibacterial mode of action of essential oils and their constituents is provided.

Potential of Plant Essential Oils and Their Components in Animal Agriculture – in vitro Studies on Antibacterial Mode of Action

PubMed Central

O’Bryan, Corliss A.; Pendleton, Sean J.; Crandall, Philip G.; Ricke, Steven C.

2015-01-01

The antimicrobial activity of essential oils and their components has been recognized for several years. Essential oils are produced as secondary metabolites by many plants and can be distilled from all different portions of plants. The recent emergence of bacteria resistant to multiple antibiotics has spurred research into the use of essential oils as alternatives. Recent research has demonstrated that many of these essential oils have beneficial effects for livestock, including reduction of foodborne pathogens in these animals. Numerous studies have been made into the mode of action of essential oils, and the resulting elucidation of bacterial cell targets has contributed to new perspectives on countering antimicrobial resistance and pathogenicity of these bacteria. In this review, an overview of the current knowledge about the antibacterial mode of action of essential oils and their constituents is provided. PMID:26664964

Low-Voltage Continuous Electrospinning Patterning.

PubMed

Li, Xia; Li, Zhaoying; Wang, Liyun; Ma, Guokun; Meng, Fanlong; Pritchard, Robyn H; Gill, Elisabeth L; Liu, Ye; Huang, Yan Yan Shery

2016-11-30

Electrospinning is a versatile technique for the construction of microfibrous and nanofibrous structures with considerable potential in applications ranging from textile manufacturing to tissue engineering scaffolds. In the simplest form, electrospinning uses a high voltage of tens of thousands volts to draw out ultrafine polymer fibers over a large distance. However, the high voltage limits the flexible combination of material selection, deposition substrate, and control of patterns. Prior studies show that by performing electrospinning with a well-defined "near-field" condition, the operation voltage can be decreased to the kilovolt range, and further enable more precise patterning of fibril structures on a planar surface. In this work, by using solution dependent "initiators", we demonstrate a further lowering of voltage with an ultralow voltage continuous electrospinning patterning (LEP) technique, which reduces the applied voltage threshold to as low as 50 V, simultaneously permitting direct fiber patterning. The versatility of LEP is shown using a wide range of combination of polymer and solvent systems for thermoplastics and biopolymers. Novel functionalities are also incorporated when a low voltage mode is used in place of a high voltage mode, such as direct printing of living bacteria; the construction of suspended single fibers and membrane networks. The LEP technique reported here should open up new avenues in the patterning of bioelements and free-form nano- to microscale fibrous structures.

Synthesis, crystal structures, spectral, thermal and antimicrobial properties of new Zn(II) 5-iodo- and 5-bromosalicylates

NASA Astrophysics Data System (ADS)

Košická, Petra; Győryová, Katarína; Smolko, Lukáš; Gyepes, Róbert; Hudecová, Daniela

2018-03-01

Two new analogous zinc(II) complexes containing 5-iodo- and 5-bromosalicylate ligands, respectively, were prepared in single-crystal form and characterized by IR spectroscopy, thermal analysis and elemental analysis. The solid-state structures of prepared complexes were determined by single crystal X-ray crystallography. Both complexes are isostructural and their crystal structures composed of neutral molecules [Zn(5-Xsal)2(H2O)2] (where X = Br, I, sal = salicylato). Central Zn(II) atom is in both complexes coordinated by six oxygen atoms, four of which are from two chelate bonded 5-halosalicylates and remaining two from coordinated water molecules. The found chelate binding mode is in line with the Δ values calculated from IR spectral data. Antimicrobial activity of prepared complexes was studied against selected bacteria, yeast and filamentous fungi. Obtained results indicate that 5-iodosalicylate complex is more antimicrobially active than its 5-bromo substituted analogue.

Bisphosphocins: novel antimicrobials for enhanced killing of drug-resistant and biofilm-forming bacteria.

PubMed

Wong, Jonathan P; DiTullio, Paul; Parkinson, Steve

2015-01-01

The global prevalence of antibiotic resistance and the threat posed by drug-resistant superbugs are a leading challenge confronting modern medicine in the 21st century. However, the progress on the development of novel antibiotics to combat this problem is severely lagging. A more concerted effort to develop novel therapeutic agents with robust activity and unique mechanisms of action will be needed to overcome the problem of drug resistance. Furthermore, biofilm forming bacteria are known to be increasingly resistant to the actions of antibiotics and are a leading cause of mortality or morbidity in nosocomial infections. Bisphosphocins (also scientifically known as nubiotics) are novel small protonated deoxynucleotide molecules, and exert their antibacterial activity by depolarization of the bacterial cell membrane, causing bacterial cell death. Bisphosphocins may represent an effective weapon against antibiotic-resistant and biofilm-forming pathogenic bacteria. Preclinical efficacy studies in animals have shown that the compounds are safe and, efficacious against various bacterial infections, including drug-resistant pathogens. In vitro biochemical analysis confirmed that the bactericidal activity of bisphosphocins is mediated by depolarization of the bacterial cell membrane, and these compounds are better able to penetrate through bacterial biofilm and kill the biofilm encased bacteria. This article will cover the structure, mode of action, safety, efficacy and the current state of development of bisphosphocins. Together, the information presented here will present a strong case for bisphosphocins to be considered for use as new weapons to complement the existing arsenal of antimicrobial drugs and as a first line defence against drug-resistant and biofilm-forming bacteria.

The Gram-positive model organism Bacillus subtilis does not form microscopically detectable cardiolipin-specific lipid domains.

PubMed

Pogmore, Alex-Rose; Seistrup, Kenneth H; Strahl, Henrik

2018-04-01

Rather than being homogenous diffusion-dominated structures, biological membranes can exhibit areas with distinct composition and characteristics, commonly termed as lipid domains. Arguably the most comprehensively studied examples in bacteria are domains formed by cardiolipin, which have been functionally linked to protein targeting, the cell division process and the mode of action of membrane-targeting antimicrobials. Cardiolipin domains were originally identified in the Gram-negative model organism Escherichia coli based on preferential staining by the fluorescent membrane dye nonylacridine orange (NAO), and later reported to also exist in other Gram-negative and -positive bacteria. Recently, the lipid-specificity of NAO has been questioned based on studies conducted in E. coli. This prompted us to reanalyse cardiolipin domains in the Gram-positive model organism Bacillus subtilis. Here we show that logarithmically growing B. subtilis does not form microscopically detectable cardiolipin-specific lipid domains, and that NAO is not a specific stain for cardiolipin in this organism.

The clpB gene of Bifidobacterium breve UCC 2003: transcriptional analysis and first insights into stress induction.

PubMed

Ventura, Marco; Kenny, John G; Zhang, Ziding; Fitzgerald, Gerald F; van Sinderen, Douwe

2005-09-01

The so-called clp genes, which encode components of the Clp proteolytic complex, are widespread among bacteria. The Bifidobacterium breve UCC 2003 genome contains a clpB gene with significant homology to predicted clpB genes from other members of the Actinobacteridae group. The heat- and osmotic-inducibility of the B. breve UCC 2003 clpB homologue was verified by slot-blot analysis, while Northern blot and primer extension analyses showed that the clpB gene is transcribed as a monocistronic unit with a single promoter. The role of a hspR homologue, known to control the regulation of clpB and dnaK gene expression in other high G+C content bacteria was investigated by gel mobility shift assays. Moreover the predicted 3D structure of HspR provides further insight into the binding mode of this protein to the clpB promoter region, and highlights the key amino acid residues believed to be involved in the protein-DNA interaction.

Spatio-temporal patterns of bacteria caused by collective motion

NASA Astrophysics Data System (ADS)

Kitsunezaki, So

2006-04-01

In incubation experiments on bacterial colonies of Proteus mirabilis, collective motion of bacteria is found to generate macroscopic turbulent patterns on the surface of agar media. We propose a mathematical model to describe the time evolution of the positional and directional distributions of motile bacteria in such systems, and investigate this model both numerically and analytically. It is shown that as the average density of bacteria increases, nonuniform swarming patterns emerge from a uniform stationary state. For a sufficient large density, we find that spiral patterns are caused by interactions between the local bacteria densities and the rotational mode of the collective motion. Unidirectional spiral patterns similar to those observed in experiments appear in the case in which the equilibrium directional distribution is asymmetric.

Atomic resolution crystal structure of VcLMWPTP-1 from Vibrio cholerae O395: Insights into a novel mode of dimerization in the low molecular weight protein tyrosine phosphatase family

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nath, Seema; Banerjee, Ramanuj; Sen, Udayaditya, E-mail: udayaditya.sen@saha.ac.in

Highlights: • VcLMWPTP-1 forms dimer in solution. • The dimer is catalytically active unlike other reported dimeric LMWPTPs. • The formation of extended dimeric surface excludes the active site pocket. • The surface bears closer resemblance to eukaryotic LMWPTPs. - Abstract: Low molecular weight protein tyrosine phosphatase (LMWPTP) is a group of phosphotyrosine phosphatase ubiquitously found in a wide range of organisms ranging from bacteria to mammals. Dimerization in the LMWPTP family has been reported earlier which follows a common mechanism involving active site residues leading to an enzymatically inactive species. Here we report a novel form of dimerization inmore » a LMWPTP from Vibrio cholera 0395 (VcLMWPTP-1). Studies in solution reveal the existence of the dimer in solution while kinetic study depicts the active form of the enzyme. This indicates that the mode of dimerization in VcLMWPTP-1 is different from others where active site residues are not involved in the process. A high resolution (1.45 Å) crystal structure of VcLMWPTP-1 confirms a different mode of dimerization where the active site is catalytically accessible as evident by a tightly bound substrate mimicking ligand, MOPS at the active site pocket. Although being a member of a prokaryotic protein family, VcLMWPTP-1 structure resembles very closely to LMWPTP from a eukaryote, Entamoeba histolytica. It also delineates the diverse surface properties around the active site of the enzyme.« less

Biofilms produced by Burkholderia cenocepacia: influence of media and solid supports on composition of matrix exopolysaccharides.

PubMed

Pellizzoni, Elena; Ravalico, Fabio; Scaini, Denis; Delneri, Ambra; Rizzo, Roberto; Cescutti, Paola

2016-02-01

Bacteria usually grow forming biofilms, which are communities of cells embedded in a self-produced dynamic polymeric matrix, characterized by a complex three-dimensional structure. The matrix holds cells together and above a surface, and eventually releases them, resulting in colonization of other surfaces. Although exopolysaccharides (EPOLs) are important components of the matrix, determination of their structure is usually performed on samples produced in non-biofilm conditions, or indirectly through genetic studies. Among the Burkholderia cepacia complex species, Burkholderia cenocepacia is an important pathogen in cystic fibrosis (CF) patients and is generally more aggressive than other species. In the present investigation, B. cenocepacia strain BTS2, a CF isolate, was grown in biofilm mode on glass slides and cellulose membranes, using five growth media, one of which mimics the nutritional content of CF sputum. The structure of the matrix EPOLs was determined by 1H-NMR spectroscopy, while visualization of the biofilms on glass slides was obtained by means of confocal laser microscopy, phase-contrast microscopy and atomic force microscopy. The results confirmed that the type of EPOLs biosynthesized depends both on the medium used and on the type of support, and showed that mucoid conditions do not always lead to significant biofilm production, while bacteria in a non-mucoid state can still form biofilm containing EPOLs.

Structures of Arg- and Gln-type bacterial cysteine dioxygenase homologs: Arg- and Gln-type Bacterial CDO Homologs

DOE PAGES

Driggers, Camden M.; Hartman, Steven J.; Karplus, P. Andrew

2015-01-01

In some bacteria, cysteine is converted to cysteine sulfinic acid by cysteine dioxygenases (CDO) that are only ~15–30% identical in sequence to mammalian CDOs. Among bacterial proteins having this range of sequence similarity to mammalian CDO are some that conserve an active site Arg residue (“Arg-type” enzymes) and some having a Gln substituted for this Arg (“Gln-type” enzymes). Here, we describe a structure from each of these enzyme types by analyzing structures originally solved by structural genomics groups but not published: a Bacillus subtilis “Arg-type” enzyme that has cysteine dioxygenase activity (BsCDO), and a Ralstonia eutropha “Gln-type” CDO homolog ofmore » uncharacterized activity (ReCDOhom). The BsCDO active site is well conserved with mammalian CDO, and a cysteine complex captured in the active site confirms that the cysteine binding mode is also similar. The ReCDOhom structure reveals a new active site Arg residue that is hydrogen bonding to an iron-bound diatomic molecule we have interpreted as dioxygen. Notably, the Arg position is not compatible with the mode of Cys binding seen in both rat CDO and BsCDO. As sequence alignments show that this newly discovered active site Arg is well conserved among “Gln-type” CDO enzymes, we conclude that the “Gln-type” CDO homologs are not authentic CDOs but will have substrate specificity more similar to 3-mercaptopropionate dioxygenases.« less

Antimicrobial Activity of Cationic Antimicrobial Peptides against Gram-Positives: Current Progress Made in Understanding the Mode of Action and the Response of Bacteria.

PubMed

Omardien, Soraya; Brul, Stanley; Zaat, Sebastian A J

2016-01-01

Antimicrobial peptides (AMPs) have been proposed as a novel class of antimicrobials that could aid the fight against antibiotic resistant bacteria. The mode of action of AMPs as acting on the bacterial cytoplasmic membrane has often been presented as an enigma and there are doubts whether the membrane is the sole target of AMPs. Progress has been made in clarifying the possible targets of these peptides, which is reported in this review with as focus gram-positive vegetative cells and spores. Numerical estimates are discussed to evaluate the possibility that targets, other than the membrane, could play a role in susceptibility to AMPs. Concerns about possible resistance that bacteria might develop to AMPs are addressed. Proteomics, transcriptomics, and other molecular techniques are reviewed in the context of explaining the response of bacteria to the presence of AMPs and to predict what resistance strategies might be. Emergent mechanisms are cell envelope stress responses as well as enzymes able to degrade and/or specifically bind (and thus inactivate) AMPs. Further studies are needed to address the broadness of the AMP resistance and stress responses observed.

Antimicrobial Activity of Cationic Antimicrobial Peptides against Gram-Positives: Current Progress Made in Understanding the Mode of Action and the Response of Bacteria

PubMed Central

Omardien, Soraya; Brul, Stanley; Zaat, Sebastian A. J.

2016-01-01

Antimicrobial peptides (AMPs) have been proposed as a novel class of antimicrobials that could aid the fight against antibiotic resistant bacteria. The mode of action of AMPs as acting on the bacterial cytoplasmic membrane has often been presented as an enigma and there are doubts whether the membrane is the sole target of AMPs. Progress has been made in clarifying the possible targets of these peptides, which is reported in this review with as focus gram-positive vegetative cells and spores. Numerical estimates are discussed to evaluate the possibility that targets, other than the membrane, could play a role in susceptibility to AMPs. Concerns about possible resistance that bacteria might develop to AMPs are addressed. Proteomics, transcriptomics, and other molecular techniques are reviewed in the context of explaining the response of bacteria to the presence of AMPs and to predict what resistance strategies might be. Emergent mechanisms are cell envelope stress responses as well as enzymes able to degrade and/or specifically bind (and thus inactivate) AMPs. Further studies are needed to address the broadness of the AMP resistance and stress responses observed. PMID:27790614

Structure of a Type-1 Secretion System ABC Transporter.

PubMed

Morgan, Jacob L W; Acheson, Justin F; Zimmer, Jochen

2017-03-07

Type-1 secretion systems (T1SSs) represent a widespread mode of protein secretion across the cell envelope in Gram-negative bacteria. The T1SS is composed of an inner-membrane ABC transporter, a periplasmic membrane-fusion protein, and an outer-membrane porin. These three components assemble into a complex spanning both membranes and providing a conduit for the translocation of unfolded polypeptides. We show that ATP hydrolysis and assembly of the entire T1SS complex is necessary for protein secretion. Furthermore, we present a 3.15-Å crystal structure of AaPrtD, the ABC transporter found in the Aquifex aeolicus T1SS. The structure suggests a substrate entry window just above the transporter's nucleotide binding domains. In addition, highly kinked transmembrane helices, which frame a narrow channel not observed in canonical peptide transporters, are likely involved in substrate translocation. Overall, the AaPrtD structure supports a polypeptide transport mechanism distinct from alternating access. Copyright © 2017 Elsevier Ltd. All rights reserved.

In situ environment rather than substrate type dictates microbial community structure of biofilms in a cold seep system

PubMed Central

Lee, On On; Wang, Yong; Tian, Renmao; Zhang, Weipeng; Shek, Chun Shum; Bougouffa, Salim; Al-Suwailem, Abdulaziz; Batang, Zenon B.; Xu, Wei; Wang, Guang Chao; Zhang, Xixiang; Lafi, Feras F.; Bajic, Vladmir B.; Qian, Pei-Yuan

2014-01-01

Using microscopic and molecular techniques combined with computational analysis, this study examined the structure and composition of microbial communities in biofilms that formed on different artificial substrates in a brine pool and on a seep vent of a cold seep in the Red Sea to test our hypothesis that initiation of the biofilm formation and spreading mode of microbial structures differs between the cold seep and the other aquatic environments. Biofilms on different substrates at two deployment sites differed morphologically, with the vent biofilms having higher microbial abundance and better structural features than the pool biofilms. Microbes in the pool biofilms were more taxonomically diverse and mainly composed of various sulfate-reducing bacteria whereas the vent biofilms were exclusively dominated by sulfur-oxidizing Thiomicrospira. These results suggest that the redox environments at the deployment sites might have exerted a strong selection on microbes in the biofilms at two sites whereas the types of substrates had limited effects on the biofilm development. PMID:24399144

Biomarkers: d13C and d15N Distribution Tightly Coupled to Nutrient Dynamics and Viral Lysing in a Microbial Mat From Death Valley, California

NASA Astrophysics Data System (ADS)

Hewson, I.; Archer, R.; Mahaffey, C.; Scott, J.; Tsapin, A.

2002-12-01

Extrapolations into ancient biomes make many assumptions and inferences regarding life modes and environmental habitat. While definition of a stromatolite as an extinct microbial biome by petrographic analysis is promising, Life interacts with is environment, actively manipulating energy flow across chemical disequilibria gradients, harvesting energy crucial for physiological maintenance and reproduction. Such structuring of communities in turn, leaves specific chemical/isotopic imprints related to physiological processes of prokaryotic communities specific to each oxidation/redox horizon. We examine stable isotopic d13C signals (d13C and d15N) as potential biomarkers reflecting bacterial physiology and microbial community nutrient-energy dynamics. While isotopes may reveal ancient chemical structuring of microbial mats, we also turn to invoking viral lysing of bacterial hosts in nutrient cycling within modern extreme environments as well as ancient stromatic structures of early Earth. Our records of d13C indicate extreme enrichment(-12%) for Corg in our extant mat due to CO2 limitation across a hypersaline diffusive barrier at the mat's surface. d15N is lowest at the mat's surface (indicating N2- fixation) where nitrogen- fixing cyanobacteria Microcoleus sp. are present . Viruses are extremely abundant in the microbial mat, exceeding bacterial abundances by a factor of ten. The ratio of viruses to bacteria was very high (VBR = 39 ñ 10) compared with abundances in marine sediments. Distribution of viruses closely follows distribution of bacteria, suggesting bacteria as primary hosts. The ratio of viruses to bacteria is inversely correlated to the concentration of organic C suggesting virus abundance is responsive to host substrate availability. High ratios of viruses to bacteria in mid-mat horizons (2.5 - 3.7 cm) above increasing levels of d13C in deeper horizons, coupled with a lack of increase in bacteria, suggests that viral lysis contributes to significant downward organic C (polysaccaride exudates) transport within the mat. Subsequent accumulation of d13C as well as heavier d15N in deeper sediment(denitrification)horizons elucidates tight nutrient coupling between evaporite substrate, nitrogen fixing primary producers and downcore zones of active denitrification and sulphate reduction. Discrepencies between d13C of ancient stromatolites (in line with C-3 photosynthetic pathways) and modern analogues (Badwater, CA) suggest a migration of microbial mats towards more extreme environments through time. A methodology for isotopically testing environmental and physiological responses in the geological record is presented here.

Effect of diesel leakage in circulating cooling water system on preponderant bacteria diversity and bactericidal effect of biocides.

PubMed

Zhong, Huiyun; Liu, Fang; Lu, Jinjin; Yang, Wei; Zhao, Chaocheng

2015-01-01

Petroleum products leakage results in adverse effect on the normal operation of a circulating cooling water system. However, relatively little research has been done to explore the effect of petroleum products leakage on circulating cooling water quality and biofilm preponderant bacteria diversity. Also, normal biocides application modes cannot fulfil the need for biofilm control. In this study, diesel oil was used as the experimental subject representing leaking petroleum products; the effect of diesel addition on biofilm preponderant bacteria diversity and the bactericidal effect of chlorine dioxide and tetradecyl dimethyl benzyl ammonium chloride (1427) was investigated. Bacterial community structures were examined by PCR-denaturing gradient gel electrophoresis and PCR cloning of 16S rDNA genes. Except for 100 mg/L diesel, increasing diesel concentration enhanced the biofilm detachment ratio compared with the control test. The microstructure of biofilm samples with 0, 300 and 900 mg/L diesel addition was observed. The species of preponderant bacteria in the biofilm sample with 300 mg/L diesel addition were more and the bacterial distribution was more uniform than those in the biofilm sample with 900 mg/L diesel addition. With ClO2 and 1427 addition, chemical oxygen demand increased, lipid phosphorus and bacterial count first decreased and then remained stable, and the bactericidal ratio first increased and then remained stable. Diesel addition variation has more obvious effect on ClO2 than 1427.

Got bacteria? The astounding, yet not-so-surprising, microbiome of human milk.

PubMed

McGuire, Michelle K; McGuire, Mark A

2017-04-01

Contrary to long-held dogma, human milk is not sterile. Instead, it provides infants a rich source of diverse bacteria, particularly microbes belonging to the Staphylococcus, Streptococcus, and Pseudomonas genera. Very little is known about factors that influence variation in the milk microbiome among women and populations, although time postpartum, delivery mode, and maternal factors such as diet and antibiotic use might be important. The origins of the bacteria in milk are thought to include the maternal gastrointestinal tract (via an entero-mammary pathway) and through bacterial exposure of the breast during nursing. Currently, almost nothing is known about whether variation in microbe consumption by the infant via human milk and that of the mammary gland, itself, impacts short-term and/or long-term infant and maternal health although several studies suggest this is likely. We urge the clinical and public health communities to be patient, however, in order to allow human milk and lactation researchers to first understand what constitutes 'normal' in terms of the milk microbiome (as well as factors that impact microbial community structure) prior to jumping the gun to investigate if and how this important source of microbes impacts maternal and infant health. Copyright © 2016. Published by Elsevier Ltd.

Gram positive and Gram negative bacteria differ in their sensitivity to cold plasma

NASA Astrophysics Data System (ADS)

Mai-Prochnow, Anne; Clauson, Maryse; Hong, Jungmi; Murphy, Anthony B.

2016-12-01

Cold atmospheric-pressure plasma (CAP) is a relatively new method being investigated for antimicrobial activity. However, the exact mode of action is still being explored. Here we report that CAP efficacy is directly correlated to bacterial cell wall thickness in several species. Biofilms of Gram positive Bacillus subtilis, possessing a 55.4 nm cell wall, showed the highest resistance to CAP, with less than one log10 reduction after 10 min treatment. In contrast, biofilms of Gram negative Pseudomonas aeruginosa, possessing only a 2.4 nm cell wall, were almost completely eradicated using the same treatment conditions. Planktonic cultures of Gram negative Pseudomonas libanensis also had a higher log10 reduction than Gram positive Staphylococcus epidermidis. Mixed species biofilms of P. aeruginosa and S. epidermidis showed a similar trend of Gram positive bacteria being more resistant to CAP treatment. However, when grown in co-culture, Gram negative P. aeruginosa was more resistant to CAP overall than as a mono-species biofilm. Emission spectra indicated OH and O, capable of structural cell wall bond breakage, were present in the plasma. This study indicates that cell wall thickness correlates with CAP inactivation times of bacteria, but cell membranes and biofilm matrix are also likely to play a role.

Crystal structure of RuvC resolvase in complex with Holliday junction substrate

PubMed Central

Górecka, Karolina M.; Komorowska, Weronika; Nowotny, Marcin

2013-01-01

The key intermediate in genetic recombination is the Holliday junction (HJ), a four-way DNA structure. At the end of recombination, HJs are cleaved by specific nucleases called resolvases. In Gram-negative bacteria, this cleavage is performed by RuvC, a dimeric endonuclease that belongs to the retroviral integrase superfamily. Here, we report the first crystal structure of RuvC in complex with a synthetic HJ solved at 3.75 Å resolution. The junction in the complex is in an unfolded 2-fold symmetrical conformation, in which the four arms point toward the vertices of a tetrahedron. The two scissile phosphates are located one nucleotide from the strand exchange point, and RuvC approaches them from the minor groove side. The key protein–DNA contacts observed in the structure were verified using a thiol-based site-specific cross-linking approach. Compared with known complex structures of the phage resolvases endonuclease I and endonuclease VII, the RuvC structure exhibits striking differences in the mode of substrate binding and location of the cleavage site. PMID:23980027

Abstracts of Manuscripts Submitted in 1989 for Publication

DTIC Science & Technology

1990-07-01

determine by anthropogenic inputs to the ecosystem. The A. the contribution of the symbionts to host nutrition zebra deployed in Hamilton Harbor had...composition profiles for the study of relationship of gonadal resorption following nutrition in animal-bacteria symbioses. The small exposure to...bacteria highly competent in this mode of nutrition . and protozoa became abundant in the incubation In Press: Lirnnology and Oceanography. vessels, most

Directed-assembled multi-band moiré plasmonic metasurfaces

NASA Astrophysics Data System (ADS)

Nagavalli Yogeesh, Maruthi; Wu, Zilong; Li, Wei; Akinwande, Deji; Zheng, Yuebing

With the large number of component sets and high rotational symmetry, plasmonic metamaterials with moiré patterns can support multiple plasmonic modes for multi-functional applications. Herein, we introduce moiré plasmonic metasurfaces using both gold and graphene, by a recently developed directed-assembled method known as moiré nanosphere lithography (MNSL). The graphene moiré metasurfaces show multiple and tunable resonance modes in the mid-infrared wavelength regime. The number and wavelength of the resonance modes can be tuned by controlling the moiré patterns, which can be easily achieved by changing the relative in-plane rotation angle during MNSL. Furthermore, we have designed a metal-insulator-metal (MIM) patch structure with a thin Au moiré metasurface layer and an optically thick Au layer separated by a dielectric spacer layer. Benefiting from the combination of moiré patterns and field enhancement from the MIM configuration, the moiré metasurface patch exhibits strong broadband absorption in the NIR ( 1.3 μm) and MIR ( 5 μm) range. The dual-band optical responses make moiré metasurface patch a multi-functional platform for surface-enhanced infrared spectroscopy, optical capture and patterning of bacteria, and photothermal denaturation of proteins.

Bacterial cell wall composition and the influence of antibiotics by cell-wall and whole-cell NMR

PubMed Central

Romaniuk, Joseph A. H.; Cegelski, Lynette

2015-01-01

The ability to characterize bacterial cell-wall composition and structure is crucial to understanding the function of the bacterial cell wall, determining drug modes of action and developing new-generation therapeutics. Solid-state NMR has emerged as a powerful tool to quantify chemical composition and to map cell-wall architecture in bacteria and plants, even in the context of unperturbed intact whole cells. In this review, we discuss solid-state NMR approaches to define peptidoglycan composition and to characterize the modes of action of old and new antibiotics, focusing on examples in Staphylococcus aureus. We provide perspectives regarding the selected NMR strategies as we describe the exciting and still-developing cell-wall and whole-cell NMR toolkit. We also discuss specific discoveries regarding the modes of action of vancomycin analogues, including oritavancin, and briefly address the reconsideration of the killing action of β-lactam antibiotics. In such chemical genetics approaches, there is still much to be learned from perturbations enacted by cell-wall assembly inhibitors, and solid-state NMR approaches are poised to address questions of cell-wall composition and assembly in S. aureus and other organisms. PMID:26370936

"Leaching or not leaching": an alternative approach to antimicrobial materials via copolymers containing crown ethers as active groups.

PubMed

De Rosa, M; Vigliotta, G; Soriente, A; Capaccio, V; Gorrasi, G; Adami, R; Reverchon, E; Mella, M; Izzo, L

2017-03-28

In this work, new copolymers containing either MMA and 18C6 crown-ether pendants, or PEG, MMA and 18C6 crown-ether pendants were synthesized to test the idea that sequestering structural alkali-earth ions from the bacterial outer membrane (OM) may lead to bacterial death. The copolymers were obtained either via uncontrolled radical polymerization or ATRP; the latter approached allowed us to produce not only linear copolymers but also branched Y-like structures. After checking for the capability of complexing magnesium and calcium ions, the antimicrobial activity of all copolymers was tested placing their casted plaques in contact with pure water E. coli suspensions. All plaques adsorbed alkali-earth ions and killed bacteria, albeit with different antimicrobial efficiencies. Differences in the latter characteristic were attributed to different plaque roughness. The role of the 18C6 crown-ether pendants was elucidated by pre-saturating plaques with Mg/Ca ions, the marked reduction in antimicrobial efficiency indicating that losing the latter from OM due to surface complexation does play an important role in killing bacteria at short (<5 h) contact times. At longer times, the mode of action is instead related to the poly-cationic nature acquired by the plaques due to ion sequestering.

Cytidine derivatives as IspF inhibitors of Burkolderia pseudomallei

PubMed Central

Zhang, Zheng; Jakkaraju, Sriram; Blain, Joy; Gogol, Kenneth; Zhao, Lei; Hartley, Robert C.; Karlsson, Courtney A.; Staker, Bart L.; Stewart, Lance J.; Myler, Peter J.; Clare, Michael; Begley, Darren W.; Horn, James R.; Hagen, Timothy J

2013-01-01

Published biological data suggest that the methyl erythritol phosphate (MEP) pathway, a non-mevalonate isoprenoid biosynthetic pathway, is essential for certain bacteria and other infectious disease organisms. One highly conserved enzyme in the MEP pathway is 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF). Fragment-bound complexes of IspF from Burkholderia pseudomallei were used to design and synthesize a series of molecules linking the cytidine moiety to different zinc pocket fragment binders. Testing by surface plasmon resonance (SPR) found one molecule in the series to possess binding affinity equal to that of cytidine diphosphate, despite lacking any metal-coordinating phosphate groups. Close inspection of the SPR data suggest different binding stoichiometries between IspF and test compounds. Crystallographic analysis shows important variations between the binding mode of one synthesized compound and the pose of the bound fragment from which it was designed. The binding modes of these molecules add to our structural knowledge base for IspF and suggest future refinements in this compound series. PMID:24157367

Axinellamines as Broad-Spectrum Antibacterial Agents: Scalable Synthesis and Biology

PubMed Central

2015-01-01

Antibiotic-resistant bacteria present an ongoing challenge to both chemists and biologists as they seek novel compounds and modes of action to out-maneuver continually evolving resistance pathways, especially against Gram-negative strains. The dimeric pyrrole–imidazole alkaloids represent a unique marine natural product class with diverse primary biological activity and chemical architecture. This full account traces the strategy used to develop a second-generation route to key spirocycle 9, culminating in a practical synthesis of the axinellamines and enabling their discovery as broad-spectrum antibacterial agents, with promising activity against both Gram-positive and Gram-negative bacteria. While their detailed mode of antibacterial action remains unclear, the axinellamines appear to cause secondary membrane destabilization and impart an aberrant cellular morphology consistent with the inhibition of normal septum formation. This study serves as a rare example of a natural product initially reported to be devoid of biological activity surfacing as an active antibacterial agent with an intriguing mode of action. PMID:25328977

Biochemical and Structural Characterization of Bisubstrate Inhibitors of BasE, the Self-standing Non-Ribosomal Peptide Synthetase Adenylate-Forming Enzyme of Acinetobactin Synthesis†,‡

PubMed Central

Drake, Eric J.; Duckworth, Benjamin P.; Neres, João; Aldrich, Courtney C.; Gulick, Andrew M.

2010-01-01

The human pathogen Acinetobacter baumannii produces a siderophore called acinetobactin that is derived from one molecule each of threonine, histidine, and 2,3-dihydroxybenzoic acid (DHB). The activity of several non-ribosomal peptide synthetase (NRPS) enzymes is used to combine the building blocks into the final molecule. The acinetobactin synthesis pathway initiates with a self-standing adenylation enzyme, BasE, that activates the DHB molecule and covalently transfers it to the pantetheine cofactor of an aryl-carrier protein of BasF, a strategy that is shared with many siderophore-producing NRPS clusters. In this reaction, DHB reacts with ATP to form the aryl adenylate and pyrophosphate. In a second partial reaction, the DHB is transferred to the carrier protein. Inhibitors of BasE and related enzymes have been identified that prevent growth of bacteria on iron-limiting media. Recently, a new inhibitor of BasE has been identified via high-throughput screening using a fluorescence polarization displacement assay. We present here biochemical and structural studies to examine the binding mode of this inhibitor. The kinetics of the wild-type BasE enzyme is shown and inhibition studies demonstrate that the new compound exhibits competitive inhibition against both ATP and 2,3-dihydroxybenzoate. Structural examination of BasE bound to this inhibitor illustrates a novel binding mode in which the phenyl moiety partially fills the enzyme pantetheine binding tunnel. Structures of rationally designed bisubstrate inhibitors are also presented. PMID:20853905

New Features in the Lipid A Structure of Brucella suis and Brucella abortus Lipopolysaccharide

NASA Astrophysics Data System (ADS)

Casabuono, Adriana C.; Czibener, Cecilia; Del Giudice, Mariela G.; Valguarnera, Ezequiel; Ugalde, Juan E.; Couto, Alicia S.

2017-12-01

Brucellaceae are Gram-negative bacteria that cause brucellosis, one of the most distributed worldwide zoonosis, transmitted to humans by contact with either infected animals or their products. The lipopolysaccharide exposed on the cell surface has been intensively studied and is considered a major virulence factor of Brucella. In the last years, structural studies allowed the determination of new structures in the core oligosaccharide and the O-antigen of this lipopolysaccharide. In this work, we have reinvestigated the lipid A structure isolated from B. suis and B. abortus lipopolysaccharides. A detailed study by MALDI-TOF mass spectrometry in the positive and negative ion modes of the lipid A moieties purified from both species was performed. Interestingly, a new feature was detected: the presence of a pyrophosphorylethanolamine residue substituting the backbone. LID-MS/MS analysis of some of the detected ions allowed assurance that the Lipid A structure composed by the diGlcN3N disaccharide, mainly hexa-acylated and penta-acylated, bearing one phosphate and one pyrophosphorylethanolamine residue. [Figure not available: see fulltext.

New Features in the Lipid A Structure of Brucella suis and Brucella abortus Lipopolysaccharide.

PubMed

Casabuono, Adriana C; Czibener, Cecilia; Del Giudice, Mariela G; Valguarnera, Ezequiel; Ugalde, Juan E; Couto, Alicia S

2017-12-01

Brucellaceae are Gram-negative bacteria that cause brucellosis, one of the most distributed worldwide zoonosis, transmitted to humans by contact with either infected animals or their products. The lipopolysaccharide exposed on the cell surface has been intensively studied and is considered a major virulence factor of Brucella. In the last years, structural studies allowed the determination of new structures in the core oligosaccharide and the O-antigen of this lipopolysaccharide. In this work, we have reinvestigated the lipid A structure isolated from B. suis and B. abortus lipopolysaccharides. A detailed study by MALDI-TOF mass spectrometry in the positive and negative ion modes of the lipid A moieties purified from both species was performed. Interestingly, a new feature was detected: the presence of a pyrophosphorylethanolamine residue substituting the backbone. LID-MS/MS analysis of some of the detected ions allowed assurance that the Lipid A structure composed by the diGlcN3N disaccharide, mainly hexa-acylated and penta-acylated, bearing one phosphate and one pyrophosphorylethanolamine residue. Graphical abstract ᅟ.

Enteric bacteria boost defences against oxidative stress in Entamoeba histolytica.

PubMed

Varet, Hugo; Shaulov, Yana; Sismeiro, Odile; Trebicz-Geffen, Meirav; Legendre, Rachel; Coppée, Jean-Yves; Ankri, Serge; Guillen, Nancy

2018-06-13

Oxidative stress is one of the strongest toxic factors in nature: it can harm or even kill cells. Cellular means of subverting the toxicity of oxidative stress are important for the success of infectious diseases. Many types of bacterium inhabit the intestine, where they can encounter pathogens. During oxidative stress, we analyzed the interplay between an intestinal parasite (the pathogenic amoeba Entamoeba histolytica - the agent of amoebiasis) and enteric bacteria (microbiome residents, pathogens and probiotics). We found that live enteric bacteria protected E. histolytica against oxidative stress. By high-throughput RNA sequencing, two amoebic regulatory modes were observed with enteric bacteria but not with probiotics. The first controls essential elements of homeostasis, and the second the levels of factors required for amoeba survival. Characteristic genes of both modes have been acquired by the amoebic genome through lateral transfer from the bacterial kingdom (e.g. glycolytic enzymes and leucine-rich proteins). Members of the leucine-rich are homologous to proteins from anti-bacterial innate immune such as Toll-like receptors. The factors identified here suggest that despite its old age in evolutionary terms, the protozoan E. histolytica displays key characteristics of higher eukaryotes' innate immune systems indicating that components of innate immunity existed in the common ancestor of plants and animals.

Synergistic interaction and mode of action of Citrus hystrix essential oil against bacteria causing periodontal diseases.

PubMed

Wongsariya, Karn; Phanthong, Phanida; Bunyapraphatsara, Nuntavan; Srisukh, Vimol; Chomnawang, Mullika Traidej

2014-03-01

Citrus hystrix de Candolle (Rutaceae), an edible plant regularly used as a food ingredient, possesses antibacterial activity, but there is no current data on the activity against bacteria causing periodontal diseases. C. hystrix essential oil from leaves and peel were investigated for antibiofilm formation and mode of action against bacteria causing periodontal diseases. In vitro antibacterial and antibiofilm formation activities were determined by broth microdilution and time kill assay. Mode of action of essential oil was observed by SEM and the active component was identified by bioautography and GC/MS. C. hystrix leaves oil exhibited antibacterial activity at the MICs of 1.06 mg/mL for P. gingivalis and S. mutans and 2.12 mg/mL for S. sanguinis. Leaf oil at 4.25 mg/mL showed antibiofilm formation activity with 99% inhibition. The lethal effects on P. gingivalis were observed within 2 and 4 h after treated with 4 × MIC and 2 × MIC, respectively. S. sanguinis and S. mutans were completely killed within 4 and 8 h after exposed to 4 × MIC and 2 × MIC of oil. MICs of tested strains showed 4 times reduction suggesting synergistic interaction of oil and chlorhexidine. Bacterial outer membrane was disrupted after treatment with leaves oil. Additionally, citronellal was identified as the major active compound of C. hystrix oil. C. hystrix leaf oil could be used as a natural active compound or in combination with chlorhexidine in mouthwash preparations to prevent the growth of bacteria associated with periodontal diseases and biofilm formation.

Bacterial-Fungal Interactions: Hyphens between Agricultural, Clinical, Environmental, and Food Microbiologists

PubMed Central

Frey-Klett, P.; Burlinson, P.; Deveau, A.; Barret, M.; Tarkka, M.; Sarniguet, A.

2011-01-01

Summary: Bacteria and fungi can form a range of physical associations that depend on various modes of molecular communication for their development and functioning. These bacterial-fungal interactions often result in changes to the pathogenicity or the nutritional influence of one or both partners toward plants or animals (including humans). They can also result in unique contributions to biogeochemical cycles and biotechnological processes. Thus, the interactions between bacteria and fungi are of central importance to numerous biological questions in agriculture, forestry, environmental science, food production, and medicine. Here we present a structured review of bacterial-fungal interactions, illustrated by examples sourced from many diverse scientific fields. We consider the general and specific properties of these interactions, providing a global perspective across this emerging multidisciplinary research area. We show that in many cases, parallels can be drawn between different scenarios in which bacterial-fungal interactions are important. Finally, we discuss how new avenues of investigation may enhance our ability to combat, manipulate, or exploit bacterial-fungal complexes for the economic and practical benefit of humanity as well as reshape our current understanding of bacterial and fungal ecology. PMID:22126995

[Analysis of the swimming pattern and the velocity of bacteria using video tracking method].

PubMed

Shigematsu, M

1997-04-01

The swimming patterns and the velocities of several flagellated bacteria were measured by a computer assisted video tracking method. The moving path of the individual bacterium revealed that the bacterium frequently changed its swimming direction and velocity. The velocity among bacterial strains varies widely. In low viscous environment. Campylobacter jejuni has characteristic swimming pattern with frequent changes in their swimming direction. As the viscosity increase, C. jejuni increases its velocity at a little higher viscosity of 3 centipoise (cP) and secondly increases at about 40 cP. Different from other flagellated bacteria, the swimming pattern of C. jejuni in these two velocity peaks were changed. C. jejuni exhibited continuously forward moving path in the first peak, but in the second it repeated back and forth swimming pattern. We thus assumed that C. jejuni may use a different swimming mode in high viscous media from the original mode mediated by the propelling force of the flagella. This method is useful for a detail analysis of bacterial movement and moving patterns in different environmental conditions.

Helical Antimicrobial Sulfono- {gamma} -AApeptides

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Yaqiong; Wu, Haifan; Teng, Peng

Host-defense peptides (HDPs) such as magainin 2 have emerged as potential therapeutic agents combating antibiotic resistance. Inspired by their structures and mechanism of action, herein we report the fi rst example of antimicrobial helical sulfono- γ - AApeptide foldamers. The lead molecule displays broad-spectrum and potent antimicrobial activity against multi-drug-resistant Gram- positive and Gram-negative bacterial pathogens. Time-kill studies and fl uorescence microscopy suggest that sulfono- γ -AApeptides eradicate bacteria by taking a mode of action analogous to that of HDPs. Clear structure - function relationships exist in the studied sequences. Longer sequences, presumably adopting more-de fi ned helical structures, aremore » more potent than shorter ones. Interestingly, the sequence with less helical propensity in solution could be more selective than the stronger helix-forming sequences. Moreover, this class of antimicrobial agents are resistant to proteolytic degradation. These results may lead to the development of a new class of antimicrobial foldamers combating emerging antibiotic-resistant pathogens.« less

The antigen 43 structure reveals a molecular Velcro-like mechanism of autotransporter-mediated bacterial clumping

PubMed Central

Heras, Begoña; Totsika, Makrina; Peters, Kate M.; Paxman, Jason J.; Gee, Christine L.; Jarrott, Russell J.; Perugini, Matthew A.; Whitten, Andrew E.; Schembri, Mark A.

2014-01-01

Aggregation and biofilm formation are critical mechanisms for bacterial resistance to host immune factors and antibiotics. Autotransporter (AT) proteins, which represent the largest group of outer-membrane and secreted proteins in Gram-negative bacteria, contribute significantly to these phenotypes. Despite their abundance and role in bacterial pathogenesis, most AT proteins have not been structurally characterized, and there is a paucity of detailed information with regard to their mode of action. Here we report the structure–function relationships of Antigen 43 (Ag43a), a prototypic self-associating AT protein from uropathogenic Escherichia coli. The functional domain of Ag43a displays a twisted L-shaped β-helical structure firmly stabilized by a 3D hydrogen-bonded scaffold. Notably, the distinctive Ag43a L shape facilitates self-association and cell aggregation. Combining all our data, we define a molecular “Velcro-like” mechanism of AT-mediated bacterial clumping, which can be tailored to fit different bacterial lifestyles such as the formation of biofilms. PMID:24335802

Structural basis for the recognition of guide RNA and target DNA heteroduplex by Argonaute

PubMed Central

Miyoshi, Tomohiro; Ito, Kosuke; Murakami, Ryo; Uchiumi, Toshio

2016-01-01

Argonaute proteins are key players in the gene silencing mechanisms mediated by small nucleic acids in all domains of life from bacteria to eukaryotes. However, little is known about the Argonaute protein that recognizes guide RNA/target DNA. Here, we determine the 2 Å crystal structure of Rhodobacter sphaeroides Argonaute (RsAgo) in a complex with 18-nucleotide guide RNA and its complementary target DNA. The heteroduplex maintains Watson–Crick base-pairing even in the 3′-region of the guide RNA between the N-terminal and PIWI domains, suggesting a recognition mode by RsAgo for stable interaction with the target strand. In addition, the MID/PIWI interface of RsAgo has a system that specifically recognizes the 5′ base-U of the guide RNA, and the duplex-recognition loop of the PAZ domain is important for the DNA silencing activity. Furthermore, we show that Argonaute discriminates the nucleic acid type (RNA/DNA) by recognition of the duplex structure of the seed region. PMID:27325485

Structural basis for the recognition of guide RNA and target DNA heteroduplex by Argonaute.

PubMed

Miyoshi, Tomohiro; Ito, Kosuke; Murakami, Ryo; Uchiumi, Toshio

2016-06-21

Argonaute proteins are key players in the gene silencing mechanisms mediated by small nucleic acids in all domains of life from bacteria to eukaryotes. However, little is known about the Argonaute protein that recognizes guide RNA/target DNA. Here, we determine the 2 Å crystal structure of Rhodobacter sphaeroides Argonaute (RsAgo) in a complex with 18-nucleotide guide RNA and its complementary target DNA. The heteroduplex maintains Watson-Crick base-pairing even in the 3'-region of the guide RNA between the N-terminal and PIWI domains, suggesting a recognition mode by RsAgo for stable interaction with the target strand. In addition, the MID/PIWI interface of RsAgo has a system that specifically recognizes the 5' base-U of the guide RNA, and the duplex-recognition loop of the PAZ domain is important for the DNA silencing activity. Furthermore, we show that Argonaute discriminates the nucleic acid type (RNA/DNA) by recognition of the duplex structure of the seed region.

Snakin: Structure, Roles and Applications of a Plant Antimicrobial Peptide.

PubMed

Oliveira-Lima, Marx; Benko-Iseppon, Ana Maria; Neto, Jose Ribamar Costa Ferreira; Rodriguez-Decuadro, Susana; Kido, Ederson Akio; Crovella, Sergio; Pandolfi, Valesca

2017-01-01

Snakins are plant antimicrobial peptides (AMPs) of the Snakin/GASA family, formed by three distinct regions: an N-terminal signal peptide; a variable site; and the GASA domain in the Cterminal region composed by twelve conserved cysteine residues that contribute to the biochemical stability of the molecule. These peptides are known to play different roles in response to a variety of biotic (i.e., induced by bacteria, fungi and nematode pathogens) and abiotic (salinity, drought and ROS) stressors, as well as in crosstalk promoted by plant hormones, with emphasis on abscisic and salicylic acid (ABA and SA, respectively). Such properties make snakin/GASA members promising biotechnological sources for potential therapeutic and agricultural applications. However, information regarding their tertiary structure, mode of action and function are not yet completely elucidated. The present review presents aspects of snakin structure, expression, functional studies and perspectives about the potential applications for agricultural and medical purposes. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Cache domains that are homologous to, but different from PAS domains comprise the largest superfamily of extracellular sensors in prokaryotes

DOE PAGES

Upadhyay, Amit A.; Fleetwood, Aaron D.; Adebali, Ogun; ...

2016-04-06

Cellular receptors usually contain a designated sensory domain that recognizes the signal. Per/Arnt/Sim (PAS) domains are ubiquitous sensors in thousands of species ranging from bacteria to humans. Although PAS domains were described as intracellular sensors, recent structural studies revealed PAS-like domains in extracytoplasmic regions in several transmembrane receptors. However, these structurally defined extracellular PAS-like domains do not match sequence-derived PAS domain models, and thus their distribution across the genomic landscape remains largely unknown. Here we show that structurally defined extracellular PAS-like domains belong to the Cache superfamily, which is homologous to, but distinct from the PAS superfamily. Our newly builtmore » computational models enabled identification of Cache domains in tens of thousands of signal transduction proteins including those from important pathogens and model organisms.Moreover, we show that Cache domains comprise the dominant mode of extracellular sensing in prokaryotes.« less

Cache domains that are homologous to, but different from PAS domains comprise the largest superfamily of extracellular sensors in prokaryotes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Upadhyay, Amit A.; Fleetwood, Aaron D.; Adebali, Ogun

Cellular receptors usually contain a designated sensory domain that recognizes the signal. Per/Arnt/Sim (PAS) domains are ubiquitous sensors in thousands of species ranging from bacteria to humans. Although PAS domains were described as intracellular sensors, recent structural studies revealed PAS-like domains in extracytoplasmic regions in several transmembrane receptors. However, these structurally defined extracellular PAS-like domains do not match sequence-derived PAS domain models, and thus their distribution across the genomic landscape remains largely unknown. Here we show that structurally defined extracellular PAS-like domains belong to the Cache superfamily, which is homologous to, but distinct from the PAS superfamily. Our newly builtmore » computational models enabled identification of Cache domains in tens of thousands of signal transduction proteins including those from important pathogens and model organisms.Moreover, we show that Cache domains comprise the dominant mode of extracellular sensing in prokaryotes.« less

Insight into the Mechanism of Hydrolysis of Meropenem by OXA-23 Serine-β-lactamase Gained by Quantum Mechanics/Molecular Mechanics Calculations.

PubMed

Sgrignani, Jacopo; Grazioso, Giovanni; De Amici, Marco

2016-09-13

The fast and constant development of drug resistant bacteria represents a serious medical emergency. To overcome this problem, the development of drugs with new structures and modes of action is urgently needed. In this work, we investigated, at the atomistic level, the mechanisms of hydrolysis of Meropenem by OXA-23, a class D β-lactamase, combining unbiased classical molecular dynamics and umbrella sampling simulations with classical force field-based and quantum mechanics/molecular mechanics potentials. Our calculations provide a detailed structural and dynamic picture of the molecular steps leading to the formation of the Meropenem-OXA-23 covalent adduct, the subsequent hydrolysis, and the final release of the inactive antibiotic. In this mechanistic framework, the predicted activation energy is in good agreement with experimental kinetic measurements, validating the expected reaction path.

The Antibiotic CJ-15,801 is an Antimetabolite which Hijacks and then Inhibits CoA Biosynthesis

PubMed Central

van der Westhuyzen, Renier; Hammons, Justin C.; Meier, Jordan L.; Dahesh, Samira; Moolman, Wessel J. A.; Pelly, Stephen C.; Nizet, Victor; Burkart, Michael D.; Strauss, Erick

2012-01-01

SUMMARY The natural product CJ-15,801 is an inhibitor of Staphylococcus aureus, but not other bacteria. Its close structural resemblance to pantothenic acid, the vitamin precursor of coenzyme A (CoA), and its Michael acceptor moiety suggest that it irreversibly inhibits an enzyme involved in CoA biosynthesis or utilization. However, its mode of action and the basis for its specificity have not been elucidated to date. We demonstrate that CJ-15,801 is transformed by the uniquely selective S. aureus pantothenate kinase, the first CoA biosynthetic enzyme, into a substrate for the next enzyme, phosphopantothenoylcysteine synthetase, which is inhibited through formation of a tight-binding structural mimic of its native reaction intermediate. These findings reveal CJ-15,801 as a vitamin biosynthetic pathway antimetabolite with a mechanism similar to that of the sulfonamide antibiotics, and highlight CoA biosynthesis as a viable antimicrobial drug target. PMID:22633408

Assembly of three new POM-based Ag(I) coordination polymers with antibacterial and photocatalytic properties

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lu, Xin-Xin; Luo, Yu-Hui; Lu, Chen

Three new silver coordination polymers, namely, {Ag_3(bpy)_6[PW_1_2O_4_0]} (1), {Ag_5(H_2biim)_2(Hbiim-NO_2)_2[PW_1_2O_4_0]} (2), {Ag_7(pytz)_4[PW_1_2O_4_0]} (3) (bpy=2,2′-bipyridine, H{sub 2}biim=2,2′-biimidazole, pytz=4-(1H-tetrazol-5-yl)pyridine), have been synthesized under hydrothermal condition. Compound 1 shows a 3D supramolecular framework based on 0D moieties. Compound 2 exhibits an attractive 2D biologic screw axis. Compound 3 displays a 3D structure, which consists of Ag(I)···π interactions, π···π stacking and weak Ag···Ag interactions. It is noteworthy that nitration happens to compound 2 during the hydrothermal condition, which is quite rare. Through contrasting the antibacterial activities of gram negative and gram positive bacteria, we find compounds 1–3 have better antibacterial property in gram negative bacteriamore » than gram positive bacteria. In addition, compounds 1–3 also exhibit efficiency of photocatalytic decomposition of organic dyes. Those compounds may be used as potential multifunctional materials in wastewater treatment, because they not only can kill bacteria but also degrade organic pollutants. - Highlights: • Three new silver coordination polymers have been synthesized under hydrothermal condition. • Due to different coordination modes of rigid N-donor ligands, structures of the title compounds vary from 0D to 3D frameworks. • It is noteworthy that nitration happens to compound 2 during the hydrothermal condition, which is quite rare. • In addition, these compounds exhibit efficiency of photocatalytic decomposition of dyes and antibacterial activities.« less

Holding a grudge

PubMed Central

Mick, Eran; Stern, Adi; Sorek, Rotem

2013-01-01

The CRISPR (clustered regularly interspaced short palindromic repeats)/Cas (CRISPR-associated) system of bacteria and archaea constitutes a mechanism of acquired adaptive immunity against phages, which is based on genome-encoded markers of previously infecting phage sequences (“spacers”). As a repository of phage sequences, these spacers make the system particularly suitable for elucidating phage-bacteria interactions in metagenomic studies. Recent metagenomic analyses of CRISPRs associated with the human microbiome intriguingly revealed conserved “memory spacers” shared by bacteria in multiple unrelated, geographically separated individuals. Here, we discuss possible avenues for explaining this phenomenon by integrating insights from CRISPR biology and phage-bacteria ecology, with a special focus on the human gut. We further explore the growing body of evidence for the role of CRISPR/Cas in regulating the interplay between bacteria and lysogenic phages, which may be intimately related to the presence of memory spacers and sheds new light on the multifaceted biological and ecological modes of action of CRISPR/Cas. PMID:23439321

[Effects of different catch modes on soil enzyme activities and bacterial community in the rhizosphere of cucumber].

PubMed

Li, Min; Wu, Feng-zhi

2014-12-01

Effects of different catch modes on soil enzyme activities and bacterial community in the rhizosphere of cucumber (Cucumis sativus) were analyzed by conventional chemical method, PCR-denaturing gradient gel electrophoresis (DGGE) and real-time PCR methods. Pot experiment was carried out in the greenhouse for three consecutive years with cucumber as the main crop, and scallion (Allium fistulosum), wheat (Triticum aestivum) and oilseed rape (Brassica campestri) as catch crops. Results showed that, with the increase of crop planting times, soil urease, neutral phosphatase and invertase activities in the wheat treatment were significantly) higher than in the scallion and oilseed rape treatments, and these enzyme activities in the oilseed rape treatment were significantly higher than in the scallion treatment. PCR-DGGR analysis showed that cucumber rhizosphere bacterial community structures were different among treatments. Scallion and wheat treatments maintained relatively higher diversity indices of bacterial community structure. qPCR results showed that the abundance of soil bacterial community in the wheat treatment was significantly higher than in the scallion and oilseed rape treatments. In conclusion, different catch treatments affected soil enzyme activities and bacteria community and changed the soil environment. Wheat used as summer catch crop could maintain relatively higher soil enzyme activities, bacterial community diversity and abundance.

Microfluidic cantilever detects bacteria and measures their susceptibility to antibiotics in small confined volumes

NASA Astrophysics Data System (ADS)

Etayash, Hashem; Khan, M. F.; Kaur, Kamaljit; Thundat, Thomas

2016-10-01

In the fight against drug-resistant bacteria, accurate and high-throughput detection is essential. Here, a bimaterial microcantilever with an embedded microfluidic channel with internal surfaces chemically or physically functionalized with receptors selectively captures the bacteria passing through the channel. Bacterial adsorption inside the cantilever results in changes in the resonance frequency (mass) and cantilever deflection (adsorption stress). The excitation of trapped bacteria using infrared radiation (IR) causes the cantilever to deflect in proportion to the infrared absorption of the bacteria, providing a nanomechanical infrared spectrum for selective identification. We demonstrate the in situ detection and discrimination of Listeria monocytogenes at a concentration of single cell per μl. Trapped Escherichia coli in the microchannel shows a distinct nanomechanical response when exposed to antibiotics. This approach, which combines enrichment with three different modes of detection, can serve as a platform for the development of a portable, high-throughput device for use in the real-time detection of bacteria and their response to antibiotics.

Acyl-homoserine lactone-based quorum sensing and quorum quenching hold promise to determine the performance of biological wastewater treatments: An overview.

PubMed

Huang, Jinhui; Shi, Yahui; Zeng, Guangming; Gu, Yanling; Chen, Guiqiu; Shi, Lixiu; Hu, Yi; Tang, Bi; Zhou, Jianxin

2016-08-01

Quorum sensing (QS) is a communication process between cells, in which bacteria secrete and sense the specific chemicals, and regulate gene expression in response to population density. Quorum quenching (QQ) blocks QS system, and inhibits gene expression mediating bacterial behaviors. Given the extensive research of acyl-homoserine lactone (AHL) signals, existences and effects of AHL-based QS and QQ in biological wastewater treatments are being subject to high concern. This review summarizes AHL structure, synthesis mode, degradation mechanisms, analytical methods, environmental factors, AHL-based QS and QQ mechanisms. The existences and roles of AHL-based QS and QQ in biomembrane processes, activated sludge processes and membrane bioreactors are summarized and discussed, and corresponding exogenous regulation strategy by selective enhancement of AHL-based QS or QQ coexisting in biological wastewater treatments is suggested. Such strategies including the addition of AHL signals, AHL-producing bacteria as well as quorum quenching enzyme or bacteria can effectively improve wastewater treatment performance without killing or limiting bacterial survival and growth. This review will present the theoretical and practical cognition for bacterial AHL-based QS and QQ, suggest the feasibility of exogenous regulation strategies in biological wastewater treatments, and provide useful information to scientists and engineers who work in this field. Copyright © 2016 Elsevier Ltd. All rights reserved.

Structurally altered capsular polysaccharides produced by mutant bacteria

NASA Technical Reports Server (NTRS)

Petersen, Gene R. (Inventor); Kern, Roger G. (Inventor); Richards, Gil F. (Inventor)

1995-01-01

Structurally altered capsular polysaccharides are produced by mutant bacteria. These polysaccharides are isolated by selecting a wild type bacterial strain and a phage producing degradative enzymes that have substrate specificity for the capsular polysaccharides produced by the wild type bacteria. Phage-resistant mutants producing capsular polysaccharides are selected and the structurally altered capsular polysaccharide is isolated therefrom.

Computational Analysis of Cysteine and Methionine Metabolism and Its Regulation in Dairy Starter and Related Bacteria

PubMed Central

Liu, Mengjin; Prakash, Celine; Nauta, Arjen; Siezen, Roland J.

2012-01-01

Sulfuric volatile compounds derived from cysteine and methionine provide many dairy products with a characteristic odor and taste. To better understand and control the environmental dependencies of sulfuric volatile compound formation by the dairy starter bacteria, we have used the available genome sequence and experimental information to systematically evaluate the presence of the key enzymes and to reconstruct the general modes of transcription regulation for the corresponding genes. The genomic organization of the key genes is suggestive of a subdivision of the reaction network into five modules, where we observed distinct differences in the modular composition between the families Lactobacillaceae, Enterococcaceae, and Leuconostocaceae, on the one hand, and the family Streptococcaceae, on the other. These differences are mirrored by the way in which transcription regulation of the genes is structured in these families. In the Lactobacillaceae, Enterococcaceae, and Leuconostocaceae, the main shared mode of transcription regulation is methionine (Met) T-box-mediated regulation. In addition, the gene metK, encoding S-adenosylmethionine (SAM) synthetase, is controlled via the SMK box (SAM). The SMK box is also found upstream of metK in species of the family Streptococcaceae. However, the transcription control of the other modules is mediated via three different LysR-family regulators, MetR/MtaR (methionine), CmbR (O-acetyl[homo]serine), and HomR (O-acetylhomoserine). Redefinition of the associated DNA-binding motifs helped to identify/disentangle the related regulons, which appeared to perfectly match the proposed subdivision of the reaction network. PMID:22522891

Helicobacter pylori Biofilm Formation and Its Potential Role in Pathogenesis.

PubMed

Hathroubi, Skander; Servetas, Stephanie L; Windham, Ian; Merrell, D Scott; Ottemann, Karen M

2018-06-01

Despite decades of effort, Helicobacter pylori infections remain difficult to treat. Over half of the world's population is infected by H. pylori , which is a major cause of duodenal and gastric ulcers as well as gastric cancer. During chronic infection, H. pylori localizes within the gastric mucosal layer, including deep within invaginations called glands; thanks to its impressive ability to survive despite the harsh acidic environment, it can persist for the host's lifetime. This ability to survive and persist in the stomach is associated with urease production, chemotactic motility, and the ability to adapt to the fluctuating environment. Additionally, biofilm formation has recently been suggested to play a role in colonization. Biofilms are surface-associated communities of bacteria that are embedded in a hydrated matrix of extracellular polymeric substances. Biofilms pose a substantial health risk and are key contributors to many chronic and recurrent infections. This link between biofilm-associated bacteria and chronic infections likely results from an increased tolerance to conventional antibiotic treatments as well as immune system action. The role of this biofilm mode in antimicrobial treatment failure and H. pylori survival has yet to be determined. Furthermore, relatively little is known about the H. pylori biofilm structure or the genes associated with this mode of growth. In this review, therefore, we aim to highlight recent findings concerning H. pylori biofilms and the molecular mechanism of their formation. Additionally, we discuss the potential roles of biofilms in the failure of antibiotic treatment and in infection recurrence. Copyright © 2018 American Society for Microbiology.

Exploring the selectivity of auto-inducer complex with LuxR using molecular docking, mutational studies and molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Rajamanikandan, Sundaraj; Srinivasan, Pappu

2017-03-01

Bacteria communicate with one another using extracellular signaling molecules called auto-inducers (AHLs), a process termed as quorum sensing. The quorum sensing process allows bacteria to regulate various physiological activities. In this regard, quorum sensing master regulator LuxR from Vibrio harveyi represents an attractive therapeutic target for the development of novel anti-quorum sensing agents. Eventhough the binding of AHL complex with LuxR is evidenced in earlier reports, but their mode of binding is not clearly determined. Therefore, in the present work, molecular docking, in silico mutational studies, molecular dynamics simulations and free energy calculations were performed to understand the selectivity of AHL into the binding site of LuxR. The results revealed that Asn133 and Gln137 residues play a crucial role in recognizing AHL more effectively into the binding site of LuxR with good binding free energy. In addition to that, the carbonyl group presents in the lactone ring and amide group of AHL plays a vital role in the formation of hydrogen bond interactions with the protein. Further, structure based virtual screening was performed using ChemBridge database to screen potent lead molecules against LuxR. 4-benzyl-2-pyrrolidinone and N-[2(1-cyclohexen-1-yl) enthyl]-N'(2-ethoxyphenyl) were selected based on dock score, binding affinity and mode of interactions with the receptor. Furthermore, binding free energy, density functional theory and ADME prediction were performed to rank the lead molecules. Thus, the identified lead molecules can be used for the development of anti-quorum sensing drugs.

[Competition between redox mediator and oxygen in the microbial fuel cell].

PubMed

Alferov, S V; Vozchikova, S V; Arlyapov, V A; Alferov, V A; Reshetilov, A N

2017-01-01

The maximal rates and effective constants of 2,6-dichlorphenolindophenol and oxygen reduction by bacterim Gluconobacter oxydans in bacterial fuel cells under different conditions were evaluated. In an open-circuit mode, the rate of 2,6-dichlorphenolindophenol reduction coupled with ethanol oxidation under oxygen and nirogen atmospheres were 1.0 and 1.1 μM s–1 g–1, respectively. In closed-circuit mode, these values were 0.4 and 0.44 μM s–1 g–1, respectively. The initial rate of mediator reduction with the use of membrane fractions of bacteria in oxygen and nitrogen atmospheres in open-circuit mode were 6.3 and 6.9 μM s–1 g–1, whereas these values in closed-circuit mode comprised 2.2 and 2.4 μM s–1 g–1, respectively. The oxygen reduction rates in the presence and absence of 2,6-dichlorphenolindophenol were 0.31 and 0.32 μM s–1 g–1, respectively. The data obtained in this work demonstrated independent electron transfer from bacterial redox centers to the mediator and the absence of competition between the redox mediator and oxygen. The results can make it possible to reduce costs of microbial fuel cells based on activity of acetic acid bacteria G. oxydans.

Rheological effects of micropolar slime on the gliding motility of bacteria with slip boundary condition

NASA Astrophysics Data System (ADS)

Asghar, Z.; Ali, N.; Anwar Bég, O.; Javed, T.

2018-06-01

Gliding bacteria are virtually everywhere. These organisms are phylogenetically diverse with their hundreds of types, different shapes and several modes of motility. One possible mode of gliding motility in the rod shaped bacteria is that they propel themselves by producing undulating waves in their body. Few bacteria glides near the solid surface over the slime without any aid of flagella so the classical Navier-Stokes equations are incapable of explaining the slime rheology at the microscopic level. Micropolar fluid dynamics however provides a solid framework for mimicking bacterial physical phenomena at both micro and nano-scales, and therefore we use the micropolar fluid to characterize the rheology of a thin layer of slime and its dominant microrotation effects. It is also assumed that there is a certain degree of slip between slime and bacterial undulating surface and also between slime and solid substrate. The flow equations are formulated under long wavelength and low Reynolds number assumptions. Exact expressions for stream function and pressure gradient are obtained. The speed of the gliding bacteria is numerically calculated by using a modified Newton-Raphson method. Slip effects and effects of non-Newtonian slime parameters on bacterial speed and power are also quantified. In addition, when the glider is fixed, the effects of slip and rheological properties of micropolar slime parameters on the velocity, micro-rotation (angular velocity) of spherical slime particles, pressure rise per wavelength, pumping and trapping phenomena are also shown graphically and discussed in detail. The study is relevant to emerging biofuel cell technologies and also bacterial biophysics.

E. coli chemotaxis and super-diffusion

NASA Astrophysics Data System (ADS)

Dobnikar, Jure; Matthäus, Franziska; Jagodic, Marko

2010-03-01

The bacteria E. coli actively propel by switching between clockwise and anti-clockwise rotation of the flagella attached to their cell membranes. This results in two modes of motion: tumbling and swimming. The switching between the two modes is coupled to the ligand sensing through the chemotactic signalling pathway inside the cell. We modelled the signalling pathway and performed numerical simulations of the chemotactic motion of a large number of E. coli bacteria under various external conditions. We have shown that under certain conditions the thermal noise in the level of receptor-bound CheR (an enzyme responsible for methylation of the receptor sites) leads to super-diffusive behaviour (L'evy walk) which is advantageous for the bacterial populations in environments with scarce food. Exerting external pressure we might observe evolution of the wild-type to the super-diffusive populations.

Bacteriagenic silver nanoparticles: synthesis, mechanism, and applications.

PubMed

Singh, Richa; Shedbalkar, Utkarsha U; Wadhwani, Sweety A; Chopade, Balu A

2015-06-01

Silver nanoparticles (AgNPs) have received tremendous attention due to their significant antimicrobial properties. Large numbers of reports are available on the physical, chemical, and biological syntheses of colloidal AgNPs. Since there is a great need to develop ecofriendly and sustainable methods, biological systems like bacteria, fungi, and plants are being employed to synthesize these nanoparticles. The present review focuses specifically on bacteria-mediated synthesis of AgNPs, its mechanism, and applications. Bacterial synthesis of extra- and intracellular AgNPs has been reported using biomass, supernatant, cell-free extract, and derived components. The extracellular mode of synthesis is preferred over the intracellular mode owing to easy recovery of nanoparticles. Silver-resistant genes, c-type cytochromes, peptides, cellular enzymes like nitrate reductase, and reducing cofactors play significant roles in AgNP synthesis in bacteria. Organic materials released by bacteria act as natural capping and stabilizing agents for AgNPs, thereby preventing their aggregation and providing stability for a longer time. Regulation over reaction conditions has been suggested to control the morphology, dispersion, and yield of nanoparticles. Bacterial AgNPs have anticancer and antioxidant properties. Moreover, the antimicrobial activity of AgNPs in combination with antibiotics signifies their importance in combating the multidrug-resistant pathogenic microorganisms. Multiple microbicidal mechanisms exhibited by AgNPs, depending upon their size and shape, make them very promising as novel nanoantibiotics.

Lipopolysaccharides from Commensal and Opportunistic Bacteria: Characterization and Response of the Immune System of the Host Sponge Suberites domuncula

PubMed Central

Gardères, Johan; Bedoux, Gilles; Koutsouveli, Vasiliki; Crequer, Sterenn; Desriac, Florie; Le Pennec, Gaël

2015-01-01

Marine sponges harbor a rich bacterioflora with which they maintain close relationships. However, the way these animals make the distinction between bacteria which are consumed to meet their metabolic needs and opportunistic and commensal bacteria which are hosted is not elucidated. Among the elements participating in this discrimination, bacterial cell wall components such as lipopolysaccharides (LPS) could play a role. In the present study, we investigated the LPS chemical structure of two bacteria associated with the sponge Suberites domuncula: a commensal Endozoicomonas sp. and an opportunistic Pseudoalteromonas sp. Electrophoretic patterns indicated different LPS structures for these bacteria. The immunomodulatory lipid A was isolated after mild acetic acid hydrolysis. The electrospray ionization ion-trap mass spectra revealed monophosphorylated molecules corresponding to tetra- and pentaacylated structures with common structural features between the two strains. Despite peculiar structural characteristics, none of these two LPS influenced the expression of the macrophage-expressed gene S. domuncula unlike the Escherichia coli ones. Further research will have to include a larger number of genes to understand how this animal can distinguish between LPS with resembling structures and discriminate between bacteria associated with it. PMID:26262625

Hit 'em where it hurts: The growing and structurally diverse family of peptides that target lipid-II.

PubMed

Oppedijk, Sabine F; Martin, Nathaniel I; Breukink, Eefjan

2016-05-01

Understanding the mode of action of antibiotics is becoming more and more important in the time that microorganisms start to develop resistance. One very well validated target of several classes of antibiotics is the peptidoglycan precursor lipid II. In this review different classes of lipid II targeting antibiotics will be discussed in detail, including the lantibiotics, human invertebrate defensins and the recently discovered teixobactin. By hitting bacteria where it hurts, at the level of lipid II, we expect to be able to develop efficient antibacterial agents in the future. This article is part of a Special Issue entitled: Antimicrobial peptides edited by Karl Lohner and Kai Hilpert. Copyright © 2015 Elsevier B.V. All rights reserved.

It is all about location: how to pinpoint microorganisms and their functions in multispecies biofilms.

PubMed

Costa, Angela M; Mergulhão, Filipe J; Briandet, Romain; Azevedo, Nuno F

2017-09-01

Multispecies biofilms represent the dominant mode of life for the vast majority of microorganisms. Bacterial spatial localization in such biostructures governs ecological interactions between different populations and triggers the overall community functions. Here, we discuss the pros and cons of fluorescence-based techniques used to decipher bacterial species patterns in biofilms at single cell level, including fluorescence in situ hybridization and the use of genetically modified bacteria that express fluorescent proteins, reporting the significant improvements of those techniques. The development of tools for spatial and temporal study of multispecies biofilms will allow live imaging and spatial localization of cells in naturally occurring biofilms coupled with metabolic information, increasing insight of microbial community and the relation between its structure and functions.

Thickness shear mode (TSM) resonators used for biosensing

NASA Astrophysics Data System (ADS)

Bailey, Claude A.; Fiebor, Ben; Yen, Wei; Vodyanoy, Vitaly; Cernosek, Richard W.; Chin, Bryan A.

2002-02-01

The Auburn University Detection and Food Safety Center has demonstrated real-time biosensor for the detection of Salmonella typimhurium, consisting of a thickness shear-mode (TSM) quartz resonator with antibodies immobilized in a Langmuir-Blodgett surface film. Scanning Electron Microscopy (SEM) images of bound Salmonella bacteria to both polished and unpolished TSM resonators were taken to correlate the mass of the bound organism to the Sauerbrey equation. Theoretical frequency shifts for unpolished TSM resonators predicted by the Sauerbrey equation are much smaller than experimentally measured frequency shift. The Salmonella detector operates in a liquid environment. The viscous properties of this liquid overlayer could influence the TSM resonator's response. Various liquid media were studied as a function of temperature (0 to 50 degree(s)C). The chicken exudate samples with varying fat content show coagulation occurring at temperatures above 35 degree(s)C. Kinematic viscosity test were performed with buffer solutions containing varying quantities of Salmonella bacteria. Since the TSM resonators only entrain a boundary layer of fluid near the surface, they do not respond to these background viscous property changes. Bilk viscosity increases when bacteria concentrations are high. This paper describes investigations of TSM resonator surface acoustic interactions - mass, fluid viscosity, and viscoelasticity - that affect the sensor.

Multidrug-Resistant Enterococcal Infections: New Compounds, Novel Antimicrobial Therapies?

PubMed

van Harten, Roel M; Willems, Rob J L; Martin, Nathaniel I; Hendrickx, Antoni P A

2017-06-01

Over the past two decades infections due to antibiotic-resistant bacteria have escalated world-wide, affecting patient morbidity, mortality, and health care costs. Among these bacteria, Enterococcus faecium and Enterococcus faecalis represent opportunistic nosocomial pathogens that cause difficult-to-treat infections because of intrinsic and acquired resistance to a plethora of antibiotics. In recent years, a number of novel antimicrobial compound classes have been discovered and developed that target Gram-positive bacteria, including E. faecium and E. faecalis. These new antibacterial agents include teixobactin (targeting lipid II and lipid III), lipopeptides derived from nisin (targeting lipid II), dimeric vancomycin analogues (targeting lipid II), sortase transpeptidase inhibitors (targeting the sortase enzyme), alanine racemase inhibitors, lipoteichoic acid synthesis inhibitors (targeting LtaS), various oxazolidinones (targeting the bacterial ribosome), and tarocins (interfering with teichoic acid biosynthesis). The targets of these novel compounds and mode of action make them very promising for further antimicrobial drug development and future treatment of Gram-positive bacterial infections. Here we review current knowledge of the most favorable anti-enterococcal compounds along with their implicated modes of action and efficacy in animal models to project their possible future use in the clinical setting. Copyright © 2017 Elsevier Ltd. All rights reserved.

Structural characterization of Helicobacter pylori dethiobiotin synthetase reveals differences between family members

DOE Office of Scientific and Technical Information (OSTI.GOV)

Porebski, Przemyslaw J.; Klimecka, Maria; Chruszcz, Maksymilian

2012-07-11

Dethiobiotin synthetase (DTBS) is involved in the biosynthesis of biotin in bacteria, fungi, and plants. As humans lack this pathway, DTBS is a promising antimicrobial drug target. We determined structures of DTBS from Helicobacter pylori (hpDTBS) bound with cofactors and a substrate analog, and described its unique characteristics relative to other DTBS proteins. Comparison with bacterial DTBS orthologs revealed considerable structural differences in nucleotide recognition. The C-terminal region of DTBS proteins, which contains two nucleotide-recognition motifs, differs greatly among DTBS proteins from different species. The structure of hpDTBS revealed that this protein is unique and does not contain a C-terminalmore » region containing one of the motifs. The single nucleotide-binding motif in hpDTBS is similar to its counterpart in GTPases; however, isothermal titration calorimetry binding studies showed that hpDTBS has a strong preference for ATP. The structural determinants of ATP specificity were assessed with X-ray crystallographic studies of hpDTBS-ATP and hpDTBS-GTP complexes. The unique mode of nucleotide recognition in hpDTBS makes this protein a good target for H. pylori-specific inhibitors of the biotin synthesis pathway.« less

Molecular structure of EmbR, a response element of Ser/Thr kinase signaling in Mycobacterium tuberculosis

PubMed Central

Alderwick, Luke J.; Molle, Virginie; Kremer, Laurent; Cozzone, Alain J.; Dafforn, Timothy R.; Besra, Gurdyal S.; Fütterer, Klaus

2006-01-01

Ser/Thr phosphorylation has emerged as a critical regulatory mechanism in a number of bacteria, including Mycobacterium tuberculosis. This problematic pathogen encodes 11 eukaryotic-like Ser/Thr kinases, yet few substrates or signaling targets have been characterized. Here, we report the structure of EmbR (2.0 Å), a putative transcriptional regulator of key arabinosyltransferases (EmbC, -A, and -B), and an endogenous substrate of the Ser/Thr-kinase PknH. EmbR presents a unique domain architecture: the N-terminal winged-helix DNA-binding domain forms an extensive interface with the all-helical central bacterial transcriptional activation domain and is positioned adjacent to the regulatory C-terminal forkhead-associated (FHA) domain, which mediates binding to a Thr-phosphorylated site in PknH. The structure in complex with a phospho-peptide (1.9 Å) reveals a conserved mode of phospho-threonine recognition by the FHA domain and evidence for specific recognition of the cognate kinase. The present structures suggest hypotheses as to how EmbR might propagate the phospho-relay signal from its cognate kinase, while serving as a template for the structurally uncharacterized Streptomyces antibiotic regulatory protein family of transcription factors. PMID:16477027

Structural Analysis of the Tobramycin and Gentamicin Clinical Resistome Reveals Limitations for Next-generation Aminoglycoside Design.

PubMed

Bassenden, Angelia V; Rodionov, Dmitry; Shi, Kun; Berghuis, Albert M

2016-05-20

Widespread use and misuse of antibiotics has allowed for the selection of resistant bacteria capable of avoiding the effects of antibiotics. The primary mechanism for resistance to aminoglycosides, a broad-spectrum class of antibiotics, is through covalent enzymatic modification of the drug, waning their bactericidal effect. Tobramycin and gentamicin are two medically important aminoglycosides targeted by several different resistance factors, including aminoglycoside 2″-nucleotidyltransferase [ANT(2″)], the primary cause of aminoglycoside resistance in North America. We describe here two crystal structures of ANT(2″), each in complex with AMPCPP, Mn(2+), and either tobramycin or gentamicin. Together these structures outline ANT(2″)'s specificity for clinically used substrates. Importantly, these structures complete our structural knowledge for the set of enzymes that most frequently confer clinically observed resistance to tobramycin and gentamicin. Comparison of tobramycin and gentamicin binding to enzymes in this resistome, as well as to the intended target, the bacterial ribosome, reveals surprising diversity in observed drug-target interactions. Analysis of the diverse binding modes informs that there are limited opportunities for developing aminoglycoside analogs capable of evading resistance.

Detection specificity studies of bacteriophage adhesin-coated long-period grating-based biosensor

NASA Astrophysics Data System (ADS)

Koba, Marcin; Śmietana, Mateusz; Brzozowska, Ewa; Górska, Sabina; Mikulic, Predrag; Cusano, Andrea; Bock, Wojtek J.

2015-09-01

In this work, we present a label-free detection specificity study of an optical fiber long-period grating (LPG) biosensor working near the dispersion turning point of higher order cladding modes. The LPG sensor functionalized with bacteriophage adhesin is tested with specific and non-specific bacteria dry weight. We show that such biosensor is able to selectively bind, thus recognize different bacteria. We use bacteria dry weights of E. coli B as positive test and E. coli K12 and Salmonella enterica as negative tests. The resonance wavelength shift induced by E. coli B reaches over 90 nm, while for E. coli K12 and Salmonella enterica approximately 40 and 20 nm, respectively.

Control of microfabricated structures powered by flagellated bacteria using phototaxis

NASA Astrophysics Data System (ADS)

Steager, Edward; Kim, Chang-Beom; Patel, Jigarkumar; Bith, Socheth; Naik, Chandan; Reber, Lindsay; Kim, Min Jun

2007-06-01

Flagellated bacteria have been employed as microactuators in low Reynolds number fluidic environments. SU-8 microstructures have been fabricated and released on the surface of swarming Serratia marcescens, and the flagella propel the structures along the swarm surface. Phototactic control of these structures is demonstrated by exposing the localized regions of the swarm to ultraviolet light. The authors additionally discuss the control of microstructures in an open channel powered by bacteria which have been docked through a blotting technique. A tracking algorithm has been developed to analyze swarming patterns of the bacteria as well as the kinematics of the microstructures.

Initiation of translation in bacteria by a structured eukaryotic IRES RNA.

PubMed

Colussi, Timothy M; Costantino, David A; Zhu, Jianyu; Donohue, John Paul; Korostelev, Andrei A; Jaafar, Zane A; Plank, Terra-Dawn M; Noller, Harry F; Kieft, Jeffrey S

2015-03-05

The central dogma of gene expression (DNA to RNA to protein) is universal, but in different domains of life there are fundamental mechanistic differences within this pathway. For example, the canonical molecular signals used to initiate protein synthesis in bacteria and eukaryotes are mutually exclusive. However, the core structures and conformational dynamics of ribosomes that are responsible for the translation steps that take place after initiation are ancient and conserved across the domains of life. We wanted to explore whether an undiscovered RNA-based signal might be able to use these conserved features, bypassing mechanisms specific to each domain of life, and initiate protein synthesis in both bacteria and eukaryotes. Although structured internal ribosome entry site (IRES) RNAs can manipulate ribosomes to initiate translation in eukaryotic cells, an analogous RNA structure-based mechanism has not been observed in bacteria. Here we report our discovery that a eukaryotic viral IRES can initiate translation in live bacteria. We solved the crystal structure of this IRES bound to a bacterial ribosome to 3.8 Å resolution, revealing that despite differences between bacterial and eukaryotic ribosomes this IRES binds directly to both and occupies the space normally used by transfer RNAs. Initiation in both bacteria and eukaryotes depends on the structure of the IRES RNA, but in bacteria this RNA uses a different mechanism that includes a form of ribosome repositioning after initial recruitment. This IRES RNA bridges billions of years of evolutionary divergence and provides an example of an RNA structure-based translation initiation signal capable of operating in two domains of life.

Inactivation/reactivation of antibiotic-resistant bacteria by a novel UVA/LED/TiO2 system.

PubMed

Xiong, Pei; Hu, Jiangyong

2013-09-01

In this study, an effective photocatalytic disinfection system was established using the newly emerged high power UVA/LED lamp. Crystallizing dish coated with TiO2 was prepared by 32-times impregnation-drying processes, and served as the supporting container for water samples. This study focused on the application of this UVA/LED system for the photocatalytic disinfection of selected antibiotic-resistant bacteria, Escherichia coli ATCC 700891. The disinfection performances were studied under various light intensities and illumination modes. Results show that higher light intensity could reach more significant inactivation of E. coli ATCC 700891. With the same UV dose, log-removal of antibiotic-resistant bacteria decreased with circle time in the studied range, while increased with duty circle. A "residual disinfecting effect" was found in the following dark period for bacteria collected at different phases of photocatalytic process. Residual disinfecting effect was found not significant for bacteria with 30 min periodic illumination. While residual disinfecting effect could kill almost all bacteria after 90 min UV periodic illumination within the following 240 min dark period. Copyright © 2013 Elsevier Ltd. All rights reserved.

Growth of Bacterial Colonies

NASA Astrophysics Data System (ADS)

Warren, Mya; Hwa, Terence

2013-03-01

On hard agar gel, there is insufficient surface hydration for bacteria to swim or swarm. Instead, growth occurs in colonies of close-packed cells, which expand purely due to repulsive interactions: individual bacteria push each other out of the way through the force of their growth. In this way, bacterial colonies represent a new type of ``active'' granular matter. In this study, we investigate the physical, biochemical, and genetic elements that determine the static and dynamic aspects of this mode of bacterial growth for E. coli. We characterize the process of colony expansion empirically, and use discrete and continuum models to examine the extent to which our observations can be explained by the growth characteristics of non-communicating cells, coupled together by physical forces, nutrients, and waste products. Our results challenge the commonly accepted modes of bacterial colony growth and provide insight into sources of growth limitation in crowded bacterial communities.

Common Virulence Factors and Tissue Targets of Entomopathogenic Bacteria for Biological Control of Lepidopteran Pests

PubMed Central

Castagnola, Anaïs; Stock, S. Patricia

2014-01-01

This review focuses on common insecticidal virulence factors from entomopathogenic bacteria with special emphasis on two insect pathogenic bacteria Photorhabdus (Proteobacteria: Enterobacteriaceae) and Bacillus (Firmicutes: Bacillaceae). Insect pathogenic bacteria of diverse taxonomic groups and phylogenetic origin have been shown to have striking similarities in the virulence factors they produce. It has been suggested that the detection of phage elements surrounding toxin genes, horizontal and lateral gene transfer events, and plasmid shuffling occurrences may be some of the reasons that virulence factor genes have so many analogs throughout the bacterial kingdom. Comparison of virulence factors of Photorhabdus, and Bacillus, two bacteria with dissimilar life styles opens the possibility of re-examining newly discovered toxins for novel tissue targets. For example, nematodes residing in the hemolymph may release bacteria with virulence factors targeting neurons or neuromuscular junctions. The first section of this review focuses on toxins and their context in agriculture. The second describes the mode of action of toxins from common entomopathogens and the third draws comparisons between Gram positive and Gram negative bacteria. The fourth section reviews the implications of the nervous system in biocontrol. PMID:24634779

A Rapid and Quantitative Flow Cytometry Method for the Analysis of Membrane Disruptive Antimicrobial Activity.

PubMed

O'Brien-Simpson, Neil M; Pantarat, Namfon; Attard, Troy J; Walsh, Katrina A; Reynolds, Eric C

2016-01-01

We describe a microbial flow cytometry method that quantifies within 3 hours antimicrobial peptide (AMP) activity, termed Minimum Membrane Disruptive Concentration (MDC). Increasing peptide concentration positively correlates with the extent of bacterial membrane disruption and the calculated MDC is equivalent to its MBC. The activity of AMPs representing three different membranolytic modes of action could be determined for a range of Gram positive and negative bacteria, including the ESKAPE pathogens, E. coli and MRSA. By using the MDC50 concentration of the parent AMP, the method provides high-throughput, quantitative screening of AMP analogues. A unique feature of the MDC assay is that it directly measures peptide/bacteria interactions and lysed cell numbers rather than bacteria survival as with MIC and MBC assays. With the threat of multi-drug resistant bacteria, this high-throughput MDC assay has the potential to aid in the development of novel antimicrobials that target bacteria with improved efficacy.

An intermolecular binding mechanism involving multiple LysM domains mediates carbohydrate recognition by an endopeptidase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wong, Jaslyn E. M. M.; Midtgaard, Søren Roi; Gysel, Kira

The crystal and solution structures of the T. thermophilus NlpC/P60 d, l-endopeptidase as well as the co-crystal structure of its N-terminal LysM domains bound to chitohexaose allow a proposal to be made regarding how the enzyme recognizes peptidoglycan. LysM domains, which are frequently present as repetitive entities in both bacterial and plant proteins, are known to interact with carbohydrates containing N-acetylglucosamine (GlcNAc) moieties, such as chitin and peptidoglycan. In bacteria, the functional significance of the involvement of multiple LysM domains in substrate binding has so far lacked support from high-resolution structures of ligand-bound complexes. Here, a structural study of themore » Thermus thermophilus NlpC/P60 endopeptidase containing two LysM domains is presented. The crystal structure and small-angle X-ray scattering solution studies of this endopeptidase revealed the presence of a homodimer. The structure of the two LysM domains co-crystallized with N-acetyl-chitohexaose revealed a new intermolecular binding mode that may explain the differential interaction between LysM domains and short or long chitin oligomers. By combining the structural information with the three-dimensional model of peptidoglycan, a model suggesting how protein dimerization enhances the recognition of peptidoglycan is proposed.« less

Spontaneous bacteriocin resistance in Listeria monocytogenes as a susceptibility screen for identifying different mechanisms of resistance and modes of action by bacteriocins of lactic acid bacteria.

PubMed

Macwana, Sunita; Muriana, Peter M

2012-01-01

A practical system was devised for grouping bacteriocins of lactic acid bacteria (LAB) based on mode of action as determined by changes in inhibitory activity to spontaneously-acquired bacteriocin resistance (Bac(R)). Wild type Listeria monocytogenes 39-2 was sensitive to five bacteriocins produced by 3 genera of LAB: pediocin PA-1 and pediocin Bac3 (Pediococcus), lacticin FS97 and lacticin FS56 (Lactococcus), and curvaticin FS47 (Lactobacillus). A spontaneous Bac(R) derivative of L. monocytogenes 39-2 obtained by selective recovery against lacticin FS56 provided complete resistance to the bacteriocin made by Lactococcus lactis FS56. The lacticin FS56-resistant strain of L. monocyotgenes 39-2 was also cross-resistant to curvaticin FS47 and pediocin PA-1, but not to lacticin FS97 or pediocin Bac3. The same pattern of cross-resistance was also observed with Bac(R) isolates obtained with L. monocytogenes Scott A-2. A spontaneous mutation that renders a strain cross-resistant to different bacteriocins indicates that they share a common mechanism of resistance due to similar modes of action of the bacteriocins. Spontaneous resistance was acquired to other bacteriocins (in aggregate) by following the same procedure against which the Bac(R) strain was still sensitive. In subsequent challenge assays, mixtures of bacteriocins of different modes of action provided greater inhibition than mixtures of bacteriocins of the same mode of action (as determined by our screening method). This study identifies a methodical approach to classify bacteriocins into functional groups based on mechanism of resistance (i.e., mode of action) that could be used for identifying the best mixture of bacteriocins for use as biopreservatives. Copyright © 2011 Elsevier B.V. All rights reserved.

Faunal Burrows Alter the Diversity, Abundance, and Structure of AOA, AOB, Anammox and n-Damo Communities in Coastal Mangrove Sediments.

PubMed

Chen, Jing; Gu, Ji-Dong

2017-07-01

In the present work, the diversity, community structures, and abundances of aerobic ammonia-oxidizing archaea (AOA) and bacteria (AOB), anaerobic ammonium-oxidizing (anammox) bacteria, and denitrifying anaerobic methane oxidization (n-damo) bacteria were unraveled in the bioturbated areas of the coastal Mai Po mangrove sediments. Results indicated that the bioturbation by burrowing in mangrove sediments was associated with higher concentration of NH 4 + but lower concentrations of both NO 2 - and NO 3 - , and increase in diversity and richness of both AOA and AOB, but relatively lower diversity and richness of n-damo bacteria. The phylotypes of anammox bacterial community were significantly increased while their phylogenetic lineages observed in the less bioturbated areas were also maintained. Infauna also showed a great impact on the composition of n-damo bacterial phylotypes and burrowing activity altered the n-damo community structure profoundly in the sampled areas. The communities of n-damo bacteria in the surrounding bulk sediments showed similar structures to marine n-damo communities, but those on the burrow wall and in the ambient surface layer had a freshwater pattern, which was different from previous findings in Mai Po wetland. On the other hand, the abundances of AOA, AOB, and n-damo bacteria were greatly stimulated on burrow walls while the abundance of anammox bacteria remained unchanged. Infaunal burrows and mangrove roots affected the relative abundance of AOA and AOB. The benthic infauna stimulated the abundances of AOA, AOB, anammox, and n-damo bacteria. Furthermore, NH 4 + and NO 2 - were important environmental factors changing the structure of each group. The communities of anammox and n-damo bacteria in bioturbated areas showed a competitive relationship.

Unraveling the antibacterial mode of action of a clay from the Colombian Amazon.

PubMed

Londono, Sandra Carolina; Williams, Lynda B

2016-04-01

Natural antibacterial clays can inhibit growth of human pathogens; therefore, understanding the antibacterial mode of action may lead to new applications for health. The antibacterial modes of action have shown differences based on mineralogical constraints. Here we investigate a natural clay from the Colombian Amazon (AMZ) known to the Uitoto natives as a healing clay. The physical and chemical properties of the AMZ clay were compared to standard reference materials: smectite (SWy-1) and kaolinite (API #5) that represent the major minerals in AMZ. We tested model Gram-negative (Escherichia coli ATCC #25922) and Gram-positive (Bacillus subtilis ATCC #6633) bacteria to assess the clay's antibacterial effectiveness against different bacterial types. The chemical and physical changes in the microbes were examined using bioimaging and mass spectrometry of clay digests and aqueous leachates. Results indicate that a single dose of AMZ clay (250 mg/mL) induced a 4-6 order of magnitude reduction in cell viability, unlike the reference clays that did not impact bacterial survival. AMZ clay possesses a relatively high specific surface area (51.23 m(2)/g) and much higher total surface area (278.82 m(2)/g) than the reference clays. In aqueous suspensions (50 mg clay/mL water), soluble metals are released and the minerals buffer fluid pH between 4.1 and 4.5. We propose that the clay facilitates chemical interactions detrimental to bacteria by absorbing nutrients (e.g., Mg, P) and potentially supplying metals (e.g., Al) toxic to bacteria. This study demonstrates that native traditional knowledge can direct scientific studies.

Resurrecting Inactive Antimicrobial Peptides from the Lipopolysaccharide Trap

PubMed Central

Mohanram, Harini

2014-01-01

Host defense antimicrobial peptides (AMPs) are a promising source of antibiotics for the treatment of multiple-drug-resistant pathogens. Lipopolysaccharide (LPS), the major component of the outer leaflet of the outer membrane of Gram-negative bacteria, functions as a permeability barrier against a variety of molecules, including AMPs. Further, LPS or endotoxin is the causative agent of sepsis killing 100,000 people per year in the United States alone. LPS can restrict the activity of AMPs inducing aggregations at the outer membrane, as observed for frog AMPs, temporins, and also in model AMPs. Aggregated AMPs, “trapped” by the outer membrane, are unable to traverse the cell wall, causing their inactivation. In this work, we show that these inactive AMPs can overcome LPS-induced aggregations while conjugated with a short LPS binding β-boomerang peptide motif and become highly bactericidal. The generated hybrid peptides exhibit activity against Gram-negative and Gram-positive bacteria in high-salt conditions and detoxify endotoxin. Structural and biophysical studies establish the mechanism of action of these peptides in LPS outer membrane. Most importantly, this study provides a new concept for the development of a potent broad-spectrum antibiotic with efficient outer membrane disruption as the mode of action. PMID:24419338

Alcohol dehydrogenase of acetic acid bacteria: structure, mode of action, and applications in biotechnology.

PubMed

Yakushi, Toshiharu; Matsushita, Kazunobu

2010-05-01

Pyrroquinoline quinone-dependent alcohol dehydrogenase (PQQ-ADH) of acetic acid bacteria is a membrane-bound enzyme involved in the acetic acid fermentation by oxidizing ethanol to acetaldehyde coupling with reduction of membranous ubiquinone (Q), which is, in turn, re-oxidized by ubiquinol oxidase, reducing oxygen to water. PQQ-ADHs seem to have co-evolved with the organisms fitting to their own habitats. The enzyme consists of three subunits and has a pyrroloquinoline quinone, 4 heme c moieties, and a tightly bound Q as the electron transfer mediators. Biochemical, genetic, and electrochemical studies have revealed the unique properties of PQQ-ADH since it was purified in 1978. The enzyme is unique to have ubiquinol oxidation activity in addition to Q reduction. This mini-review focuses on the molecular properties of PQQ-ADH, such as the roles of the subunits and the cofactors, particularly in intramolecular electron transport of the enzyme from ethanol to Q. Also, we summarize biotechnological applications of PQQ-ADH as to enantiospecific oxidations for production of the valuable chemicals and bioelectrocatalysis for sensors and fuel cells using indirect and direct electron transfer technologies and discuss unsolved issues and future prospects related to this elaborate enzyme.

Dual-mode acoustic wave biosensors microarrays

NASA Astrophysics Data System (ADS)

Auner, Gregory W.; Shreve, Gina; Ying, Hao; Newaz, Golam; Hughes, Chantelle; Xu, Jianzeng

2003-04-01

We have develop highly sensitive and selective acoustic wave biosensor arrays with signal analysis systems to provide a fingerprint for the real-time identification and quantification of a wide array of bacterial pathogens and environmental health hazards. We have developed an unique highly sensitive dual mode acoustic wave platform prototype that, when combined with phage based selective detection elements, form a durable bacteria sensor. Arrays of these new real-time biosensors are integrated to form a biosensor array on a chip. This research and development program optimizes advanced piezoelectric aluminum nitride wide bandgap semiconductors, novel micromachining processes, advanced device structures, selective phage displays development and immobilization techniques, and system integration and signal analysis technology to develop the biosensor arrays. The dual sensor platform can be programmed to sense in a gas, vapor or liquid environment by switching between acoustic wave resonate modes. Such a dual mode sensor has tremendous implications for applications involving monitoring of pathogenic microorganisms in the clinical setting due to their ability to detect airborne pathogens. This provides a number of applications including hospital settings such as intensive care or other in-patient wards for the reduction of nosocomial infections and maintenance of sterile environments in surgical suites. Monitoring for airborn pathogen transmission in public transportation areas such as airplanes may be useful for implementation of strategies for redution of airborn transmission routes. The ability to use the same sensor in the liquid sensing mode is important for tracing the source of airborn pathogens to local liquid sources. Sensing of pathogens in saliva will be useful for sensing oral pathogens and support of decision-making strategies regarding prevention of transmission and support of treatment strategies.

Proteinaceous determinants of surface colonization in bacteria: bacterial adhesion and biofilm formation from a protein secretion perspective

PubMed Central

Chagnot, Caroline; Zorgani, Mohamed A.; Astruc, Thierry; Desvaux, Mickaël

2013-01-01

Bacterial colonization of biotic or abiotic surfaces results from two quite distinct physiological processes, namely bacterial adhesion and biofilm formation. Broadly speaking, a biofilm is defined as the sessile development of microbial cells. Biofilm formation arises following bacterial adhesion but not all single bacterial cells adhering reversibly or irreversibly engage inexorably into a sessile mode of growth. Among molecular determinants promoting bacterial colonization, surface proteins are the most functionally diverse active components. To be present on the bacterial cell surface, though, a protein must be secreted in the first place. Considering the close association of secreted proteins with their cognate secretion systems, the secretome (which refers both to the secretion systems and their protein substrates) is a key concept to apprehend the protein secretion and related physiological functions. The protein secretion systems are here considered in light of the differences in the cell-envelope architecture between diderm-LPS (archetypal Gram-negative), monoderm (archetypal Gram-positive) and diderm-mycolate (archetypal acid-fast) bacteria. Besides, their cognate secreted proteins engaged in the bacterial colonization process are regarded from single protein to supramolecular protein structure as well as the non-classical protein secretion. This state-of-the-art on the complement of the secretome (the secretion systems and their cognate effectors) involved in the surface colonization process in diderm-LPS and monoderm bacteria paves the way for future research directions in the field. PMID:24133488

Bactericidal assessment of nano-silver on emerging and re-emerging human pathogens.

PubMed

Anuj, Samir A; Gajera, Harsukh P; Hirpara, Darshna G; Golakiya, Baljibhai A

2018-04-24

With the threat of the growing number of bacteria resistant to antibiotics, the re-emergence of previously deadly infections and the emergence of new infections, there is an urgent need for novel therapeutic agent. Silver in the nano form, which is being used increasingly as antibacterial agents, may extend its antibacterial application to emerging and re-emerging multidrug-resistant pathogens, the main cause of nosocomial diseases worldwide. In the present study, a completely bottom up method to prepare green nano-silver was used. To explore the action of nano-silver on emerging Bacillus megaterium MTCC 7192 and re-emerging Pseudomonas aeruginosa MTCC 741 pathogenic bacteria, the study includes an analysis of the bacterial membrane damage through Scanning Electron Microscope (SEM) as well as alternation of zeta potential and intracellular leakages. In this work, we observed genuine bactericidal property of nano-silver as compare to broad spectrum antibiotics against emerging and re-emerging mode. After being exposed to nano-silver, the membrane becomes scattered from their original ordered arrangement based on SEM observation. Moreover, our results also suggested that alternation of zeta potential enhanced membrane permeability, and beyond a critical point, it leads to cell death. The leakages of intracellular constituents were confirmed by Gas Chromatography-Mass Spectrometry (GC-MS). In conclusion, the combine results suggested that at a specific dose, nano-silver may destroy the structure of bacterial membrane and depress its activity, which causes bacteria to die eventually. Copyright © 2018 Elsevier GmbH. All rights reserved.

Enhancing nitrogen removal in an Orbal oxidation ditch by optimization of oxygen supply: practice in a full-scale municipal wastewater treatment plant.

PubMed

Zhou, Xin; Guo, Xuesong; Han, Yunping; Liu, Junxin; Ren, Jincheng; Wang, Yu; Guo, Yantao

2012-09-01

Seven different aeration modes, in which oxygen supply was changed by adjusting the number of aerators, were designed and applied in a full-scale municipal wastewater treatment plant with Orbal oxidation ditch to investigate the influence of dissolved oxygen (DO) on nitrogen removal performance. The full-scale experiment results of 574 days showed that nitrogen removal efficiency depended on the degree of nitrification and denitrification in the outer channel, which was the largest contributor for TN removal in the Orbal oxidation ditch. Appropriate aeration control in the outer channel was essential to balance nitrification and denitrification in the Orbal oxidation ditch. When DO was as low as about 0.2 mg/L in the outer channel, the highest TN removal efficiency of 75% was obtained. Microbial analysis confirmed that aerobic and anaerobic bacteria coexisted in the outer channel. The greater species diversity and more intensive activities of these bacteria in aeration Mode V may be responsible for the higher TN removal efficiency compared with Mode III. These results suggest that different aerated conditions in the Orbal oxidation ditch might have a significant effect on microbial community characteristics and nitrogen removal efficiencies.

Strong and Nonspecific Synergistic Antibacterial Efficiency of Antibiotics Combined with Silver Nanoparticles at Very Low Concentrations Showing No Cytotoxic Effect.

PubMed

Panáček, Aleš; Smékalová, Monika; Kilianová, Martina; Prucek, Robert; Bogdanová, Kateřina; Večeřová, Renata; Kolář, Milan; Havrdová, Markéta; Płaza, Grażyna Anna; Chojniak, Joanna; Zbořil, Radek; Kvítek, Libor

2015-12-28

The resistance of bacteria towards traditional antibiotics currently constitutes one of the most important health care issues with serious negative impacts in practice. Overcoming this issue can be achieved by using antibacterial agents with multimode antibacterial action. Silver nano-particles (AgNPs) are one of the well-known antibacterial substances showing such multimode antibacterial action. Therefore, AgNPs are suitable candidates for use in combinations with traditional antibiotics in order to improve their antibacterial action. In this work, a systematic study quantifying the synergistic effects of antibiotics with different modes of action and different chemical structures in combination with AgNPs against Escherichia coli, Pseudomonas aeruginosa and Staphylococcus aureus was performed. Employing the microdilution method as more suitable and reliable than the disc diffusion method, strong synergistic effects were shown for all tested antibiotics combined with AgNPs at very low concentrations of both antibiotics and AgNPs. No trends were observed for synergistic effects of antibiotics with different modes of action and different chemical structures in combination with AgNPs, indicating non-specific synergistic effects. Moreover, a very low amount of silver is needed for effective antibacterial action of the antibiotics, which represents an important finding for potential medical applications due to the negligible cytotoxic effect of AgNPs towards human cells at these concentration levels.

Structure and function of POTRA domains of Omp85/TPS superfamily.

PubMed

Simmerman, Richard F; Dave, Ashita M; Bruce, Barry D

2014-01-01

The Omp85/TPS (outer-membrane protein of 85 kDa/two-partner secretion) superfamily is a ubiquitous and major class of β-barrel proteins. This superfamily is restricted to the outer membranes of gram-negative bacteria, mitochondria, and chloroplasts. The common architecture, with an N-terminus consisting of repeats of soluble polypeptide-transport-associated (POTRA) domains and a C-terminal β-barrel pore is highly conserved. The structures of multiple POTRA domains and one full-length TPS protein have been solved, yet discovering roles of individual POTRA domains has been difficult. This review focuses on similarities and differences between POTRA structures, emphasizing POTRA domains in autotrophic organisms including plants and cyanobacteria. Unique roles, specific for certain POTRA domains, are examined in the context of POTRA location with respect to their attachment to the β-barrel pore, and their degree of biological dispensability. Finally, because many POTRA domains may have the ability to interact with thousands of partner proteins, possible modes of these interactions are also explored. © 2014 Elsevier Inc. All rights reserved.

Chemotaxis in P. Aeruginosa Biofilm Formation

NASA Astrophysics Data System (ADS)

Bienvenu, Samuel; Strain, Shinji; Thatcher, Travis; Gordon, Vernita

2010-10-01

Pseudomonas biofilms form infections in the lungs of Cystic Fibrosis (CF) patients that damage lung tissue and lead to death. Previous work shows chemotaxis is important for Pseudomonas in CF lungs. The work studied swimming bacteria at high concentrations. In contrast, medically relevant biofilms initiate from sparse populations of surface-bound bacteria. The recent development of software techniques for automated, high-throughput bacteria tracking leaves us well-poised to quantitatively study these chemotactic conditions. We will develop experimental systems for such studies, focusing on L-Arginine (an amino acid), D-Galactose (a sugar present in lungs), and succinate and glucose (carbon sources for bacteria). This suite of chemoattractants will allow us to study how chemoattractant characteristics--size and diffusion behavior--change bacterial response; the interaction of competing chemoattractants; and, differences in bacterial behaviors, like motility modes, in response to different types of chemoattractions and varying neighbor cell density.

Dimorphism in methane seep-dwelling ecotypes of the largest known bacteria

PubMed Central

Bailey, Jake V; Salman, Verena; Rouse, Gregory W; Schulz-Vogt, Heide N; Levin, Lisa A; Orphan, Victoria J

2011-01-01

We present evidence for a dimorphic life cycle in the vacuolate sulfide-oxidizing bacteria that appears to involve the attachment of a spherical Thiomargarita-like cell to the exteriors of invertebrate integuments and other benthic substrates at methane seeps. The attached cell elongates to produce a stalk-like form before budding off spherical daughter cells resembling free-living Thiomargarita that are abundant in surrounding sulfidic seep sediments. The relationship between the attached parent cell and free-living daughter cell is reminiscent of the dimorphic life modes of the prosthecate Alphaproteobacteria, but on a grand scale, with individual elongate cells reaching nearly a millimeter in length. Abundant growth of attached Thiomargarita-like bacteria on the integuments of gastropods and other seep fauna provides not only a novel ecological niche for these giant bacteria, but also for animals that may benefit from epibiont colonization. PMID:21697959

Mesosomes are a definite event in antibiotic-treated Staphylococcus aureus ATCC 25923.

PubMed

Santhana Raj, L; Hing, H L; Baharudin, Omar; Teh Hamidah, Z; Aida Suhana, R; Nor Asiha, C P; Vimala, B; Paramsarvaran, S; Sumarni, G; Hanjeet, K

2007-06-01

Mesosomes of Staphylococcus aureus ATCC 25923 treated with antibiotics were examined morphologically under the electron microscope. The Transmission Electron Microscope Rapid Method was used to eliminate the artifacts due to sample processing. Mesosomes were seen in all the antibiotic treated bacteria and not in the control group. The main factor that contributes to the formation of mesosomes in the bacteria was the mode of action of the antibiotics. The continuous cytoplasmic membrane with infolding (mesosomes) as in the S. aureus ATCC 25923 is therefore confirmed as a definite pattern of membrane organization in gram positive bacteria assaulted by amikacin, gentamicin, ciprofloxacin, vancomycin and oxacillin antibiotics. Our preliminary results show oxacillin and vancomycin treated bacteria seemed to have deeper and more mesosomes than those treated with amikacin, gentamicin and ciprofloxacin. Further research is needed to ascertain whether the deep invagination and the number of mesosomes formed is associated with the types of antibiotic used.

The Pseudomonas fluorescens Siderophore Pyoverdine Weakens Arabidopsis thaliana Defense in Favor of Growth in Iron-Deficient Conditions1

PubMed Central

Trapet, Pauline; Avoscan, Laure; Klinguer, Agnès; Pateyron, Stéphanie; Chervin, Christian; Mazurier, Sylvie; Lemanceau, Philippe; Wendehenne, David; Besson-Bard, Angélique

2016-01-01

Pyoverdines are siderophores synthesized by fluorescent Pseudomonas spp. Under iron-limiting conditions, these high-affinity ferric iron chelators are excreted by bacteria in the soil to acquire iron. Pyoverdines produced by beneficial Pseudomonas spp. ameliorate plant growth. Here, we investigate the physiological incidence and mode of action of pyoverdine from Pseudomonas fluorescens C7R12 on Arabidopsis (Arabidopsis thaliana) plants grown under iron-sufficient or iron-deficient conditions. Pyoverdine was provided to the medium in its iron-free structure (apo-pyoverdine), thus mimicking a situation in which it is produced by bacteria. Remarkably, apo-pyoverdine abolished the iron-deficiency phenotype and restored the growth of plants maintained in the iron-deprived medium. In contrast to a P. fluorescens C7R12 strain impaired in apo-pyoverdine production, the wild-type C7R12 reduced the accumulation of anthocyanins in plants grown in iron-deficient conditions. Under this condition, apo-pyoverdine modulated the expression of around 2,000 genes. Notably, apo-pyoverdine positively regulated the expression of genes related to development and iron acquisition/redistribution while it repressed the expression of defense-related genes. Accordingly, the growth-promoting effect of apo-pyoverdine in plants grown under iron-deficient conditions was impaired in iron-regulated transporter1 and ferric chelate reductase2 knockout mutants and was prioritized over immunity, as highlighted by an increased susceptibility to Botrytis cinerea. This process was accompanied by an overexpression of the transcription factor HBI1, a key node for the cross talk between growth and immunity. This study reveals an unprecedented mode of action of pyoverdine in Arabidopsis and demonstrates that its incidence on physiological traits depends on the plant iron status. PMID:26956666

Multispectroscopic DNA-Binding studies and antimicrobial evaluation of new mixed-ligand Silver(I) complex and nanocomplex: A comparative study

NASA Astrophysics Data System (ADS)

Movahedi, Elaheh; Rezvani, Ali Reza

2018-05-01

A novel mixed-ligand Ag(I) complex, , has been synthesized and characterized by the elemental analysis, IR spectroscopy and 1HNMR. In the formula, dian and phen are N-(4,5-diazafluoren-9-ylidene)aniline and 1,10-phenanthroline, respectively. This complex also has been prepared at nano size by sonochemical technique and characterized by the FTIR and scanning electron microscopy (SEM). To evaluate the biological preferences of the Ag(I) complex and nanocomplex and verify the relationships between the structure and biological function, in vitro DNA binding and antibacterial experiments have been carried out. DNA-complex interaction has been pursued by electronic absorption titration, luminescence titration, competitive binding experiment, effect of ionic strength, thermodynamic studies, viscometric evaluation and circular dichroism spectroscopy in the physiological pH. Each compound displays significant binding trend to the CT-DNA. The mode of binding to the CT-DNA probably is a moderate intercalation mode with the partial insertion of the planar ligands between the base stacks of double-stranded DNA. The relative viscosities and circular dichroism spectra of the CT-DNA with the complex solutions, confirm the intense interactions of the Ag(I) complex and nanocomplex with DNA. An in vitro antibacterial test of the complex and nanocomplex on a series of the Gram-positive bacteria (Staphylococcus aureus, Enterococcus faecalis) and the Gram-negative bacteria (Escherichia coli, Pseudomonas aeruginosa) shows a remarkable antibacterial feature of the Ag(I) complex. The MIC values (minimum inhibitory concentration) of the compounds compare with silver nitrate and silver sulfadiazine. The bacterial inhibitions of the Ag(I) complex and nanocomplex are agreed to their DNA binding affinities.

Synergy of brushing mode and antibacterial use on in vivo biofilm formation.

PubMed

Jongsma, Marije A; van de Lagemaat, Marieke; Busscher, Henk J; Geertsema-Doornbusch, Gesinda I; Atema-Smit, Jelly; van der Mei, Henny C; Ren, Yijin

2015-12-01

Orthodontic, multi-strand retention-wires are used as a generalized model for oral retention sites to investigate whether biofilm left-behind after powered toothbrushing in-vivo enabled better penetration of antibacterials as compared with manual brushing. 2-cm multi-strand, stainless-steel retention-wires were placed in brackets bonded bilaterally in the upper arches of 10-volunteers. Volunteers used NaF-sodium-lauryl-sulphate-containing toothpaste and antibacterial, triclosan-containing toothpaste supplemented or not with an essential-oils containing mouthrinse. Opposite sides of the dentition including the retention-wires, were brushed manually or with a powered toothbrush. Health-care-regimens were maintained for 1-week, after which wires were removed and oral biofilm was collected. When powered toothbrushing was applied, slightly less bacteria were collected than after manual brushing, regardless whether an antibacterial-regimen was used or not. Powered-toothbrushing combined with antibacterial-regimens yielded lower biofilm viability than manual brushing, indicating better antibacterial penetration into biofilm left-behind after powered brushing. Major shifts in biofilm composition, with a decrease in prevalence of both cariogenic species and periodontopathogens, were induced after powered brushing using an antibacterial-regimen. Oral biofilm left-behind after powered brushing in-vivo enabled better penetration of antibacterials than after manual brushing. Mechanical removal of oral biofilm is important for prevention of dental pathologies, but biofilm is always left-behind, such as in fissures, buccal pits, interproximal areas and gingival margins and around orthodontic appliances. Use of antibacterial toothpastes or mouthrinses can contribute to removal or killing of biofilm bacteria, but biofilm structure hampers antibacterial penetration. A synergy between brushing mode and antibacterial-regimen applied exists with clinically demonstrable effects. Copyright © 2015 Elsevier Ltd. All rights reserved.

Symbiotic interaction of endophytic bacteria with arbuscular mycorrhizal fungi and its antagonistic effect on Ganoderma boninense.

PubMed

Sundram, Shamala; Meon, Sariah; Seman, Idris Abu; Othman, Radziah

2011-08-01

Endophytic bacteria (Pseudomonas aeruginosa UPMP3 and Burkholderia cepacia UMPB3), isolated from within roots of oil palm (Elaeis guineensis Jacq.) were tested for their presymbiotic effects on two arbuscular mcorrhizal fungi, Glomus intraradices UT126 and Glomus clarum BR152B). These endophytic bacteria were also tested for antagonistic effects on Ganoderma boninense PER 71, a white wood rot fungal pathogen that causes a serious disease in oil palm. Spore germination and hyphal length of each arbuscular mycorrhizal fungal (AMF) pairing with endophytic bacteria was found to be significantly higher than spores plated in the absence of bacteria. Scanning electron microscopy (SEM) showed that the endophytic bacteria were scattered, resting or embedded on the surface hyaline layer or on the degraded walls of AMF spores, possibly feeding on the outer hyaline spore wall. The antagonistic effect of the endophytic bacteria was expressed as severe morphological abnormalities in the hyphal structures of G. boninense PER 71. The effects of the endophytic bacteria on G. boninense PER 71 hyphal structures were observed clearly under SEM. Severe inter-twisting, distortion, lysis and shriveling of the hyphal structures were observed. This study found that the effect of endophytic bacteria on G. intraradices UT126 and G. clarum BR152B resembled that of a mycorrhiza helper bacteria (MHB) association because the association significantly promoted AMF spore germination and hyphal length. However, the endophytic bacteria were extremely damaging to G. boninense PER 71.

Pleomorphic Structures in Human Blood Are Red Blood Cell-Derived Microparticles, Not Bacteria.

PubMed

Mitchell, Adam J; Gray, Warren D; Schroeder, Max; Yi, Hong; Taylor, Jeannette V; Dillard, Rebecca S; Ke, Zunlong; Wright, Elizabeth R; Stephens, David; Roback, John D; Searles, Charles D

2016-01-01

Red blood cell (RBC) transfusions are a common, life-saving therapy for many patients, but they have also been associated with poor clinical outcomes. We identified unusual, pleomorphic structures in human RBC transfusion units by negative-stain electron microscopy that appeared identical to those previously reported to be bacteria in healthy human blood samples. The presence of viable, replicating bacteria in stored blood could explain poor outcomes in transfusion recipients and have major implications for transfusion medicine. Here, we investigated the possibility that these structures were bacteria. Flow cytometry, miRNA analysis, protein analysis, and additional electron microscopy studies strongly indicated that the pleomorphic structures in the supernatant of stored RBCs were RBC-derived microparticles (RMPs). Bacterial 16S rDNA PCR amplified from these samples were sequenced and was found to be highly similar to species that are known to commonly contaminate laboratory reagents. These studies suggest that pleomorphic structures identified in human blood are RMPs and not bacteria, and they provide an example in which laboratory contaminants may can mislead investigators.

Nanoforms: a new type of protein-associated mineralization

NASA Astrophysics Data System (ADS)

Vali, Hojatollah; McKee, Marc D.; Çiftçioglu, Neva; Sears, S. Kelly; Plows, Fiona L.; Chevet, Eric; Ghiabi, Pegah; Plavsic, Marc; Kajander, E. Olavi; Zare, Richard N.

2001-01-01

Controversy surrounds the interpretation of various nano-phenomena as being living organisms. Incubation of fetal bovine serum under standard cell culture conditions results in the formation of free entities in solution, here referred to as nanoforms. These nanoforms, when examined by transmission electron microscopy, have a distinct ovoid morphology ranging in size from tens to hundreds of nanometers. They are composed of hydroxyapatite and proteins and constitute a novel form of protein-associated mineralization. No detectable cell structure resembling bacteria is apparent. However, immunodetection of the proteins associated with the nanoforms, by two specific monoclonal antibodies, suggests a possible biogenic origin. The significance of nanoforms for the recognition of biological activity in ancient geological systems is discussed. The mode of mineralization in nanoforms is also compared to matrix-mediated calcification in vertebrates.

Structure-guided optimization of protein kinase inhibitors reverses aminoglycoside antibiotic resistance

PubMed Central

Stogios, Peter J.; Spanogiannopoulos, Peter; Evdokimova, Elena; Egorova, Olga; Shakya, Tushar; Todorovic, Nick; Capretta, Alfredo; Wright, Gerard D.; Savchenko, Alexei

2013-01-01

SYNOPSIS Activity of the aminoglycoside phosphotransferase APH(3’)-Ia leads to resistance to aminoglycoside antibiotics in pathogenic Gram-negative bacteria, and contributes to the clinical obsolescence of this class of antibiotics. One strategy to rescue compromised antibiotics such as aminoglycosides is targeting the enzymes that confer resistance with small molecules. Previously we demonstrated that eukaryotic protein kinase (ePK) inhibitors could inhibit APH enzymes, due to the structural similarity between these two enzyme families. However, limited structural information of enzyme-inhibitor complexes hindered interpretation of the results. As well, cross-reactivity of compounds between APHs and ePKs represents an obstacle to their use as aminoglycoside adjuvants to rescue aminoglycoside antibiotic activity. Here, we structurally and functionally characterize inhibition of APH(3’)-Ia by three diverse chemical scaffolds – anthrapyrazolone, 4-anilinoquinazoline and pyrazolopyrimidine (PP) – and reveal distinctions in the binding mode of anthrapyrazolone and PP compounds to APH(3’)-Ia versus ePKs. Using this observation, we identify PP-derivatives that select against ePKs, attenuate APH(3’)-Ia activity and rescue aminoglycoside antibiotic activity against a resistant E. coli strain. The structures presented here and these inhibition studies provide an important opportunity for structure-based design of compounds to target aminoglycoside phosphotransferases for inhibition, potentially overcoming this form of antibiotic resistance. PMID:23758273

Polar bears, antibiotics, and the evolving ribosome (Nobel Lecture).

PubMed

Yonath, Ada

2010-06-14

High-resolution structures of ribosomes, the cellular machines that translate the genetic code into proteins, revealed the decoding mechanism, detected the mRNA path, identified the sites of the tRNA molecules in the ribosome, elucidated the position and the nature of the nascent proteins exit tunnel, illuminated the interactions of the ribosome with non-ribosomal factors, such as the initiation, release and recycling factors, and provided valuable information on ribosomal antibiotics, their binding sites, modes of action, principles of selectivity and the mechanisms leading to their resistance. Notably, these structures proved that the ribosome is a ribozyme whose active site, namely where the peptide bonds are being formed, is situated within a universal symmetrical region that is embedded in the otherwise asymmetric ribosome structure. As this symmetrical region is highly conserved and provides the machinery required for peptide bond formation and for ribosome polymerase activity, it may be the remnant of the proto-ribosome, a dimeric prebiotic machine that formed peptide bonds and non-coded polypeptide chains. Structures of complexes of ribosomes with antibiotics targeting them revealed the principles allowing for their clinical use, identified resistance mechanisms and showed the structural bases for discriminating pathogenic bacteria from hosts, hence providing valuable structural information for antibiotics improvement and for the design of novel compounds that can serve as antibiotics.

Crystal structure of E. coli ZinT with one zinc-binding mode and complexed with citrate.

PubMed

Chen, Jinli; Wang, Lulu; Shang, Fei; Dong, Yuesheng; Ha, Nam-Chul; Nam, Ki Hyun; Quan, Chunshan; Xu, Yongbin

2018-06-02

The ZnuABC ATP-binding cassette transporter found in gram-negative bacteria has been implicated in ensuring adequate zinc import into Zn(II)-poor environments. ZinT is an essential component of ZnuABC and contributes to metal transport by transferring metals to ZnuA, which delivers them to ZnuB in periplasmic zinc recruitment. Although several structures of E. coli ZinT have been reported, its zinc-binding sites and oligomeric state have not been clearly identified. Here, we report the crystal structure of E. coli ZinT at 1.76 Å resolution. This structure contains one zinc ion in its calycin-like domain, and this ion is coordinated by three highly conserved histidine residues (His167, His176 and His178). Moreover, three oxygen atoms (O 1 , O 6 and O 7 ) from the citrate molecule interact with zinc, giving the zinc ion stable octahedral coordination. Our EcZinT structure shows the fewest zinc ions bound of all reported EcZinT structures. Crystallographic packing and size exclusion chromatography suggest that EcZinT prefers to form monomers in solution. Our results provide insights into the molecular function of ZinT. Copyright © 2018. Published by Elsevier Inc.

Bacteriophage T4 Infection of Stationary Phase E. coli: Life after Log from a Phage Perspective

PubMed Central

Bryan, Daniel; El-Shibiny, Ayman; Hobbs, Zack; Porter, Jillian; Kutter, Elizabeth M.

2016-01-01

Virtually all studies of phage infections investigate bacteria growing exponentially in rich media. In nature, however, phages largely encounter non-growing cells. Bacteria entering stationary phase often activate well-studied stress defense mechanisms that drastically alter the cell, facilitating its long-term survival. An understanding of phage-host interactions in such conditions is of major importance from both an ecological and therapeutic standpoint. Here, we show that bacteriophage T4 can efficiently bind to, infect and kill E. coli in stationary phase, both in the presence and absence of a functional stationary-phase sigma factor, and explore the response of T4-infected stationary phase cells to the addition of fresh nutrients 5 or 24 h after that infection. An unexpected new mode of response has been identified. “Hibernation” mode is a persistent but reversible dormant state in which the infected cells make at least some phage enzymes, but halt phage development until appropriate nutrients become available before producing phage particles. Our evidence indicates that the block in hibernation mode occurs after the middle-mode stage of phage development; host DNA breakdown and the incorporation of the released nucleotides into phage DNA indicate that the enzymes of the nucleotide synthesizing complex, under middle-mode control, have been made and assembled into a functional state. Once fresh glucose and amino acids become available, the standard lytic infection process rapidly resumes and concentrations of up to 1011 progeny phage (an average of about 40 phage per initially present cell) are produced. All evidence is consistent with the hibernation-mode control point lying between middle mode and late mode T4 gene expression. We have also observed a “scavenger” response, where the infecting phage takes advantage of whatever few nutrients are available to produce small quantities of progeny within 2 to 5 h after infection. The scavenger response seems able to produce no more than an average of one phage per originally available cell, and few if any further progeny are produced by cells in this mode even if fresh nutrients are made available later. PMID:27660625

Detection and Quantification of Ribosome Inhibition by Aminoglycoside Antibiotics in Living Bacteria Using an Orthogonal Ribosome-Controlled Fluorescent Reporter.

PubMed

Huang, Shijie; Zhu, Xuechen; Melançon, Charles E

2016-01-15

The ribosome is the quintessential antibacterial drug target, with many structurally and mechanistically distinct classes of antibacterial agents acting by inhibiting ribosome function. Detecting and quantifying ribosome inhibition by small molecules and investigating their binding modes and mechanisms of action are critical to antibacterial drug discovery and development efforts. To develop a ribosome inhibition assay that is operationally simple, yet provides direct information on the drug target and the mechanism of action, we have developed engineered E. coli strains harboring an orthogonal ribosome-controlled green fluorescent protein (GFP) reporter that produce fluorescent signal when the orthogonal ribosome is inhibited. As a proof of concept, we demonstrate that these strains, when coexpressing homogeneous populations of aminoglycoside resistant ribosomes, act as sensitive and quantitative detectors of ribosome inhibition by a set of 12 structurally diverse aminoglycoside antibiotics. We suggest that this strategy can be extended to quantifying ribosome inhibition by other drug classes.

The antibiotic CJ-15,801 is an antimetabolite that hijacks and then inhibits CoA biosynthesis.

PubMed

van der Westhuyzen, Renier; Hammons, Justin C; Meier, Jordan L; Dahesh, Samira; Moolman, Wessel J A; Pelly, Stephen C; Nizet, Victor; Burkart, Michael D; Strauss, Erick

2012-05-25

The natural product CJ-15,801 is an inhibitor of Staphylococcus aureus, but not other bacteria. Its close structural resemblance to pantothenic acid, the vitamin precursor of coenzyme A (CoA), and its Michael acceptor moiety suggest that it irreversibly inhibits an enzyme involved in CoA biosynthesis or utilization. However, its mode of action and the basis for its specificity have not been elucidated to date. We demonstrate that CJ-15,801 is transformed by the uniquely selective S. aureus pantothenate kinase, the first CoA biosynthetic enzyme, into a substrate for the next enzyme, phosphopantothenoylcysteine synthetase, which is inhibited through formation of a tight-binding structural mimic of its native reaction intermediate. These findings reveal CJ-15,801 as a vitamin biosynthetic pathway antimetabolite with a mechanism similar to that of the sulfonamide antibiotics and highlight CoA biosynthesis as a viable antimicrobial drug target. Copyright © 2012 Elsevier Ltd. All rights reserved.

Perversions driven spontaneous symmetry breaking in heterogeneous elastic ribbons

NASA Astrophysics Data System (ADS)

Liu, Shuangping; Yao, Zhenwei; Olvera de La Cruz, Monica

2015-03-01

Perversion structures in an otherwise uniform helical structure are associated with several important concepts in fundamental physics and materials science, including the spontaneous symmetry breaking and the elastic buckling. They also have strong connections with biological motifs (e.g., bacteria shapes and plant tendrils) and have potential applications in micro-muscles and soft robotics. In this work, using a three-dimensional elastomeric bi-stripe model, we investigate the properties of perversions that are independent of the specific ribbon shapes. Several intrinsic features of perversions are revealed, including the spontaneous condensation of energy as well as the distinct energy transfer modes within the perversion region. These properties of perversions associated with the storage of elastic energies can be exploited in the design of actuator devices. We thank the financial support from the U.S. Department of Commerce, National Institute of Standards and Technology, the Office of the Director of Defense Research and Engineering (DDR&E) and the Air Force Office of Scientific Research.

CexTi1-xO 2 nanomaterials applied as photocatalyst and disinfectants

NASA Astrophysics Data System (ADS)

Ancha, Bhumika

The thesis extensively studied the synthesis, characterization and photocatalyticity of Ce-dopedTiO2 (CTO-NPs). An environmental-friendly and cost-effective Sol-Gel approach was used to prepare different formulations of CTO-NPs.The starting materials of Ce(NO3)3 and Ti(nOBu) 4 were used and water iso-proponol mixture was used as a solvent to ensure the solubility of the above starting materials. The fabrication variables of CTO-NPs were optimized according to the photocatalytical reactivity and antibacterial activities. The powders of CTO-NPs were prepared after calculation at 200-400 °C with an increment of 50 °C for 2 hours. These so-prepared CTO-NPs were characterized using X-ray powder diffraction, scanning & transmission electron microscopy, ultra-violet and Raman spectroscopy, to evaluate their crystalline structure, morphology, and vibrational modes. It was found that the TiO2 tetragonal anatase structure (PDF 01-086-1157, 3.7852 x 9.5139 A and 90x90 °) was obtained. The cerium cation substituted the lattice Ti, leading to one phase formation. These CTO-NPs were found to be effective at decomposing methylene blue under visible light. Both Gram-negative (S. marcescens, ATCC 49732) and Gram-positive (M. luteus, ATCC 13880) bacteria were also tested using CTO-NPs as disinfectants. The maximum bactericidal concentrations (MBCs) were found to be 0.6 ppm to inactivate both bacteria within 1 hr.

Viscoelasticity of biofilms and their recalcitrance to mechanical and chemical challenges

PubMed Central

Peterson, Brandon W.; He, Yan; Ren, Yijin; Zerdoum, Aidan; Libera, Matthew R.; Sharma, Prashant K.; van Winkelhoff, Arie-Jan; Neut, Danielle; Stoodley, Paul; van der Mei, Henny C.; Busscher, Henk J.

2015-01-01

We summarize different studies describing mechanisms through which bacteria in a biofilm mode of growth resist mechanical and chemical challenges. Acknowledging previous microscopic work describing voids and channels in biofilms that govern a biofilms response to such challenges, we advocate a more quantitative approach that builds on the relation between structure and composition of materials with their viscoelastic properties. Biofilms possess features of both viscoelastic solids and liquids, like skin or blood, and stress relaxation of biofilms has been found to be a corollary of their structure and composition, including the EPS matrix and bacterial interactions. Review of the literature on viscoelastic properties of biofilms in ancient and modern environments as well as of infectious biofilms reveals that the viscoelastic properties of a biofilm relate with antimicrobial penetration in a biofilm. In addition, also the removal of biofilm from surfaces appears governed by the viscoelasticity of a biofilm. Herewith, it is established that the viscoelasticity of biofilms, as a corollary of structure and composition, performs a role in their protection against mechanical and chemical challenges. Pathways are discussed to make biofilms more susceptible to antimicrobials by intervening with their viscoelasticity, as a quantifiable expression of their structure and composition. PMID:25725015

Raman spectroscopy for the microbiological characterization and identification of medically relevant bacteria

NASA Astrophysics Data System (ADS)

Hamasha, Khozima Mahmoud

The detection and identification of pathogenic bacteria has become more important than ever due to the increase of potential bioterrorism threats and the high mortality rate of bacterial infections worldwide. Raman spectroscopy has recently gained popularity as an attractive robust approach for the molecular characterization, rapid identification, and accurate classification of a wide range of bacteria. In this dissertation, Raman spectroscopy utilizing advanced statistical techniques was used to identify and discriminate between different pathogenic and non-pathogenic bacterial strains of E. coli and Staphylococcus aureus bacterial species by probing the molecular compositions of the cells. The five-carbon sugar xylitol, which cannot be metabolized by the oral and nasopharyngeal bacteria, had been recognized by clinicians as a preventive agents for dental caries and many studies have demonstrated that xylitol causes a reduction in otitis media (chronic inner ear infections) and other nasopharyngeal infections. Raman spectroscopy was used to characterize the uptake and metabolic activity of xylitol in pathogenic (viridans group Streptococcus) and nonpathogenic (E. coli) bacteria by taking their Raman spectra before xylitol exposure and after growing with xylitol and quantifying the significant differences in the molecular vibrational modes due to this exposure. The results of this study showed significant stable spectral changes in the S. viridians bacteria induced by xylitol and those changes were not the same as in some E. coli strains. Finally, Raman spectroscopy experiments were conducted to provide important information about the function of a certain protein (wag31) of Mycobacterium tuberculosis using a relative non-pathogenic bacterium called Mycobacterium smegmatis. Raman spectra of conditional mutants of bacteria expressing three different phosphorylation forms of wag31 were collected and analyzed. The results show that that the phosphorylation of wag31 causes significant differences in the molecular structure, namely the quantity of amino acids associated with peptidoglycan precursor proteins and lipid II as observed in the Raman spectra of these cells. Raman spectra were also acquired from the isolated cell envelope fraction of the cells expressing different forms of wag31 and the results showed that a significant number of the molecular vibrational differences observed in the cells were also observed in the cell envelope fraction, indicating that these differences are localized in the cell envelope.

Mixotrophy in the marine red-tide cryptophyte Teleaulax amphioxeia and ingestion and grazing impact of cryptophytes on natural populations of bacteria in Korean coastal waters.

PubMed

Yoo, Yeong Du; Seong, Kyeong Ah; Jeong, Hae Jin; Yih, Wonho; Rho, Jung-Rae; Nam, Seung Won; Kim, Hyung Seop

2017-09-01

Cryptophytes are ubiquitous and one of the major phototrophic components in marine plankton communities. They often cause red tides in the waters of many countries. Understanding the bloom dynamics of cryptophytes is, therefore, of great importance. A critical step in this understanding is unveiling their trophic modes. Prior to this study, several freshwater cryptophyte species and marine Cryptomonas sp. and Geminifera cryophila were revealed to be mixotrophic. The trophic mode of the common marine cryptophyte species, Teleaulax amphioxeia has not been investigated yet. Thus, to explore the mixotrophic ability of T. amphioxeia by assessing the types of prey species that this species is able to feed on, the protoplasms of T. amphioxeia cells were carefully examined under an epifluorescence microscope and a transmission electron microscope after adding each of the diverse prey species. Furthermore, T. amphioxeia ingestion rates heterotrophic bacteria and the cyanobacterium Synechococcus sp. were measured as a function of prey concentration. Moreover, the feeding of natural populations of cryptophytes on natural populations of heterotrophic bacteria was assessed in Masan Bay in April 2006. This study reported for the first time, to our knowledge, that T. amphioxeia is a mixotrophic species. Among the prey organisms offered, T. amphioxeia fed only on heterotrophic bacteria and Synechococcus sp. The ingestion rates of T. amphioxeia on heterotrophic bacteria or Synechococcus sp. rapidly increased with increasing prey concentrations up to 8.6×10 6 cells ml -1 , but slowly at higher prey concentrations. The maximum ingestion rates of T. amphioxeia on heterotrophic bacteria and Synechococcus sp. reached 0.7 and 0.3 cells predator -1  h -1 , respectively. During the field experiments, the ingestion rates and grazing coefficients of cryptophytes on natural populations of heterotrophic bacteria were 0.3-8.3 cells predator -1 h -1 and 0.012-0.033d -1 , respectively. Marine cryptophytes, including T. amphioxeia, are known to be favorite prey species for many mixotrophic and heterotrophic dinoflagellates and ciliates. Cryptophytes, therefore, likely play important roles in marine food webs and may exert a considerable potential grazing impact on the populations of marine bacteria. Copyright © 2017 Elsevier B.V. All rights reserved.

Co-existence of Anaerobic Ammonium Oxidation Bacteria and Denitrifying Anaerobic Methane Oxidation Bacteria in Sewage Sludge: Community Diversity and Seasonal Dynamics.

PubMed

Xu, Sai; Lu, Wenjing; Mustafa, Muhammad Farooq; Caicedo, Luis Miguel; Guo, Hanwen; Fu, Xindi; Wang, Hongtao

2017-11-01

Anaerobic ammonium oxidation (ANAMMOX) and denitrifying anaerobic methane oxidation (DAMO) have been recently discovered as relevant processes in the carbon and nitrogen cycles of wastewater treatment plants. In this study, the seasonal dynamics of ANAMMOX and DAMO bacterial community structures and their abundance in sewage sludge collected from wastewater treatment plants were analysed. Results indicated that ANAMMOX and DAMO bacteria co-existed in sewage sludge in different seasons and their abundance was positively correlated (P < 0.05). The high abundance of ANAMMOX and DAMO bacteria in autumn and winter indicated that these seasons were the preferred time to favour the growth of ANAMMOX and DAMO bacteria. The community structure of ANNAMOX and DAMO bacteria could also shift with seasonal changes. The "Candidatus Brocadia" genus of ANAMMOX bacteria was mainly recovered in spring and summer, and an unknown cluster was primarily detected in autumn and winter. Similar patterns of seasonal variation in the community structure of DAMO bacteria were also observed. Group B was the dominant in spring and summer, whereas in autumn and winter, group A and group B presented almost the same proportion. The redundancy analysis revealed that pH and nitrate were the most significant factors affecting community structures of these two groups (P < 0.01). This study reported the diversity of ANAMMOX and DAMO in wastewater treatment plants that may be the basis for new nitrogen removal technologies.

[Diversity and community structure of soil ammonia-oxidizing bacteria in Hulunbeier Grassland, Inner Mongolia].

PubMed

Wendu, Ri-le; Li, Gang; Yang, Dian-lin; Zhang, Jing-ni; Yi, Jin

2011-04-01

By the methods of polymerase chain reaction-denaturing gradient gel electrophoresis and sequence analysis, a comparative study was conducted on the diversity and community structure of soil ammonia-oxidizing bacteria in the Filifolium sibiricum steppe, Stipa baicalensis steppe, Leymus chinensis steppe, Stipa grandis steppe, and Stipa kryrowi steppe in Hulunbeier Grassland, Inner Mongolia. A significant difference was observed in the community structure of soil ammonia-oxidizing bacteria among the five steppes, with the similarity lower than 50%. The diversity of soil ammonia-oxidizing bacteria was the highest in F. sibiricum steppe, followed by in S. baicalensis steppe, L. chinensis steppe, S. kryrowi steppe, and S. grandis steppe. In the five steppes, Nitrosospira cluster 3 was the dominant group, and the Nitrosospira cluster 1, 2, and 4 as well as Nitrosomonas were also found. The community structure of soil ammonia oxidizing bacteria in F. sibiricum steppe was most complex, while that in L. chinensis steppe and S. grandis steppe was relatively simple. Correlation analysis indicated that there existed significant positive correlations between the diversity of soil ammonia-oxidizing bacteria and the soil moisture, total nitrogen, total organic carbon, and C/N ratio (P<0.05).

Combined effect of enterocin and lipase from Enterococcus faecium NCIM5363 against food borne pathogens: mode of action studies.

PubMed

Ramakrishnan, Vrinda; Narayan, Bhaskar; Halami, Prakash M

2012-08-01

Food borne diseases have a major impact on public health whose epidemiology is rapidly changing. The whole cells of pathogens involved or their toxins/metabolites affect the human health apart from spoiling sensory properties of the food products finally affecting the food industry as well as consumer health. With pathogens developing mechanisms of antibiotic resistance, there has been an increased need to replace antibiotics as well as chemical additives with naturally occurring bacteriocins. Bacteriocins are known to act mainly against Gram-positive pathogens and with little or no effect towards Gram-negative enteric bacteria. In the present study, combination effect of lipase and bacteriocin produced by Enterococcus faecium NCIM5363, a highly lipolytic lactic acid bacterium against various food pathogens was assessed. The lipase in combination with enterocin exhibited a lethal effect against Gram-negative pathogens. Scanning electron microscopy studies carried out to ascertain the constitutive mode of action of lipase and enterocin revealed that the lipase degrades the cell wall of Gram-negative bacteria and creates a pore through which enterocin enters thereby resulting in cell death. The novelty of this work is the fact that this is the first report revealing the synergistic effect of lipase with enterocin against Gram-negative bacteria.

Effect of a blend of essential oil compounds on the colonization of starch-rich substrates by bacteria in the rumen.

PubMed

Duval, S M; McEwan, N R; Graham, R C; Wallace, R J; Newbold, C J

2007-12-01

To investigate the mode of action of a blend of essential oil compounds on the colonization of starch-rich substrates by rumen bacteria. Starch-rich substrates were incubated, in nylon bags, in the rumen of sheep organized in a 4 x 4 latin square design and receiving a 60:40 silage : concentrate diet. The concentrate was either high or low in crude protein, and the diet was supplemented or not with a commercial blend of essential oil compounds (110 mg per day). The total genomic DNA was extracted from the residues in the bags. The total eubacterial DNA was quantified by real-time PCR and the proportion of Ruminobacter amylophilus, Streptococcus bovis and Prevotella bryantii was determined. Neither the supplementation with essential oil compounds nor the amount of crude protein affected the colonization of the substrates by the bacteria quantified. However, colonization was significantly affected by the substrate colonized. The effect of essential oils on the colonization of starch-rich substrates is not mediated through the selective inhibition of R. amylophilus. This study enhances our understanding of the colonization of starch-rich substrates, as well as of the mode of action of the essential oils as rumen manipulating agents.

Optimization of Plant Growth-Promoting Bacteria-Assisted Phytostabilization of Mine Tailings

PubMed Central

Grandlic, Christopher J.; Palmer, Michael W.; Maier, Raina M.

2009-01-01

Recent studies have indicated that plant growth-promoting bacteria (PGPB) can improve revegetation of arid mine tailings as measured by increased biomass production. The goals of the present study were first to evaluate how mode of application of known PGPB affects plant growth, and second to evaluate the effect of this inoculation on rhizosphere microbial community structure. PGPB application strategies investigated include preliminary surface sterilization of seeds (a common practice in phytoremediation trials) followed by a comparison of two application methods; immersion and alginate encapsulation. Results with two native desert plant species, Atriplex lentiformis and Buchloe dactyloides, suggest that seed surface sterilization prior to inoculation is not necessary to achieve beneficial effects of introduced PGPB. Both PGPB application techniques generally enhanced plant growth although results were both plant and PGPB specific. These results demonstrate that alginate encapsulation, which allows for long-term storage and easier application to seeds, is an effective way to inoculate PGPB. In addition, the influence of PGPB application on B. dactyloides rhizosphere community structure was evaluated using PCR-DGGE (denaturing gradient gel electrophoresis) analysis of bacterial DNA extracted from rhizosphere samples collected 75 d following planting. A comparative analysis of DGGE profiles was performed using canonical correspondence analysis (CCA). DGGE-CCA showed that rhizosphere community profiles from PGPB-inoculated treatments are significantly different from both uninoculated tailings rhizosphere profiles and profiles from the compost used to amend the tailings. Further, community profiles from B. dactyloides inoculated with the best performing PGPB (Arthro mix) were significantly different from two other PGPB tested. These results suggest that introduced PGPB have the potential to influence the development of the rhizosphere community structure found in plants grown in mine tailings. PMID:20161141

Probing the structural dynamics of the CRISPR-Cas9 RNA-guided DNA-cleavage system by coarse-grained modeling.

PubMed

Zheng, Wenjun

2017-02-01

In the adaptive immune systems of many bacteria and archaea, the Cas9 endonuclease forms a complex with specific guide/scaffold RNA to identify and cleave complementary target sequences in foreign DNA. This DNA targeting machinery has been exploited in numerous applications of genome editing and transcription control. However, the molecular mechanism of the Cas9 system is still obscure. Recently, high-resolution structures have been solved for Cas9 in different structural forms (e.g., unbound forms, RNA-bound binary complexes, and RNA-DNA-bound tertiary complexes, corresponding to an inactive state, a pre-target-bound state, and a cleavage-competent or product state), which offered key structural insights to the Cas9 mechanism. To further probe the structural dynamics of Cas9 interacting with RNA and DNA at the amino-acid level of details, we have performed systematic coarse-grained modeling using an elastic network model and related analyses. Our normal mode analysis predicted a few key modes of collective motions that capture the observed conformational changes featuring large domain motions triggered by binding of RNA and DNA. Our flexibility analysis identified specific regions with high or low flexibility that coincide with key functional sites (such as DNA/RNA-binding sites, nuclease cleavage sites, and key hinges). We also identified a small set of hotspot residues that control the energetics of functional motions, which overlap with known functional sites and offer promising targets for future mutagenesis efforts to improve the specificity of Cas9. Finally, we modeled the conformational transitions of Cas9 from the unbound form to the binary complex and then the tertiary complex, and predicted a distinct sequence of domain motions. In sum, our findings have offered rich structural and dynamic details relevant to the Cas9 machinery, and will guide future investigation and engineering of the Cas9 systems. Proteins 2017; 85:342-353. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

[Antimicrobial effect on some zoonotic bacteria, of the cell-free fermentation fluid and purified peptide fraction of the entomopathogenic bacterium, Xenorhabdus budapestensis].

PubMed

Burgettiné Böszörményi, Erzsébet; Barcs, István; Domján, Gyula; Bélafiné Bakó, Katalin; Fodor, András; Makrai, László; Vozik, Dávid

2015-11-01

Many multi-resistant patogens appear continuously resulting in a permanent need for the development of novel antibiotics. A large number of antibiotics introduced in clinical and veterinary practices are not effective. Antibacterial peptides with unusual mode of action may represent a promising option against multi-resistant pathogens. The entomopathogenic Xenorhabdus budapestensis bacteria produce several different antimicrobial peptides compounds such as bicornutin-A and fabclavin. The aim of the authors was to evaluate the in vitro antibacterial effect of Xenorhabdus budapestensis using zoonotic patogen bacteria. Cell-free conditioned media and purified peptide fractions of Xenorhabdus budapestensis were tested on Gram-positive (Rhodococcus equi, Erysipelothrix rhusiopathia, Staphylococcus aureus, Streptococcus equi, Corynebacterium pseudotuberculosis, Listeria monocytagenes) and Gram-negative bacteria (Salmonella gallinarum, Salmonella derbi, Bordatella bronchoseptica, Escherichia coli, Pasteurella multocida, Aeromonas hydrophila) using agar diffusion test on blood agar plates. It was found that Xenorhabdus budapestensis bacteria produced compounds with strong and dose-dependent effects on the tested organisms. Purified peptid fraction exerted a more marked effect than cell free conditioned media. Gram-positive bacteria were more sensitive to this antibacterial effect than Gram-negative bacteria. Antibacterial peptide compound from Xenorhabdus budapestensis exert marked antibacterial effect on zoonotic patogen bacteria and they should be further evaluated in future for their potential use in the control or prevention of zoonoses.

[Effects of traditional Chinese medicine on oral bacteria biofilm].

PubMed

Zhao, Jin; Li, Ji-yao; Zhu, Bing; Zhou, Xue-dong

2007-10-01

To investigate the effects of compounds of Galla chinensis extract (GCE) and Nidus vespae extract-1 (WVE1) on oral bacteria biofilm structure and activity and to determine the possibility of caries prevention by the compounds. The morphology and activity of treated-oral bacterial biofilm and untreated-oral bacterial biofilm were observed by using fluorescence microscope in combination of idio-fluorochrome to label the died and living bacteria. The visible light semiquantitative method was used to measure biomass glucosyltransferase (GTF, A620) values and to determine the effects of active compounds of GCE and NVE1 on GTF of oral bacteria biofilm. The living bacteria in the untreated 24 h bacterial biofilm was dominant, and only a small number of died bacteria were found, the biofilm structure was regular and clear. GCE, GCE-B and NVE1 could inhibit the bacteria in the dental biofilm, which showed significant difference with the negative control. GCE and NVE1 could also inhibit GTF activity of 24 h bacterial biofilm in comparison with the negative control. The traditional Chinese medicine Galla chinensis and Nidus vespae could not only inhibit bacteria growth on oral bacterial biofilm, but also function by adjusting biofilm structure, composition and GTF activity of 24 h bacterial biofilm.

Depth-Related Changes in Community Structure of Culturable Mineral Weathering Bacteria and in Weathering Patterns Caused by Them along Two Contrasting Soil Profiles

PubMed Central

Huang, Jing; Xi, Jun; Huang, Zhi; Wang, Qi; Zhang, Zhen-Dong

2014-01-01

Bacteria play important roles in mineral weathering and soil formation. However, few reports of mineral weathering bacteria inhabiting subsurfaces of soil profiles have been published, raising the question of whether the subsurface weathering bacteria are fundamentally distinct from those in surface communities. To address this question, we isolated and characterized mineral weathering bacteria from two contrasting soil profiles with respect to their role in the weathering pattern evolution, their place in the community structure, and their depth-related changes in these two soil profiles. The effectiveness and pattern of bacterial mineral weathering were different in the two profiles and among the horizons within the respective profiles. The abundance of highly effective mineral weathering bacteria in the Changshu profile was significantly greater in the deepest horizon than in the upper horizons, whereas in the Yanting profile it was significantly greater in the upper horizons than in the deeper horizons. Most of the mineral weathering bacteria from the upper horizons of the Changshu profile and from the deeper horizons of the Yanting profile significantly acidified the culture media in the mineral weathering process. The proportion of siderophore-producing bacteria in the Changshu profile was similar in all horizons except in the Bg2 horizon, whereas the proportion of siderophore-producing bacteria in the Yanting profile was higher in the upper horizons than in the deeper horizons. Both profiles existed in different highly depth-specific culturable mineral weathering community structures. The depth-related changes in culturable weathering communities were primarily attributable to minor bacterial groups rather than to a change in the major population structure. PMID:24077700

Quantification of two forms of green sulfur bacteria in their natural habitat using bacteriochlorophyll fluorescence spectra

NASA Astrophysics Data System (ADS)

Kharcheva, Anastasia V.; Zhiltsova, Anna A.; Lunina, Olga N.; Savvichev, Alexander S.; Patsaeva, Svetlana V.

2016-04-01

Detection of phototropic organisms in their natural habitat using optical instruments operating under water is urgently needed for many tasks of ecological monitoring. While fluorescence methods are widely applied nowadays to detect and characterize phytoplankton communities, the techniques for detection and recognition of anoxygenic phototrophs are considered challenging. Differentiation of the forms of anoxygenic green sulfur bacteria in natural water using spectral techniques remains problematic. Green sulfur bacteria could be found in two forms, green-colored (containing BChl d in pigment compound) and brown-colored (containing BChl e), have the special ecological niche in such reservoirs. Separate determination of these microorganisms by spectral methods is complicated because of similarity of spectral characteristics of their pigments. We describe the novel technique of quantification of two forms of green sulfur bacteria directly in water using bacteriochlorophyll fluorescence without pigment extraction. This technique is noninvasive and could be applied in remote mode in the water bodies with restricted water circulation to determine simultaneously concentrations of two forms of green sulfur bacteria in their natural habitat.

Inhibitory Spectra and Modes of Antimicrobial Action of Gallotannins from Mango Kernels (Mangifera indica L.) ▿ †

PubMed Central

Engels, Christina; Schieber, Andreas; Gänzle, Michael G.

2011-01-01

This study investigated the antimicrobial activities and modes of action of penta-, hexa-, hepta-, octa-, nona-, and deca-O-galloylglucose (gallotannins) isolated from mango kernels. The MICs and minimum bactericidal concentrations (MBCs) against food-borne bacteria and fungi were determined using a critical dilution assay. Gram-positive bacteria were generally more susceptible to gallotannins than were Gram-negative bacteria. The MICs of gallotannins against Bacillus subtilis, Bacillus cereus, Clostridium botulinum, Campylobacter jejuni, Listeria monocytogenes, and Staphylococcus aureus were 0.2 g liter−1 or less; enterotoxigenic Escherichia coli and Salmonella enterica were inhibited by 0.5 to 1 g liter−1, and lactic acid bacteria were resistant. The use of lipopolysaccharide mutants of S. enterica indicated that the outer membrane confers resistance toward gallotannins. Supplementation of LB medium with iron eliminated the inhibitory activity of gallotannins against Staphylococcus aureus, and siderophore-deficient mutants of S. enterica were less resistant toward gallotannins than was the wild-type strain. Hepta-O-galloylglucose sensitized Lactobacillus plantarum TMW1.460 to hop extract, indicating inactivation of hop resistance mechanisms, e.g., the multidrug resistance (MDR) transporter HorA. Carbohydrate metabolism of Lactococcus lactis MG1363, a conditionally respiring organism, was influenced by hepta-O-galloylglucose when grown under aerobic conditions and in the presence of heme but not under anaerobic conditions, indicating that gallotannins influence the respiratory chain. In conclusion, the inhibitory activities of gallotannins are attributable to their strong affinity for iron and likely additionally relate to the inactivation of membrane-bound proteins. PMID:21317249

Inhibitory spectra and modes of antimicrobial action of gallotannins from mango kernels (Mangifera indica L.).

PubMed

Engels, Christina; Schieber, Andreas; Gänzle, Michael G

2011-04-01

This study investigated the antimicrobial activities and modes of action of penta-, hexa-, hepta-, octa-, nona-, and deca-O-galloylglucose (gallotannins) isolated from mango kernels. The MICs and minimum bactericidal concentrations (MBCs) against food-borne bacteria and fungi were determined using a critical dilution assay. Gram-positive bacteria were generally more susceptible to gallotannins than were Gram-negative bacteria. The MICs of gallotannins against Bacillus subtilis, Bacillus cereus, Clostridium botulinum, Campylobacter jejuni, Listeria monocytogenes, and Staphylococcus aureus were 0.2 g liter(-1) or less; enterotoxigenic Escherichia coli and Salmonella enterica were inhibited by 0.5 to 1 g liter(-1), and lactic acid bacteria were resistant. The use of lipopolysaccharide mutants of S. enterica indicated that the outer membrane confers resistance toward gallotannins. Supplementation of LB medium with iron eliminated the inhibitory activity of gallotannins against Staphylococcus aureus, and siderophore-deficient mutants of S. enterica were less resistant toward gallotannins than was the wild-type strain. Hepta-O-galloylglucose sensitized Lactobacillus plantarum TMW1.460 to hop extract, indicating inactivation of hop resistance mechanisms, e.g., the multidrug resistance (MDR) transporter HorA. Carbohydrate metabolism of Lactococcus lactis MG1363, a conditionally respiring organism, was influenced by hepta-O-galloylglucose when grown under aerobic conditions and in the presence of heme but not under anaerobic conditions, indicating that gallotannins influence the respiratory chain. In conclusion, the inhibitory activities of gallotannins are attributable to their strong affinity for iron and likely additionally relate to the inactivation of membrane-bound proteins.

Development of nanostructured biocompatible materials for chemical and biological sensors

NASA Astrophysics Data System (ADS)

Curley, Michael; Chilvery, Ashwith K.; Kukhatreva, Tatiana; Sharma, Anup; Corda, John; Farley, Carlton

2012-10-01

This research is focused on the fabrication of thin films followed by Surface Enhanced Raman Spectroscopy (SERS) testing of these films for various applications. One technique involves the mixture of nanoparticles with twophoton material to be used as an indicator dye. Another method involved embedding silver nanoparticles in a ceramic nano-membrane. The substrates were characterized by both Atom Force Microscopy (AFM) and Scanning Electron Microscopy (SEM). We applied the nanostructured substrate to measure the SERS spectra of 10-6 Mol/L Rhodomine 6G(Rh6G), e-coli bacteria and RDX explosive. Our results showed that silver coated ceramic membranes can serve as appropriate substrates to enhance Raman signals. In addition, we demonstrated that the in-house-made colloidal silver can work for enhancement of the Raman spectra for bacteria. We measured the Raman spectra of Rh6G molecules on a substrate absorbed by a nanofluid of silver. We observed several strong Raman bands - 613cm-1,768 cm-1,1308cm-1 1356 cm-1,1510cm-1, which correspond to Rh6G vibrational modes υ53,υ65,υ115,υ117,υ146 respectively, using a ceramic membrane coated by silver. The Raman spectra of Rh6G absorbed by silver nanofluid showed strong enhancement of Raman bands 1175cm-1 and 1529cm-1, 1590 cm-1. Those correspond to vibrational frequency modes - υ103,υ151,152. We also measured the Raman spectra of e-coli bacteria, both absorbed by silver nanofluid, and on nanostructured substrate. In addition, the Fourier Transfer Infrared Spectra (FTIR) of the bacteria was measured.

Structure and Function of p97 and Pex1/6 Type II AAA+ Complexes.

PubMed

Saffert, Paul; Enenkel, Cordula; Wendler, Petra

2017-01-01

Protein complexes of the Type II AAA+ (ATPases associated with diverse cellular activities) family are typically hexamers of 80-150 kDa protomers that harbor two AAA+ ATPase domains. They form double ring assemblies flanked by associated domains, which can be N-terminal, intercalated or C-terminal to the ATPase domains. Most prominent members of this family include NSF (N-ethyl-maleimide sensitive factor), p97/VCP (valosin-containing protein), the Pex1/Pex6 complex and Hsp104 in eukaryotes and ClpB in bacteria. Tremendous efforts have been undertaken to understand the conformational dynamics of protein remodeling type II AAA+ complexes. A uniform mode of action has not been derived from these works. This review focuses on p97/VCP and the Pex1/6 complex, which both structurally remodel ubiquitinated substrate proteins. P97/VCP plays a role in many processes, including ER- associated protein degradation, and the Pex1/Pex6 complex dislocates and recycles the transport receptor Pex5 from the peroxisomal membrane during peroxisomal protein import. We give an introduction into existing knowledge about the biochemical and cellular activities of the complexes before discussing structural information. We particularly emphasize recent electron microscopy structures of the two AAA+ complexes and summarize their structural differences.

THE FINE STRUCTURE OF GREEN BACTERIA

PubMed Central

Cohen-Bazire, Germaine; Pfennig, Norbert; Kunisawa, Riyo

1964-01-01

The fine structure of several strains of green bacteria belonging to the genus Chlorobium has been studied in thin sections with the electron microscope. In addition to having general cytological features typical of Gram-negative bacteria, the cells of these organisms always contain membranous mesosomal elements, connected with the cytoplasmic membrane, and an elaborate system of isolated cortical vesicles, some 300 to 400 A wide and 1000 to 1500 A long. The latter structures, chlorobium vesicles, have been isolated in a partly purified state by differential centrifugation of cell-free extracts. They are associated with a centrifugal fraction that has a very high specific chlorophyll content. In all probability, therefore, the chlorobium vesicles are the site of the photosynthetic apparatus of green bacteria. PMID:14195611

Antimicrobial Peptides Derived from Fusion Peptides of Influenza A Viruses, a Promising Approach to Designing Potent Antimicrobial Agents.

PubMed

Wang, Jingyu; Zhong, Wenjing; Lin, Dongguo; Xia, Fan; Wu, Wenjiao; Zhang, Heyuan; Lv, Lin; Liu, Shuwen; He, Jian

2015-10-01

The emergence and dissemination of antibiotic-resistant bacterial pathogens have spurred the urgent need to develop novel antimicrobial agents with different mode of action. In this respect, we turned several fusogenic peptides (FPs) derived from the hemagglutinin glycoproteins (HAs) of IAV into potent antibacterials by replacing the negatively or neutrally charged residues of FPs with positively charged lysines. Their antibacterial activities were evaluated by testing the MICs against a panel of bacterial strains including S. aureus, S. mutans, P. aeruginosa, and E. coli. The results showed that peptides HA-FP-1, HA-FP-2-1, and HA-FP-3-1 were effective against both Gram-positive and Gram-negative bacteria with MICs ranging from 1.9 to 16.0 μm, while the toxicities toward mammalian cells were low. In addition, the mode of action and the secondary structure of these peptides were also discussed. These data not only provide several potent peptides displaying promising potential in development as broad antimicrobial agents, but also present a useful strategy in designing new antimicrobial agents. © 2015 John Wiley & Sons A/S.

Antibiotics: Precious Goods in Changing Times.

PubMed

Sass, Peter

2017-01-01

Antibiotics represent a first line of defense of diverse microorganisms, which produce and use antibiotics to counteract natural enemies or competitors for nutritional resources in their nearby environment. For antimicrobial activity, nature has invented a great variety of mechanisms of antibiotic action that involve the perturbation of essential bacterial structures or biosynthesis pathways of macromolecules such as the bacterial cell wall, DNA, RNA, or proteins, thereby threatening the specific microbial lifestyle and eventually even survival. However, along with highly inventive modes of antibiotic action, nature also developed a comparable set of resistance mechanisms that help the bacteria to circumvent antibiotic action. Microorganisms have evolved specific adaptive responses that allow appropriately reacting to the presence of antimicrobial agents, ensuring survival during antimicrobial stress. In times of rapid development and spread of antibiotic (multi-)resistance, we need to explore new, resistance-breaking strategies to counteract bacterial infections. This chapter intends to give an overview of common antibiotics and their target pathways. It will also discuss recent advances in finding new antibiotics with novel modes of action, illustrating that nature's repertoire of innovative new antimicrobial agents has not been fully exploited yet, and we still might find new drugs that help to evade established antimicrobial resistance strategies.

Oligonucleotide recombination enabled site-specific mutagenesis in bacteria

USDA-ARS?s Scientific Manuscript database

Recombineering refers to a strategy for engineering DNA sequences using a specialized mode of homologous recombination. This technology can be used for rapidly constructing precise changes in bacterial genome sequences in vivo. Oligo recombination is one type of recombineering that uses ssDNA olig...

Community structures of actively growing bacteria shift along a north-south transect in the western North Pacific

PubMed Central

Taniguchi, Akito; Hamasaki, Koji

2008-01-01

Bacterial community structures and their activities in the ocean are tightly coupled with organic matter fluxes and thus control ocean biogeochemical cycles. Bromodeoxyuridine (BrdU), halogenated nucleoside and thymidine analogue, has been recently used to monitor actively growing bacteria (AGB) in natural environments. We labelled DNA of proliferating cells in seawater bacterial assemblages with BrdU and determined community structures of the bacteria that were possible key species in mediating biochemical reactions in the ocean. Surface seawater samples were collected along a north-south transect in the North Pacific in October 2003 and subjected to BrdU magnetic beads immunocapture and PCR-DGGE (BUMP-DGGE) analysis. Change of BrdU-incorporated community structures reflected the change of water masses along a north-south transect from subarctic to subtropical gyres in the North Pacific. We identified 25 bands referred to AGB as BrdU-incorporated phylotypes, belonging to Alphaproteobacteria (5 bands), Betaproteobacteria (1 band), Gammaproteobacteria (4 bands), Cytophaga-Flavobacterium-Bacteroides (CFB) group bacteria (5 bands), Gram-positive bacteria (6 bands), and Cyanobacteria (4 bands). BrdU-incorporated phylotypes belonging to Vibrionales, Alteromonadales and Gram-positive bacteria appeared only at sampling stations in a subtropical gyre, while those belonging to Roseobacter-related bacteria and CFB group bacteria appeared at the stations in both subarctic and subtropical gyres. Our result revealed phylogenetic affiliation of AGB and their dynamic change along with north-south environmental gradients in open oceans. Different species of AGB utilize different amount and kinds of substrates, which can affect the change of organic matter fluxes along transect. PMID:18177366

[Quantum differences of ortho/para H2O2 spin-isomers as a factor of the femtosecond charge separation kinetics modulation in reaction centers of purple bacteria].

PubMed

Pishchal'nikov, R Iu; Pershin, S M; Bunkin, A F

2012-01-01

We have proposed the mechanism of coherent modulations of the P* state in the transient absorption spectra of the reaction center isolated from purple bacteria. Two water molecules, located between special pair, Ba, Bb chlorophylls and histidine L173 and M202, are supposed to be ortho-H2O and para-H2O isomers with different magnetic properties. The distinctive modulation frequencies were labeling as rotational resonances of ortho-H2O. According to our assumption, the interaction of rotational modes of water isomers with the charge-transfer states is a reason of coherent modulations of kinetics. We have modified a Hamiltonian system in order to take into account the rotational modes of ortho-H2O. Evolution of the density matrix was calculated in Liouville space. The Redfield relaxation theory for molecular aggregates was used to model kinetics up to 3 ps.

Bioprospecting for Exopolysaccharides from Deep-Sea Hydrothermal Vent Bacteria: Relationship between Bacterial Diversity and Chemical Diversity

PubMed Central

Delbarre-Ladrat, Christine; Leyva Salas, Marcia; Zykwinska, Agata; Colliec-Jouault, Sylvia

2017-01-01

Many bacteria biosynthesize structurally diverse exopolysaccharides (EPS) and excrete them into their surrounding environment. The EPS functional features have found many applications in industries such as cosmetics and pharmaceutics. In particular, some EPS produced by marine bacteria are composed of uronic acids, neutral sugars, and N-acetylhexosamines, and may also bear some functional sulfate groups. This suggests that they can share common structural features with glycosaminoglycans (GAG) like the two EPS (HE800 and GY785) originating from the deep sea. In an attempt to discover new EPS that may be promising candidates as GAG-mimetics, fifty-one marine bacterial strains originating from deep-sea hydrothermal vents were screened. The analysis of the EPS chemical structure in relation to bacterial species showed that Vibrio, Alteromonas, and Pseudoalteromonas strains were the main producers. Moreover, they produced EPS with distinct structural features, which might be useful for targeting marine bacteria that could possibly produce structurally GAG-mimetic EPS. PMID:28930185

Bacteria causing important diseases of citrus utilise distinct modes of pathogenesis to attack a common host.

PubMed

Vojnov, Adrián Alberto; do Amaral, Alexandre Morais; Dow, John Maxwell; Castagnaro, Atilio Pedro; Marano, Marìa Rosa

2010-06-01

In this review, we summarise the current knowledge on three pathogens that exhibit distinct tissue specificity and modes of pathogenesis in citrus plants. Xanthomonas axonopodis pv. citri causes canker disease and invades the host leaf mesophyll tissue through natural openings and can also survive as an epiphyte. Xylella fastidiosa and Candidatus Liberibacter are vectored by insects and proliferate in the vascular system of the host, either in the phloem (Candidatus Liberibacter) or xylem (X. fastidiosa) causing variegated chlorosis and huanglongbing diseases, respectively. Candidatus Liberibacter can be found within host cells and is thus unique as an intracellular phytopathogenic bacterium. Genome sequence comparisons have identified groups of species-specific genes that may be associated with the particular lifestyle, mode of transmission or symptoms produced by each phytopathogen. In addition, components that are conserved amongst bacteria may have diverse regulatory actions underpinning the different bacterial lifestyles; one example is the divergent role of the Rpf/DSF cell-cell signalling system in X. citri and X. fastidiosa. Biofilm plays a key role in epiphytic fitness and canker development in X. citri and in the symptoms produced by X. fastidiosa. Bacterial aggregation may be associated with vascular occlusion of the xylem vessels and symptomatology of variegated chlorosis.

Unified approach for calculating the number of confined modes in multilayered waveguiding structures

NASA Astrophysics Data System (ADS)

Ruschin, S.; Griffel, G.; Hardy, A.; Croitoru, N.

1986-01-01

A general formalism is developed in order to find the number of modes and mode cutoff conditions in multilayer waveguiding structures. An explicit expression is presented for the number of confined modes that allows the modes to be counted without having to analyze the specific eigenvalue equation of the structure. The method is illustrated by its application to several structures: the buried layer, the directional coupler, and the three-guide symmetrical arrangement. By a suitable extension of the formalism, the number of well-confined modes is found for a four-layer structure.

Application of attachment modes in the control of large space structures

NASA Technical Reports Server (NTRS)

Craig, Roy R., Jr.

1989-01-01

Various ways are examined to obtain reduced order mathematical models of structures for use in dynamic response analyses and in controller design studies. Attachment modes are deflection shapes of a structure subjected to specified unit load distributions. Attachment modes are frequently employed to supplement free-interface normal modes to improve the modeling of components (structures) employed in component mode synthesis analyses. Deflection shapes of structures subjected to generalized loads of some specified distribution and of unit magnitude can also be considered to be attachment modes. Several papers which were written under this contract are summarized herein.

Devescovinid features, a remarkable surface cytoskeleton, and epibiotic bacteria revisited in Mixotricha paradoxa, a parabasalid flagellate.

PubMed

Brugerolle, G

2004-10-01

This work reports on the flagellate systematics and phylogeny, cytoskeleton, prokaryote-eukaryote cell junction organisation, and epibiotic bacteria identification. It confirms the pioneer 1964 study on Mixotricha paradoxa and supplies new information. Mixotricha paradoxa has a cresta structure specific to devescovinid parabasalid flagellates, a slightly modified recurrent flagellum, and an axostylar tube containing two lamina-shaped parabasal fibres. However, many parabasal profiles are distributed throughout the cell body. There is a conspicuous cortical microfibrillar network whose strands are related to cell junction structures subjacent to epibiotic bacteria. The supposed actin composition of this network could not be demonstrated with anti-actin antibodies or phalloidin labelling. Four types of epibiotic bacteria were described. Bacillus-shaped bacteria with a Gram-negative organisation are nested in alternate rows on most of the surface of the protozoon. They induce a striated calyxlike junction structure beneath the adhesion zone linked to the cortical microfibrillar network. Slender spirochetes are attached by one differentiated end to the plasma membrane of the protozoon, forming knobs on the cell surface. Two very similar long rod-shaped bacteria are also attached on the knobs of the plasma membrane. A large spirochete attributed to the genus Canaleparolina is also attached to the protozoon. Observations on epibiotic bacteria and of their attachments are compared with several described epibiotic bacteria of symbiotic protozoa and with the results of the molecular identification of the epibiotic bacteria of M. paradoxa.

The flagellar motor of Caulobacter crescentus generates more torque when a cell swims backward

PubMed Central

Lele, Pushkar P.; Roland, Thibault; Shrivastava, Abhishek; Chen, Yihao; Berg, Howard C.

2016-01-01

Caulobacter crescentus, a monotrichous bacterium, swims by rotating a single right-handed helical filament. CW motor rotation thrusts the cell forward 1, a mode of motility known as the pusher mode; CCW motor rotation pulls the cell backward, a mode of motility referred to as the puller mode 2. The situation is opposite in E. coli, a peritrichous bacterium, where CCW rotation of multiple left-handed filaments drives the cell forward. The flagellar motor in E. coli generates more torque in the CCW direction than the CW direction in swimming cells 3,4. However, monotrichous bacteria including C. crescentus swim forward and backward at similar speeds, prompting the assumption that motor torques in the two modes are the same 5,6. Here, we present evidence that motors in C. crescentus develop higher torques in the puller mode than in the pusher mode, and suggest that the anisotropy in torque-generation is similar in two species, despite the differences in filament handedness and motor bias (probability of CW rotation). PMID:27499800

Genetics and Assembly Line Enzymology of Siderophore Biosynthesis in Bacteria

PubMed Central

Crosa, Jorge H.; Walsh, Christopher T.

2002-01-01

The regulatory logic of siderophore biosynthetic genes in bacteria involves the universal repressor Fur, which acts together with iron as a negative regulator. However in other bacteria, in addition to the Fur-mediated mechanism of regulation, there is a concurrent positive regulation of iron transport and siderophore biosynthetic genes that occurs under conditions of iron deprivation. Despite these regulatory differences the mechanisms of siderophore biosynthesis follow the same fundamental enzymatic logic, which involves a series of elongating acyl-S-enzyme intermediates on multimodular protein assembly lines: nonribosomal peptide synthetases (NRPS). A substantial variety of siderophore structures are produced from similar NRPS assembly lines, and variation can come in the choice of the phenolic acid selected as the N-cap, the tailoring of amino acid residues during chain elongation, the mode of chain termination, and the nature of the capturing nucleophile of the siderophore acyl chain being released. Of course the specific parts that get assembled in a given bacterium may reflect a combination of the inventory of biosynthetic and tailoring gene clusters available. This modular assembly logic can account for all known siderophores. The ability to mix and match domains within modules and to swap modules themselves is likely to be an ongoing process in combinatorial biosynthesis. NRPS evolution will try out new combinations of chain initiation, elongation and tailoring, and termination steps, possibly by genetic exchange with other microorganisms and/or within the same bacterium, to create new variants of iron-chelating siderophores that can fit a particular niche for the producer bacterium. PMID:12040125

Impact of a Recombinant Biocontrol Bacterium, Pseudomonas fluorescens pc78, on Microbial Community in Tomato Rhizosphere.

PubMed

Kong, Hyun Gi; Kim, Nam Hee; Lee, Seung Yeup; Lee, Seon-Woo

2016-04-01

Pseudomonas fluorescens pc78 is an effective biocontrol agent for soil-borne fungal diseases. We previously constructed a P43-gfp tagged biocontrol bacteria P. fluorescens pc78-48 to investigate bacterial traits in natural ecosystem and the environmental risk of genetically modified biocontrol bacteria in tomato rhizosphere. Fluctuation of culturable bacteria profile, microbial community structure, and potential horizontal gene transfer was investigated over time after the bacteria treatment to the tomato rhizosphere. Tagged gene transfer to other organisms such as tomato plants and bacteria cultured on various media was examined by polymerase chain reaction, using gene specific primers. Transfer of chromosomally integrated P43-gfp from pc78 to other organisms was not apparent. Population and colony types of culturable bacteria were not significantly affected by the introduction of P. fluorescens pc78 or pc78-48 into tomato rhizosphere. Additionally, terminal restriction fragment length polymorphism profiles were investigated to estimate the influence on the microbial community structure in tomato rhizosphere between non-treated and pc78-48-treated samples. Interestingly, rhizosphere soil treated with strain pc78-48 exhibited a significantly different bacterial community structure compared to that of non-treated rhizosphere soil. Our results suggest that biocontrol bacteria treatment influences microbial community in tomato rhizosphere, while the chromosomally modified biocontrol bacteria may not pose any specific environmental risk in terms of gene transfer.

Establishing bacterial communities by 'word of mouth': LuxS and autoinducer 2 in biofilm development.

PubMed

Hardie, Kim Rachael; Heurlier, Karin

2008-08-01

Multicellular bacterial communities (biofilms) abound in nature, and their successful formation and survival is likely to require cell-cell communication--including quorum sensing--to co-ordinate appropriate gene expression. The only mode of quorum sensing that is shared by both Gram-positive and Gram-negative bacteria involves the production of the signalling molecule autoinducer 2 by LuxS. A survey of the current literature reveals that luxS contributes to biofilm development in some bacteria. However, inconsistencies prevent biofilm development being attributed to the production of AI2 in all cases.

Bacteriocins from Lactobacillus plantarum – production, genetic organization and mode of action

PubMed Central

Todorov, Svetoslav D.

2009-01-01

Bacteriocins are biologically active proteins or protein complexes that display a bactericidal mode of action towards usually closely related species. Numerous strains of bacteriocin producing Lactobacillus plantarum have been isolated in the last two decades from different ecological niches including meat, fish, fruits, vegetables, and milk and cereal products. Several of these plantaricins have been characterized and the aminoacid sequence determined. Different aspects of the mode of action, fermentation optimization and genetic organization of the bacteriocin operon have been studied. However, numerous of bacteriocins produced by different Lactobacillus plantarum strains have not been fully characterized. In this article, a brief overview of the classification, genetics, characterization, including mode of action and production optimization for bacteriocins from Lactic Acid Bacteria in general, and where appropriate, with focus on bacteriocins produced by Lactobacillus plantarum, is presented. PMID:24031346

[Effect of mechanical grinding of Sphagnum on the structure and physiological state of bacterial communities].

PubMed

Dobrovol'skaya, T G; Golovchenko, A V; Yakushev, A V; Manucharova, N A; Yurchenko, E N

2014-01-01

The microcosm method was used to demonstrate an increase in bacterial numbers and drastic changes in the taxonomic structure of saprotrophic bacteria as a result of mechanical grinding of Sphagnum moss. Ekkrisotrophic agrobacteria predominant in untreated moss were replaced by hydrolytic bacteria. Molecular biological approaches revealed such specific hydrolytic bacteria as Janthinobacterium agaricum and Streptomyces purpurascens among the dominant taxa. The application of kinetic technique for determination of the physiological state of bacteria in situ revealed higher functional diversity of hydrolytic bacteria in ground moss than in untreated samples. A considerable decrease of the C/N ratio in ground samples of living Sphagnum incubated using the microcosm technique indicated decomposition of this substrate.

[Microflora of damaged ferroconcrete structures under the conditions of inhibitory protection].

PubMed

Kopteva, Zh P; Zanina, V V; Purish, L M; Piliashenko-Novokhatnyĭ, A I; Kozlova, I A

2004-01-01

Thionic, sulphate-reducing, denitrifying and ammonifying bacteria widely distributed in the sewer system on various structure elements have been isolated from damaged ferroconcrete samples. Effect of protective materials on microbe-induced corrosion of metal famework of concrete samples has been studied. Selective effect of corrosion inhibitors and coatings on the growth of corrosion-active bacteria of sulphur and nitrogen cycle has been revealed. It is shown that acid medium formed by thionic bacteria is more aggressive than ammonium-hydrosulphide one formed by denitrifying and sulphate-reducing bacteria. It has been established that the corrosion inhibitor--pyrquin, organosilicon coating CO-FMI and epoxyorganosilicon coating 4sk are most effective materials as to the action of thionic bacteria--dangerous agents of ferroconcrete aerobic corrosion.

An SMS (single mode - multi mode - single mode) fiber structure for vibration sensing

NASA Astrophysics Data System (ADS)

Waluyo, T. B.; Bayuwati, D.

2017-04-01

We describe an SMS (single mode - multi mode - single mode) fiber structure to be used in a vibration sensing system. The fiber structure was fabricated by splicing a section (about 300 mm in length) of a step index multi mode fiber between two single mode fibers obtained from a communication grade fiber patchcord. Interference between higher order modes occurs while light from a narrow band light source travels along the multi mode fiber. When the multi mode fiber vibrates, the refractive index profile is changed because of the photo-elastics effect and the amplitude of the interference pattern is changed accordingly. To simulate a vibrating structure we used a loudspeaker to vibrate a wooden table. By using a digital oscilloscope, we recorded and analysed the vibrating signals obtained from the SMS fiber structure as well as from a GS-32CT geophone for referencing. We observed that this SMS fiber structure was potential to be used in a vibration sensing system with a measurement range from 30 to 180 Hz with inherent optical fiber sensor advantages such as light weight, immune to electromagnetic interference, and no electricity in the sensing part.

Potential Applications of the Cyclic Peptide Enterocin AS-48 in the Preservation of Vegetable Foods and Beverages.

PubMed

Abriouel, Hikmate; Lucas, Rosario; Omar, Nabil Ben; Valdivia, Eva; Gálvez, Antonio

2010-06-01

Bacteriocins are antimicrobial peptides produced by bacteria. Among them, the enterococcal bacteriocin (enterocin) AS-48 stands for its peculiar characteristics and broad-spectrum antimicrobial activity. AS-48 belongs to the class of circular bacteriocins and has been studied in depth in several aspects: peptide structure, genetic determinants, and mode of action. Recently, a wealth of knowledge has accumulated on the antibacterial activity of this bacteriocin against foodborne pathogenic and spoilage bacteria in food systems, especially in vegetable foods and drinks. This work provides a general overview on the results from tests carried out with AS-48 in different vegetable food categories (such as fruit juices, ciders, sport and energy drinks, fresh fruits and vegetables, pre-cooked ready to eat foods, canned vegetables, and bakery products). Depending on the food substrate, the bacteriocin has been tested alone or as part of hurdle technology, in combination with physico-chemical treatments (such as mild heat treatments or high-intensity pulsed electric fields) and other antimicrobial substances (such as essential oils, phenolic compounds, and chemical preservatives). Since the work carried out on bacteriocins in preservation of vegetable foods and drinks is much more limited compared to meat and dairy products, the results reported for AS-48 may open new possibilities in the field of bacteriocin applications.

Use of nitrogen-fixing bacteria as biofertiliser for non-legumes: prospects and challenges.

PubMed

Bhattacharjee, Rumpa Biswas; Singh, Aqbal; Mukhopadhyay, S N

2008-08-01

The potential of nitrogen-fixing (NF) bacteria to form a symbiotic relationship with leguminous plants and fix atmospheric nitrogen has been exploited in the field to meet the nitrogen requirement of the latter. This phenomenon provides an alternative to the use of the nitrogenous fertiliser whose excessive and imbalanced use over the decades has contributed to green house emission (N2O) and underground water leaching. Recently, it was observed that non-leguminous plants like rice, sugarcane, wheat and maize form an extended niche for various species of NF bacteria. These bacteria thrive within the plant, successfully colonizing roots, stems and leaves. During the association, the invading bacteria benefit the acquired host with a marked increase in plant growth, vigor and yield. With increasing population, the demand of non-leguminous plant products is growing. In this regard, the richness of NF flora within non-leguminous plants and extent of their interaction with the host definitely shows a ray of hope in developing an ecofriendly alternative to the nitrogenous fertilisers. In this review, we have discussed the association of NF bacteria with various non-leguminous plants emphasizing on their potential to promote host plant growth and yield. In addition, plant growth-promoting traits observed in these NF bacteria and their mode of interaction with the host plant have been described briefly.

Differentiating the growth phases of single bacteria using Raman spectroscopy

NASA Astrophysics Data System (ADS)

Strola, S. A.; Marcoux, P. R.; Schultz, E.; Perenon, R.; Simon, A.-C.; Espagnon, I.; Allier, C. P.; Dinten, J.-M.

2014-03-01

In this paper we present a longitudinal study of bacteria metabolism performed with a novel Raman spectrometer system. Longitudinal study is possible with our Raman setup since the overall procedure to localize a single bacterium and collect a Raman spectrum lasts only 1 minute. Localization and detection of single bacteria are performed by means of lensfree imaging, whereas Raman signal (from 600 to 3200 cm-1) is collected into a prototype spectrometer that allows high light throughput (HTVS technology, Tornado Spectral System). Accomplishing time-lapse Raman spectrometry during growth of bacteria, we observed variation in the net intensities for some band groups, e.g. amides and proteins. The obtained results on two different bacteria species, i.e. Escherichia coli and Bacillus subtilis clearly indicate that growth affects the Raman chemical signature. We performed a first analysis to check spectral differences and similarities. It allows distinguishing between lag, exponential and stationary growth phases. And the assignment of interest bands to vibration modes of covalent bonds enables the monitoring of metabolic changes in bacteria caused by growth and aging. Following the spectra analysis, a SVM (support vector machine) classification of the different growth phases is presented. In sum this longitudinal study by means of a compact and low-cost Raman setup is a proof of principle for routine analysis of bacteria, in a real-time and non-destructive way. Real-time Raman studies on metabolism and viability of bacteria pave the way for future antibiotic susceptibility testing.

Specialized cell surface structures in cellulolytic bacteria.

PubMed Central

Lamed, R; Naimark, J; Morgenstern, E; Bayer, E A

1987-01-01

The cell surface topology of various gram-negative and -positive, anaerobic and aerobic, mesophilic and thermophilic, cellulolytic and noncellulolytic bacteria was investigated by scanning electron microscopic visualization using cationized ferritin. Characteristic protuberant structures were observed on cells of all cellulolytic strains. These structures appeared to be directly related to the previously described exocellular cellulase-containing polycellulosomes of Clostridium thermocellum YS (E. A. Bayer and R. Lamed, J. Bacteriol. 167:828-836, 1986). Immunochemical evidence and lectin-binding studies suggested a further correlation on the molecular level among cellulolytic bacteria. The results indicate that such cell surface cellulase-containing structures may be of general consequence to the bacterial interaction with and degradation of cellulose. Images PMID:3301817

Complex community of nitrite-dependent anaerobic methane oxidation bacteria in coastal sediments of the Mai Po wetland by PCR amplification of both 16S rRNA and pmoA genes.

PubMed

Chen, Jing; Zhou, Zhichao; Gu, Ji-Dong

2015-02-01

In the present work, both 16S rRNA and pmoA gene-based PCR primers were employed successfully to study the diversity and distribution of n-damo bacteria in the surface and lower layer sediments at the coastal Mai Po wetland. The occurrence of n-damo bacteria in both the surface and subsurface sediments with high diversity was confirmed in this study. Unlike the two other known n-damo communities from coastal areas, the pmoA gene-amplified sequences in the present work clustered not only with some freshwater subclusters but also within three newly erected marine subclusters mostly, indicating the unique niche specificity of n-damo bacteria in this wetland. Results suggested vegetation affected the distribution and community structures of n-damo bacteria in the sediments and n-damo could coexist with sulfate-reducing methanotrophs in the coastal ecosystem. Community structures of the Mai Po n-damo bacteria based on 16S rRNA gene were different from those of either the freshwater or the marine. In contrast, structures of the Mai Po n-damo communities based on pmoA gene grouped with the marine ones and were clearly distinguished from the freshwater ones. The abundance of n-damo bacteria at this wetland was quantified using 16S rRNA gene PCR primers to be 2.65-6.71 × 10(5) copies/g dry sediment. Ammonium and nitrite strongly affected the community structures and distribution of n-damo bacteria in the coastal Mai Po wetland sediments.

Designed β-Boomerang Antiendotoxic and Antimicrobial Peptides

PubMed Central

Bhunia, Anirban; Mohanram, Harini; Domadia, Prerna N.; Torres, Jaume; Bhattacharjya, Surajit

2009-01-01

Lipopolysaccharide (LPS), an integral part of the outer membrane of Gram-negative bacteria, is involved in a variety of biological processes including inflammation, septic shock, and resistance to host-defense molecules. LPS also provides an environment for folding of outer membrane proteins. In this work, we describe the structure-activity correlation of a series of 12-residue peptides in LPS. NMR structures of the peptides derived in complex with LPS reveal boomerang-like β-strand conformations that are stabilized by intimate packing between the two aromatic residues located at the 4 and 9 positions. This structural feature renders these peptides with a high ability to neutralize endotoxicity, >80% at 10 nm concentration, of LPS. Replacements of these aromatic residues either with Ala or with Leu destabilizes the boomerang structure with the concomitant loss of antiendotoxic and antimicrobial activities. Furthermore, the aromatic packing stabilizing the β-boomerang structure in LPS is found to be maintained even in a truncated octapeptide, defining a structured LPS binding motif. The mode of action of the active designed peptides correlates well with their ability to perturb LPS micelle structures. Fourier transform infrared spectroscopy studies of the peptides delineate β-type conformations and immobilization of phosphate head groups of LPS. Trp fluorescence studies demonstrated selective interactions with LPS and the depth of insertion into the LPS bilayer. Our results demonstrate the requirement of LPS-specific structures of peptides for endotoxin neutralizations. In addition, we propose that structures of these peptides may be employed to design proteins for the outer membrane. PMID:19520860

Structural basis for diversity in the SAM clan of riboswitches.

PubMed

Trausch, Jeremiah J; Xu, Zhenjiang; Edwards, Andrea L; Reyes, Francis E; Ross, Phillip E; Knight, Rob; Batey, Robert T

2014-05-06

In bacteria, sulfur metabolism is regulated in part by seven known families of riboswitches that bind S-adenosyl-l-methionine (SAM). Direct binding of SAM to these mRNA regulatory elements governs a downstream secondary structural switch that communicates with the transcriptional and/or translational expression machinery. The most widely distributed SAM-binding riboswitches belong to the SAM clan, comprising three families that share a common SAM-binding core but differ radically in their peripheral architecture. Although the structure of the SAM-I member of this clan has been extensively studied, how the alternative peripheral architecture of the other families supports the common SAM-binding core remains unknown. We have therefore solved the X-ray structure of a member of the SAM-I/IV family containing the alternative "PK-2" subdomain shared with the SAM-IV family. This structure reveals that this subdomain forms extensive interactions with the helix housing the SAM-binding pocket, including a highly unusual mode of helix packing in which two helices pack in a perpendicular fashion. Biochemical and genetic analysis of this RNA reveals that SAM binding induces many of these interactions, including stabilization of a pseudoknot that is part of the regulatory switch. Despite strong structural similarity between the cores of SAM-I and SAM-I/IV members, a phylogenetic analysis of sequences does not indicate that they derive from a common ancestor.

The Extreme Mechanics of Soft Structures

NASA Astrophysics Data System (ADS)

Reis, Pedro

2015-03-01

I will present a series of experimental investigations on the rich behavior of soft mechanical structures, which, similarly to soft materials, can undergo large deformations under a variety of loading conditions. Soft structures typically comprise slender elements that can readily undergo mechanical instabilities to achieve extreme flexibility and reversible reconfigurations. This field has came to be warmly known as `Extreme Mechanics', where one of the fundamental challenges lies in rationalizing the geometric nonlinearities that arise in the post-buckling regime. I shall focus on problems involving thin elastic rods and shells, through examples ranging from the deployment of submarine cables onto the seabed, locomotion of uniflagellar bacteria, crystallography of curved wrinkling and its usage for active aerodynamic drag reduction. The main common feature underlying this series of studies is the prominence of geometry, and its interplay with mechanics, in dictating complex mechanical behavior that is relevant and applicable over a wide range of length scales. Moreover, our findings suggest that we rethink our relationship with mechanical instabilities which, rather than modes of failure, can be embraced as opportunities for functionality that are scalable, reversible, and robust. The author knowledges financial support from the National Science Foundation, CMMI-1351449 (CAREER).

Structural, antimicrobial and computational characterization of 1-benzoyl-3-(5-chloro-2-hydroxyphenyl)thiourea.

PubMed

Atiş, Murat; Karipcin, Fatma; Sarıboğa, Bahtiyar; Taş, Murat; Çelik, Hasan

2012-12-01

A new thiourea derivative, 1-benzoyl-3-(5-chloro-2-hydroxyphenyl)thiourea (bcht) has been synthesized from the reaction of 2-amino-4-chlorophenol with benzoyl isothiocyanate. The title compound has been characterized by elemental analyses, FT-IR, (13)C, (1)H NMR spectroscopy and the single crystal X-ray diffraction analysis. The structure of bcht derived from X-ray diffraction of a single crystal has been presented. The structural and spectroscopic data of the molecule in the ground state were calculated by using density functional method using 6-311++G(d,p) basis set. The complete assignments of all vibrational modes were performed on the basis of the total energy distributions (TED). Isotropic chemical shifts ((13)C NMR and (1)H NMR) were calculated using the gauge-invariant atomic orbital (GIAO) method. Theoretical calculations of bond parameters, harmonic vibration frequencies and nuclear magnetic resonance are in good agreement with experimental results. The UV absorption spectra of the compound that dissolved in ACN and MeOH were recorded. Bcht was also screened for antimicrobial activity against pathogenic bacteria and fungi. Copyright © 2012 Elsevier B.V. All rights reserved.

Molecular structure, chemical synthesis, and antibacterial activity of ABP-dHC-cecropin A from drury (Hyphantria cunea).

PubMed

Zhang, Jiaxin; Movahedi, Ali; Wang, Xiaoli; Wu, Xiaolong; Yin, Tongming; Zhuge, Qiang

2015-06-01

The increasing resistance of bacteria and fungi to currently available antibiotics is a major concern worldwide, leading to enormous efforts to develop new antibiotics with new modes of actions. In this paper, cDNA encoding cecropin A was amplified from drury (Hyphantria cunea) (dHC) pupa fatbody total RNA using RT-PCR. The full-length dHC-cecropin A cDNA encoded a protein of 63 amino acids with a predicted 26-amino acid signal peptide and a 37-amino acid functional domain. We synthesized the antibacterial peptide (ABP) from the 37-amino acid functional domain (ABP-dHC-cecropin A), and amidated it via the C-terminus. Time-of-flight mass spectrometry showed its molecular weight to be 4058.94. The ABP-dHC-cecropin A was assessed in terms of its protein structure using bioinformatics and CD spectroscopy. The protein's secondary structure was predicted to be α-helical. In an antibacterial activity analysis, the ABP-dHC-cecropin A exhibited strong antibacterial activity against E. coli K12D31 and Agrobacterium EHA105. Copyright © 2014 Elsevier Inc. All rights reserved.

Nature's Way to Make the Lantibiotics

ERIC Educational Resources Information Center

Relyea, Heather A.; van der Donk, Wilfred A.

2006-01-01

The biosynthesis and mode of action of a class of compounds called lantibiotics, a peptide with antibacterial activity against multi-drug resistant bacteria as well as food-borne pathogens like Listeria monocytogenes and Clostridium botulinum is described. These peptide-derived compounds are especially interesting because they could be used as…

Potential probiotic effects of lactic acid bacteria on ruminant performance

USDA-ARS?s Scientific Manuscript database

Probiotics are microbial feed supplements that benefit animals by improving the microbial community of the digestive tract. In humans, probiotics are species that can survive the stomach and influence the intestinal microflora. The mode of action of human probiotics is not as yet proven. However, th...

Cell wall elongation mode in Gram-negative bacteria is determined by peptidoglycan architecture.

PubMed

Turner, Robert D; Hurd, Alexander F; Cadby, Ashley; Hobbs, Jamie K; Foster, Simon J

2013-01-01

Cellular integrity and morphology of most bacteria is maintained by cell wall peptidoglycan, the target of antibiotics essential in modern healthcare. It consists of glycan strands, cross-linked by peptides, whose arrangement determines cell shape, prevents lysis due to turgor pressure and yet remains dynamic to allow insertion of new material, and hence growth. The cellular architecture and insertion pattern of peptidoglycan have remained elusive. Here we determine the peptidoglycan architecture and dynamics during growth in rod-shaped Gram-negative bacteria. Peptidoglycan is made up of circumferentially oriented bands of material interspersed with a more porous network. Super-resolution fluorescence microscopy reveals an unexpected discontinuous, patchy synthesis pattern. We present a consolidated model of growth via architecture-regulated insertion, where we propose only the more porous regions of the peptidoglycan network that are permissive for synthesis.

Generalization of soft phonon modes

NASA Astrophysics Data System (ADS)

Rudin, Sven P.

2018-04-01

Soft phonon modes describe a collective movement of atoms that transform a higher-symmetry crystal structure into a lower-symmetry crystal structure. Such structural transformations occur at finite temperatures, where the phonons (i.e., the low-temperature vibrational modes) and the static perfect crystal structures provide an incomplete picture of the dynamics. Here, principal vibrational modes (PVMs) are introduced as descriptors of the dynamics of a material system with N atoms. The PVMs represent the independent collective movements of the atoms at a given temperature. Molecular dynamics (MD) simulations, here in the form of quantum MD using density functional theory calculations, provide both the data describing the atomic motion and the data used to construct the PVMs. The leading mode, PVM0, represents the 3 N -dimensional direction in which the system moves with greatest amplitude. For structural phase transitions, PVM0 serves as a generalization of soft phonon modes. At low temperatures, PVM0 reproduces the soft phonon mode in systems where one phonon dominates the phase transformation. In general, multiple phonon modes combine to describe a transformation, in which case PVM0 culls these phonon modes. Moreover, while soft phonon modes arise in the higher-symmetry crystal structure, PVM0 can be equally well calculated on either side of the structural phase transition. Two applications demonstrate these properties: first, transitions into and out of bcc titanium, and, second, the two crystal structures proposed for the β phase of uranium, the higher-symmetry structure of which stabilizes with temperature.

Chemometric Analysis of Bacterial Peptidoglycan Reveals Atypical Modifications That Empower the Cell Wall against Predatory Enzymes and Fly Innate Immunity.

PubMed

Espaillat, Akbar; Forsmo, Oskar; El Biari, Khouzaima; Björk, Rafael; Lemaitre, Bruno; Trygg, Johan; Cañada, Francisco Javier; de Pedro, Miguel A; Cava, Felipe

2016-07-27

Peptidoglycan is a fundamental structure for most bacteria. It contributes to the cell morphology and provides cell wall integrity against environmental insults. While several studies have reported a significant degree of variability in the chemical composition and organization of peptidoglycan in the domain Bacteria, the real diversity of this polymer is far from fully explored. This work exploits rapid ultraperformance liquid chromatography and multivariate data analysis to uncover peptidoglycan chemical diversity in the Class Alphaproteobacteria, a group of Gram negative bacteria that are highly heterogeneous in terms of metabolism, morphology and life-styles. Indeed, chemometric analyses revealed novel peptidoglycan structures conserved in Acetobacteria: amidation at the α-(l)-carboxyl of meso-diaminopimelic acid and the presence of muropeptides cross-linked by (1-3) l-Ala-d-(meso)-diaminopimelate cross-links. Both structures are growth-controlled modifications that influence sensitivity to Type VI secretion system peptidoglycan endopeptidases and recognition by the Drosophila innate immune system, suggesting relevant roles in the environmental adaptability of these bacteria. Collectively our findings demonstrate the discriminative power of chemometric tools on large cell wall-chromatographic data sets to discover novel peptidoglycan structural properties in bacteria.

Recognition of LPS by TLR4: Potential for Anti-Inflammatory Therapies

PubMed Central

Nijland, Reindert; Hofland, Tom; van Strijp, Jos A. G.

2014-01-01

LPS molecules of marine bacteria show structures distinct from terrestrial bacteria, due to the different environment that marine bacteria live in. Because of these different structures, lipid A molecules from marine bacteria are most often poor stimulators of the Toll-like receptor 4 (TLR4) pathway. Due to their low stimulatory potential, these lipid A molecules are suggested to be applicable as antagonists of TLR4 signaling in sepsis patients, where this immune response is amplified and unregulated. Antagonizing lipid A molecules might be used for future therapies against sepsis, therapies that currently do not exist. In this review, we will discuss these differences in lipid A structures and their recognition by the immune system. The modifications present in marine lipid A structures are described, and their potential as LPS antagonists will be discussed. Finally, since clinical trials built on antagonizing lipid A molecules have proven unsuccessful, we propose to also focus on different aspects of the TLR4 signaling pathway when searching for new potential drugs. Furthermore, we put forward the notion that bacteria probably already produce inhibitors of TLR4 signaling, making these bacterial products interesting molecules to investigate for future sepsis therapies. PMID:25056632

Protein structure, electron transfer and evolution of prokaryotic photosynthetic reaction centers

NASA Technical Reports Server (NTRS)

Blankenship, R. E.

1994-01-01

Photosynthetic reaction centers from a variety of organisms have been isolated and characterized. The groups of prokaryotic photosynthetic organisms include the purple bacteria, the filamentous green bacteria, the green sulfur bacteria and the heliobacteria as anoxygenic representatives as well as the cyanobacteria and prochlorophytes as oxygenic representatives. This review focuses on structural and functional comparisons of the various groups of photosynthetic reaction centers and considers possible evolutionary scenarios to explain the diversity of existing photosynthetic organisms.

Dietary Probiotics Affect Gastrointestinal Microbiota, Histological Structure and Shell Mineralization in Turtles

PubMed Central

Rawski, Mateusz; Kierończyk, Bartosz; Długosz, Jakub; Świątkiewicz, Sylwester; Józefiak, Damian

2016-01-01

Probiotics are widely used in nutrition, and their mode of action is intensively studied in mammals and birds; however, it is almost unknown in reptiles. In the present study, Trachemys scripta scripta and Sternotherus odoratus were used to assess the effects of dietary probiotics on chelonian gastrointestinal tract microecology. In the first, 20-week experiment, 40 young T. s. scripta were randomly distributed to four experimental groups: 1st, (CON)–with no additives; 2nd, (SSPA) with Bacillus subtilis PB6; 3rd, (MSP)–with multiple strain probiotic; and 4th, (SSPB) with Bacillus subtilis C-3102. The first study has shown that SSPA and MSP decreased the numbers of total bacteria, Enterobacteriace, Staphylococcus sp. and Streptococcus sp. excreted to water and increased the villous height and mucosa thickness in duodenum. SSPB improved the duodenal microstructure; however, it also increased numbers of kanamycin and vancomycin resistant bacteria, Staphylococcus sp. and Streptococcus sp., in water. In the second, 52-week experiment, 30 S. odoratus were randomly assigned to three dietary treatments. CON, SSPA and MSP groups. The MSP preparation increased the body weight gain, crude ash, Ca and P share in the turtles’ shells. Both probiotics affected duodenal histomorphology. SSPA decreased the villous height, while MSP increased the villous height and mucosa thickness, and decreased the crypt depth. SSPA decreased the concentrations of bacteria excreted to water. In the case of intestinal microbiota, bacteria suppressing effects were observed in the case of both probiotics. MSP increased the number of Bifidobacterium sp. and Lactobacillus sp./Enteroccoccus sp., and decreased the number of Clostridium perfringens and Campylobacter sp. in the small intestine. In the large intestine it lowered, amongst others, Bacteroides–Pervotella cluster, Clostridium leptum subgroup and Clostridium perfringens numbers. The above-mentioned results suggest that probiotics are useful in turtle nutrition due to their positive effects on growth performance, shell mineralization, duodenal histomorphology and microbiota. PMID:26828367

Antibacterial Activity of Blue Light against Nosocomial Wound Pathogens Growing Planktonically and as Mature Biofilms.

PubMed

Halstead, Fenella D; Thwaite, Joanne E; Burt, Rebecca; Laws, Thomas R; Raguse, Marina; Moeller, Ralf; Webber, Mark A; Oppenheim, Beryl A

2016-07-01

The blue wavelengths within the visible light spectrum are intrinisically antimicrobial and can photodynamically inactivate the cells of a wide spectrum of bacteria (Gram positive and negative) and fungi. Furthermore, blue light is equally effective against both drug-sensitive and -resistant members of target species and is less detrimental to mammalian cells than is UV radiation. Blue light is currently used for treating acnes vulgaris and Helicobacter pylori infections; the utility for decontamination and treatment of wound infections is in its infancy. Furthermore, limited studies have been performed on bacterial biofilms, the key growth mode of bacteria involved in clinical infections. Here we report the findings of a multicenter in vitro study performed to assess the antimicrobial activity of 400-nm blue light against bacteria in both planktonic and biofilm growth modes. Blue light was tested against a panel of 34 bacterial isolates (clinical and type strains) comprising Acinetobacter baumannii, Enterobacter cloacae, Stenotrophomonas maltophilia, Pseudomonas aeruginosa, Escherichia coli, Staphylococcus aureus, Enterococcus faecium, Klebsiella pneumoniae, and Elizabethkingia meningoseptica All planktonic-phase bacteria were susceptible to blue light treatment, with the majority (71%) demonstrating a ≥5-log10 decrease in viability after 15 to 30 min of exposure (54 J/cm(2) to 108 J/cm(2)). Bacterial biofilms were also highly susceptible to blue light, with significant reduction in seeding observed for all isolates at all levels of exposure. These results warrant further investigation of blue light as a novel decontamination strategy for the nosocomial environment, as well as additional wider decontamination applications. Blue light shows great promise as a novel decontamination strategy for the nosocomial environment, as well as additional wider decontamination applications (e.g., wound closure during surgery). This warrants further investigation. © Crown copyright 2016.

Antibacterial Activity of Blue Light against Nosocomial Wound Pathogens Growing Planktonically and as Mature Biofilms

PubMed Central

Thwaite, Joanne E.; Burt, Rebecca; Laws, Thomas R.; Raguse, Marina; Moeller, Ralf; Webber, Mark A.; Oppenheim, Beryl A.

2016-01-01

ABSTRACT The blue wavelengths within the visible light spectrum are intrinisically antimicrobial and can photodynamically inactivate the cells of a wide spectrum of bacteria (Gram positive and negative) and fungi. Furthermore, blue light is equally effective against both drug-sensitive and -resistant members of target species and is less detrimental to mammalian cells than is UV radiation. Blue light is currently used for treating acnes vulgaris and Helicobacter pylori infections; the utility for decontamination and treatment of wound infections is in its infancy. Furthermore, limited studies have been performed on bacterial biofilms, the key growth mode of bacteria involved in clinical infections. Here we report the findings of a multicenter in vitro study performed to assess the antimicrobial activity of 400-nm blue light against bacteria in both planktonic and biofilm growth modes. Blue light was tested against a panel of 34 bacterial isolates (clinical and type strains) comprising Acinetobacter baumannii, Enterobacter cloacae, Stenotrophomonas maltophilia, Pseudomonas aeruginosa, Escherichia coli, Staphylococcus aureus, Enterococcus faecium, Klebsiella pneumoniae, and Elizabethkingia meningoseptica. All planktonic-phase bacteria were susceptible to blue light treatment, with the majority (71%) demonstrating a ≥5-log10 decrease in viability after 15 to 30 min of exposure (54 J/cm2 to 108 J/cm2). Bacterial biofilms were also highly susceptible to blue light, with significant reduction in seeding observed for all isolates at all levels of exposure. These results warrant further investigation of blue light as a novel decontamination strategy for the nosocomial environment, as well as additional wider decontamination applications. IMPORTANCE Blue light shows great promise as a novel decontamination strategy for the nosocomial environment, as well as additional wider decontamination applications (e.g., wound closure during surgery). This warrants further investigation. PMID:27129967

Label-free bimodal waveguide immunosensor for rapid diagnosis of bacterial infections in cirrhotic patients.

PubMed

Maldonado, Jesús; González-Guerrero, Ana Belén; Domínguez, Carlos; Lechuga, Laura M

2016-11-15

Spontaneous bacterial peritonitis is an acute bacterial infection of ascitic fluid; it has a high incidence in cirrhotic patients and it is associated with high mortality. In such a situation, early diagnosis and treatment is crucial for the survival of the patient. However, bacterial analysis in ascitic fluid is currently based on culture methods, which are time-consuming and laborious. We report here the application of a photonic interferometer biosensor based on a bimodal waveguide (BiMW) for the rapid and label-free detection of bacteria directly in ascitic fluid. The device consists of a straight waveguide in which two modes of the same polarization interfere while interacting with the external medium through their evanescent fields. A bimolecular event occurring on the sensor area of the device (e.g. capturing bacteria) will differently affect each light mode, inducing a variation in the phase of the light exiting at the output of the waveguide. In this work, we demonstrate the quantitative detection of Bacillus cereus in buffer medium and Escherichia coli in undiluted ascitic fluid from cirrhotic patients. In the case of Bacillus cereus detection, the device was able to specifically detect bacteria at relevant concentrations in 12.5min and in the case of Escherichia coli detection, the analysis time was 25min. Extrapolation of the data demonstrated that the detection limits of the biosensor could reach few bacteria per milliliter. Based on the results obtained, we consider that the BiMW biosensor is positioned as a promising new clinical tool for user-friendly, cost-effective and real-time microbiological analysis. Copyright © 2016 Elsevier B.V. All rights reserved.

[Community structure and diversity of culturable moderate halophilic bacteria isolated from Qrhan salt lake on Qinghai-Tibet Plateau].

PubMed

Shen, Shuo

2017-04-04

I studied the community structure and diversity of culturable moderate halophilic bacteria isolated from Qrhan Salt Lake. I isolated and cultured the moderate halophilic bacteria on different selective media. After the 16S rRNA gene sequences was amplified and measured, I constructed the phylogenic tree, analyzed the community structure and calculated the diversity indexes according to the 16S rRNA gene information. A total of 421 moderate halophilic bacteria were isolated from water and mud samples in Qrhan Salt Lake. The 16S rRNA gene information showed that 4 potential novel species belonged to the family Bacillaceae. Eighty-three model strains belonged to 3 phylurms 6 families 16 genus. Among them, Bacillus sp., Oceanobacillus sp. and Halomonas sp. were dominant species. Diversity analysis showed that the diversity of strains isolated from water sample was higher than that from mud sample, but the dominance degree of strains isolated from mud sample was higher than that from water sample. The genetic diversity of moderate halophilic bacteria isolated from Qrhan Salt Lake was abundant. Also, there were dominant and novel species of culturable moderate halophilic bacteria in this lake.

The inhibitory effect of Thymus vulgaris extracts on the planktonic form and biofilm structures of six human pathogenic bacteria

PubMed Central

Mohsenipour, Zeinab; Hassanshahian, Mehdi

2015-01-01

Objective: Microorganisms are responsible for many problems in industry and medicine because of biofilm formation. Therefore, this study was aimed to examine the effect of Thymus vulgaris (T. vulgaris) extracts on the planktonic form and biofilm structures of six pathogenic bacteria. Materials and methods: Antimicrobial activities of the plant extracts against the planktonic form of the bacteria were determined using the disc diffusion method. MIC and MBC values were evaluated using macrobroth dilution technique. Anti-biofilm effects were assessed by microtiter plate method. Results: According to disc diffusion test (MIC and MBC), the ability of Thymus vulgaris (T. vulgaris ) extracts for inhibition of bacteria in planktonic form was confirmed. In dealing with biofilm structures, the inhibitory effect of the extracts was directly correlated to their concentration. Except for the inhibition of biofilm formation, efficacy of each extract was independent from type of solvent. Conclusion: According to the potential of Thymus vulgaris (T. vulgaris) extracts to inhibit the test bacteria in planktonic and biofilm form, it can be suggested that Thymus vulgaris (T. vulgaris) extracts can be applied as antimicrobial agents against the pathogenic bacteria particularly in biofilm forms. PMID:26442753

Quantification of biofilm structures by the novel computer program COMSTAT.

PubMed

Heydorn, A; Nielsen, A T; Hentzer, M; Sternberg, C; Givskov, M; Ersbøll, B K; Molin, S

2000-10-01

The structural organization of four microbial communities was analysed by a novel computer program, COMSTAT, which comprises ten features for quantifying three-dimensional biofilm image stacks. Monospecies biofilms of each of the four bacteria, Pseudomonas: putida, P. aureofaciens, P. fluorescens and P. aeruginosa, tagged with the green fluorescent protein (GFP) were grown in flow chambers with a defined minimal medium as substrate. Analysis by the COMSTAT program of four variables describing biofilm structure - mean thickness, roughness, substratum coverage and surface to volume ratio - showed that the four Pseudomonas: strains represent different modes of biofilm growth. P. putida had a unique developmental pattern starting with single cells on the substratum growing into micro-colonies, which were eventually succeeded by long filaments and elongated cell clusters. P. aeruginosa colonized the entire substratum, and formed flat, uniform biofilms. P. aureofaciens resembled P. aeruginosa, but had a stronger tendency to form micro-colonies. Finally, the biofilm structures of P. fluorescens had a phenotype intermediate between those of P. putida and P. aureofaciens. Analysis of biofilms of P. aureofaciens growing on 0.03 mM, 0.1 mM or 0.5 mM citrate minimal media showed that mean biofilm thickness increased with increasing citrate concentration. Moreover, biofilm roughness increased with lower citrate concentrations, whereas surface to volume ratio increased with higher citrate concentrations.

The structure of human ADP-ribosylhydrolase 3 (ARH3) provides insights into the reversibility of protein ADP-ribosylation

PubMed Central

Mueller-Dieckmann, Christoph; Kernstock, Stefan; Lisurek, Michael; von Kries, Jens Peter; Haag, Friedrich; Weiss, Manfred S.; Koch-Nolte, Friedrich

2006-01-01

Posttranslational modifications are used by cells from all kingdoms of life to control enzymatic activity and to regulate protein function. For many cellular processes, including DNA repair, spindle function, and apoptosis, reversible mono- and polyADP-ribosylation constitutes a very important regulatory mechanism. Moreover, many pathogenic bacteria secrete toxins which ADP-ribosylate human proteins, causing diseases such as whooping cough, cholera, and diphtheria. Whereas the 3D structures of numerous ADP-ribosylating toxins and related mammalian enzymes have been elucidated, virtually nothing is known about the structure of protein de-ADP-ribosylating enzymes. Here, we report the 3Dstructure of human ADP-ribosylhydrolase 3 (hARH3). The molecular architecture of hARH3 constitutes the archetype of an all-α-helical protein fold and provides insights into the reversibility of protein ADP-ribosylation. Two magnesium ions flanked by highly conserved amino acids pinpoint the active-site crevice. Recombinant hARH3 binds free ADP-ribose with micromolar affinity and efficiently de-ADP-ribosylates poly- but not monoADP-ribosylated proteins. Docking experiments indicate a possible binding mode for ADP-ribose polymers and suggest a reaction mechanism. Our results underscore the importance of endogenous ADP-ribosylation cycles and provide a basis for structure-based design of ADP-ribosylhydrolase inhibitors. PMID:17015823

Raman spectroscopy, electronic microscopy and SPME-GC-MS to elucidate the mode of action of a new antimicrobial food packaging material.

PubMed

Clemente, Isabel; Aznar, Margarita; Salafranca, Jesús; Nerín, Cristina

2017-02-01

One critical challenge when developing a new antimicrobial packaging material is to demonstrate the mode of action of the antimicrobials incorporated into the packaging. For this task, several analytical techniques as well as microbiology are required. In this work, the antimicrobial properties of benzyl isothiocyanate, allyl isothiocyanate and essential oils of cinnamon and oregano against several moulds and bacteria have been evaluated. Benzyl isothiocyanate showed the highest antimicrobial activity and it was selected for developing the new active packaging material. Scanning electron microscopy and Raman spectroscopy were successfully used to demonstrate the mode of action of benzyl isothiocyanate on Escherichia coli. Bacteria exhibited external modifications such as oval shape and the presence of septum surface, but they did not show any disruption or membrane damage. To provide data on the in vitro action of benzyl isothiocyanate and the presence of inhibition halos, the transfer mechanism to the cells was assessed using solid-phase microextraction-gas chromatography-mass spectrometry. Based on the transfer system, action mechanism and its stronger antimicrobial activity, benzyl isothiocyanate was incorporated to two kinds of antimicrobial labels. The labels were stable and active for 140 days against two mould producers of ochratoxin A; Penicillium verrucosum is more sensitive than Aspergillus ochraceus. Details about the analytical techniques and the results obtained are shown and discussed. Graphical Abstract Antimicrobial evaluation of pure compounds, incorporation in the packaging and study for mode of action on S. coli by Raman, SEM and SPME-GC-MS.

Impact of delivery mode on the colostrum microbiota composition.

PubMed

Toscano, Marco; De Grandi, Roberta; Peroni, Diego Giampietro; Grossi, Enzo; Facchin, Valentina; Comberiati, Pasquale; Drago, Lorenzo

2017-09-25

Breast milk is a rich nutrient with a temporally dynamic nature. In particular, numerous alterations in the nutritional, immunological and microbiological content occur during the transition from colostrum to mature milk. The objective of our study was to evaluate the potential impact of delivery mode on the microbiota of colostrum, at both the quantitative and qualitative levels (bacterial abundance and microbiota network). Twenty-nine Italian mothers (15 vaginal deliveries vs 14 Cesarean sections) were enrolled in the study. The microbiota of colostrum samples was analyzed by next generation sequencing (Ion Torrent Personal Genome Machine). The colostrum microbiota network associated with Cesarean section and vaginal delivery was evaluated by means of the Auto Contractive Map (AutoCM), a mathematical methodology based on Artificial Neural Network (ANN) architecture. Numerous differences between Cesarean section and vaginal delivery colostrum were observed. Vaginal delivery colostrum had a significant lower abundance of Pseudomonas spp., Staphylococcus spp. and Prevotella spp. when compared to Cesarean section colostrum samples. Furthermore, the mode of delivery had a strong influence on the microbiota network, as Cesarean section colostrum showed a higher number of bacterial hubs if compared to vaginal delivery, sharing only 5 hubs. Interestingly, the colostrum of mothers who had a Cesarean section was richer in environmental bacteria than mothers who underwent vaginal delivery. Finally, both Cesarean section and vaginal delivery colostrum contained a greater number of anaerobic bacteria genera. The mode of delivery had a large impact on the microbiota composition of colostrum. Further studies are needed to better define the meaning of the differences we observed between Cesarean section and vaginal delivery colostrum microbiota.

Bacterial associations with decaying wood : a review

Treesearch

C. A. Clausen

1996-01-01

Wood-inhabiting bacteria are associated with wood decay and may have an indirect influence on the decay process. Bacteria are able to affect wood permeability, attack wood structure, or work synergistically with other bacteria and soft-rot fungi to predispose wood to fungal attack. Bacteria that can inhabit chemically treated wood are recognized. The natural ability of...

Structural, electronic structure and antibacterial properties of graphene-oxide nano-sheets

NASA Astrophysics Data System (ADS)

Sharma, Aditya; Varshney, Mayora; Nanda, Sitansu Sekhar; Shin, Hyun Joon; Kim, Namdong; Yi, Dong Kee; Chae, Keun-Hwa; Ok Won, Sung

2018-04-01

Correlation between the structural/electronic structure properties and bio-activity of graphene-based materials need to be thoroughly evaluated before their commercial implementation in the health and environment precincts. To better investigate the local hybridization of sp2/sp3 orbitals of the functional groups of graphene-oxide (GO) and their execution in the antimicrobial mechanism, we exemplify the antibacterial activity of GO sheets towards the Escherichia coli bacteria (E. coli) by applying the field-emission scanning electron microscopy (FESEM), near edge X-ray absorption fine structure (NEXAFS) and scanning transmission X-ray microscope (STXM) techniques. C K-edge and O K-edge NEXAFS spectra have revealed lesser sp2 carbon atoms in the aromatic ring and attachment of functional oxygen groups at GO sheets. Entrapment of E. coli bacteria by GO sheets is evidenced by FESEM investigations and has also been corroborated by nano-scale imaging of bacteria using the STXM. Spectroscopy evidence of functional oxygen moieties with GO sheets and physiochemical entrapment of E. coli bacteria have assisted us to elaborate the mechanism of cellular oxidative stress-induced disruption of bacterial membrane.

Influence of human milk oligosaccharides on adherence of bifidobacteria and clostridia to cell lines.

PubMed

Musilova, Sarka; Modrackova, Nikol; Doskocil, Ivo; Svejstil, Roman; Rada, Vojtech

2017-12-01

Adhesion of gut bacteria to the intestinal epithelium is the first step in their colonization of the neonatal immature gut. Bacterial colonization of the infant gut is influenced by several factors, of which the most important are the mode of delivery and breast-feeding. Breast-fed infants ingest several grams of human milk oligosaccharides (HMOs) per day, which can become receptor decoys for intestinal bacteria. The most abundant intestinal bacteria in vaginally delivered infants are bifidobacteria, whereas infants born by cesarean section are colonized by clostridia. The influence of HMOs on the adhesion of five strains of intestinal bacteria (three bifidobacterial strains and two clostridial strains) to mucus-secreting and non-mucus-secreting human epithelial cells was investigated. Bifidobacterium bifidum 1 and Bifidobacterium longum displayed almost the same level of adhesion in the presence and absence of HMOs. By contrast, adhesion of Clostridium butyricum 1 and 2 decreased from 14.41% to 6.72% and from 41.54% to 30.91%, respectively, in the presence of HMOs. The results of this study indicate that HMOs affect bacterial adhesion and are an important factor influencing bacterial colonization of the gut. Adhesion of the tested bacteria correlates with their ability to autoaggregate.

Bacterialike (filamentous) structures associated with pyritized burrow linings, Arnheim Formation (Upper Ordovician), southeastern Indiana

DOE Office of Scientific and Technical Information (OSTI.GOV)

Blackwell, W.H.; Martin, A.J.

Much naturally occurring pyritization is biologically mediated, with specific types of bacteria (sulfate reducers) promoting the reactions. Among the criteria required for pyritization in a marine environment are the presence of: (1) interstitial iron ions, (2) a primarily anaerobic (reducing) environment; (3) an organic-rich substrate, and (4) sulfate-reducing bacteria (releasing sulfide). However, the direct connection between pyritization and bacteria (microfloral remains) is difficult to visualize in the fossil record. This study focuses specifically on pyritized burrow linings that occur in strongly bioturbated wackestones from the Arnheim Formation (Cincinnatian Series, Upper Ordovician). Specific reducing microenvironments (i.e. mucoidal burrow linings) were themore » sites of early diagenetic pyritization in otherwise oxygenated, organic-rich sediments. Material examined under both the light and electron microscopes revealed occasional evidence of pyrite associated with filamentous structures. These structures possess a shape and size consistent with certain types of bacteria. This relationship, bacterialike structures with pyrite, may be more common in the fossil record than previously suspected.« less

Diverse structural approaches to haem appropriation by pathogenic bacteria.

PubMed

Hare, Stephen A

2017-04-01

The critical need for iron presents a challenge for pathogenic bacteria that must survive in an environment bereft of accessible iron due to a natural low bioavailability and their host's nutritional immunity. Appropriating haem, either direct from host haemoproteins or by secreting haem-scavenging haemophores, is one way pathogenic bacteria can overcome this challenge. After capturing their target, haem appropriation systems must remove haem from a high-affinity binding site (on the host haemoprotein or bacterial haemophore) and transfer it to a binding site of lower affinity on a bacterial receptor. Structural information is now available to show how, using a combination of induced structural changes and steric clashes, bacteria are able to extract haem from haemophores, haemopexin and haemoglobin. This review focuses on structural descriptions of these bacterial haem acquisition systems, summarising how they bind haem and their target haemoproteins with particularly emphasis on the mechanism of haem extraction. Copyright © 2017 The Author. Published by Elsevier B.V. All rights reserved.

Bacteriocins from Lactobacillus plantarum - production, genetic organization and mode of action: produção, organização genética e modo de ação.

PubMed

Todorov, Svetoslav D

2009-04-01

Bacteriocins are biologically active proteins or protein complexes that display a bactericidal mode of action towards usually closely related species. Numerous strains of bacteriocin producing Lactobacillus plantarum have been isolated in the last two decades from different ecological niches including meat, fish, fruits, vegetables, and milk and cereal products. Several of these plantaricins have been characterized and the aminoacid sequence determined. Different aspects of the mode of action, fermentation optimization and genetic organization of the bacteriocin operon have been studied. However, numerous of bacteriocins produced by different Lactobacillus plantarum strains have not been fully characterized. In this article, a brief overview of the classification, genetics, characterization, including mode of action and production optimization for bacteriocins from Lactic Acid Bacteria in general, and where appropriate, with focus on bacteriocins produced by Lactobacillus plantarum, is presented.

IspE Inhibitors Identified by a Combination of In Silico and In Vitro High-Throughput Screening

PubMed Central

Tidten-Luksch, Naomi; Grimaldi, Raffaella; Torrie, Leah S.; Frearson, Julie A.; Hunter, William N.; Brenk, Ruth

2012-01-01

CDP-ME kinase (IspE) contributes to the non-mevalonate or deoxy-xylulose phosphate (DOXP) pathway for isoprenoid precursor biosynthesis found in many species of bacteria and apicomplexan parasites. IspE has been shown to be essential by genetic methods and since it is absent from humans it constitutes a promising target for antimicrobial drug development. Using in silico screening directed against the substrate binding site and in vitro high-throughput screening directed against both, the substrate and co-factor binding sites, non-substrate-like IspE inhibitors have been discovered and structure-activity relationships were derived. The best inhibitors in each series have high ligand efficiencies and favourable physico-chemical properties rendering them promising starting points for drug discovery. Putative binding modes of the ligands were suggested which are consistent with established structure-activity relationships. The applied screening methods were complementary in discovering hit compounds, and a comparison of both approaches highlights their strengths and weaknesses. It is noteworthy that compounds identified by virtual screening methods provided the controls for the biochemical screens. PMID:22563402

Generalization of soft phonon modes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rudin, Sven P.

Soft phonon modes describe a collective movement of atoms that transform a higher-symmetry crystal structure into a lower-symmetry crystal structure. Such structural transformations occur at finite temperatures, where the phonons (i.e., the low-temperature vibrational modes) and the static perfect crystal structures provide an incomplete picture of the dynamics. In this paper, principal vibrational modes (PVMs) are introduced as descriptors of the dynamics of a material system withmore » $N$ atoms. The PVMs represent the independent collective movements of the atoms at a given temperature. Molecular dynamics (MD) simulations, here in the form of quantum MD using density functional theory calculations, provide both the data describing the atomic motion and the data used to construct the PVMs. The leading mode, $${\\mathrm{PVM}}_{0}$$, represents the $3N$-dimensional direction in which the system moves with greatest amplitude. For structural phase transitions, $${\\mathrm{PVM}}_{0}$$ serves as a generalization of soft phonon modes. At low temperatures, $${\\mathrm{PVM}}_{0}$$ reproduces the soft phonon mode in systems where one phonon dominates the phase transformation. In general, multiple phonon modes combine to describe a transformation, in which case $${\\mathrm{PVM}}_{0}$$ culls these phonon modes. Moreover, while soft phonon modes arise in the higher-symmetry crystal structure, $${\\mathrm{PVM}}_{0}$$ can be equally well calculated on either side of the structural phase transition. Finally, two applications demonstrate these properties: first, transitions into and out of bcc titanium, and, second, the two crystal structures proposed for the $${\\beta}$$ phase of uranium, the higher-symmetry structure of which stabilizes with temperature.« less

Generalization of soft phonon modes

DOE PAGES

Rudin, Sven P.

2018-04-27

Soft phonon modes describe a collective movement of atoms that transform a higher-symmetry crystal structure into a lower-symmetry crystal structure. Such structural transformations occur at finite temperatures, where the phonons (i.e., the low-temperature vibrational modes) and the static perfect crystal structures provide an incomplete picture of the dynamics. In this paper, principal vibrational modes (PVMs) are introduced as descriptors of the dynamics of a material system withmore » $N$ atoms. The PVMs represent the independent collective movements of the atoms at a given temperature. Molecular dynamics (MD) simulations, here in the form of quantum MD using density functional theory calculations, provide both the data describing the atomic motion and the data used to construct the PVMs. The leading mode, $${\\mathrm{PVM}}_{0}$$, represents the $3N$-dimensional direction in which the system moves with greatest amplitude. For structural phase transitions, $${\\mathrm{PVM}}_{0}$$ serves as a generalization of soft phonon modes. At low temperatures, $${\\mathrm{PVM}}_{0}$$ reproduces the soft phonon mode in systems where one phonon dominates the phase transformation. In general, multiple phonon modes combine to describe a transformation, in which case $${\\mathrm{PVM}}_{0}$$ culls these phonon modes. Moreover, while soft phonon modes arise in the higher-symmetry crystal structure, $${\\mathrm{PVM}}_{0}$$ can be equally well calculated on either side of the structural phase transition. Finally, two applications demonstrate these properties: first, transitions into and out of bcc titanium, and, second, the two crystal structures proposed for the $${\\beta}$$ phase of uranium, the higher-symmetry structure of which stabilizes with temperature.« less

Influence of modes of metal transfer on grain structure and direction of grain growth in low nickel austenitic stainless steel weld metals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mukherjee, Manidipto; Saha, Saptarshi; Pal, Tapan Kumar, E-mail: tkpal.ju@gmail.com

2015-04-15

The present study elaborately discussed the effect of different modes of metal transfer (i.e., short circuit mode, spray mode and pulse mode) on grain structure and direction of grain growth in low nickel austenitic stainless steel weld metals. Electron backscattered diffraction (EBSD) analysis was used to study the grain growth direction and grain structure in weld metals. The changes in grain structure and grain growth direction were found to be essentially varied with the weld pool shape and acting forces induced by modes of metal transfer at a constant welding speed. Short circuit mode of metal transfer owing to highermore » Marangoni force (M{sub a}) and low electromagnetic force (R{sub m}) promotes the lower weld pool volume (Γ) and higher weld pool maximum radius (r{sub m}). Short circuit mode also shows curved and tapered columnar grain structures and the grain growth preferentially occurred in <001> direction. In contrast, spray mode of metal transfer increases the Γ and reduces the r{sub m} values due to very high R{sub m} and typically reveals straight and broad columnar grain structures with preferential growth direction in <111>. In the pulse mode of metal transfer relatively high M{sub a} and R{sub m} simultaneously increase the weld pool width and the primary penetration which might encourage relatively complex grain growth directions in the weld pool and cause a shift of major intensity from <001> to <111> direction. It can also be concluded that the fusion zone grain structure and direction of grain growth are solely dependent on modes of metal transfer and remain constant for a particular mode of metal transfer irrespective of filler wire used. - Highlights: • Welded joints of LNiASS were prepared by varying modes of metal transfer. • Weld pool shape, grain structure and grain growth direction were studied. • Short circuit mode shows curved and tapered grain growth in <001> direction. • Spray mode shows straight and broad columnar grain growth in <111> direction. • Pulse mode shows complex grain growth with a shift in growth direction.« less

Measurement of fluid dynamic loading on staphylococci bacteria bio-film structures using μPIV

NASA Astrophysics Data System (ADS)

Sherman, Erica; Moormeier, Derek; Bayles, Kenneth; Davidson, John; Ryu, Sangjin; Wei, Timothy

2013-11-01

Staphylococci bacteria are recognized as the most frequent cause of biofilm-associated infections. Although humans are regularly exposed to these bacteria without consequence, a localized infection can enter the bloodstream and lead to serious infections such as endocarditis, pneumonia, or toxic shock syndrome. The mechanics of staphylococci biofilm formation and dispersion through the bloodstream are not well known. It has recently been observed that under certain flow conditions, bacteria organize in tower-like structures which break and are transported downstream by the flow. The fundamental questions of interest are i) whether or not fluid mechanics plays a role in differentiating between film or tower formation and ii) whether or not the faulty towers are a bio-film propagation mechanism. This talk focuses on the application of μPIV to study this problem. Staphylococcus aureus bacteria were cultured in the Bioflux Fluxion square microchannel of a 65 by 65 um cross section, and subjected to a steady shear rate of 0.5 dynes. μPIV measurements were made to map the flow over and around a biofilm tower structure which occluded approximately 66% of the channel width. Data were recorded around the structure at a series of two dimensional planes, which when stacked vertically show a two dimensional flow field as a function of tower height. Measurements and control volume analysis will be presented quantifying forces acting on these structures.

Production of Value-added Products by Lactic Acid Bacteria

USDA-ARS?s Scientific Manuscript database

Lactic acid bacteria (LAB) are a group of facultative anaerobic, catalase negative, nonmotile and nonsporeforming–Gram positive bacteria. Most LAB utilize high energy C sources including monomer sugars to produce energy to maintain cellular structure and function. This anaerobic fermentation proce...

Biotechnological potential for degradation of isoprene: a review.

PubMed

Srivastva, Navnita; Singh, Abhishek; Bhardwaj, Yashpal; Dubey, Suresh Kumar

2018-06-01

Isoprene, the ubiquitous, highly emitted non-methane volatile hydrocarbon, affects atmospheric chemistry and human health, and this makes its removal from the contaminated environment imperative. Physicochemical degradation of isoprene is inefficient and generates secondary pollutants. Therefore, biodegradation can be considered as the safer approach for its efficient abatement. This review summarizes efforts in this regard that led to tracking the diverse groups of isoprene degrading bacteria such as Methanotrophs, Xanthobacter, Nocardia, Alcaligenes, Rhodococcus, Actinobacteria, Alphaproteobacteria, Bacteriodetes, Pseudomonas, and Alcanivorax. Biodegradation of isoprene by such bacteria in batch and continuous modes has been elaborated. The products, pathways and the key enzymes associated with isoprene biodegradation have also been presented.

Learning from Bacteriophages - Advantages and Limitations of Phage and Phage-Encoded Protein Applications

PubMed Central

Drulis-Kawa, Zuzanna; Majkowska-Skrobek, Grażyna; Maciejewska, Barbara; Delattre, Anne-Sophie; Lavigne, Rob

2012-01-01

The emergence of bacteria resistance to most of the currently available antibiotics has become a critical therapeutic problem. The bacteria causing both hospital and community-acquired infections are most often multidrug resistant. In view of the alarming level of antibiotic resistance between bacterial species and difficulties with treatment, alternative or supportive antibacterial cure has to be developed. The presented review focuses on the major characteristics of bacteriophages and phage-encoded proteins affecting their usefulness as antimicrobial agents. We discuss several issues such as mode of action, pharmacodynamics, pharmacokinetics, resistance and manufacturing aspects of bacteriophages and phage-encoded proteins application. PMID:23305359

Phage-bacteria infection networks: From nestedness to modularity

NASA Astrophysics Data System (ADS)

Flores, Cesar O.; Valverde, Sergi; Weitz, Joshua S.

2013-03-01

Bacteriophages (viruses that infect bacteria) are the most abundant biological life-forms on Earth. However, very little is known regarding the structure of phage-bacteria infections. In a recent study we re-evaluated 38 prior studies and demonstrated that phage-bacteria infection networks tend to be statistically nested in small scale communities (Flores et al 2011). Nestedness is consistent with a hierarchy of infection and resistance within phages and bacteria, respectively. However, we predicted that at large scales, phage-bacteria infection networks should be typified by a modular structure. We evaluate and confirm this hypothesis using the most extensive study of phage-bacteria infections (Moebus and Nattkemper 1981). In this study, cross-infections were evaluated between 215 marine phages and 286 marine bacteria. We develop a novel multi-scale network analysis and find that the Moebus and Nattkemper (1981) study, is highly modular (at the whole network scale), yet also exhibits nestedness and modularity at the within-module scale. We examine the role of geography in driving these modular patterns and find evidence that phage-bacteria interactions can exhibit strong similarity despite large distances between sites. CFG acknowledges the support of CONACyT Foundation. JSW holds a Career Award at the Scientific Interface from the Burroughs Wellcome Fund and acknowledges the support of the James S. McDonnell Foundation

Monitoring biodegradation of diesel fuel in bioventing processes using in situ respiration rate.

PubMed

Lee, T H; Byun, I G; Kim, Y O; Hwang, I S; Park, T J

2006-01-01

An in situ measuring system of respiration rate was applied for monitoring biodegradation of diesel fuel in a bioventing process for bioremediation of diesel contaminated soil. Two laboratory-scale soil columns were packed with 5 kg of soil that was artificially contaminated by diesel fuel as final TPH (total petroleum hydrocarbon) concentration of 8,000 mg/kg soil. Nutrient was added to make a relative concentration of C:N:P = 100:10:1. One soil column was operated with continuous venting mode, and the other one with intermittent (6 h venting/6 h rest) venting mode. On-line O2 and CO2 gas measuring system was applied to measure O2 utilisation and CO2 production during biodegradation of diesel for 5 months. Biodegradation rate of TPH was calculated from respiration rate measured by the on-line gas measuring system. There were no apparent differences between calculated biodegradation rates from two columns with different venting modes. The variation of biodegradation rates corresponded well with trend of the remaining TPH concentrations comparing other biodegradation indicators, such as C17/pristane and C18/phytane ratio, dehydrogenase activity, and the ratio of hydrocarbon utilising bacteria to total heterotrophic bacteria. These results suggested that the on-line measuring system of respiration rate would be applied to monitoring biodegradation rate and to determine the potential applicability of bioventing process for bioremediation of oil contaminated soil.

Identification of Microbial Communities in Open and Closed Circuit Bioelectrochemical MBRs by High-Throughput 454 Pyrosequencing

PubMed Central

Huang, Jian; Wang, Zhiwei; Zhu, Chaowei; Ma, Jinxing; Zhang, Xingran; Wu, Zhichao

2014-01-01

Two bioelectrochemical membrane bioreactors (MBRs) developed by integrating microbial fuel cell and MBR technology were operated under closed-circuit and open-circuit modes, and high-throughput 454 pyrosequencing was used to investigate the effects of the power generation on the microbial community of bio-anode and bio-cathode. Microbes on the anode under open-circuit operation (AO) were enriched and highly diverse when compared to those on the anode under closed-circuit operation (AC). However, among the cathodes the closed-circuit mode (CC) had richer and more diverse microbial community compared to the cathode under open-circuit mode (CO). On the anodes AO and AC, Proteobacteria and Bacteroidetes were the dominant phyla, while Firmicutes was enriched only on AC. Deltaproteobacteria affiliated to Proteobacteria were also more abundant on AC than AO. Furthermore, the relative abundance of Desulfuromonas, which are well-known electrogenic bacteria, were much higher on AC (10.2%) when compared to AO (0.11%), indicating that closed-circuit operation was more conducive for the growth of electrogenic bacteria on the anodes. On the cathodes, Protebacteria was robust on CC while Bacteroidetes was more abundant on CO. Rhodobacter and Hydrogenophaga were also enriched on CC than CO, suggesting that these genera play a role in electron transfer from the cathode surface to the terminal electron acceptors in the bioelectrochemical MBR under closed-circuit operation. PMID:24705450

Electron microscopic examination of uncultured soil-dwelling bacteria.

PubMed

Amako, Kazunobu; Takade, Akemi; Taniai, Hiroaki; Yoshida, Shin-ichi

2008-05-01

Bacteria living in soil collected from a rice paddy in Fukuoka, Japan, were examined by electron microscopy using a freeze-substitution fixation method. Most of the observed bacteria could be categorized, based on the structure of the cell envelope and overall morphology, into one of five groups: (i) bacterial spore; (ii) Gram-positive type; (iii) Gram-negative type; (iv) Mycobacterium like; and (v) Archaea like. However, a few of the bacteria could not be readily categorized into one of these groups because they had unique cell wall structures, basically resembling those of Gram-negative bacteria, but with the layer corresponding to the peptidoglycan layer in Gram-negative bacteria being extremely thick, like that of the cortex of a bacterial spore. The characteristic morphological features found in many of these uncultured, soil-dwelling cells were the nucleoid being in a condensed state and the cytoplasm being shrunken. We were able to produce similar morphologies in vitro using a Salmonella sp. by culturing under low-temperature, low-nutrient conditions, similar to those found in some natural environments. These unusual morphologies are therefore hypothesized to be characteristic of bacteria in resting or dormant stages.

Bacteria can mobilize nematode-trapping fungi to kill nematodes

PubMed Central

Wang, Xin; Li, Guo-Hong; Zou, Cheng-Gang; Ji, Xing-Lai; Liu, Tong; Zhao, Pei-Ji; Liang, Lian-Ming; Xu, Jian-Ping; An, Zhi-Qiang; Zheng, Xi; Qin, Yue-Ke; Tian, Meng-Qing; Xu, You-Yao; Ma, Yi-Cheng; Yu, Ze-Fen; Huang, Xiao-Wei; Liu, Shu-Qun; Niu, Xue-Mei; Yang, Jin-Kui; Huang, Ying; Zhang, Ke-Qin

2014-01-01

In their natural habitat, bacteria are consumed by bacterivorous nematodes; however, they are not simply passive preys. Here we report a defensive mechanism used by certain bacteria to mobilize nematode-trapping fungi to kill nematodes. These bacteria release urea, which triggers a lifestyle switch in the fungus Arthrobotrys oligospora from saprophytic to nematode–predatory form; this predacious form is characterized by formation of specialized cellular structures or ‘traps’. The bacteria significantly promote the elimination of nematodes by A. oligospora. Disruption of genes involved in urea transport and metabolism in A. oligospora abolishes the urea-induced trap formation. Furthermore, the urea metabolite ammonia functions as a signal molecule in the fungus to initiate the lifestyle switch to form trap structures. Our findings highlight the importance of multiple predator–prey interactions in prey defense mechanisms. PMID:25514608

Use of the gram stain in microbiology.

PubMed

Beveridge, T J

2001-05-01

The Gram stain differentiates bacteria into two fundamental varieties of cells. Bacteria that retain the initial crystal violet stain (purple) are said to be "gram-positive," whereas those that are decolorized and stain red with carbol fuchsin (or safranin) are said to be "gram-negative." This staining response is based on the chemical and structural makeup of the cell walls of both varieties of bacteria. Gram-positives have a thick, relatively impermeable wall that resists decolorization and is composed of peptidoglycan and secondary polymers. Gram-negatives have a thin peptidoglycan layer plus an overlying lipid-protein bilayer known as the outer membrane, which can be disrupted by decolorization. Some bacteria have walls of intermediate structure and, although they are officially classified as gram-positives because of their linage, they stain in a variable manner. One prokaryote domain, the Archaea, have such variability of wall structure that the Gram stain is not a useful differentiating tool.

Changes in the structure of bacterial complexes of vegetable crops in the course of their growth on a cultivated soddy-podzolic soil

NASA Astrophysics Data System (ADS)

Dobrovol'skaya, T. G.; Khusnetdinova, K. A.

2017-11-01

The dynamics of population density and taxonomic structure of epiphytic bacterial communities on the leaves and roots of potatoes, carrots, and beets have been studied. Significant changes take place in the ontogenesis of these vegetables with substitution of hydrolytic bacteria for eccrisotrophic bacteria feeding on products of plant exosmosis. The frequency of domination of representatives of different taxa of epiphytic bacteria on the studied plants has been determined for the entire period of their growth. Bacteria of different genera have been isolated from the aboveground and underground organs of vegetables; their functions are discussed. It is shown that the taxonomic structure of bacterial communities in the soil under studied plants is not subjected to considerable changes and is characterized by the domination of typical soil bacteria— Arthrobacter and bacilli—with the appearance of Rhodococcus as a codominant at the end of the season (before harvesting).

Mechanism of endonuclease cleavage by the HigB toxin

PubMed Central

Schureck, Marc A.; Repack, Adrienne; Miles, Stacey J.; Marquez, Jhomar; Dunham, Christine M.

2016-01-01

Bacteria encode multiple type II toxin–antitoxin modules that cleave ribosome-bound mRNAs in response to stress. All ribosome-dependent toxin family members structurally characterized to date adopt similar microbial RNase architectures despite possessing low sequence identities. Therefore, determining which residues are catalytically important in this specialized RNase family has been a challenge in the field. Structural studies of RelE and YoeB toxins bound to the ribosome provided significant insights but biochemical experiments with RelE were required to clearly demonstrate which residues are critical for acid-base catalysis of mRNA cleavage. Here, we solved an X-ray crystal structure of the wild-type, ribosome-dependent toxin HigB bound to the ribosome revealing potential catalytic residues proximal to the mRNA substrate. Using cell-based and biochemical assays, we further determined that HigB residues His54, Asp90, Tyr91 and His92 are critical for activity in vivo, while HigB H54A and Y91A variants have the largest effect on mRNA cleavage in vitro. Comparison of X-ray crystal structures of two catalytically inactive HigB variants with 70S-HigB bound structures reveal that HigB active site residues undergo conformational rearrangements likely required for recognition of its mRNA substrate. These data support the emerging concept that ribosome-dependent toxins have diverse modes of mRNA recognition. PMID:27378776

Structural characterization of new Schiff bases of sulfamethoxazole and sulfathiazole, their antibacterial activity and docking computation with DHPS protein structure.

PubMed

Mondal, Sudipa; Mandal, Santi M; Mondal, Tapan Kumar; Sinha, Chittaranjan

2015-01-01

New Schiff bases (1, 2) of substituted salicylaldehydes and sulfamethoxazole (SMX)/sulfathiazole (STZ) are synthesized and characterized by elemental analysis and spectroscopic data. Single crystal X-ray structure of one of the compounds (E)-4-((3,5-dichloro-2-hydroxybenzylidene)amino)-N-(5-methylisoxazol-3-yl)benzenesulfonamide (1c) has been determined. Antimicrobial activities of the Schiff bases and parent sulfonamides (SMX, STZ) have been examined against several Gram-positive and Gram-negative bacteria and sulfonamide resistant pathogens; the lowest MIC is observed for (E)-4-((3,5-dichloro-2-hydroxybenzylidene)amino)-N-(thiazol-2-yl)benzene sulfonamide (2c) (8.0 μg mL(-1)) and (E)-4-((3,5-dichloro-2-hydroxybenzylidene)amino)-N-(5-methylisoxazol-3-yl)benzene sulfonamide (1c) (16.0 μg mL(-1)) against sulfonamide resistant pathogens. DFT optimized structures of the Schiff bases have been used to carry out molecular docking studies with DHPS (dihydropteroate synthase) protein structure (downloaded from Protein Data Bank) using Discovery Studio 3.5 to find the most preferred binding mode of the ligand inside the protein cavity. The theoretical data have been well correlated with the experimental results. Cell viability assay and ADMET studies predict that 1c and 2c have good drug like characters. Copyright © 2015 Elsevier B.V. All rights reserved.

Cuticular bacteria appear detrimental to social spiders in mixed but not monoculture exposure

PubMed Central

Keiser, Carl N.; Shearer, Taylor A.; DeMarco, Alexander E.; Brittingham, Hayley A.; Knutson, Karen A.; Kuo, Candice; Zhao, Katherine; Pruitt, Jonathan N.

2016-01-01

Abstract Much of an animal’s health status, life history, and behavior are dictated by interactions with its endogenous and exogenous bacterial communities. Unfortunately, interactions between hosts and members of their resident bacterial community are often ignored in animal behavior and behavioral ecology. Here, we aim to identify the nature of host–microbe interactions in a nonmodel organism, the African social spider Stegodyphus dumicola. We collected and identified bacteria from the cuticles of spiders in situ and then exposed spiders to bacterial monocultures cultures via topical application or injection. We also topically inoculated spiders with a concomitant “cocktail” of bacteria and measured the behavior of spiders daily for 24 days after inoculation. Lastly, we collected and identified bacteria from the cuticles of prey items in the capture webs of spiders, and then fed spiders domestic crickets which had been injected with these bacteria. We also injected 1 species of prey-borne bacteria into the hemolymph of spiders. Only Bacillus thuringiensis caused increased mortality when injected into the hemolymph of spiders, whereas no bacterial monocultures caused increased mortality when applied topically, relative to control solutions. However, a bacterial cocktail of cuticular bacteria caused weight loss and mortality when applied topically, yet did not detectibly alter spider behavior. Consuming prey injected with prey-borne bacteria was associated with an elongated lifespan in spiders. Thus, indirect evidence from multiple experiments suggests that the effects of these bacteria on spider survivorship appear contingent on their mode of colonization and whether they are applied in monoculture or within a mixed cocktail. We urge that follow-up studies should test these host–microbe interactions across different social contexts to determine the role that microbes play in colony performance. PMID:29491926

Switch from intracellular to intercellular invasion during water stress-tolerant legume nodulation

PubMed Central

Goormachtig, Sofie; Capoen, Ward; James, Euan K.; Holsters, Marcelle

2004-01-01

Rhizobia colonize their legume hosts by different modes of entry while initiating symbiotic nitrogen fixation. Most legumes are invaded via growing root hairs by the root hair-curl mechanism, which involves epidermal cell responses. However, invasion of a number of tropical legumes happens through fissures at lateral root bases by cortical, intercellular crack entry. In the semiaquatic Sesbania rostrata, the bacteria entered via root hair curls under nonflooding conditions. Upon flooding, root hair growth was prevented, invasion on accessible root hairs was inhibited, and intercellular invasion was recruited. The plant hormone ethylene was involved in these processes. The occurrence of both invasion pathways on the same host plant enabled a comparison to be made of the structural requirements for the perception of nodulation factors, which were more stringent for the epidermal root hair invasion than for the cortical intercellular invasion at lateral root bases. PMID:15079070

Biofilm growth program and architecture revealed by single-cell live imaging

NASA Astrophysics Data System (ADS)

Yan, Jing; Sabass, Benedikt; Stone, Howard; Wingreen, Ned; Bassler, Bonnie

Biofilms are surface-associated bacterial communities. Little is known about biofilm structure at the level of individual cells. We image living, growing Vibrio cholerae biofilms from founder cells to ten thousand cells at single-cell resolution, and discover the forces underpinning the architectural evolution of the biofilm. Mutagenesis, matrix labeling, and simulations demonstrate that surface-adhesion-mediated compression causes V. cholerae biofilms to transition from a two-dimensional branched morphology to a dense, ordered three-dimensional cluster. We discover that directional proliferation of rod-shaped bacteria plays a dominant role in shaping the biofilm architecture, and this growth pattern is controlled by a single gene. Competition analyses reveal the advantages of the dense growth mode in providing the biofilm with superior mechanical properties. We will further present continuum theory to model the three-dimensional growth of biofilms at the solid-liquid interface as well as solid-air interface.

Ligand-Induced Asymmetry in Histidine Sensor Kinase Complex Regulates Quorum Sensing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Neiditch,M.; Federle, M.; Pompeani, A.

2006-01-01

Bacteria sense their environment using receptors of the histidine sensor kinase family, but how kinase activity is regulated by ligand binding is not well understood. Autoinducer-2 (AI-2), a secreted signaling molecule originally identified in studies of the marine bacterium Vibrio harveyi, regulates quorum-sensing responses and allows communication between different bacterial species. AI-2 signal transduction in V. harveyi requires the integral membrane receptor LuxPQ, comprised of periplasmic binding protein (LuxP) and histidine sensor kinase (LuxQ) subunits. Combined X-ray crystallographic and functional studies show that AI-2 binding causes a major conformational change within LuxP, which in turn stabilizes a quaternary arrangement inmore » which two LuxPQ monomers are asymmetrically associated. We propose that formation of this asymmetric quaternary structure is responsible for repressing the kinase activity of both LuxQ subunits and triggering the transition of V. harveyi into quorum-sensing mode.« less

Inhibition of fructan-fermenting equine fecal bacteria and Streptococcus bovis by hops (Humulus lupulus L.) ß-acid

USDA-ARS?s Scientific Manuscript database

Aims: The goals were to determine if the '-acid from hops (Humulus lupulus L.) could be used to control fructan fermentation by equine hindgut microorganisms, and to verify the antimicrobial mode of action on the Streptococcus bovis, which has been implicated in fructan fermentation, hindgut acidos...

Active depinning of bacterial droplets: The collective surfing of Bacillus subtilis

PubMed Central

Hennes, Marc; Tailleur, Julien; Charron, Gaëlle

2017-01-01

How systems are endowed with migration capacity is a fascinating question with implications ranging from the design of novel active systems to the control of microbial populations. Bacteria, which can be found in a variety of environments, have developed among the richest set of locomotion mechanisms both at the microscopic and collective levels. Here, we uncover, experimentally, a mode of collective bacterial motility in humid environment through the depinning of bacterial droplets. Although capillary forces are notoriously enormous at the bacterial scale, even capable of pinning water droplets of millimetric size on inclined surfaces, we show that bacteria are able to harness a variety of mechanisms to unpin contact lines, hence inducing a collective slipping of the colony across the surface. Contrary to flagella-dependent migration modes like swarming, we show that this much faster “colony surfing” still occurs in mutant strains of Bacillus subtilis lacking flagella. The active unpinning seen in our experiments relies on a variety of microscopic mechanisms, which could each play an important role in the migration of microorganisms in humid environment. PMID:28536199

Antibacterial free fatty acids: activities, mechanisms of action and biotechnological potential.

PubMed

Desbois, Andrew P; Smith, Valerie J

2010-02-01

Amongst the diverse and potent biological activities of free fatty acids (FFAs) is the ability to kill or inhibit the growth of bacteria. The antibacterial properties of FFAs are used by many organisms to defend against parasitic or pathogenic bacteria. Whilst their antibacterial mode of action is still poorly understood, the prime target of FFA action is the cell membrane, where FFAs disrupt the electron transport chain and oxidative phosphorylation. Besides interfering with cellular energy production, FFA action may also result from the inhibition of enzyme activity, impairment of nutrient uptake, generation of peroxidation and auto-oxidation degradation products or direct lysis of bacterial cells. Their broad spectrum of activity, non-specific mode of action and safety makes them attractive as antibacterial agents for various applications in medicine, agriculture and food preservation, especially where the use of conventional antibiotics is undesirable or prohibited. Moreover, the evolution of inducible FFA-resistant phenotypes is less problematic than with conventional antibiotics. The potential for commercial or biomedical exploitation of antibacterial FFAs, especially for those from natural sources, is discussed.

Assessing acute toxicity of effluent from a textile industry and nearby river waters using sulfur-oxidizing bacteria in continuous mode.

PubMed

Gurung, Anup; Hassan, Sedky H A; Oh, Sang-Eun

2011-10-01

Bioassays are becoming an important tool for assessing the toxicity of complex mixtures of substances in aquatic environments in which Daphnia magna is routinely used as a test organism. Bioassays outweigh physicochemical analyses and are valuable in the decision-making process pertaining to the final discharge of effluents from wastewater treatment plants as they measure the total effect of the discharge which is ecologically relevant. In this study, the aquatic toxicity of a textile plant effluent and river water downstream from the plant were evaluated with sulfur-oxidizing bacterial biosensors in continuous mode. Collected samples were analysed for different physicochemical parameters and 1,4-dioxane was detected in the effluent. The effluent contained a relatively high chemical oxygen demand of 60 mg L(-1), which exceeded the limit set by the Korean government for industrial effluent discharges. Results showed that both the effluent and river waters were toxic to sulfur-oxidizing bacteria. These results show the importance of incorporating bioassays to detect toxicity in wastewater effluents for the sustainable management of water resources.

Plasmids of corynebacteria.

PubMed

Deb, J K; Nath, N

1999-06-01

Corynebacteria are pleomorphic, asporogenous, Gram-positive bacteria. Included in this group are nonpathogenic soil corynebacteria, which are widely used for the industrial production of amino acids and detergents, and in biotransformation of steroids. Other members of this group are plant and animal pathogens. This review summarizes the current information available about the plasmids of corynebacteria. The emphasis is mainly on the small plasmids, which have been used for construction of vectors for expression of genes in these bacteria. Moreover, considerable information is now available on their nucleotide sequence, gene organization and modes of replication, which would make it possible to further manipulate these plasmids. Other plasmid properties, such as incompatibility and host range, are also discussed. Finally, use of these plasmids as cloning vectors for the expression of heterologous proteins using corynebacteria as hosts is also summarized to highlight the potential of these bacteria as hosts for recombinant DNA.

Bacterial cooperative organization under antibiotic stress

NASA Astrophysics Data System (ADS)

Ben-Jacob, Eshel; Cohen, Inon; Golding, Ido; Gutnick, David L.; Tcherpakov, Marianna; Helbing, Dirk; Ron, Ilan G.

2000-07-01

Bacteria have developed sophisticated modes of cooperative behavior to cope with unfavorable environmental conditions. Here we report the effect of antibiotic stress on the colonial development of Paenibacillus dendritiformis and P. vortex. We focus on the effect of co-trimoxazole on the colonial organization of P. dendritiformis. We find that the exposure to non-lethal concentrations of antibiotic leads to dramatic changes in the colonial growth patterns. Branching, tip-splitting patterns are affected by reduction in the colonial fractal dimension from Df=2.0 to 1.7, appearance of pronounced weak chirality and pronounced radial orientation of the growth. We combine the experimental observations with numerical studies of both discrete and continuous generic models to reveal the causes for the modifications in the patterns. We conclude that the bacteria adjust their chemotactic signaling together with variations in the bacteria length and increase in the metabolic load.

Dietary choice behavior in Caenorhabditis elegans

PubMed Central

Shtonda, Boris Borisovich; Avery, Leon

2005-01-01

Animals have evolved diverse behaviors that serve the purpose of finding food in the environment. We investigated the food seeking strategy of the soil bacteria-eating nematode Caenorhabditis elegans. C. elegans bacterial food varies in quality: some species are easy to eat and support worm growth well, while others do not. We show that worms exhibit dietary choice: they hunt for high quality food and leave hard-to-eat bacteria. This food seeking behavior is enhanced in animals that have already experienced good food. When hunting for good food, worms alternate between two modes of locomotion, known as dwelling: movement with frequent stops and reversals; and roaming: straight rapid movement. On good food, roaming is very rare, while on bad food it is common. Using laser ablations and mutant analysis, we show that the AIY neurons serve to extend roaming periods, and are essential for efficient food seeking. PMID:16354781

Sexually transmitted bacteria affect female cloacal assemblages in a wild bird

USGS Publications Warehouse

White, Joël; Mirleau, Pascal; Danchin, Etienne; Mulard, Hervé; Hatch, Scott A.; Heeb, Phillipp; Wagner, Richard H.

2010-01-01

Sexual transmission is an important mode of disease propagation, yet its mechanisms remain largely unknown in wild populations. Birds comprise an important model for studying sexually transmitted microbes because their cloaca provides a potential for both gastrointestinal pathogens and endosymbionts to become incorporated into ejaculates. We experimentally demonstrate in a wild population of kittiwakes (Rissa tridactyla) that bacteria are transmitted during copulation and affect the composition and diversity of female bacterial communities. We used an anti-insemination device attached to males in combination with a molecular technique (automated ribosomal intergenic spacer analysis) that describes bacterial communities. After inseminations were experimentally blocked, the cloacal communities of mates became increasingly dissimilar. Moreover, female cloacal diversity decreased and the extinction of mate-shared bacteria increased, indicating that female cloacal assemblages revert to their pre-copulatory state and that the cloaca comprises a resilient microbial ecosystem.

Rapid prototyping and parametric optimization of plastic acoustofluidic devices for blood-bacteria separation.

PubMed

Silva, R; Dow, P; Dubay, R; Lissandrello, C; Holder, J; Densmore, D; Fiering, J

2017-09-01

Acoustic manipulation has emerged as a versatile method for microfluidic separation and concentration of particles and cells. Most recent demonstrations of the technology use piezoelectric actuators to excite resonant modes in silicon or glass microchannels. Here, we focus on acoustic manipulation in disposable, plastic microchannels in order to enable a low-cost processing tool for point-of-care diagnostics. Unfortunately, the performance of resonant acoustofluidic devices in plastic is hampered by a lack of a predictive model. In this paper, we build and test a plastic blood-bacteria separation device informed by a design of experiments approach, parametric rapid prototyping, and screening by image-processing. We demonstrate that the new device geometry can separate bacteria from blood while operating at 275% greater flow rate as well as reduce the power requirement by 82%, while maintaining equivalent separation performance and resolution when compared to the previously published plastic acoustofluidic separation device.

Stress of algicidal substances from a bacterium Exiguobacterium sp. h10 on Microcystis aeruginosa.

PubMed

Li, Y; Liu, L; Xu, Y; Li, P; Zhang, K; Jiang, X; Zheng, T; Wang, H

2017-01-01

Microcystis aeruginosa is a cyanobacterial bloom-causing species and is considered a serious threat to human health and biological safety. In this study, the algicidal bacterium h10 showed high algicidal effects on M. aeruginosa 7820, and strain h10 was confirmed to belong to the genus Exiguobacterium, for which the name Exiguobacterium sp. h10 is proposed. Algicidal activity and mode analysis revealed that the supernatant, rather than the bacterial cells, was responsible for the algicidal activity, indicating that the algicidal mode of strain h10 is by indirect attack through the production of algicidal substances. Analysis of the algicidal substance characteristics showed a molecular weight of <1000 Da and that algicidal substances exhibit high thermal stability and pH instability, and the characteristic functional groups of the algicidal substance mainly included carbonyl, amino and hydroxyl groups. Under the effects of the algicidal substance, the cellular pigment content was significantly decreased, and the algal cell structure and morphology were seriously damaged. The results indicate that the algicidal bacterium Exiguobacterium sp. h10 could be a potential bio-agent for controlling cyanobacterial blooms of M. aeruginosa. In this study, the effects of algicidal substances from an algicidal bacterium Exiguobacterium sp. h10 on the toxic cyanobacterium, Microcystis aeruginosa 7820, were first investigated. The algicidal mode of action was confirmed as an indirect attack through the production of algicidal substances. The characteristics of the algicidal substance were determined, especially the functional groups analysis that confirmed the algicidal substances were glycolipid mixtures. With the stress of algicidal substances, the algal chlorophyll a synthesis, cell structure and morphology were seriously damaged. This study proved that algicidal bacteria are promising sources of potential cyanobacterial bloom-control, and provided good procedures for the identification and analysis of an algicidal bacterium and substances. Letters in Applied Microbiology © 2016 The Society for Applied Microbiology.

Inoculation of a phenanthrene-degrading endophytic bacterium reduces the phenanthrene level and alters the bacterial community structure in wheat.

PubMed

Liu, Juan; Xiang, Yanbing; Zhang, Zhiming; Ling, Wanting; Gao, Yanzheng

2017-06-01

Colonization by polycyclic aromatic hydrocarbon (PAH)-degrading endophytic bacteria (PAHDEB) can reduce the PAH contamination risk in plant. However, little information is available on the impact of PAHDEB colonization on the endophytic bacterial community of inner plant tissues. A phenanthrene-degrading endophytic bacterium (PDEB), Massilia sp. Pn2, was inoculated onto the roots of wheat and subjected to greenhouse container experiments. The endophytic bacterial community structure in wheat was investigated using high-throughput sequencing technology. The majority of endophytic bacteria in wheat were Proteobacteria, and the dominant genus was Pseudomonas. Phenanthrene contamination clearly increased the diversity of endophytic bacteria in wheat. The cultivable endophytic bacteria counts in wheat decreased with increasing the level of phenanthrene contamination; the endophytic bacterial community structure changed correspondingly, and the bacterial richness first increased and then decreased. Inoculation of strain Pn2 reduced the phenanthrene contamination in wheat, enlarged the biomass of wheat roots, changed the bacterial community structure and enhanced the cell counts, diversity and richness of endophytic bacteria in phenanthrene-contaminated wheat in a contamination level-dependent manner. The findings of this investigation provide insight into the responses of endophytic bacterial community in plant to external PAH contamination and PAHDEB colonization.

Designed beta-boomerang antiendotoxic and antimicrobial peptides: structures and activities in lipopolysaccharide.

PubMed

Bhunia, Anirban; Mohanram, Harini; Domadia, Prerna N; Torres, Jaume; Bhattacharjya, Surajit

2009-08-14

Lipopolysaccharide (LPS), an integral part of the outer membrane of Gram-negative bacteria, is involved in a variety of biological processes including inflammation, septic shock, and resistance to host-defense molecules. LPS also provides an environment for folding of outer membrane proteins. In this work, we describe the structure-activity correlation of a series of 12-residue peptides in LPS. NMR structures of the peptides derived in complex with LPS reveal boomerang-like beta-strand conformations that are stabilized by intimate packing between the two aromatic residues located at the 4 and 9 positions. This structural feature renders these peptides with a high ability to neutralize endotoxicity, >80% at 10 nM concentration, of LPS. Replacements of these aromatic residues either with Ala or with Leu destabilizes the boomerang structure with the concomitant loss of antiendotoxic and antimicrobial activities. Furthermore, the aromatic packing stabilizing the beta-boomerang structure in LPS is found to be maintained even in a truncated octapeptide, defining a structured LPS binding motif. The mode of action of the active designed peptides correlates well with their ability to perturb LPS micelle structures. Fourier transform infrared spectroscopy studies of the peptides delineate beta-type conformations and immobilization of phosphate head groups of LPS. Trp fluorescence studies demonstrated selective interactions with LPS and the depth of insertion into the LPS bilayer. Our results demonstrate the requirement of LPS-specific structures of peptides for endotoxin neutralizations. In addition, we propose that structures of these peptides may be employed to design proteins for the outer membrane.

Investigation of energy gene expressions and community structures of free and attached acidophilic bacteria in chalcopyrite bioleaching.

PubMed

Zhu, Jianyu; Jiao, Weifeng; Li, Qian; Liu, Xueduan; Qin, Wenqing; Qiu, Guanzhou; Hu, Yuehua; Chai, Liyuan

2012-12-01

In order to better understand the bioleaching mechanism, expression of genes involved in energy conservation and community structure of free and attached acidophilic bacteria in chalcopyrite bioleaching were investigated. Using quantitative real-time PCR, we studied the expression of genes involved in energy conservation in free and attached Acidithiobacillus ferrooxidans during bioleaching of chalcopyrite. Sulfur oxidation genes of attached A. ferrooxidans were up-regulated while ferrous iron oxidation genes were down-regulated compared with free A. ferrooxidans in the solution. The up-regulation may be induced by elemental sulfur on the mineral surface. This conclusion was supported by the results of HPLC analysis. Sulfur-oxidizing Acidithiobacillus thiooxidans and ferrous-oxidizing Leptospirillum ferrooxidans were the members of the mixed culture in chalcopyrite bioleaching. Study of the community structure of free and attached bacteria showed that A. thiooxidans dominated the attached bacteria while L. ferrooxidans dominated the free bacteria. With respect to available energy sources during bioleaching of chalcopyrite, sulfur-oxidizers tend to be on the mineral surfaces whereas ferrous iron-oxidizers tend to be suspended in the aqueous phase. Taken together, these results indicate that the main role of attached acidophilic bacteria was to oxidize elemental sulfur and dissolution of chalcopyrite involved chiefly an indirect bioleaching mechanism.

Caenorhabditis elegans star formation and negative chemotaxis induced by infection with corynebacteria.

PubMed

Antunes, Camila Azevedo; Clark, Laura; Wanuske, Marie-Therès; Hacker, Elena; Ott, Lisa; Simpson-Louredo, Liliane; de Luna, Maria das Gracas; Hirata, Raphael; Mattos-Guaraldi, Ana Luíza; Hodgkin, Jonathan; Burkovski, Andreas

2016-01-01

Caenorhabditis elegans is one of the major model systems in biology based on advantageous properties such as short life span, transparency, genetic tractability and ease of culture using an Escherichia coli diet. In its natural habitat, compost and rotting plant material, this nematode lives on bacteria. However, C. elegans is a predator of bacteria, but can also be infected by nematopathogenic coryneform bacteria such Microbacterium and Leucobacter species, which display intriguing and diverse modes of pathogenicity. Depending on the nematode pathogen, aggregates of worms, termed worm-stars, can be formed, or severe rectal swelling, so-called Dar formation, can be induced. Using the human and animal pathogens Corynebacterium diphtheriae and Corynebacterium ulcerans as well as the non-pathogenic species Corynebacterium glutamicum, we show that these coryneform bacteria can also induce star formation slowly in worms, as well as a severe tail-swelling phenotype. While C. glutamicum had a significant, but minor influence on survival of C. elegans, nematodes were killed after infection with C. diphtheriae and C. ulcerans. The two pathogenic species were avoided by the nematodes and induced aversive learning in C. elegans.

Removal of fluoride, arsenic and coliform bacteria by modified homemade filter media from drinking water.

PubMed

Devi, Rani; Alemayehu, Esayas; Singh, Vijender; Kumar, Ashok; Mengistie, Embialle

2008-05-01

An attempt was made to investigate the removal of fluoride, arsenic and coliform bacteria from drinking water using modified homemade filter media. Batch mode experimental study was conducted to test the efficiency of modified homemade filter for reduction of impurities under the operating condition of treatment time. The physico-chemical and biological analysis of water samples had been done before and after the treatment with filter media, using standard methods. Optimum operating treatment time was determined for maximum removal of these impurities by running the experiment for 2, 4, 6, 8, 10 and 12h, respectively. The maximum reduction of fluoride, arsenic and coliform bacteria in percentage was 85.60%, 93.07% and 100% and their residual values were 0.72 mg/l, 0.009 mg/l and 0 coliform cells/100ml, respectively after a treatment time of 10h. These residual values were under the permissible limits prescribed by WHO. Hence this could be a cheap, easy and an efficient technique for removal of fluoride, arsenic and coliform bacteria from drinking water.

Algae-bacteria interactions: Evolution, ecology and emerging applications.

PubMed

Ramanan, Rishiram; Kim, Byung-Hyuk; Cho, Dae-Hyun; Oh, Hee-Mock; Kim, Hee-Sik

2016-01-01

Algae and bacteria have coexisted ever since the early stages of evolution. This coevolution has revolutionized life on earth in many aspects. Algae and bacteria together influence ecosystems as varied as deep seas to lichens and represent all conceivable modes of interactions - from mutualism to parasitism. Several studies have shown that algae and bacteria synergistically affect each other's physiology and metabolism, a classic case being algae-roseobacter interaction. These interactions are ubiquitous and define the primary productivity in most ecosystems. In recent years, algae have received much attention for industrial exploitation but their interaction with bacteria is often considered a contamination during commercialization. A few recent studies have shown that bacteria not only enhance algal growth but also help in flocculation, both essential processes in algal biotechnology. Hence, there is a need to understand these interactions from an evolutionary and ecological standpoint, and integrate this understanding for industrial use. Here we reflect on the diversity of such relationships and their associated mechanisms, as well as the habitats that they mutually influence. This review also outlines the role of these interactions in key evolutionary events such as endosymbiosis, besides their ecological role in biogeochemical cycles. Finally, we focus on extending such studies on algal-bacterial interactions to various environmental and bio-technological applications. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Atmospheric pressure resistive barrier air plasma jet induced bacterial inactivation in aqueous environment

NASA Astrophysics Data System (ADS)

Thiyagarajan, Magesh; Sarani, Abdollah; Gonzales, Xavier

2013-03-01

An atmospheric pressure resistive barrier air plasma jet is designed to inactivate bacteria in aqueous media in direct and indirect exposure modes of treatment. The resistive barrier plasma jet is designed to operate at both dc and standard 50-60 Hz low frequency ac power input and the ambient air at 50% humidity level was used as the operating gas. The voltage-current characteristics of the plasma jet were analyzed and the operating frequency of the discharge was measured to be 20 kHz and the plasma power was measured to be 26 W. The plasma jet rotational temperatures (Trot) are obtained from the optical emission spectra, from the N2C-B(2+) transitions by matching the experimental spectrum results with the Spectra Air (SPECAIR) simulation spectra. The reactive oxygen and nitrogen species were measured using optical emission spectroscopy and gas analyzers, for direct and indirect treatment modes. The nitric oxides (NO) were observed to be the predominant long lived reactive nitrogen species produced by the plasma. Three different bacteria including Staphylococcus aureus (Gram-positive), Escherichia coli (Gram-negative), and Neisseria meningitidis (Gram-negative) were suspended in an aqueous media and treated by the resistive barrier air plasma jet in direct and indirect exposure modes. The results show that a near complete bacterial inactivation was achieved within 120 s for both direct and indirect plasma treatment of S. aureus and E. coli bacteria. Conversely, a partial inactivation of N. meningitidis was observed by 120 s direct plasma exposure and insignificant inactivation was observed for the indirect plasma exposure treatment. Plasma induced shifts in N. meningitidis gene expression was analyzed using pilC gene expression as a representative gene and the results showed a reduction in the expression of the pilC gene compared to untreated samples suggesting that the observed protection against NO may be regulated by other genes.

Acquisition of Uropygial Gland Microbiome by Hoopoe Nestlings.

PubMed

Martín-Vivaldi, Manuel; Soler, Juan José; Martínez-García, Ángela; Arco, Laura; Juárez-García-Pelayo, Natalia; Ruiz-Rodríguez, Magdalena; Martínez-Bueno, Manuel

2017-12-18

Mutualistic symbioses between animals and bacteria depend on acquisition of appropriate symbionts while avoiding exploitation by non-beneficial microbes. The mode of acquisition of symbionts would determine, not only the probability of encountering but also evolutionary outcomes of mutualistic counterparts. The microbiome inhabiting the uropygial gland of the European hoopoe (Upupa epops) includes a variety of bacterial strains, some of them providing antimicrobial benefits. Here, the mode of acquisition and stability of this microbiome is analyzed by means of Automated rRNA Intergenic Spacer Analysis and two different experiments. The first experiment impeded mothers' access to their glands, thus avoiding direct transmission of microorganisms from female to offspring secretions. The second experiment explored the stability of the microbiomes by inoculating glands with secretions from alien nests. The first experiment provoked a reduction in similarity of microbiomes of mother and nestlings. Interestingly, some bacterial strains were more often detected when females had not access to their glands, suggesting antagonistic effects among bacteria from different sources. The second experiment caused an increase in richness of the microbiome of receivers in terms of prevalence of Operational Taxonomic Units (OTUs) that reduced differences in microbiomes of donors and receivers. That occurred because OTUs that were present in donors but not in receivers incorporated to the microbiome of the latter, which provoked that cross-inoculated nestlings got similar final microbiomes that included the most prevalent OTUs. The results are therefore consistent with a central role of vertical transmission in bacterial acquisition by nestling hoopoes and support the idea that the typical composition of the hoopoe gland microbiome is reached by the incorporation of some bacteria during the nestling period. This scenario suggests the existence of a coevolved core microbiome composed by a mix of specialized vertically transmitted strains and facultative symbionts able to coexist with them. The implications of this mixed mode of transmission for the evolution of the mutualism are discussed.

Effects of bacteriocins on methicillin-resistant Staphylococcus aureus biofilm.

PubMed

Okuda, Ken-ichi; Zendo, Takeshi; Sugimoto, Shinya; Iwase, Tadayuki; Tajima, Akiko; Yamada, Satomi; Sonomoto, Kenji; Mizunoe, Yoshimitsu

2013-11-01

Control of biofilms formed by microbial pathogens is an important subject for medical researchers, since the development of biofilms on foreign-body surfaces often causes biofilm-associated infections in patients with indwelling medical devices. The present study examined the effects of different kinds of bacteriocins, which are ribosomally synthesized antimicrobial peptides produced by certain bacteria, on biofilms formed by a clinical isolate of methicillin-resistant Staphylococcus aureus (MRSA). The activities and modes of action of three bacteriocins with different structures (nisin A, lacticin Q, and nukacin ISK-1) were evaluated. Vancomycin, a glycopeptide antibiotic used in the treatment of MRSA infections, showed bactericidal activity against planktonic cells but not against biofilm cells. Among the tested bacteriocins, nisin A showed the highest bactericidal activity against both planktonic cells and biofilm cells. Lacticin Q also showed bactericidal activity against both planktonic cells and biofilm cells, but its activity against biofilm cells was significantly lower than that of nisin A. Nukacin ISK-1 showed bacteriostatic activity against planktonic cells and did not show bactericidal activity against biofilm cells. Mode-of-action studies indicated that pore formation leading to ATP efflux is important for the bactericidal activity against biofilm cells. Our results suggest that bacteriocins that form stable pores on biofilm cells are highly potent for the treatment of MRSA biofilm infections.

Effects of Bacteriocins on Methicillin-Resistant Staphylococcus aureus Biofilm

PubMed Central

Zendo, Takeshi; Sugimoto, Shinya; Iwase, Tadayuki; Tajima, Akiko; Yamada, Satomi; Sonomoto, Kenji

2013-01-01

Control of biofilms formed by microbial pathogens is an important subject for medical researchers, since the development of biofilms on foreign-body surfaces often causes biofilm-associated infections in patients with indwelling medical devices. The present study examined the effects of different kinds of bacteriocins, which are ribosomally synthesized antimicrobial peptides produced by certain bacteria, on biofilms formed by a clinical isolate of methicillin-resistant Staphylococcus aureus (MRSA). The activities and modes of action of three bacteriocins with different structures (nisin A, lacticin Q, and nukacin ISK-1) were evaluated. Vancomycin, a glycopeptide antibiotic used in the treatment of MRSA infections, showed bactericidal activity against planktonic cells but not against biofilm cells. Among the tested bacteriocins, nisin A showed the highest bactericidal activity against both planktonic cells and biofilm cells. Lacticin Q also showed bactericidal activity against both planktonic cells and biofilm cells, but its activity against biofilm cells was significantly lower than that of nisin A. Nukacin ISK-1 showed bacteriostatic activity against planktonic cells and did not show bactericidal activity against biofilm cells. Mode-of-action studies indicated that pore formation leading to ATP efflux is important for the bactericidal activity against biofilm cells. Our results suggest that bacteriocins that form stable pores on biofilm cells are highly potent for the treatment of MRSA biofilm infections. PMID:23979748

The Evolution of Two-Component Systems in Bacteria Reveals Different Strategies for Niche Adaptation

PubMed Central

Arkin, Adam

2006-01-01

Two-component systems including histidine protein kinases represent the primary signal transduction paradigm in prokaryotic organisms. To understand how these systems adapt to allow organisms to detect niche-specific signals, we analyzed the phylogenetic distribution of nearly 5,000 histidine protein kinases from 207 sequenced prokaryotic genomes. We found that many genomes carry a large repertoire of recently evolved signaling genes, which may reflect selective pressure to adapt to new environmental conditions. Both lineage-specific gene family expansion and horizontal gene transfer play major roles in the introduction of new histidine kinases into genomes; however, there are differences in how these two evolutionary forces act. Genes imported via horizontal transfer are more likely to retain their original functionality as inferred from a similar complement of signaling domains, while gene family expansion accompanied by domain shuffling appears to be a major source of novel genetic diversity. Family expansion is the dominant source of new histidine kinase genes in the genomes most enriched in signaling proteins, and detailed analysis reveals that divergence in domain structure and changes in expression patterns are hallmarks of recent expansions. Finally, while these two modes of gene acquisition are widespread across bacterial taxa, there are clear species-specific preferences for which mode is used. PMID:17083272

Mode conversion in metal-insulator-metal waveguide with a shifted cavity

NASA Astrophysics Data System (ADS)

Wang, Yueke; Yan, Xin

2018-01-01

We propose a method, which is utilized to achieve the plasmonic mode conversion in metal-insulator-metal (MIM) waveguide, theoretically. Our proposed structure is composed of bus waveguides and a shifted cavity. The shifted cavity can choose out a plasmonic mode (a- or s-mode) when it is in Fabry-Perot (FP) resonance. The length of the shifted cavity L is carefully chosen, and our structure can achieve the mode conversion between a- and s-mode in the communication region. Besides, our proposed structure can also achieve plasmonic mode-division multiplexing. All the numerical simulations are carried on by the finite element method to verify our design.

Mode of action of the 2-phenylquinoline efflux inhibitor PQQ4R against Escherichia coli

PubMed Central

Machado, Diana; Fernandes, Laura; Costa, Sofia S.; Cannalire, Rolando; Manfroni, Giuseppe; Tabarrini, Oriana; Couto, Isabel; Sabatini, Stefano

2017-01-01

Efflux pump inhibitors are of great interest since their use as adjuvants of bacterial chemotherapy can increase the intracellular concentrations of the antibiotics and assist in the battle against the rising of antibiotic-resistant bacteria. In this work, we have described the mode of action of the 2-phenylquinoline efflux inhibitor (4-(2-(piperazin-1-yl)ethoxy)-2-(4-propoxyphenyl) quinolone – PQQ4R), against Escherichia coli, by studding its efflux inhibitory ability, its synergistic activity in combination with antibiotics, and compared its effects with the inhibitors phenyl-arginine-β-naphthylamide (PAβN) and chlorpromazine (CPZ). The results showed that PQQ4R acts synergistically, in a concentration dependent manner, with antibiotics known to be subject to efflux in E. coli reducing their MIC in correlation with the inhibition of their efflux. Real-time fluorometry assays demonstrated that PQQ4R at sub-inhibitory concentrations promote the intracellular accumulation of ethidium bromide inhibiting its efflux similarly to PAβN or CPZ, well-known and described efflux pump inhibitors for Gram-negative bacteria and whose clinical usage is limited by their levels of toxicity at clinical and bacteriological effective concentrations. The time-kill studies showed that PQQ4R, at bactericidal concentrations, has a rapid antimicrobial activity associated with a fast decrease of the intracellular ATP levels. The results also indicated that the mode of action of PQQ4R involves the destabilization of the E. coli inner membrane potential and ATP production impairment, ultimately leading to efflux pump inhibition by interference with the energy required by the efflux systems. At bactericidal concentrations, membrane permeabilization increases and finally ATP is totally depleted leading to cell death. Since drug resistance mediated by the activity of efflux pumps depends largely on the proton motive force (PMF), dissipaters of PMF such as PQQ4R, can be regarded as future adjuvants of conventional therapy against E. coli and other Gram-negative bacteria, especially their multidrug resistant forms. Their major limitation is the high toxicity for human cells at the concentrations needed to be effective against bacteria. Their future molecular optimization to improve the efflux inhibitory properties and reduce relative toxicity will optimize their potential for clinical usage against multi-drug resistant bacterial infections due to efflux. PMID:28516003

Carbonate Biogenic Structures in Storrs Lake, Bahamas

NASA Technical Reports Server (NTRS)

Byrne, Monica; Morris, Penny A.; Wentworth, Susan J.; Brigmon, Robin L.; McKay, David S.

2001-01-01

Storr's Lake, an inland hypersaline lake on San Salvador Island, Bahamas, contains calcium carbonate-rich lithified mats of filamentous microorganisms, diatoms, associated photosynthetic and chemotrophic bacteria, and trapped sediment. In addition, 16S rRNA analysis indicates the presence of five sulfur-reducing genera of bacteria. These microbes are potential modern-day analogs to some ancient stromatolitic structures. The goals of this study are to identify unique compositional and biogenic features, possibly correlating some of these with some of the sulfate-reducing bacteria. Additional information is contained in the original extended abstract.

Potential Bacillus probiotics enhance bacterial numbers, water quality and growth during early development of white shrimp (Litopenaeus vannamei).

PubMed

Nimrat, Subuntith; Suksawat, Sunisa; Boonthai, Traimat; Vuthiphandchai, Verapong

2012-10-12

Epidemics of epizootics and occurrence of multiresistant antibiotics of pathogenic bacteria in aquaculture have put forward a development of effective probiotics for the sustainable culture. This study examined the effectiveness of forms of mixed Bacillus probiotics (probiotic A and probiotic B) and mode of probiotic administration on growth, bacterial numbers and water quality during rearing of white shrimp (Litopenaeus vannamei) in two separated experiments: (1) larval stages and (2) postlarval (PL) stages. Forms of Bacillus probiotics and modes of probiotic administration did not affect growth and survival of larval to PL shrimp. The compositions of Bacillus species in probiotic A and probiotic B did not affect growth and survival of larvae. However, postlarvae treated with probiotic B exhibited higher (P<0.05) growth than probiotic A and controls, indicating Bacillus probiotic composition affects the growth of PL shrimp. Total heterotrophic bacteria and Bacillus numbers in larval and PL shrimp or culture water of the treated groups were higher (P<0.05) than in controls. Levels of pH, ammonia and nitrite of the treated shrimp were significantly decreased, compared to the controls. Microencapsulated Bacillus probiotic was effective for rearing of PL L. vannamei. This investigation showed that administration of mixed Bacillus probiotics significantly improved growth and survival of PL shrimp, increased beneficial bacteria in shrimp and culture water and enhanced water quality for the levels of pH, ammonia and nitrite of culture water. Copyright © 2012 Elsevier B.V. All rights reserved.

Effectiveness of Active Packaging on Control of Escherichia Coli O157:H7 and Total Aerobic Bacteria on Iceberg Lettuce.

PubMed

Lu, Haixia; Zhu, Junli; Li, Jianrong; Chen, Jinru

2015-06-01

Contaminated leafy green vegetables have been linked to several outbreaks of human gastrointestinal infections. Antimicrobial interventions that are adoptable by the fresh produce industry for control of pathogen contamination are in great demand. This study was undertaken to evaluate the efficacy of sustained active packaging on control of Escherichia coli O157:H7 and total aerobic bacteria on lettuce. Commercial Iceberg lettuce was inoculated with a 3-strain mixture of E. coli O157:H7 at 10(2) or 10(4) CFU/g. The contaminated lettuce and un-inoculated controls were placed respectively in 5 different active packaging structures. Traditional, nonactive packaging structure was included as controls. Packaged lettuce was stored at 4, 10, or 22 °C for 3 wk and sampled weekly for the population of E. coli O157:H7 and total aerobic bacteria. Results showed that packaging structures with ClO2 generator, CO2 generator, or one of the O2 scavengers effectively controlled the growth of E. coli O157:H7 and total aerobic bacteria under all storage conditions. Packaging structure with the ClO2 generator was most effective and no E. coli O157:H7 was detected in samples packaged in this structure except for those that were inoculated with 4 log CFU/g of E. coli O157:H7 and stored at 22 °C. Packaging structures with an oxygen scavenger and the allyl isothiocyanate generator were mostly ineffective in control of the growth of the bacteria on Iceberg lettuce. The research suggests that some of the packaging structures evaluated in the study can be used to control the presence of foodborne pathogens on leafy green vegetables. © 2015 Institute of Food Technologists®

Method for producing capsular polysaccharides

NASA Technical Reports Server (NTRS)

Richards, Gil F. (Inventor); Kern, Roger G. (Inventor); Petersen, Gene R. (Inventor)

1994-01-01

Structurally altered capsular polysaccharides are produced by mutant bacteria. These polysaccharides are isolated by selecting a wild type bacterial strain and a phage producing degradative enzymes that have substrate specificity for the capsular polysaccharides produced by the wild type bacteria. Phage-resistant mutants producing capsular polysaccharides are selected and the structurally altered capsular polysaccharide is isolated therefrom.

Coupling of small, low-loss hexapole mode with photonic crystal slab waveguide mode.

PubMed

Kim, Guk-Hyun; Lee, Yong-Hee; Shinya, Akihiko; Notomi, Masaya

2004-12-27

Coupling characteristics between the single-cell hexapole mode and the triangular-lattice photonic crystal slab waveguide mode is studied by the finite-difference time-domain method. The single-cell hexapole mode has a high quality factor (Q) of 3.3Chi106 and a small modal volume of 1.18(lambda/n)3. Based on the symmetry, three representative types of coupling geometries (shoulder-couple, butt-couple and side-couple structures) are selected and tested. The coupling efficiency shows strong dependence on the transverse overlap of the cavity mode and the waveguide mode over the region of the waveguide. The shoulder-couple structure shows best coupling characteristics among three tested structures. For example, two shouldercouple waveguides and a hexapole cavity result in a high performance resonant-tunneling-filter with Q of 9.7Chi105 and transmittance of 0.48. In the side-couple structure, the coupling strength is much weaker than that of the shoulder-couple structure because of the poor spatial overlap between the mode profiles. In the direct-couple structure, the energy transfer from the cavity to the waveguide is prohibited because of the symmetry mismatch and no coupling is observed.

Effects of the dose and viability of Saccharomyces cerevisiae. 1. Diversity of ruminal microbes as analyzed by Illumina MiSeq sequencing and quantitative PCR.

PubMed

Jiang, Y; Ogunade, I M; Qi, S; Hackmann, T J; Staples, C R; Adesogan, A T

2017-01-01

This study was conducted to examine effects of the dose and viability of supplemental Saccharomyces cerevisiae on the ruminal fermentation and bacteria population and the performance of lactating dairy cows. Four ruminally cannulated lactating cows averaging 284±18d in milk were assigned to 4 treatments arranged in a 4×4 Latin square design with four 21-d periods. Cows were fed a total mixed ration containing 41.7% corn silage, 12.1% brewer's grains, and 46.2% concentrate on a dry matter basis. The diet was supplemented with no yeast (control) or with a low dose of live yeast (5.7×10 7 cfu/cow per day; LLY), a high dose of live yeast (6.0×10 8 cfu/cow per day; HLY), or a high dose of killed yeast (6.0×10 8 cfu/cow per day; HDY). Microbial diversity was examined by high-throughput Illumina MiSeq sequencing (Illumina Inc., San Diego, CA) of the V4 region of the 16S rRNA gene. The relative abundance of select ruminal bacteria was also quantified by quantitative PCR (qPCR). Adding LLY to the diet increased the relative abundance of some ruminal cellulolytic bacteria (Ruminococcus and Fibrobacter succinogenes) and amylolytic bacteria (Ruminobacter, Bifidobacterium, and Selenomonas ruminantium). Adding live instead of killed yeast increased the relative abundance of Ruminococcus and F. succinogenes; adding HDY increased the relative abundance of Ruminobacter, Bifidobacterium, Streptococcus bovis, and Selenomonas ruminantium. The most dominant (≥1% of total sequences) bacteria that responded to LLY addition whose functions are among the least understood in relation to the mode of action of yeast include Paraprevotellaceae, CF231, Treponema, and Lachnospiraceae. Future studies should aim to speciate, culture, and examine the function of these bacteria to better understand their roles in the mode of action of yeast. A relatively precise relationship was detected between the relative abundance of F. succinogenes (R 2 =0.67) from qPCR and MiSeq sequencing, but weak relationships were detected for Megasphaera elsdenii, Ruminococcus flavefaciens, and S. ruminantium (R 2 ≤0.19). Copyright © 2017 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Improvement of indoor air quality in pet shop using gaseous chlorine dioxide.

PubMed

Lu, Ming-Chun; Huang, Da-Ji; Hsu, Ching-Shan; Liang, Chih-Kuo; Chen, Geng-Min

2018-06-01

Many studies have shown that pet shops have a high concentration of bioaerosols. Thus, effective disinfection protocols are essential to protect the pet shop staff and visitors to the store. The present study examines the effectiveness of gaseous chlorine dioxide (ClO 2 ) fogging in minimizing the residual bacteria and fungi levels in a typical pet shop in Taiwan consisting of a commodity area, a lodging area, and a grooming area. This investigation uses three disinfection modes (DMs) according to different disinfection periods, namely once every hour (1DM), once every 2 h (2DM), and once every 3 h (3DM). The bacteria and fungi concentrations are measured before and after disinfection treatment, and the effectiveness of each disinfection mode is evaluated using standard statistical techniques. To assess the effect of the environmental factors on the disinfection efficiency, measurements are taken of temperature, relative humidity, airflow velocity, the carbon dioxide concentration, the PM 1 , PM 2.5 , PM 7 , PM 10 , and TSP level at each sampling locations. The results reveal that the effectiveness of the three disinfection modes depends on both the environmental parameters and the use of the three areas (e.g., commodity, lodging, or grooming). Hence, the choice of disinfection method should be adjusted accordingly. For all three disinfection modes, a faster air velocity is beneficial in spreading the disinfectant throughout the indoor space and improving the disinfection performance. Overall, the results presented in this study confirm that gaseous chlorine dioxide disinfection improves the air quality in the pet shop interior, and thus beneficial in safeguarding the health of the pet shop staff and visitors.

Enhanced Raman scattering of biological molecules

NASA Astrophysics Data System (ADS)

Montoya, Joseph R.

The results presented in this thesis, originate from the aspiration to develop an identification algorithm for Salmonella enterica Serovar Enteritidis (S. enterica), Escherichia coli (E. coli), Bacillus globigii ( B. globigii), and Bacillus megaterium ( B. megaterium) using "enhanced" Raman scattering. We realized our goal, with a method utilizing an immunoassay process in a spectroscopic technique, and the direct use of the enhanced spectral response due to bacterial surface elements. The enhanced Raman signal originates from Surface Enhanced Raman Scattering (SERS) and/or Morphological Dependent Resonances (MDR's). We utilized a modified Lee-Meisel colloidal production method to produce a SERS active substrate, which was applied to a SERS application for the amino acid Glycine. The comparison indicates that the SERS/FRACTAL/MDR process can produce an increase of 107 times more signal than the bulk Raman signal from Glycine. In the extension of the Glycine results, we studied the use of SERS related to S. enterica, where we have shown that the aromatic amino acid contribution from Phenylalanine, Tyrosine, and Tryptophan produces a SERS response that can be used to identify the associated SERS vibrational modes of a S. enterica one or two antibody complexes. The "fingerprint" associated with the spectral signature in conjunction with an enhanced Raman signal allows conclusions to be made: (1) about the orientation of the secondary structure on the metal; (2) whether bound/unbound antibody can be neglected; (3) whether we can lower the detection limit. We have lowered the detection limit of S. enterica to 106 bacteria/ml. We also show a profound difference between S. enterica and E. coli SERS spectra even when there exists non-specific binding on E. coli indicating a protein conformation change induced by the addition of the antigen S. enterica. We confirm TEM imagery data, indicating that the source of the aromatic amino acid SERS response is originating from fractal structures on the surface of the bacteria with appropriate associated absorption spectra. In addition, we show that SERS may be used by directly detecting cell surface chemistry, with a report of a SERS response from gram-positive bacteria, B. globigii and B. megaterium combined, with silver fractal aggregates.

Methodologies for screening of bacteria-carbohydrate interactions: anti-adhesive milk oligosaccharides as a case study.

PubMed

Lane, Jonathan A; Mariño, Karina; Rudd, Pauline M; Carrington, Stephen D; Slattery, Helen; Hickey, Rita M

2012-07-01

Many studies have demonstrated the capacity of glycan-based compounds to disrupt microbial binding to mucosal epithelia. Therefore, oligosaccharides have potential application in the prevention of certain bacterial diseases. However, current screening methods for the identification of anti-adhesive oligosaccharides have limitations: they are time-consuming and require large amounts of oligosaccharides. There is a need to develop analytical techniques which can quickly screen for, and structurally define, anti-adhesive oligosaccharides prior to using human cell line models of infection. Considering this, we have developed a rapid method for screening complex oligosaccharide mixtures for potential anti-adhesive activity against bacteria. Our approach involves the use of whole bacterial cells to "deplete" free oligosaccharides from solution. As a case study, the free oligosaccharides from the colostrum of Holstein Friesian cows were screened for interactions with whole Escherichia coli cells. Reductions in oligosaccharide concentrations were determined by High pH Anion Exchange Chromatography and Hydrophilic Interaction Liquid Chromatography (HILIC-HPLC). Oligosaccharide structures were confirmed by a combination of HILIC-HPLC, exoglycosidase digestion and off-line negative ion mode MS/MS. The depletion assay confirmed selective bacterial interaction with certain bovine oligosaccharides which in previous studies, by other methodologies, had been shown to interact with E. coli. In particular, the bacterial cells depleted the following oligosaccharides in a population dependent manner: 3'-sialyllactose, disialyllactose, and 6'-sialyllactosamine. The assay methodology was further validated by studies in which we demonstrated the inhibitory activity of 3'-sialyllactose, and a mixture of bovine colostrum oligosaccharides, on E. coli adhesion to differentiated HT-29 cells. Copyright © 2012 Elsevier B.V. All rights reserved.

The role of guanosine-3',5'-bis-pyrophosphate in mediating antimicrobial activity of the antibiotic 3,5-dihydroxy-4-ethyl-trans-stilbene.

PubMed Central

Sundar, L; Chang, F N

1992-01-01

The mode of action of 3,5-dihydroxy-4-ethyl-trans-stilbene (ES), an antibiotic produced by Xenorhabdus luminescens symbiotically associated with an entomopathogenic nematode, was investigated. ES was active against gram-positive and a number of gram-negative bacteria. In susceptible bacteria this antibiotic caused the inhibition of total RNA synthesis and, to a lesser extent, protein synthesis. At or above MICs, ES triggered a substantial accumulation of an intracellular regulatory compound, guanosine-3',5'-bis-pyrophosphate (ppGpp). This response was also noticed in species of bacteria which have previously not been shown to use ppGpp as a regulatory molecule. The involvement of ppGpp in antibiotic action was confirmed by using an isogenic stringent and a relaxed pair of Escherichia coli strains. The fact that the accumulation of ppGpp was correlated with the susceptibility of various gram-positive and gram-negative bacteria to ES suggests that this nucleotide is involved in the regulation of RNA synthesis and growth in all these microorganisms. Thus, inhibition of RNA synthesis via an increase in ppGpp concentrations may represent a mechanism that is prevalent among most bacteria and one that could be exploited for achieving a rapid inhibition of bacterial growth. Images PMID:1282791

Antibacterial clay against gram-negative antibiotic resistant bacteria.

PubMed

Zarate-Reyes, Luis; Lopez-Pacheco, Cynthia; Nieto-Camacho, Antonio; Palacios, Eduardo; Gómez-Vidales, Virginia; Kaufhold, Stephan; Ufer, Kristian; García Zepeda, Eduardo; Cervini-Silva, Javiera

2018-01-15

Antibiotic resistant bacteria persist throughout the world because they have evolved the ability to express various defense mechanisms to cope with antibiotics and the immune system; thus, low-cost strategies for the treatment of these bacteria are needed, such as the usage of environmental minerals. This paper reports the antimicrobial properties of a clay collected from Brunnenberg, Germany, that is composed of ferroan saponite with admixtures of quartz, feldspar and calcite as well as exposed or hidden (layered at inner regions) nano Fe(0). Based on the growth curves (log phase) of six antibiotic resistant bacteria (4 gram-negative and 2 gram-positive), we concluded that the clay acted as a bacteriostat; however, the clay was only active against the gram-negative bacteria (except for resilient Klebsiella pneumonia). The bacteriostatic mode of action was evidenced by the initial lack of Colony Forming Units on agar plates with growth registered afterward, certainly after 24h, and can be explained because interactions between membrane lipopolysaccharides and the siloxane surfaces of the clay. Labile or bioavailable Fe in the clay (extracted by EDTA or DFO-B) induced the quantitative production of HO as well as oxidative stress, which, nevertheless, did not account for by its bacteriostatic activity. Copyright © 2017 Elsevier B.V. All rights reserved.

Classification of the micro and nanoparticles and biological agents by neural network analysis of the parameters of optical resonance of whispering gallery mode in dielectric microspheres

NASA Astrophysics Data System (ADS)

Saetchnikov, Vladimir A.; Tcherniavskaia, Elina A.; Schweiger, Gustav; Ostendorf, Andreas

2011-07-01

A novel technique for the label-free analysis of micro and nanoparticles including biomolecules using optical micro cavity resonance of whispering-gallery-type modes is being developed. Various schemes of the method using both standard and specially produced microspheres have been investigated to make further development for microbial application. It was demonstrated that optical resonance under optimal geometry could be detected under the laser power of less 1 microwatt. The sensitivity of developed schemes has been tested by monitoring the spectral shift of the whispering gallery modes. Water solutions of ethanol, ascorbic acid, blood phantoms including albumin and HCl, glucose, biotin, biomarker like C reactive protein so as bacteria and virus phantoms (gels of silica micro and nanoparticles) have been used. Structure of resonance spectra of the solutions was a specific subject of investigation. Probabilistic neural network classifier for biological agents and micro/nano particles classification has been developed. Several parameters of resonance spectra as spectral shift, broadening, diffuseness and others have been used as input parameters to develop a network classifier for micro and nanoparticles and biological agents in solution. Classification probability of approximately 98% for probes under investigation have been achieved. Developed approach have been demonstrated to be a promising technology platform for sensitive, lab-on-chip type sensor which can be used for development of diagnostic tools for different biological molecules, e.g. proteins, oligonucleotides, oligosaccharides, lipids, small molecules, viral particles, cells as well as in different experimental contexts e.g. proteomics, genomics, drug discovery, and membrane studies.

Conformational and thermodynamic hallmarks of DNA operator site specificity in the copper sensitive operon repressor from Streptomyces lividans

PubMed Central

Tan, Benedict G.; Vijgenboom, Erik; Worrall, Jonathan A. R.

2014-01-01

Metal ion homeostasis in bacteria relies on metalloregulatory proteins to upregulate metal resistance genes and enable the organism to preclude metal toxicity. The copper sensitive operon repressor (CsoR) family is widely distributed in bacteria and controls the expression of copper efflux systems. CsoR operator sites consist of G-tract containing pseudopalindromes of which the mechanism of operator binding is poorly understood. Here, we use a structurally characterized CsoR from Streptomyces lividans (CsoRSl) together with three specific operator targets to reveal the salient features pertaining to the mechanism of DNA binding. We reveal that CsoRSl binds to its operator site through a 2-fold axis of symmetry centred on a conserved 5′-TAC/GTA-3′ inverted repeat. Operator recognition is stringently dependent not only on electropositive residues but also on a conserved polar glutamine residue. Thermodynamic and circular dichroic signatures of the CsoRSl–DNA interaction suggest selectivity towards the A-DNA-like topology of the G-tracts at the operator site. Such properties are enhanced on protein binding thus enabling the symmetrical binding of two CsoRSl tetramers. Finally, differential binding modes may exist in operator sites having more than one 5′-TAC/GTA-3′ inverted repeat with implications in vivo for a mechanism of modular control. PMID:24121681

Biofilm-derived Legionella pneumophila evades the innate immune response in macrophages

PubMed Central

Abu Khweek, Arwa; Fernández Dávila, Natalia S.; Caution, Kyle; Akhter, Anwari; Abdulrahman, Basant A.; Tazi, Mia; Hassan, Hoda; Novotny, Laura A.; Bakaletz, Lauren O.; Amer, Amal O.

2013-01-01

Legionella pneumophila, the causative agent of Legionnaire's disease, replicates in human alveolar macrophages to establish infection. There is no human-to-human transmission and the main source of infection is L. pneumophila biofilms established in air conditioners, water fountains, and hospital equipments. The biofilm structure provides protection to the organism from disinfectants and antibacterial agents. L. pneumophila infection in humans is characterized by a subtle initial immune response, giving time for the organism to establish infection before the patient succumbs to pneumonia. Planktonic L. pneumophila elicits a strong immune response in murine, but not in human macrophages enabling control of the infection. Interactions between planktonic L. pneumophila and murine or human macrophages have been studied for years, yet the interface between biofilm-derived L. pneumophila and macrophages has not been explored. Here, we demonstrate that biofilm-derived L. pneumophila replicates significantly more in murine macrophages than planktonic bacteria. In contrast to planktonic L. pneumophila, biofilm-derived L. pneumophila lacks flagellin expression, do not activate caspase-1 or -7 and trigger less cell death. In addition, while planktonic L. pneumophila is promptly delivered to lysosomes for degradation, most biofilm-derived bacteria were enclosed in a vacuole that did not fuse with lysosomes in murine macrophages. This study advances our understanding of the innate immune response to biofilm-derived L. pneumophila and closely reproduces the natural mode of infection in human. PMID:23750338

Bacteria-based concrete: from concept to market

NASA Astrophysics Data System (ADS)

Wiktor, V.; Jonkers, H. M.

2016-08-01

The concept of self-healing concrete—a concrete which can autonomously repair itself after crack formation, with no or limited human intervention—has received a lot of attention over the past 10 years as it could help structures to last longer and at a lower maintenance cost. This paper gives an overview on the key aspects and recent advances in the development of the bacteria-based self-healing concrete developed at the University of Technology of Delft (The Netherlands). Research started with the screening and selection of concrete compatible bacteria and nutrients. Several types of encapsulated bacteria and nutrients have been developed and tested. The functionality of these healing agents was demonstrated by showing metabolic activity of activated bacterial spores by oxygen consumption measurements and by regain of material functionality in form of regain of water tightness. Besides development of bacteria-based self-healing concrete, a bacteria-based repair mortar and liquid system were developed for the treatment of aged concrete structures. Field trials have been carried out with either type of bacteria-based systems and the promising results have led to a spinoff company Basilisk Self-Healing Concrete with the aim to further develop these systems and bring them to the market.

Community Composition and Abundance of Anammox Bacteria in Cattail Rhizosphere Sediments at Three Phenological Stages.

PubMed

Zhou, Xiaohong; Zhang, Jinping; Wen, Chunzi

2017-11-01

The distribution of anammox bacteria in rhizosphere sediments of cattail (Typha orientalis) at different phenological stages was investigated. Results showed that the number of 16S rRNA gene copies of the anammox bacteria was considerably higher in the rhizosphere sediment than in the nonrhizosphere sediment and control sediment. The abundances of the anammox bacteria exhibited striking temporal variations in the three different cattail phenological stages. In addition, the Chao1 and Shannon H indexes of the anammox bacteria in cattail rhizosphere sediments had evident spatial and temporal variations at different phenological stages. Four anammox genera (Brocadia, Kuenenia, Jettenia, and a new cluster) were detected and had proportions of 34.18, 45.57, 0.63, and 19.62%, respectively. The CCA analysis results indicated that Cu, TN, Pb, and Zn were pivotal factors that affect anammox bacteria composition. The PCoA analysis results indicated that the community structure at the rhizosphere and nonrhizosphere sediments collected on July was relatively specific and was different from sediments collected on other months, suggesting that cattail can influence the community structures of the anammox bacteria at the maturity stage.

ITG modes in the presence of inhomogeneous field-aligned flow

NASA Astrophysics Data System (ADS)

Sen, S.; McCarthy, D. R.; Lontano, M.; Lazzaro, E.; Honary, F.

2010-02-01

In a recent paper, Varischetti et al. (Plasma Phys. Contr. F. 2008, 50, 105008-1-15) have found that in a slab geometry the effect of the flow shear in the field-aligned parallel flow on the linear mode stability of the ion temperature gradient (ITG)-driven modes is not very prominent. They found that the flow shear also has a negligible effect on the mode characteristics. The work in this paper shows that the inclusion of flow curvature in the field-aligned flow can have a considerable effect on the mode stability; it can also change the mode structure so as to effect the mixing length transport in the core region of a fusion device. Flow shear, on the other hand, has indeed an insignificant role in the mode stability and mode structure. Inhomogeneous field-aligned flow should therefore still be considered for a viable candidate in controlling the ITG mode stability and mode structure.

Effect of engineered environment on microbial community structure in biofilter and biofilm on reverse osmosis membrane.

PubMed

Jeong, Sanghyun; Cho, Kyungjin; Jeong, Dawoon; Lee, Seockheon; Leiknes, TorOve; Vigneswaran, Saravanamuthu; Bae, Hyokwan

2017-11-01

Four dual media filters (DMFs) were operated in a biofiltration mode with different engineered environments (DMF I and II: coagulation with/without acidification and DMF III and IV: without/with chlorination). Designed biofilm enrichment reactors (BERs) containing the removable reverse osmosis (RO) coupons, were connected at the end of the DMFs in parallel to analyze the biofilm on the RO membrane by DMF effluents. Filtration performances were evaluated in terms of dissolved organic carbon (DOC) and assimilable organic carbon (AOC). Organic foulants on the RO membrane were also quantified and fractionized. The bacterial community structures in liquid (seawater and effluent) and biofilm (DMF and RO) samples were analyzed using 454-pyrosequencing. The DMF IV fed with the chlorinated seawater demonstrated the highest reductions of DOC including LMW-N as well as AOC among the other DMFs. The DMF IV was also effective in reducing organic foulants on the RO membrane surface. The bacterial community structure was grouped according to the sample phase (i.e., liquid and biofilm samples), sampling location (i.e., DMF and RO samples), and chlorination (chlorinated and non-chlorinated samples). In particular, the biofilm community in the DMF IV differed from the other DMF treatments, suggesting that chlorination exerted as stronger selective pressure than pH adjustment or coagulation on the biofilm community. In the DMF IV, several chemoorganotrophic chlorine-resistant biofilm-forming bacteria such as Hyphomonas, Erythrobacter, and Sphingomonas were predominant, and they may enhance organic carbon degradation efficiency. Diverse halophilic or halotolerant organic degraders were also found in other DMFs (i.e., DMF I, II, and III). Various kinds of dominant biofilm-forming bacteria were also investigated in RO membrane samples; the results provided possible candidates that cause biofouling when DMF process is applied as the pretreatment option for the RO process. Copyright © 2017 Elsevier Ltd. All rights reserved.

Conjugation of fatty acids with different lengths modulates the antibacterial and antifungal activity of a cationic biologically inactive peptide

PubMed Central

2005-01-01

Many studies have shown that an amphipathic structure and a threshold of hydrophobicity of the peptidic chain are crucial for the biological function of AMPs (antimicrobial peptides). However, the factors that dictate their cell selectivity are not yet clear. In the present study, we show that the attachment of aliphatic acids with different lengths (10, 12, 14 or 16 carbon atoms) to the N-terminus of a biologically inactive cationic peptide is sufficient to endow the resulting lipopeptides with lytic activity against different cells. Mode-of-action studies were performed with model phospholipid membranes mimicking those of bacterial, mammalian and fungal cells. These include determination of the structure in solution and membranes by using CD and ATR-FTIR (attenuated total reflectance Fourier-transform infrared) spectroscopy, membrane leakage experiments and by visualizing bacterial and fungal damage via transmission electron microscopy. The results obtained reveal that: (i) the short lipopeptides (10 and 12 carbons atoms) are non-haemolytic, active towards both bacteria and fungi and monomeric in solution. (ii) The long lipopeptides (14 and 16 carbons atoms) are highly antifungal, haemolytic only at concentrations above their MIC (minimal inhibitory concentration) values and aggregate in solution. (iii) All the lipopeptides adopt a partial α-helical structure in 1% lysophosphatidylcholine and bacterial and mammalian model membranes. However, the two short lipopeptides contain a significant fraction of random coil in fungal membranes, in agreement with their reduced antifungal activity. (iv) All the lipopeptides have a membranolytic effect on all types of cells assayed. Overall, the results reveal that the length of the aliphatic chain is sufficient to control the pathogen specificity of the lipopeptides, most probably by controlling both the overall hydrophobicity and the oligomeric state of the lipopeptides in solution. Besides providing us with basic important information, these new lipopeptides are potential candidates that can target bacteria and/or fungi, especially in cases where the bacterial flora should not be harmed. PMID:15907192

Whispering-gallery-mode-based seismometer

DOEpatents

Fourguette, Dominique Claire; Otugen, M Volkan; Larocque, Liane Marie; Ritter, Greg Aan; Meeusen, Jason Jeffrey; Ioppolo, Tindaro

2014-06-03

A whispering-gallery-mode-based seismometer provides for receiving laser light into an optical fiber, operatively coupling the laser light from the optical fiber into a whispering-gallery-mode-based optical resonator, operatively coupling a spring of a spring-mass assembly to a housing structure; and locating the whispering-gallery-mode-based optical resonator between the spring-mass assembly and the housing structure so as to provide for compressing the whispering-gallery-mode-based optical resonator between the spring-mass assembly and the housing structure responsive to a dynamic compression force from the spring-mass assembly responsive to a motion of the housing structure relative to an inertial frame of reference.

Bacteria versus selenium: A view from the inside out

USGS Publications Warehouse

Staicu, Lucian; Oremland, Ronald S.; Tobe, Ryuta; Mihara, Hisaaki

2017-01-01

Bacteria and selenium (Se) are closely interlinked as the element serves both essential nutrient requirements and energy generation functions. However, Se can also behave as a powerful toxicant for bacterial homeostasis. Conversely, bacteria play a tremendous role in the cycling of Se between different environmental compartments, and bacterial metabolism has been shown to participate to all valence state transformations undergone by Se in nature. Bacteria possess an extensive molecular repertoire for Se metabolism. At the end of the 1980s, a novel mode of anaerobic respiration based on Se oxyanions was experimentally documented for the first time. Following this discovery, specific enzymes capable of reducing Se oxyanions and harvesting energy were found in a number of anaerobic bacteria. The genes involved in the expression of these enzymes have later been identified and cloned. This iterative approach undertaken outside-in led to the understanding of the molecular mechanisms of Se transformations in bacteria. Based on the extensive knowledge accumulated over the years, we now have a full(er) view from the inside out, from DNA-encoding genes to enzymes and thermodynamics. Bacterial transformations of Se for assimilatory purposes have been the object of numerous studies predating the investigation of Se respiration. Remarkable contributions related to the understating of the molecular picture underlying seleno-amino acid biosynthesis are reviewed herein. Under certain circumstances, Se is a toxicant for bacterial metabolism and bacteria have evolved strategies to counteract this toxicity, most notably by the formation of elemental Se (nano)particles. Several biotechnological applications, such as the production of functional materials and the biofortification of crop species using Se-utilizing bacteria, are presented in this chapter.

ELM Suppression and Pedestal Structure in I-Mode Plasmas

NASA Astrophysics Data System (ADS)

Walk, John

2013-10-01

The I-mode regime is characterized by the formation of a temperature pedestal and enhanced energy confinement (H98 up to 1.2), without an accompanying density pedestal or drop in particle transport. Unlike ELMy H-modes, I-mode operation appears to have naturally-occurring suppression of large ELMs in addition to its highly favorable scalings of pedestal structure (and therefore overall performance). Instead, continuous Weakly Coherent Modes help to regulate density. Extensive study of the ELMy H-mode has led to the development of the EPED model, which utilizes calculations of coupled peeling-ballooning MHD modes and kinetic-ballooning mode (KBM) stability limits to predict the pedestal structure preceding an ELM crash. We apply similar tools to the structure and ELM stability of I-mode pedestals. Peeling-ballooning MHD calculations are completed using the ELITE code, showing I-mode pedestals to be generally MHD-stable. Under certain conditions, intermittent ELMs are observed in I-mode at reduced field, typically triggered by sawtooth crashes; modification of the temperature pedestal (and therefore the pressure profile stability) by sawtooth heat pulses is being examined in ELITE. Modeled stability to KBM turbulence in I-mode and ELMy H-mode suggests that typical I-modes are stable against KBM turbulence. Measured I-mode pedestals are significantly wider (more stable) than the width scaling with the square root of poloidal beta characteristic of the KBM-limited pedestals in ELMy H-mode. Finally, we explore scalings of pedestal structure with engineering parameters compared to ELMy H-modes on C-Mod. In particular, we focus on scalings of the pressure pedestal with heating power (and its relation to the favorable scaling of confinement with power in I-mode) and on relationships between heat flux and pedestal temperature gradients. This work is supported by DOE agreement DE-FC02-99ER54512. Theory work at General Atomics is supported by DOE agreement DE-FG02-99ER54309.

Application of micro-PIV to the study of staphylococci bacteria bio-film dynamics

NASA Astrophysics Data System (ADS)

Sherman, Erica; Bayles, Kenneth; Moormeier, Derek; Wei, Timothy

2012-11-01

Staphylococci bacteria are recognized as the most frequent cause of biofilm-associated infections. Although humans are regularly exposed to staphylococcus bacteria without consequence, a localized staph infection has the potential to enter the bloodstream and lead to serious infections such as endocarditis, pneumonia, or toxic shock syndrome. The mechanics of staphylococci biofilm formation and dispersion through the bloodstream are not well known. It has recently been observed that under certain flow conditions, bacteria grow in stable bio-films. Under other conditions, they organize in tower-like structures which break and are transported downstream by the flow. The fundamental questions addressed in this study are i) whether or not fluid mechanics plays a role in differentiating between film or tower formation and ii) whether or not the faulty towers are a bio-film propagation mechanism. This talk focuses on the application of micro-PIV to study this problem. Bacteria were cultured in a glass microchannel and subjected to a range of steady shear rates. Micro-PIV measurements were made to map the flow over and around different types of bio-film structures. Measurements and control volume analysis will be presented quantifying forces acting on these structures.

Observations of fluorescent and biological aerosol at a high-altitude site in Central France

NASA Astrophysics Data System (ADS)

Gabey, A. M.; Vaitilingom, M.; Freney, E.; Boulon, J.; Sellegri, K.; Gallagher, M. W.; Crawford, I. P.; Robinson, N. H.; Stanley, W. R.; Kaye, P. H.

2013-01-01

Total bacteria, fungal spore and yeast counts were compared with UV Light-Induced Fluorescence (UV-LIF) measurements of ambient aerosol at the summit of the Puy de Dôme (pdD) mountain in Central France (1465 m a.s.l), which represents a background elevated site. Bacteria, fungal spores and yeast were enumerated by epifluorescence microscopy (EFM) and found to number 2.2 to 23 L-1 and 0.8 to 2 L-1, respectively. Bacteria counts on two successive nights were an order of magnitude larger than in the intervening day. A Wide Issue Bioaerosol Spectrometer, version 3 (WIBS-3) was used to perform UV-LIF measurements on ambient aerosol sized 0.8 to 20 μm. Mean total number concentration was 270 L-1 (σ = 66 L-1) found predominantly in a size mode at 2 μm for most of the campaign. Total concentration (fluorescent + non-fluorescent aerosol) peaked at 500 L-1 with a size mode at 1 μm because of a change in air mass origin lasting around 48 h. The WIBS-3 features two excitation and fluorescence detection wavelengths corresponding to different biological molecules. The mean fluorescent particle concentration after short-wave (280 nm; Tryptophan) excitation was 12 L-1 (σ = 6 L-1), and did not vary much through the campaign. In contrast the mean concentration of particles fluorescent after long-wave (370 nm; NADH) excitation was 95 L-1 (σ = 25 L-1), and a nightly rise and subsequent fall of up to 100 L-1 formed a strong diurnal cycle in the latter. The fluorescent populations exhibited size modes at 3 μm and 2 to 3 μm, respectively. A hierarchical agglomerative cluster analysis algorithm was applied to the data and used to extract different particle factors. A cluster concentration time series representative of bacteria was identified. This was found to exhibit a diurnal cycle with a maximum peak appearing during the day. Analysis of organic mass spectra recorded using an Aerosol Mass Spectrometer (AMS; Aerodyne Inc.) suggests that aerosol reaching the site at night was more aged than that during the day, indicative of sampling the residual layer at night. Supplementary meteorological data and previous work also show that pdD lies in the residual layer/free troposphere at night, and this is thought to cause the observed diurnal cycles in organic-type and fluorescent aerosol particles. Based on the observed disparity between bacteria and fluorescent particle concentrations, fluorescent non-PBA is likely to be important in the WIBS-3 data and the surprisingly high fluorescent concentration in the residual layer/free troposphere raises questions about a ubiquitous background in continental air during the summer.

Structural Dissection of Crotalicidin, a Rattlesnake Venom Cathelicidin, Retrieves a Fragment with Antimicrobial and Antitumor Activity.

PubMed

Falcao, Claudio Borges; Pérez-Peinado, Clara; de la Torre, Beatriz G; Mayol, Xavier; Zamora-Carreras, Héctor; Jiménez, M Ángeles; Rádis-Baptista, Gandhi; Andreu, David

2015-11-12

In silico dissection of crotalicidin (Ctn), a cathelicidin from a South American pit viper, yielded fragments Ctn[1-14] and Ctn[15-34], which were tested to ascertain to what extent they reproduced the structure and activity of the parent peptide. NMR data showing Ctn to be α-helical at the N-terminus and unstructured at the C-terminus were matched by similar data from the fragments. The peptides were tested against Gram-positive and -negative bacteria and for toxicity against both tumor and healthy cells. Despite its amphipathic α-helical structure, Ctn[1-14] was totally inert toward bacteria or eukaryotic cells. In contrast, unstructured Ctn[15-34] replicated the activity of parent Ctn against Gram-negative bacteria and tumor cells while being significantly less toxic toward eukaryotic cells. This selectivity for bacteria and tumor cells, plus a stability to serum well above that of Ctn, portrays Ctn[15-34] as an appealing candidate for further development as an anti-infective or antitumor lead.

Mode structure of a quantum cascade laser

NASA Astrophysics Data System (ADS)

Bogdanov, A. A.; Suris, R. A.

2011-03-01

We analyze the mode structure of a quantum cascade laser (QCL) cavity considering the surface plasmon-polariton modes and familiar modes of hollow resonator jointly, within a single model. We present a comprehensive mode structure analysis of the laser cavity, varying its geometric parameters and free electron concentration inside cavity layers within a wide range. Our analysis covers, in particular, the cases of metal-insulator-metal and insulator-metal-insulator waveguides. We discuss the phenomenon of negative dispersion for eigenmodes in detail and explain the nature of this phenomenon. We specify a waveguide parameters domain in which negative dispersion exists. The mode structure of QCL cavity is considered in the case of the anisotropic electrical properties of the waveguide materials. We show that anisotropy of the waveguide core results in propagation of Langmuir modes that are degenerated in the case of the isotropic core. Comparative analysis of optical losses due to free carrier absorption is presented for different modes within the frequency range from terahertz to ultraviolet frequencies.

Elaboration of a fragment library hit produces potent and selective aspartate semialdehyde dehydrogenase inhibitors.

PubMed

Thangavelu, Bharani; Bhansali, Pravin; Viola, Ronald E

2015-10-15

Aspartate-β-semialdehyde dehydrogenase (ASADH) lies at the first branch point in the aspartate metabolic pathway which leads to the biosynthesis of several essential amino acids and some important metabolites. This pathway is crucial for many metabolic processes in plants and microbes like bacteria and fungi, but is absent in mammals. Therefore, the key microbial enzymes involved in this pathway are attractive potential targets for development of new antibiotics with novel modes of action. The ASADH enzyme family shares the same substrate binding and active site catalytic groups; however, the enzymes from representative bacterial and fungal species show different inhibition patterns when previously screened against low molecular weight inhibitors identified from fragment library screening. In the present study several approaches, including fragment based drug discovery (FBDD), inhibitor docking, kinetic, and structure-activity relationship (SAR) studies have been used to guide ASADH inhibitor development. Elaboration of a core structure identified by FBDD has led to the synthesis of low micromolar inhibitors of the target enzyme, with high selectivity introduced between the Gram-negative and Gram-positive orthologs of ASADH. This new set of structures open a novel direction for the development of inhibitors against this validated drug-target enzyme. Copyright © 2015 Elsevier Ltd. All rights reserved.

Solution conformation of a cohesin module and its scaffoldin linker from a prototypical cellulosome.

PubMed

Galera-Prat, Albert; Pantoja-Uceda, David; Laurents, Douglas V; Carrión-Vázquez, Mariano

2018-04-15

Bacterial cellulases are drawing increased attention as a means to obtain plentiful chemical feedstocks and fuels from renewable lignocellulosic biomass sources. Certain bacteria deploy a large extracellular multi-protein complex, called the cellulosome, to degrade cellulose. Scaffoldin, a key non-catalytic cellulosome component, is a large protein containing a cellulose-specific carbohydrate-binding module and several cohesin modules which bind and organize the hydrolytic enzymes. Despite the importance of the structure and protein/protein interactions of the cohesin module in the cellulosome, its structure in solution has remained unknown to date. Here, we report the backbone 1 H, 13 C and 15 N NMR assignments of the Cohesin module 5 from the highly stable and active cellulosome from Clostridium thermocellum. These data reveal that this module adopts a tightly packed, well folded and rigid structure in solution. Furthermore, since in scaffoldin, the cohesin modules are connected by linkers we have also characterized the conformation of a representative linker segment using NMR spectroscopy. Analysis of its chemical shift values revealed that this linker is rather stiff and tends to adopt extended conformations. This suggests that the scaffoldin linkers act to minimize interactions between cohesin modules. These results pave the way towards solution studies on cohesin/dockerin's fascinating dual-binding mode. Copyright © 2018 Elsevier Inc. All rights reserved.

Structure and mode of action of cyclic lipopeptide pseudofactin II with divalent metal ions.

PubMed

Janek, Tomasz; Rodrigues, Lígia R; Gudiña, Eduardo J; Czyżnikowska, Żaneta

2016-10-01

The interaction of natural lipopeptide pseudofactin II with a series of doubly charged metal cations was examined by matrix-assisted laser-desorption ionization-time of flight (MALDI-TOF) mass spectrometry and molecular modelling. The molecular modelling for metal-pseudofactin II provides information on the metal-peptide binding sites. Overall, Mg(2+), Ca(2+) and Zn(2+) favor the association with oxygen atoms spanning the peptide backbone, whereas Cu(2+) is coordinated by three nitrogens. Circular dichroism (CD) results confirmed that Zn(2+) and Cu(2+) can disrupt the secondary structure of pseudofactin II at high concentrations, while Ca(2+) and Mg(2+) did not essentially affect the structure of the lipopeptide. Interestingly, our results showed that the addition of Zn(2+) and Cu(2+) helped smaller micelles to form larger micellar aggregates. Since pseudofactin II binds metals, we tested whether this phenomena was somehow related to its antimicrobial activity against Staphylococcus epidermidis and Proteus mirabilis. We found that the antimicrobial effect of pseudofactin II was increased by supplementation of culture media with all tested divalent metal ions. Finally, by using Gram-positive and Gram-negative bacteria we showed that the higher antimicrobial activity of metal complexes of pseudofactin II is attributed to the disruption of the cytoplasmic membrane. Copyright © 2016 Elsevier B.V. All rights reserved.

Bioprocessing Data for the Production of Marine Enzymes

PubMed Central

Sarkar, Sreyashi; Pramanik, Arnab; Mitra, Anindita; Mukherjee, Joydeep

2010-01-01

This review is a synopsis of different bioprocess engineering approaches adopted for the production of marine enzymes. Three major modes of operation: batch, fed-batch and continuous have been used for production of enzymes (such as protease, chitinase, agarase, peroxidase) mainly from marine bacteria and fungi on a laboratory bioreactor and pilot plant scales. Submerged, immobilized and solid-state processes in batch mode were widely employed. The fed-batch process was also applied in several bioprocesses. Continuous processes with suspended cells as well as with immobilized cells have been used. Investigations in shake flasks were conducted with the prospect of large-scale processing in reactors. PMID:20479981

Citrate synthase proteins in extremophilic organisms: Studies within a structure-based model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Różycki, Bartosz, E-mail: rozycki@ifpan.edu.pl; Cieplak, Marek

2014-12-21

We study four citrate synthase homodimeric proteins within a structure-based coarse-grained model. Two of these proteins come from thermophilic bacteria, one from a cryophilic bacterium and one from a mesophilic organism; three are in the closed and two in the open conformations. Even though the proteins belong to the same fold, the model distinguishes the properties of these proteins in a way which is consistent with experiments. For instance, the thermophilic proteins are more stable thermodynamically than their mesophilic and cryophilic homologues, which we observe both in the magnitude of thermal fluctuations near the native state and in the kineticsmore » of thermal unfolding. The level of stability correlates with the average coordination number for amino acid contacts and with the degree of structural compactness. The pattern of positional fluctuations along the sequence in the closed conformation is different than in the open conformation, including within the active site. The modes of correlated and anticorrelated movements of pairs of amino acids forming the active site are very different in the open and closed conformations. Taken together, our results show that the precise location of amino acid contacts in the native structure appears to be a critical element in explaining the similarities and differences in the thermodynamic properties, local flexibility, and collective motions of the different forms of the enzyme.« less

Citrate synthase proteins in extremophilic organisms: Studies within a structure-based model

NASA Astrophysics Data System (ADS)

RóŻycki, Bartosz; Cieplak, Marek

2014-12-01

We study four citrate synthase homodimeric proteins within a structure-based coarse-grained model. Two of these proteins come from thermophilic bacteria, one from a cryophilic bacterium and one from a mesophilic organism; three are in the closed and two in the open conformations. Even though the proteins belong to the same fold, the model distinguishes the properties of these proteins in a way which is consistent with experiments. For instance, the thermophilic proteins are more stable thermodynamically than their mesophilic and cryophilic homologues, which we observe both in the magnitude of thermal fluctuations near the native state and in the kinetics of thermal unfolding. The level of stability correlates with the average coordination number for amino acid contacts and with the degree of structural compactness. The pattern of positional fluctuations along the sequence in the closed conformation is different than in the open conformation, including within the active site. The modes of correlated and anticorrelated movements of pairs of amino acids forming the active site are very different in the open and closed conformations. Taken together, our results show that the precise location of amino acid contacts in the native structure appears to be a critical element in explaining the similarities and differences in the thermodynamic properties, local flexibility, and collective motions of the different forms of the enzyme.

Parasitic modes removal out of operating mode neighbourhood in the DAW accelerating structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Andreev, V.G.; Belugin, V.M.; Esin, S.K.

1983-08-01

The disk and washer (DAW) accelerating structure finds its use in a number of new projects (PIGMI, SNQ etc ). It composes the main part of the accelerating structure of the meson factory now under construction in the Institute for Nuclear Research (INR), Moscow. It is known that the parasitic modes with azimuthal field variations exist at the operating mode region. In this report different methods of the parasitic modes frequency shift are considered. The main attention is given to the resonant methods, which are the most efficient.

Microbial community functional structure in response to antibiotics in pharmaceutical wastewater treatment systems.

PubMed

Zhang, Yu; Xie, Jianping; Liu, Miaomiao; Tian, Zhe; He, Zhili; van Nostrand, Joy D; Ren, Liren; Zhou, Jizhong; Yang, Min

2013-10-15

It is widely demonstrated that antibiotics in the environment affect microbial community structure. However, direct evidence regarding the impacts of antibiotics on microbial functional structures in wastewater treatment systems is limited. Herein, a high-throughput functional gene array (GeoChip 3.0) in combination with quantitative PCR and clone libraries were used to evaluate the microbial functional structures in two biological wastewater treatment systems, which treat antibiotic production wastewater mainly containing oxytetracycline. Despite the bacteriostatic effects of antibiotics, the GeoChip detected almost all key functional gene categories, including carbon cycling, nitrogen cycling, etc., suggesting that these microbial communities were functionally diverse. Totally 749 carbon-degrading genes belonging to 40 groups (24 from bacteria and 16 from fungi) were detected. The abundance of several fungal carbon-degrading genes (e.g., glyoxal oxidase (glx), lignin peroxidase or ligninase (lip), manganese peroxidase (mnp), endochitinase, exoglucanase_genes) was significantly correlated with antibiotic concentrations (Mantel test; P < 0.05), showing that the fungal functional genes have been enhanced by the presence of antibiotics. However, from the fact that the majority of carbon-degrading genes were derived from bacteria and diverse antibiotic resistance genes were detected in bacteria, it was assumed that many bacteria could survive in the environment by acquiring antibiotic resistance and may have maintained the position as a main player in nutrient removal. Variance partitioning analysis showed that antibiotics could explain 24.4% of variations in microbial functional structure of the treatment systems. This study provides insights into the impacts of antibiotics on microbial functional structure of a unique system receiving antibiotic production wastewater, and reveals the potential importance of the cooperation between fungi and bacteria with antibiotic resistance in maintaining the stability and performance of the systems. Copyright © 2013 Elsevier Ltd. All rights reserved.

Comparison of partial and full nitrification processes applied for treating high-strength nitrogen wastewaters: microbial ecology through nitrous oxide production.

PubMed

Ahn, Joon Ho; Kwan, Tiffany; Chandran, Kartik

2011-04-01

The goal of this study was to compare the microbial ecology, gene expression, biokinetics, and N2O emissions from a lab-scale bioreactor operated sequentially in full-nitrification and partial-nitrification modes. Based on sequencing of 16S rRNA and ammonia monooxygenase subunit A (amoA) genes, ammonia oxidizing bacteria (AOB) populations during full- and partial-nitrification modes were distinct from one another. The concentrations of AOB (XAOB) and their respiration rates during full- and partial-nitrification modes were statistically similar, whereas the concentrations of nitrite oxidizing bacteria (XNOB) and their respiration rates declined significantly after the switch from full- to partial-nitrification. The transition from full-nitrification to partial nitrification resulted in a protracted transient spike of nitrous oxide (N2O) and nitric oxide (NO) emissions, which later stabilized. The trends in N2O and NO emissions correlated well with trends in the expression of nirK and norB genes that code for the production of these gases in AOB. Both the transient and stabilized N2O and NO emissions during partial nitrification were statistically higher than those during steady-state full-nitrification. Based on these results, partial nitrification strategies for biological nitrogen removal, although attractive for their reduced operating costs and energy demand, may need to be optimized against the higher carbon foot-print attributed to their N2O emissions.

Multilayer-MCTDH approach to the energy transfer dynamics in the LH2 antenna complex

NASA Astrophysics Data System (ADS)

Shibl, Mohamed F.; Schulze, Jan; Al-Marri, Mohammed J.; Kühn, Oliver

2017-09-01

The multilayer multiconfiguration time-dependent Hartree method is used to study the coupled exciton-vibrational dynamics in a high-dimensional nonameric model of the LH2 antenna complex of purple bacteria. The exciton-vibrational coupling is parametrized within the Huang-Rhys model according to phonon and intramolecular vibrational modes derived from an experimental bacteriochlorophyll spectral density. In contrast to reduced density matrix approaches, the Schrödinger equation is solved explicitly, giving access to the full wave function. This facilitates an unbiased analysis in terms of the coupled dynamics of excitonic and vibrational degrees of freedom. For the present system, we identify spectator modes for the B800 to B800 transfer and we find a non-additive effect of phonon and intramolecular vibrational modes on the B800 to B850 exciton transfer.

Motility modes of the parasite Trypanosoma brucei

NASA Astrophysics Data System (ADS)

Temel, Fatma Zeynep; Qu, Zijie; McAllaster, Michael; de Graffenried, Christopher; Breuer, Kenneth

2015-11-01

The parasitic single-celled protozoan Trypanosoma brucei causes African Sleeping Sickness, which is a fatal disease in humans and animals that threatens more than 60 million people in 36 African countries. Cell motility plays a critical role in the developmental phases and dissemination of the parasite. Unlike many other motile cells such as bacteria Escherichia coli or Caulobacter crescentus, the flagellum of T. brucei is attached along the length of its awl-like body, producing a unique mode of motility that is not fully understood or characterized. Here, we report on the motility of T. brucei, which swims using its single flagellum employing both rotating and undulating propulsion modes. We tracked cells in real-time in three dimensions using fluorescent microscopy. Data obtained from experiments using both short-term tracking within the field of view and long-term tracking using a tracking microscope were analyzed. Motility modes and swimming speed were analyzed as functions of cell size, rotation rate and undulation pattern. Research supported by NSF.

Bacterial Microbiota Associated with the Glacier Ice Worm Is Dominated by Both Worm-Specific and Glacier-Derived Facultative Lineages

PubMed Central

Murakami, Takumi; Segawa, Takahiro; Dial, Roman; Takeuchi, Nozomu; Kohshima, Shiro; Hongoh, Yuichi

2017-01-01

The community structure of bacteria associated with the glacier ice worm Mesenchytraeus solifugus was analyzed by amplicon sequencing of 16S rRNA genes and their transcripts. Ice worms were collected from two distinct glaciers in Alaska, Harding Icefield and Byron Glacier, and glacier surfaces were also sampled for comparison. Marked differences were observed in bacterial community structures between the ice worm and glacier surface samples. Several bacterial phylotypes were detected almost exclusively in the ice worms, and these bacteria were phylogenetically affiliated with either animal-associated lineages or, interestingly, clades mostly consisting of glacier-indigenous species. The former included bacteria that belong to Mollicutes, Chlamydiae, Rickettsiales, and Lachnospiraceae, while the latter included Arcicella and Herminiimonas phylotypes. Among these bacteria enriched in ice worm samples, Mollicutes, Arcicella, and Herminiimonas phylotypes were abundantly and consistently detected in the ice worm samples; these phylotypes constituted the core microbiota associated with the ice worm. A fluorescence in situ hybridization analysis showed that Arcicella cells specifically colonized the epidermis of the ice worms. Other bacterial phylotypes detected in the ice worm samples were also abundantly recovered from the respective habitat glaciers; these bacteria may be food for ice worms to digest or temporary residents. Nevertheless, some were overrepresented in the ice worm RNA samples; they may also function as facultative gut bacteria. Our results indicate that the community structure of bacteria associated with ice worms is distinct from that in the associated glacier and includes worm-specific and facultative, glacier-indigenous lineages. PMID:28302989

Bacterial Microbiota Associated with the Glacier Ice Worm Is Dominated by Both Worm-Specific and Glacier-Derived Facultative Lineages.

PubMed

Murakami, Takumi; Segawa, Takahiro; Dial, Roman; Takeuchi, Nozomu; Kohshima, Shiro; Hongoh, Yuichi

2017-03-31

The community structure of bacteria associated with the glacier ice worm Mesenchytraeus solifugus was analyzed by amplicon sequencing of 16S rRNA genes and their transcripts. Ice worms were collected from two distinct glaciers in Alaska, Harding Icefield and Byron Glacier, and glacier surfaces were also sampled for comparison. Marked differences were observed in bacterial community structures between the ice worm and glacier surface samples. Several bacterial phylotypes were detected almost exclusively in the ice worms, and these bacteria were phylogenetically affiliated with either animal-associated lineages or, interestingly, clades mostly consisting of glacier-indigenous species. The former included bacteria that belong to Mollicutes, Chlamydiae, Rickettsiales, and Lachnospiraceae, while the latter included Arcicella and Herminiimonas phylotypes. Among these bacteria enriched in ice worm samples, Mollicutes, Arcicella, and Herminiimonas phylotypes were abundantly and consistently detected in the ice worm samples; these phylotypes constituted the core microbiota associated with the ice worm. A fluorescence in situ hybridization analysis showed that Arcicella cells specifically colonized the epidermis of the ice worms. Other bacterial phylotypes detected in the ice worm samples were also abundantly recovered from the respective habitat glaciers; these bacteria may be food for ice worms to digest or temporary residents. Nevertheless, some were overrepresented in the ice worm RNA samples; they may also function as facultative gut bacteria. Our results indicate that the community structure of bacteria associated with ice worms is distinct from that in the associated glacier and includes worm-specific and facultative, glacier-indigenous lineages.

Structural Analysis of the Hg(II)-Regulatory Protein Tn501 MerR from Pseudomonas aeruginosa

NASA Astrophysics Data System (ADS)

Wang, Dan; Huang, Shanqing; Liu, Pingying; Liu, Xichun; He, Yafeng; Chen, Weizhong; Hu, Qingyuan; Wei, Tianbiao; Gan, Jianhua; Ma, Jing; Chen, Hao

2016-09-01

The metalloprotein MerR is a mercury(II)-dependent transcriptional repressor-activator that responds to mercury(II) with extraordinary sensitivity and selectivity. It’s widely distributed in both Gram-negative and Gram-positive bacteria but with barely detectable sequence identities between the two sources. To provide structural basis for the considerable biochemical and biophysical experiments previously performed on Tn501 and Tn21 MerR from Gram-negative bacteria, we analyzed the crystal structure of mercury(II)-bound Tn501 MerR. The structure in the metal-binding domain provides Tn501 MerR with a high affinity for mercury(II) and the ability to distinguish mercury(II) from other metals with its unique planar trigonal coordination geometry, which is adopted by both Gram-negative and Gram-positive bacteria. The mercury(II) coordination state in the C-terminal metal-binding domain is transmitted through the allosteric network across the dimer interface to the N-terminal DNA-binding domain. Together with the previous mutagenesis analyses, the present data indicate that the residues in the allosteric pathway have a central role in maintaining the functions of Tn501 MerR. In addition, the complex structure exhibits significant differences in tertiary and quaternary structural arrangements compared to those of Bacillus MerR from Gram-positive bacteria, which probably enable them to function with specific promoter DNA with different spacers between -35 and -10 elements.

Mode structure symmetry breaking of energetic particle driven beta-induced Alfvén eigenmode

NASA Astrophysics Data System (ADS)

Lu, Z. X.; Wang, X.; Lauber, Ph.; Zonca, F.

2018-01-01

The mode structure symmetry breaking of energetic particle driven Beta-induced Alfvén Eigenmode (BAE) is studied based on global theory and simulation. The weak coupling formula gives a reasonable estimate of the local eigenvalue compared with global hybrid simulation using XHMGC. The non-perturbative effect of energetic particles on global mode structure symmetry breaking in radial and parallel (along B) directions is demonstrated. With the contribution from energetic particles, two dimensional (radial and poloidal) BAE mode structures with symmetric/asymmetric tails are produced using an analytical model. It is demonstrated that the symmetry breaking in radial and parallel directions is intimately connected. The effects of mode structure symmetry breaking on nonlinear physics, energetic particle transport, and the possible insight for experimental studies are discussed.

System for determining the angle of impact of an object on a structure

NASA Technical Reports Server (NTRS)

Prosser, William H. (Inventor); Gorman, Michael R. (Inventor)

1993-01-01

A method for determining the angle of impact of an object on a thin-walled structure which determines the angle of impact through analysis of the acoustic waves which result when an object impacts a structure is presented. Transducers are placed on and in the surface of the structure which sense the wave caused in the structure by impact. The waves are recorded and saved for analysis. For source motion normal to the surface, the antisymmetric mode has a large amplitude while that of the symmetric mode is very small. As the source angle increases with respect to the surface normal, the symmetric mode amplitude increases while the antisymmetric mode amplitude decreases. Thus, the angle of impact is determined by measuring the relative amplitudes of these two lowest order modes.

FLEXAN (version 2.0) user's guide

NASA Technical Reports Server (NTRS)

Stallcup, Scott S.

1989-01-01

The FLEXAN (Flexible Animation) computer program, Version 2.0 is described. FLEXAN animates 3-D wireframe structural dynamics on the Evans and Sutherland PS300 graphics workstation with a VAX/VMS host computer. Animation options include: unconstrained vibrational modes, mode time histories (multiple modes), delta time histories (modal and/or nonmodal deformations), color time histories (elements of the structure change colors through time), and rotational time histories (parts of the structure rotate through time). Concurrent color, mode, delta, and rotation, time history animations are supported. FLEXAN does not model structures or calculate the dynamics of structures; it only animates data from other computer programs. FLEXAN was developed to aid in the study of the structural dynamics of spacecraft.

Quantification of spatial distribution and spread of bacteria in soil at microscale

NASA Astrophysics Data System (ADS)

Juyal, Archana; Eickhorst, Thilo; Falconer, Ruth; Baveye, Philippe; Otten, Wilfred

2015-04-01

Soil bacteria play an essential role in functioning of ecosystems and maintaining of biogeochemical cycles. Soil is a complex heterogeneous environment comprising of highly variable and dynamic micro-habitats that have significant impacts on the growth and activity of resident microbiota including bacteria and fungi. Bacteria occupy a very small portion of available pore space in soil which demonstrates that their spatial arrangement in soil has a huge impact on the contact to their target and on the way they interact to carry out their functions. Due to limitation of techniques, there is scant information on spatial distribution of indigenous or introduced bacteria at microhabitat scale. There is a need to understand the interaction between soil structure and microorganisms including fungi for ecosystem-level processes such as carbon sequestration and improving the predictive models for soil management. In this work, a combination of techniques was used including X-ray CT to characterize the soil structure and in-situ detection via fluorescence microscopy to visualize and quantify bacteria in soil thin sections. Pseudomonas fluorescens bacteria were introduced in sterilized soil of aggregate size 1-2 mm and packed at bulk-densities 1.3 g cm-3 and 1.5 g cm-3. A subset of samples was fixed with paraformaldehyde and subsequently impregnated with resin. DAPI and fluorescence in situ hybridization (FISH) were used to visualize bacteria in thin sections of soil cores by epifluorescence microscopy to enumerate spatial distribution of bacteria in soil. The pore geometry of soil was quantified after X-ray microtomography scanning. The distribution of bacteria introduced locally reduced significantly (P

Pathogenesis of Human Enterovirulent Bacteria: Lessons from Cultured, Fully Differentiated Human Colon Cancer Cell Lines

PubMed Central

Liévin-Le Moal, Vanessa

2013-01-01

SUMMARY Hosts are protected from attack by potentially harmful enteric microorganisms, viruses, and parasites by the polarized fully differentiated epithelial cells that make up the epithelium, providing a physical and functional barrier. Enterovirulent bacteria interact with the epithelial polarized cells lining the intestinal barrier, and some invade the cells. A better understanding of the cross talk between enterovirulent bacteria and the polarized intestinal cells has resulted in the identification of essential enterovirulent bacterial structures and virulence gene products playing pivotal roles in pathogenesis. Cultured animal cell lines and cultured human nonintestinal, undifferentiated epithelial cells have been extensively used for understanding the mechanisms by which some human enterovirulent bacteria induce intestinal disorders. Human colon carcinoma cell lines which are able to express in culture the functional and structural characteristics of mature enterocytes and goblet cells have been established, mimicking structurally and functionally an intestinal epithelial barrier. Moreover, Caco-2-derived M-like cells have been established, mimicking the bacterial capture property of M cells of Peyer's patches. This review intends to analyze the cellular and molecular mechanisms of pathogenesis of human enterovirulent bacteria observed in infected cultured human colon carcinoma enterocyte-like HT-29 subpopulations, enterocyte-like Caco-2 and clone cells, the colonic T84 cell line, HT-29 mucus-secreting cell subpopulations, and Caco-2-derived M-like cells, including cell association, cell entry, intracellular lifestyle, structural lesions at the brush border, functional lesions in enterocytes and goblet cells, functional and structural lesions at the junctional domain, and host cellular defense responses. PMID:24006470

Mineral deposition in bacteria-filled and bacteria-free calcium bodies in the crustacean Hyloniscus riparius (Isopoda: Oniscidea).

PubMed

Vittori, Miloš; Rozman, Alenka; Grdadolnik, Jože; Novak, Urban; Štrus, Jasna

2013-01-01

Crustacean calcium bodies are epithelial sacs which contain a mineralized matrix. The objectives of this study were to describe the microscopic anatomy of calcium bodies in the terrestrial isopod Hyloniscus riparius and to establish whether they undergo molt-related structural changes. We performed 3D reconstruction of the calcium bodies from paraffin sections and analyzed their structure with light and electron microscopy. In addition, we analyzed the chemical composition of their mineralized matrices with micro-Raman spectroscopy. Two pairs of these organs are present in H. riparius. One pair is filled with bacteria while the other pair is not. In non-molting animals, the bacteria-filled calcium bodies contain apatite crystals and the bacteria-free calcium bodies enclose CaCO3-containing concretions with little organic matrix. During preparation for molt, an additional matrix layer is deposited in both pairs of calcium bodies. In the bacteria-filled calcium bodies it contains a mixture of calcium carbonate and calcium phosphate, whereas only calcium carbonate is present in bacteria-free calcium bodies. After ecdysis, all mineral components in bacteria-free calcium bodies and the additional matrix layer in bacteria-filled calcium bodies are completely resorbed. During calcium resorption, the apical surface of the calcium body epithelium is deeply folded and electron dense granules are present in spaces between epithelial cells. Our results indicate that the presence of bacteria might be linked to calcium phosphate mineralization. Calcium bodies likely provide a source of calcium and potentially phosphate for the mineralization of the new cuticle after molt. Unlike other terrestrial isopods, H. riparius does not form sternal CaCO3 deposits and the bacteria-free calcium bodies might functionally replace them in this species.

Mineral Deposition in Bacteria-Filled and Bacteria-Free Calcium Bodies in the Crustacean Hyloniscus riparius (Isopoda: Oniscidea)

PubMed Central

Vittori, Miloš; Rozman, Alenka; Grdadolnik, Jože; Novak, Urban; Štrus, Jasna

2013-01-01

Crustacean calcium bodies are epithelial sacs which contain a mineralized matrix. The objectives of this study were to describe the microscopic anatomy of calcium bodies in the terrestrial isopod Hyloniscus riparius and to establish whether they undergo molt-related structural changes. We performed 3D reconstruction of the calcium bodies from paraffin sections and analyzed their structure with light and electron microscopy. In addition, we analyzed the chemical composition of their mineralized matrices with micro-Raman spectroscopy. Two pairs of these organs are present in H. riparius. One pair is filled with bacteria while the other pair is not. In non-molting animals, the bacteria-filled calcium bodies contain apatite crystals and the bacteria-free calcium bodies enclose CaCO3-containing concretions with little organic matrix. During preparation for molt, an additional matrix layer is deposited in both pairs of calcium bodies. In the bacteria-filled calcium bodies it contains a mixture of calcium carbonate and calcium phosphate, whereas only calcium carbonate is present in bacteria-free calcium bodies. After ecdysis, all mineral components in bacteria-free calcium bodies and the additional matrix layer in bacteria-filled calcium bodies are completely resorbed. During calcium resorption, the apical surface of the calcium body epithelium is deeply folded and electron dense granules are present in spaces between epithelial cells. Our results indicate that the presence of bacteria might be linked to calcium phosphate mineralization. Calcium bodies likely provide a source of calcium and potentially phosphate for the mineralization of the new cuticle after molt. Unlike other terrestrial isopods, H. riparius does not form sternal CaCO3 deposits and the bacteria-free calcium bodies might functionally replace them in this species. PMID:23554963

Shrink-induced superhydrophobic and antibacterial surfaces in consumer plastics.

PubMed

Freschauf, Lauren R; McLane, Jolie; Sharma, Himanshu; Khine, Michelle

2012-01-01

Structurally modified superhydrophobic surfaces have become particularly desirable as stable antibacterial surfaces. Because their self-cleaning and water resistant properties prohibit bacteria growth, structurally modified superhydrophobic surfaces obviate bacterial resistance common with chemical agents, and therefore a robust and stable means to prevent bacteria growth is possible. In this study, we present a rapid fabrication method for creating such superhydrophobic surfaces in consumer hard plastic materials with resulting antibacterial effects. To replace complex fabrication materials and techniques, the initial mold is made with commodity shrink-wrap film and is compatible with large plastic roll-to-roll manufacturing and scale-up techniques. This method involves a purely structural modification free of chemical additives leading to its inherent consistency over time and successive recasting from the same molds. Finally, antibacterial properties are demonstrated in polystyrene (PS), polycarbonate (PC), and polyethylene (PE) by demonstrating the prevention of gram-negative Escherichia coli (E. coli) bacteria growth on our structured plastic surfaces.

Kdo2-lipid A: structural diversity and impact on immunopharmacology

PubMed Central

Wang, Xiaoyuan; Quinn, Peter J; Yan, Aixin

2015-01-01

3-deoxy-d-manno-octulosonic acid-lipid A (Kdo2-lipid A) is the essential component of lipopolysaccharide in most Gram-negative bacteria and the minimal structural component to sustain bacterial viability. It serves as the active component of lipopolysaccharide to stimulate potent host immune responses through the complex of Toll-like-receptor 4 (TLR4) and myeloid differentiation protein 2. The entire biosynthetic pathway of Escherichia coli Kdo2-lipid A has been elucidated and the nine enzymes of the pathway are shared by most Gram-negative bacteria, indicating conserved Kdo2-lipid A structure across different species. Yet many bacteria can modify the structure of their Kdo2-lipid A which serves as a strategy to modulate bacterial virulence and adapt to different growth environments as well as to avoid recognition by the mammalian innate immune systems. Key enzymes and receptors involved in Kdo2-lipid A biosynthesis, structural modification and its interaction with the TLR4 pathway represent a clear opportunity for immunopharmacological exploitation. These include the development of novel antibiotics targeting key biosynthetic enzymes and utilization of structurally modified Kdo2-lipid A or correspondingly engineered live bacteria as vaccines and adjuvants. Kdo2-lipid A/TLR4 antagonists can also be applied in anti-inflammatory interventions. This review summarizes recent knowledge on both the fundamental processes of Kdo2-lipid A biosynthesis, structural modification and immune stimulation, and applied research on pharmacological exploitations of these processes for therapeutic development. PMID:24838025

Shuttle structural dynamics characteristics: The analysis and verification

NASA Technical Reports Server (NTRS)

Modlin, C. T., Jr.; Zupp, G. A., Jr.

1985-01-01

The space shuttle introduced a new dimension in the complexity of the structural dynamics of a space vehicle. The four-body configuration exhibited structural frequencies as low as 2 hertz with a model density on the order of 10 modes per hertz. In the verification process, certain mode shapes and frequencies were identified by the users as more important than others and, as such, the test objectives were oriented toward experimentally extracting those modes and frequencies for analysis and test correlation purposes. To provide the necessary experimental data, a series of ground vibration tests (GVT's) was conducted using test articles ranging from the 1/4-scale structural replica of the space shuttle to the full-scale vehicle. The vibration test and analysis program revealed that the mode shapes and frequency correlations below 10 hertz were good. The quality of correlation of modes between 10 and 20 hertz ranged from good to fair and that of modes above 20 hertz ranged from poor to good. Since the most important modes, based on user preference, were below 10 hertz, it was judged that the shuttle structural dynamic models were adequate for flight certifications.

Bias field tunable magnetic configuration and magnetization dynamics in Ni80Fe20 nano-cross structures with varying arm length

NASA Astrophysics Data System (ADS)

Adhikari, K.; Choudhury, S.; Mandal, R.; Barman, S.; Otani, Y.; Barman, A.

2017-01-01

Ferromagnetic nano-cross structures promise exotic static magnetic configurations and very rich and tunable magnetization dynamics leading towards potential applications in magnetic logic and communication devices. Here, we report an experimental study of external magnetic field tunable static magnetic configurations and magnetization dynamics in Ni80Fe20 nano-cross structures with varying arm lengths (L). Broadband ferromagnetic resonance measurements showed a strong variation in the number of spin-wave (SW) modes and mode frequencies (f) with bias field magnitude (H). Simulated static magnetic configurations and SW mode profiles explain the rich variation of the SW spectra, including mode softening, mode crossover, mode splitting, and mode merging. Such variation of SW spectra is further modified by the size of the nano-cross. Remarkably, with decreasing arm length of nano-cross structures, the onion magnetization ground state becomes more stable. Calculated magnetostatic field distributions support the above observations and revealed the non-collective nature of the dynamics in closely packed nano-cross structures. The latter is useful for their possible applications in magnetic storage and memory devices.

[In vitro comparison of epidural bacteria filters permeability and screening scanning electron microscopy].

PubMed

Sener, Aysin; Erkin, Yuksel; Sener, Alper; Tasdogen, Aydin; Dokumaci, Esra; Elar, Zahide

2015-01-01

Epidural catheter bacteria filters are barriers in the patient-controlled analgesia/anaesthesia for preventing contamination at the epidural insertion site. The efficiency of these filters varies according to pore sizes and materials. The bacterial adhesion capability of the two filters was measured in vitro experiment. Adhesion capacities for standard Staphylococcus aureus (ATCC 25923) and Pseudomonas aeruginosa (ATCC 27853) strains of the two different filters (Portex and Rusch) which have the same pore size were examined. Bacterial suspension of 0.5 Mc Farland was placed in the patient-controlled analgesia pump, was filtered at a speed of 5mL/h. in continuous infusion for 48h and accumulated in bottle. The two filters were compared with colony counts of bacteria in the filters and bottles. At the same time, the filters and adhered bacteria were monitored by scanning electron microscope. Electron microscopic examination of filters showed that the Portex filter had a granular and the Rusch filter fibrillary structure. Colony counting from the catheter and bottle showed that both of the filters have significant bacterial adhesion capability (p<0.001). After the bacteria suspension infusion, colony countings showed that the Portex filter was more efficient (p<0.001). There was not any difference between S. aureus and P. aeruginosa bacteria adhesion. In the SEM monitoring after the infusion, it was physically shown that the bacteria were adhered efficiently by both of the filters. The granular structured filter was found statistically and significantly more successful than the fibrial. Although the pore sizes of the filters were same - of which structural differences shown by SEM were the same - it would not be right to attribute the changes in the efficiencies to only structural differences. Using microbiological and physical proofs with regard to efficiency at the same time has been another important aspect of this experiment. Copyright © 2013 Sociedade Brasileira de Anestesiologia. Publicado por Elsevier Editora Ltda. All rights reserved.

In vitro comparison of epidural bacteria filters permeability and screening scanning electron microscopy.

PubMed

Sener, Aysin; Erkin, Yuksel; Sener, Alper; Tasdogen, Aydin; Dokumaci, Esra; Elar, Zahide

2015-01-01

Epidural catheter bacteria filters are barriers in the patient-controlled analgesia/anaesthesia for preventing contamination at the epidural insertion site. The efficiency of these filters varies according to pore sizes and materials. The bacterial adhesion capability of the two filters was measured in vitro experiment. Adhesion capacities for standard Staphylococcus aureus (ATCC 25923) and Pseudomonas aeruginosa (ATCC 27853) strains of the two different filters (Portex and Rusch) which have the same pore size were examined. Bacterial suspension of 0.5 Mc Farland was placed in the patient-controlled analgesia pump, was filtered at a speed of 5 mL/h. in continuous infusion for 48 h and accumulated in bottle. The two filters were compared with colony counts of bacteria in the filters and bottles. At the same time, the filters and adhered bacteria were monitored by scanning electron microscope. Electron microscopic examination of filters showed that the Portex filter had a granular and the Rusch filter fibrillary structure. Colony counting from the catheter and bottle showed that both of the filters have significant bacterial adhesion capability (p<0.001). After the bacteria suspension infusion, colony countings showed that the Portex filter was more efficient (p<0.001). There was not any difference between S. aureus and P. aeruginosa bacteria adhesion. In the SEM monitoring after the infusion, it was physically shown that the bacteria were adhered efficiently by both of the filters. The granular structured filter was found statistically and significantly more successful than the fibrial. Although the pore sizes of the filters were same - of which structural differences shown by SEM were the same - it would not be right to attribute the changes in the efficiencies to only structural differences. Using microbiological and physical proofs with regard to efficiency at the same time has been another important aspect of this experiment. Copyright © 2013 Sociedade Brasileira de Anestesiologia. Published by Elsevier Editora Ltda. All rights reserved.

Lactic Acid Bacteria – Friend or Foe? Lactic Acid Bacteria in the Production of Polysaccharides and Fuel Ethanol

USDA-ARS?s Scientific Manuscript database

Lactic acid bacteria (LAB) have been widely used in the production of fermented foods and as probiotics. Alternan is a glucan with a distinctive backbone structure of alternating a-(1,6) and a-(1,3) linkages produced by the LAB Leuconostoc mesenteroides. In recent years, we have developed improved...

A glycoproteomic approach reveals that the S-layer glycoprotein of Lactobacillus kefiri CIDCA 83111 is O- and N-glycosylated.

PubMed

Cavallero, Gustavo J; Malamud, Mariano; Casabuono, Adriana C; Serradell, M de Los Ángeles; Couto, Alicia S

2017-06-06

In Gram-positive bacteria, such as lactic acid bacteria, general glycosylation systems have not been documented so far. The aim of this work was to characterize in detail the glycosylation of the S-layer protein of Lactobacillus kefiri CIDCA 83111. A reductive β-elimination treatment followed by anion exchange high performance liquid chromatography analysis was useful to characterize the O-glycosidic structures. MALDI-TOF mass spectrometry analysis confirmed the presence of oligosaccharides bearing from 5 to 8 glucose units carrying galacturonic acid. Further nanoHPLC-ESI analysis of the glycopeptides showed two O-glycosylated peptides: the peptide sequence SSASSASSA already identified as a signature glycosylation motif in L. buchneri, substituted on average with eight glucose residues and decorated with galacturonic acid and another O-glycosylated site on peptide 471-476, with a Glc 5-8 GalA 2 structure. As ten characteristic sequons (Asn-X-Ser/Thr) are present in the S-layer amino acid sequence, we performed a PNGase F digestion to release N-linked oligosaccharides. Anion exchange chromatography analysis showed mainly short N-linked chains. NanoHPLC-ESI in the positive and negative ion modes were useful to determine two different peptides substituted with short N-glycan structures. To our knowledge, this is the first description of the structure of N-glycans in S-layer glycoproteins from Lactobacillus species. A detailed characterization of protein glycosylation is essential to establish the basis for understanding and investigating its biological role. It is known that S-layer proteins from kefir-isolated L. kefiri strains are involved in the interaction of bacterial cells with yeasts present in kefir grains and are also capable to antagonize the adverse effects of different enteric pathogens. Therefore, characterization of type and site of glycosidic chains in this protein may help to understand these important properties. Furthermore, this is the first description of N-glycosidic chains in S-layer glycoprotein from Lactobacillus spp. Copyright © 2017 Elsevier B.V. All rights reserved.

Surface structure influences contact killing of bacteria by copper

PubMed Central

Zeiger, Marco; Solioz, Marc; Edongué, Hervais; Arzt, Eduard; Schneider, Andreas S

2014-01-01

Copper kills bacteria rapidly by a mechanism that is not yet fully resolved. The antibacterial property of copper has raised interest in its use in hospitals, in place of plastic or stainless steel. On the latter surfaces, bacteria can survive for days or even weeks. Copper surfaces could thus provide a powerful accessory measure to curb nosocomial infections. We here investigated the effect of the copper surface structure on the efficiency of contact killing of Escherichia coli, an aspect which so far has received very little attention. It was shown that electroplated copper surfaces killed bacteria more rapidly than either polished copper or native rolled copper. The release of ionic copper was also more rapid from electroplated copper compared to the other materials. Scanning electron microscopy revealed that the bacteria nudged into the grooves between the copper grains of deposited copper. The findings suggest that, in terms of contact killing, more efficient copper surfaces can be engineered. PMID:24740976

Regulatory mechanisms of thiol-based redox sensors: lessons learned from structural studies on prokaryotic redox sensors.

PubMed

Lee, Sang Jae; Kim, Dong-Gyun; Lee, Kyu-Yeon; Koo, Ji Sung; Lee, Bong-Jin

2018-05-17

Oxidative stresses, such as reactive oxygen species, reactive electrophilic species, reactive nitrogen species, and reactive chlorine species, can damage cellular components, leading to cellular malfunction and death. In response to oxidative stress, bacteria have evolved redox-responsive sensors that enable them to simultaneously monitor and eradicate potential oxidative stress. Specifically, redox-sensing transcription regulators react to oxidative stress by means of modifying the thiol groups of cysteine residues, functioning as part of an efficient survival mechanism for many bacteria. In general, oxidative molecules can induce changes in the three-dimensional structures of redox sensors, which, in turn, affects the transcription of specific genes in detoxification pathways and defense mechanisms. Moreover, pathogenic bacteria utilize these redox sensors for adaptation and to evade subsequent oxidative attacks from host immune defense. For this reason, the redox sensors of pathogenic bacteria are potential antibiotic targets. Understanding the regulatory mechanisms of thiol-based redox sensors in bacteria will provide insight and knowledge into the discovery of new antibiotics.

Structure and mechanism of the T-box riboswitches

PubMed Central

Zhang, Jinwei

2015-01-01

In most Gram-positive bacteria, including many clinically devastating pathogens from genera such as Bacillus, Clostridium, Listeria and Staphylococcus, T-box riboswitches sense and regulate intracellular availability of amino acids through a multipartite mRNA-tRNA interaction. The T-box mRNA leaders respond to nutrient starvation by specifically binding cognate tRNAs and sensing whether the bound tRNA is aminoacylated, as a proxy for amino acid availability. Based on this readout, T-boxes direct a transcriptional or translational switch to control the expression of downstream genes involved in various aspects of amino acid metabolism: biosynthesis, transport, aminoacylation, transamidation, etc. Two decades after its discovery, the structural and mechanistic underpinnings of the T-box riboswitch were recently elucidated, producing a wealth of insights into how two structured RNAs can recognize each other with robust affinity and exquisite selectivity. The T-box paradigm exemplifies how natural non-coding RNAs can interact not just through sequence complementarity, but can add molecular specificity by precisely juxtaposing RNA structural motifs, exploiting inherently flexible elements and the biophysical properties of post-transcriptional modifications, ultimately achieving a high degree of shape complementarity through mutually induced fit. The T-box also provides a proof-of-principle that compact RNA domains can recognize minute chemical changes (such as tRNA aminoacylation) on another RNA. The unveiling of the structure and mechanism of the T-box system thus expands our appreciation of the range of capabilities and modes of action of structured non-coding RNAs, and hints at the existence of networks of non-coding RNAs that communicate through both, structural and sequence specificity. PMID:25959893

Cellular Response of the Amoeba Acanthamoeba castellanii to Chlorine, Chlorine Dioxide, and Monochloramine Treatments ▿

PubMed Central

Mogoa, Emerancienne; Bodet, Charles; Morel, Franck; Rodier, Marie-Hélène; Legube, Bernard; Héchard, Yann

2011-01-01

Acanthamoeba castellanii is a free-living amoebae commonly found in water systems. Free-living amoebae might be pathogenic but are also known to bear phagocytosis-resistant bacteria, protecting these bacteria from water treatments. The mode of action of these treatments is poorly understood, particularly on amoebae. It is important to examine the action of these treatments on amoebae in order to improve them. The cellular response to chlorine, chlorine dioxide, and monochloramine was tested on A. castellanii trophozoites. Doses of disinfectants leading to up to a 3-log reduction were compared by flow cytometry and electron microscopy. Chlorine treatment led to size reduction, permeabilization, and retraction of pseudopods. In addition, treatment with chlorine dioxide led to a vacuolization of the cytoplasm. Monochloramine had a dose-dependent effect. At the highest doses monochloramine treatment resulted in almost no changes in cell size and permeability, as shown by flow cytometry, but the cell surface became smooth and dense, as seen by electron microscopy. We show that these disinfectants globally induced size reduction, membrane permeabilization, and morphological modifications but that they have a different mode of action on A. castellanii. PMID:21602398

Entangled singularity patterns of photons in Ince-Gauss modes

NASA Astrophysics Data System (ADS)

Krenn, Mario; Fickler, Robert; Huber, Marcus; Lapkiewicz, Radek; Plick, William; Ramelow, Sven; Zeilinger, Anton

2013-01-01

Photons with complex spatial mode structures open up possibilities for new fundamental high-dimensional quantum experiments and for novel quantum information tasks. Here we show entanglement of photons with complex vortex and singularity patterns called Ince-Gauss modes. In these modes, the position and number of singularities vary depending on the mode parameters. We verify two-dimensional and three-dimensional entanglement of Ince-Gauss modes. By measuring one photon and thereby defining its singularity pattern, we nonlocally steer the singularity structure of its entangled partner, while the initial singularity structure of the photons is undefined. In addition we measure an Ince-Gauss specific quantum-correlation function with possible use in future quantum communication protocols.

Tomography and Purification of the Temporal-Mode Structure of Quantum Light

NASA Astrophysics Data System (ADS)

Ansari, Vahid; Donohue, John M.; Allgaier, Markus; Sansoni, Linda; Brecht, Benjamin; Roslund, Jonathan; Treps, Nicolas; Harder, Georg; Silberhorn, Christine

2018-05-01

High-dimensional quantum information processing promises capabilities beyond the current state of the art, but addressing individual information-carrying modes presents a significant experimental challenge. Here we demonstrate effective high-dimensional operations in the time-frequency domain of nonclassical light. We generate heralded photons with tailored temporal-mode structures through the pulse shaping of a broadband parametric down-conversion pump. We then implement a quantum pulse gate, enabled by dispersion-engineered sum-frequency generation, to project onto programmable temporal modes, reconstructing the quantum state in seven dimensions. We also manipulate the time-frequency structure by selectively removing temporal modes, explicitly demonstrating the effectiveness of engineered nonlinear processes for the mode-selective manipulation of quantum states.

Development and applications of two computational procedures for determining the vibration modes of structural systems. [aircraft structures - aerospaceplanes

NASA Technical Reports Server (NTRS)

Kvaternik, R. G.

1975-01-01

Two computational procedures for analyzing complex structural systems for their natural modes and frequencies of vibration are presented. Both procedures are based on a substructures methodology and both employ the finite-element stiffness method to model the constituent substructures. The first procedure is a direct method based on solving the eigenvalue problem associated with a finite-element representation of the complete structure. The second procedure is a component-mode synthesis scheme in which the vibration modes of the complete structure are synthesized from modes of substructures into which the structure is divided. The analytical basis of the methods contains a combination of features which enhance the generality of the procedures. The computational procedures exhibit a unique utilitarian character with respect to the versatility, computational convenience, and ease of computer implementation. The computational procedures were implemented in two special-purpose computer programs. The results of the application of these programs to several structural configurations are shown and comparisons are made with experiment.

The interactions of bacteria with fungi in soil: emerging concepts.

PubMed

Haq, Irshad Ul; Zhang, Miaozhi; Yang, Pu; van Elsas, Jan Dirk

2014-01-01

In this chapter, we review the existing literature on bacterial-fungal interactions in soil, exploring the role fungi may play for soil bacteria as providers of hospitable niches. A focus is placed on the mycosphere, i.e., the narrow zone of influence of fungal hyphae on the external soil milieu, in which hypha-associated bacterial cells dwell. Evidence is brought forward for the contention that the hyphae of both mycorrhizal and saprotrophic fungi serve as providers of ecological opportunities in a grossly carbon-limited soil, as a result of their release of carbonaceous compounds next to the provision of a colonizable surface. Soil bacteria of particular nature are postulated to have adapted to such selection pressures, evolving to the extent that they acquired capabilities that allow them to thrive in the novel habitat created by the emerging fungal hyphae. The mechanisms involved in the interactions and the modes of genetic adaptation of the mycosphere dwellers are discussed, with an emphasis on one key mycosphere-adapted bacterium, Burkholderia terrae BS001. In this discussion, we interrogate the positive interactions between soil fungi and bacteria, and refrain from considering negative interactions. © 2014 Elsevier Inc. All rights reserved.

Method of microbially producing metal gallate spinel nano-objects, and compositions produced thereby

DOE Office of Scientific and Technical Information (OSTI.GOV)

Duty, Chad E.; Jellison, Jr., Gerald E.; Love, Lonnie J.

A method of forming a metal gallate spinel structure that includes mixing a divalent metal-containing salt and a gallium-containing salt in solution with fermentative or thermophilic bacteria. In the process, the bacteria nucleate metal gallate spinel nano-objects from the divalent metal-containing salt and the gallium-containing salt without requiring reduction of a metal in the solution. The metal gallate spinel structures, as well as light-emitting structures in which they are incorporated, are also described.

Diversity and functional traits of culturable microbiome members, including cyanobacteria in the rice phyllosphere.

PubMed

Venkatachalam, S; Ranjan, K; Prasanna, R; Ramakrishnan, B; Thapa, S; Kanchan, A

2016-07-01

The diversity and abundance of culturable microbiome members of the rice phyllosphere was investigated using cv. Pusa Punjab Basmati 1509. Both diversity and species richness of bacteria were significantly higher in plants in pots in a semi-controlled environment than those in fields. Application of fertilisers reduced both diversity and species richness in field-grown plants under a conventional flooded system of rice intensification (SRI) and in dry-seeded rice (DSR) modes. Sequence analyses of 16S rDNA of culturable bacteria, those selected after amplified ribosomal DNA restriction analysis (ARDRA), showed the dominance of α-proteobacteria (35%) and actinobacteria (38%); Pantoea, Exiguobacterium and Bacillus were common among the culturable phyllospheric bacteria. About 34% of 83 culturable bacterial isolates had higher potential (>2 μg·ml(-1) ) for indole acetic acid production in the absence of tryptophan. Interestingly, the phyllosphere bacterial isolates from the pot experiment had significantly higher potential for nitrogen fixation than isolates from the field experiment. Enrichment for cyanobacteria showed both unicellular forms and non-heterocystous filaments under aerobic as well as anaerobic conditions. PCR-DGGE analysis of these showed that aerobic and anaerobic conditions as well as the three modes of cultivation of rice in the field strongly influenced the number and abundance of phylotypes. The adaptability and functional traits of these culturable microbiome members suggest enormous diversity in the phyllosphere, including potential for plant growth promotion, which was also significantly influenced by the different methods of growing rice. © 2016 German Botanical Society and The Royal Botanical Society of the Netherlands.

Correlation among far-infrared reflection modes, crystal structures and dielectric properties of Ba(Zn{sub 1/3}Nb{sub 2/3})O{sub 3}–CaTiO{sub 3} ceramics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shi, Feng, E-mail: sf751106@sina.com.cn; Sun, Haiqing; Liu, Hongquan

Highlights: • Crystal symmetry decreases with CT concentration from cubic to hexagonal structure. • Lattice constants as well as the ordered degree change with CT concentration. • Ordered structures turn from 1:1 to 1:2 ordering with change of crystal structures. • There is a correlation between FIR phonon modes and dielectric properties. • There is a correlation between FIR phonon modes and crystal structures. - Abstract: Ba(Zn{sub 1/3}Nb{sub 2/3})O{sub 3} (BZN)–CaTiO{sub 3} (CT) microwave dielectric ceramics were synthesized at 1395 °C for 4 h using conventional solid-state sintering technique with different CT contents. The ceramics were characterized by X-ray diffractionmore » (XRD) and far-infrared reflection (FIR) spectroscopy to evaluate correlations among crystal structures, dielectric properties, and infrared modes. XRD results showed that crystal symmetry decreased with increased CT concentration from cubic to hexagonal structure, and lattice constants and ordered degree changed accordingly. Ordered phases transformed from 1:1 to 1:2 ordered structure with crystal-structure change. FIR results demonstrated that two new IR active modes appeared at 300 cm{sup −1}, and another new mode appeared at 600 cm{sup −1} for the x ≥ 0.60 sample, which agreed with the change in crystal structures as confirmed by XRD results. Correlations between FIR modes and dielectric properties were established.« less

Intramolecular energy transfer and the driving mechanisms for large-amplitude collective motions of clusters

NASA Astrophysics Data System (ADS)

Yanao, Tomohiro; Koon, Wang Sang; Marsden, Jerrold E.

2009-04-01

This paper uncovers novel and specific dynamical mechanisms that initiate large-amplitude collective motions in polyatomic molecules. These mechanisms are understood in terms of intramolecular energy transfer between modes and driving forces. Structural transition dynamics of a six-atom cluster between a symmetric and an elongated isomer is highlighted as an illustrative example of what is a general message. First, we introduce a general method of hyperspherical mode analysis to analyze the energy transfer among internal modes of polyatomic molecules. In this method, the (3n-6) internal modes of an n-atom molecule are classified generally into three coarse level gyration-radius modes, three fine level twisting modes, and (3n-12) fine level shearing modes. We show that a large amount of kinetic energy flows into the gyration-radius modes when the cluster undergoes structural transitions by changing its mass distribution. Based on this fact, we construct a reactive mode as a linear combination of the three gyration-radius modes. It is shown that before the reactive mode acquires a large amount of kinetic energy, activation or inactivation of the twisting modes, depending on the geometry of the isomer, plays crucial roles for the onset of a structural transition. Specifically, in a symmetric isomer with a spherical mass distribution, activation of specific twisting modes drives the structural transition into an elongated isomer by inducing a strong internal centrifugal force, which has the effect of elongating the mass distribution of the system. On the other hand, in an elongated isomer, inactivation of specific twisting modes initiates the structural transition into a symmetric isomer with lower potential energy by suppressing the elongation effect of the internal centrifugal force and making the effects of the potential force dominant. This driving mechanism for reactions as well as the present method of hyperspherical mode analysis should be widely applicable to molecular reactions in which a system changes its overall mass distribution in a significant way.

Topological phonon modes in filamentary structures

NASA Astrophysics Data System (ADS)

Berg, Nina; Joel, Kira; Koolyk, Miriam; Prodan, Emil

2011-02-01

This work describes a class of topological phonon modes, that is, mechanical vibrations localized at the edges of special structures that are robust against the deformations of the structures. A class of topological phonons was recently found in two-dimensional structures similar to that of microtubules. The present work introduces another class of topological phonons, this time occurring in quasi-one-dimensional filamentary structures with inversion symmetry. The phenomenon is exemplified using a structure inspired from that of actin microfilaments, present in most live cells. The system discussed here is probably the simplest structure that supports topological phonon modes, a fact that allows detailed analysis in both time and frequency domains. We advance the hypothesis that the topological phonon modes are ubiquitous in the biological world and that living organisms make use of them during various processes.

Elaboration of antibiofilm materials by chemical grafting of an antimicrobial peptide.

PubMed

Yala, Jean-Fabrice; Thebault, Pascal; Héquet, Arnaud; Humblot, Vincent; Pradier, Claire-Marie; Berjeaud, Jean-Marc

2011-02-01

A peptide antibiotic, gramicidin A, was covalently bound to cystamine self-assembled monolayers on gold surfaces. Each step of the surface functionalization was characterized by polarization modulation infrared reflection absorption spectroscopy and X-ray photoelectron spectroscopy. The antimicrobial activity of the anchored gramicidin was tested against three Gram-positive bacteria (Listeria ivanovii, Enterococcus faecalis, and Staphylococcus aureus), the Gram-negative bacterium Escherichia coli and the yeast Candida albicans. The results revealed that the adsorbed gramicidin reduced, from 60% for E. coli to 90% for C. albicans, the number of culturable microorganisms attached to the surface. The activity was proven to be persistent overtime, up to 6 months after the first use. The bacteria attached to the functionalized surfaces were permeabilized as shown by confocal microscopy. Taken together, these results indicate a bacteriostatic mode of action of the immobilized peptide. Finally, using green fluorescent protein-expressing bacteria, it was shown that the development of a bacterial biofilm was delayed on peptide-grafted surfaces for at least 24 h.

Long-term exposure to spaceflight conditions affects bacterial response to antibiotics.

PubMed

Juergensmeyer, M A; Juergensmeyer, E A; Guikema, J A

1999-01-01

Bacteria exposed to the spaceflight environment have been shown to have an increased growth rate and an increased resistance to antibiotics. The mechanism of resistance has not yet been identified, as the resistance is quickly lost upon return to Earth. To more fully characterize the spaceflight-induced resistance to antibiotics, 4 species of bacteria were exposed to microgravity for 4 months on the Space Station MIR. Upon return to Earth, these cultures were challenged with a suite of 12 antibiotics of varying modes of action. In contrast to reports from short-term space flights, we find that long-term exposure to microgravity causes bacteria to become more susceptible to most, but not all, antibiotics. Each species responds differently to the suite of antibiotics, frequently becoming less resistant, but occasionally more resistant to the antibiotic. A pattern enabling prediction of response is not yet discernible. While contradicting the results from short-term pure culture research, this experiment confirms results from astronaut and cosmonaut skin flora samples.

Establishing a laboratory model of dental unit waterlines bacterial biofilms using a CDC biofilm reactor.

PubMed

Yoon, Hye Young; Lee, Si Young

2017-11-01

In this study, a laboratory model to reproduce dental unit waterline (DUWL) biofilms was developed using a CDC biofilm reactor (CBR). Bacteria obtained from DUWLs were filtered and cultured in Reasoner's 2A (R2A) for 10 days, and were subsequently stored at -70°C. This stock was cultivated on R2A in batch mode. After culturing for five days, the bacteria were inoculated into the CBR. Biofilms were grown on polyurethane tubing for four days. Biofilm accumulation and thickness was 1.3 × 10 5  CFU cm -2 and 10-14 μm respectively, after four days. Bacteria in the biofilms included cocci and rods of short and medium lengths. In addition, 38 bacterial genera were detected in biofilms. In this study, the suitability and reproducibility of the CBR model for DUWL biofilm formation were demonstrated. The model provides a foundation for the development of bacterial control methods for DUWLs.

[Hospital infection due to Serratia marcescens and its sensitivity to antibiotics].

PubMed

Filloy, L; Serrano, D; Borjas, E

1980-01-01

A total of 164 isolations of Serratia marcescens achieved during 1978-1979 at the Hospital Infantil de México in children with various pathology due to this bacteria were studied. Most of the cases were debilitated patients from the newborns and prematures wards and contagious and surgery departments. The most frequent isolations were from wounds and abscesses (76 cases), the same as from meningitis (22 cases) and sepsis (12 patients). Serratia marcescens showed a high degree of resistance (87-100%) to the following antibiotics: carbenicillin, colimycin, chloramphenicol, phosphomicin, ampicillin and cephalothin. To gestamicin and kanamycin, 42% of strains were sensitive. Amikacin was the most effective drug with 92% of strains susceptible to it. The history of this bacteria, its mode of transmission, frequency of infections and resistance to antibiotics found in foreign institutions are commented. Likewise, the difficulty for the precision bacteriologic diagnosis is emphasized as the possible main cause for the ignorance in Mexico of infections due to this bacteria.

Transmission function properties for multi-layered structures: application to super-resolution.

PubMed

Mattiucci, N; D'Aguanno, G; Scalora, M; Bloemer, M J; Sibilia, C

2009-09-28

We discuss the properties of the transmission function in the k-space for a generic multi-layered structure. In particular we analytically demonstrate that a transmission greater than one in the evanescent spectrum (amplification of the evanescent modes) can be directly linked to the guided modes supported by the structure. Moreover we show that the slope of the phase of the transmission function in the propagating spectrum is inversely proportional to the ability of the structure to compensate the diffraction of the propagating modes. We apply these findings to discuss several examples where super-resolution is achieved thanks to the simultaneous availability of the amplification of the evanescent modes and the diffraction compensation of the propagating modes.

Structures and Antibacterial Properties of Isorugosins H-J, Oligomeric Ellagitannins from Liquidambar formosana with Characteristic Bridging Groups between Sugar Moieties.

PubMed

Shimozu, Yuuki; Kuroda, Teruo; Tsuchiya, Tomofusa; Hatano, Tsutomu

2017-10-27

Three new ellagitannin oligomers, isorugosins H (1), I (2), and J (3), together with 11 known hydrolyzable tannins were isolated from an aqueous acetone extract of the fresh leaves of Liquidambar formosana. Their chemical structures were elucidated based on spectroscopic data and chemical conversion into known hydrolyzable tannins. The bridging mode of the valoneoyl groups between their sugar moieties has been identified only in this plant species. Additionally, the effects of the isorugosins isolated from this species on drug-resistant bacteria were evaluated and showed that isorugosin A (4) exhibited the most potent antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA). The isorugosins also had a suppressing effect on pigment formation in Pseudomonas aeruginosa. The isorugosin-protein complexes were analyzed using size-exclusion chromatography and polyacrylamide gel electrophoresis to clarify the relationship of their antibacterial properties with their protein interaction potency as hydrolyzable tannins. The results suggested that the antibacterial properties of hydrolyzable tannins are not simply a result of their binding activity to proteins, but are due to other factors such as the accessibility of polyphenolic acyl groups to bacterial membranes.

Vibrio cholerae biofilm growth program and architecture revealed by single-cell live imaging

PubMed Central

Yan, Jing; Sharo, Andrew G.; Stone, Howard A.; Wingreen, Ned S.; Bassler, Bonnie L.

2016-01-01

Biofilms are surface-associated bacterial communities that are crucial in nature and during infection. Despite extensive work to identify biofilm components and to discover how they are regulated, little is known about biofilm structure at the level of individual cells. Here, we use state-of-the-art microscopy techniques to enable live single-cell resolution imaging of a Vibrio cholerae biofilm as it develops from one single founder cell to a mature biofilm of 10,000 cells, and to discover the forces underpinning the architectural evolution. Mutagenesis, matrix labeling, and simulations demonstrate that surface adhesion-mediated compression causes V. cholerae biofilms to transition from a 2D branched morphology to a dense, ordered 3D cluster. We discover that directional proliferation of rod-shaped bacteria plays a dominant role in shaping the biofilm architecture in V. cholerae biofilms, and this growth pattern is controlled by a single gene, rbmA. Competition analyses reveal that the dense growth mode has the advantage of providing the biofilm with superior mechanical properties. Our single-cell technology can broadly link genes to biofilm fine structure and provides a route to assessing cell-to-cell heterogeneity in response to external stimuli. PMID:27555592

Active Polar Two-Fluid Macroscopic Dynamics

NASA Astrophysics Data System (ADS)

Pleiner, Harald; Svensek, Daniel; Brand, Helmut R.

2014-03-01

We study the dynamics of systems with a polar dynamic preferred direction. Examples include the pattern-forming growth of bacteria (in a solvent, shoals of fish (moving in water currents), flocks of birds and migrating insects (flying in windy air). Because the preferred direction only exists dynamically, but not statically, the macroscopic variable of choice is the macroscopic velocity associated with the motion of the active units. We derive the macroscopic equations for such a system and discuss novel static, reversible and irreversible cross-couplings connected to this second velocity. We find a normal mode structure quite different compared to the static descriptions, as well as linear couplings between (active) flow and e.g. densities and concentrations due to the genuine two-fluid transport derivatives. On the other hand, we get, quite similar to the static case, a direct linear relation between the stress tensor and the structure tensor. This prominent ``active'' term is responsible for many active effects, meaning that our approach can describe those effects as well. In addition, we also deal with explicitly chiral systems, which are important for many active systems. In particular, we find an active flow-induced heat current specific for the dynamic chiral polar order.

7 CFR 201.56 - Interpretation.

Code of Federal Regulations, 2010 CFR

2010-01-01

... evaluation of such tests. (c) Seedlings infected with fungi or bacteria should be regarded as normal if all essential structures are present. A seedling that has been seriously damaged by bacteria or fungi from any...

7 CFR 201.56 - Interpretation.

Code of Federal Regulations, 2011 CFR

2011-01-01

... evaluation of such tests. (c) Seedlings infected with fungi or bacteria should be regarded as normal if all essential structures are present. A seedling that has been seriously damaged by bacteria or fungi from any...

7 CFR 201.56 - Interpretation.

Code of Federal Regulations, 2013 CFR

2013-01-01

... evaluation of such tests. (c) Seedlings infected with fungi or bacteria should be regarded as normal if all essential structures are present. A seedling that has been seriously damaged by bacteria or fungi from any...

An Innovative Structural Mode Selection Methodology: Application for the X-33 Launch Vehicle Finite Element Model

NASA Technical Reports Server (NTRS)

Hidalgo, Homero, Jr.

2000-01-01

An innovative methodology for determining structural target mode selection and mode selection based on a specific criterion is presented. An effective approach to single out modes which interact with specific locations on a structure has been developed for the X-33 Launch Vehicle Finite Element Model (FEM). We presented Root-Sum-Square (RSS) displacement method computes resultant modal displacement for each mode at selected degrees of freedom (DOF) and sorts to locate modes with highest values. This method was used to determine modes, which most influenced specific locations/points on the X-33 flight vehicle such as avionics control components, aero-surface control actuators, propellant valve and engine points for use in flight control stability analysis and for flight POGO stability analysis. Additionally, the modal RSS method allows for primary or global target vehicle modes to also be identified in an accurate and efficient manner.

The three-dimensional structure of CFA/I adhesion pili: traveler's diarrhea bacteria hang on by a spring.

PubMed

Mu, Xiang-Qi; Savarino, Stephen J; Bullitt, Esther

2008-02-22

To survive the harsh environment of a churning intestinal tract, bacteria attach to the host epithelium via thin fibers called pili (or fimbriae). Enterotoxigenic Escherichia coli bacteria expressing colonization factor antigen I (CFA/I) pili and related pili are the most common known bacterial cause of diarrheal disease, including traveler's diarrhea. CFA/I pili, assembled via the alternate chaperone pathway, are essential for binding and colonization of the small bowel by these pathogenic bacteria. Herein, we elucidate unique structural features of CFA/I pili that appear to optimize their function as bacterial tethers in the intestinal tract. Using transmission electron microscopy of negatively stained samples in combination with iterative three-dimensional helical reconstruction methods for image processing, we determined the structure of the CFA/I pilus filament. Our results indicate that strong end-to-end protein interactions and weak interactions between the coils of a sturdy spring-like helix provide the combination of strength, stability, and flexibility required to sustain bacterial adhesion and incite intestinal disease. We propose that CFA/I pili behave like a spring to maintain attachment to the gut lining during vortex mixing and downward flow of the intestinal contents, thereby persisting long enough for these bacteria to colonize the host epithelium and cause enteric disease.

Predicted Bacterial Interactions Affect in Vivo Microbial Colonization Dynamics in Nematostella

PubMed Central

Domin, Hanna; Zurita-Gutiérrez, Yazmín H.; Scotti, Marco; Buttlar, Jann; Hentschel Humeida, Ute; Fraune, Sebastian

2018-01-01

The maintenance and resilience of host-associated microbiota during development is a fundamental process influencing the fitness of many organisms. Several host properties were identified as influencing factors on bacterial colonization, including the innate immune system, mucus composition, and diet. In contrast, the importance of bacteria–bacteria interactions on host colonization is less understood. Here, we use bacterial abundance data of the marine model organism Nematostella vectensis to reconstruct potential bacteria–bacteria interactions through co-occurrence networks. The analysis indicates that bacteria–bacteria interactions are dynamic during host colonization and change according to the host’s developmental stage. To assess the predictive power of inferred interactions, we tested bacterial isolates with predicted cooperative or competitive behavior for their ability to influence bacterial recolonization dynamics. Within 3 days of recolonization, all tested bacterial isolates affected bacterial community structure, while only competitive bacteria increased bacterial diversity. Only 1 week after recolonization, almost no differences in bacterial community structure could be observed between control and treatments. These results show that predicted competitive bacteria can influence community structure for a short period of time, verifying the in silico predictions. However, within 1 week, the effects of the bacterial isolates are neutralized, indicating a high degree of resilience of the bacterial community. PMID:29740401

Assessing the interactions of a natural antibacterial clay with model Gram-positive and Gram-negative human pathogens

NASA Astrophysics Data System (ADS)

Londono, S. C.; Williams, L. B.

2013-12-01

The emergence of antibiotic resistant bacteria and increasing accumulations of antibiotics in reclaimed water, drive the quest for new natural antimicrobials. We are studying the antibacterial mechanism(s) of clays that have shown an ability to destroy bacteria or significantly inhibit their growth. One possible mode of action is from soluble transition metal species, particularly reduced Fe, capable of generating deleterious oxygen radical species. Yet another possibility is related to membrane damage as a consequence of physical or electrostatic interaction between clay and bacteria. Both mechanisms could combine to produce cell death. This study addresses a natural antibacterial clay from the NW Amazon basin, South America (AMZ clay). Clay mineralogy is composed of disordered kaolinite (28.9%), halloysite (17.8%) illite (12%) and smectite (16.7%). Mean particle size is 1.6μm and total and specific surface area 278.82 and 51.23 m2/g respectively. The pH of a suspension (200mg/ml) is 4.1 and its Eh is 361mV after 24h of equilibration. The ionic strength of the water in equilibrium with the clay after 24 h. is 6 x10-4M. These conditions, affect the element solubility, speciation, and interactions between clay and bacteria. Standard microbiological methods were used to assess the viability of two model bacteria (Escherichia coli and Bacillus subtilis) after incubation with clay at 37 degC for 24 hrs. A threefold reduction in bacterial viability was observed upon treatment with AMZ clay. We separated the cells from the clay using Nycodenz gradient media and observed the mounts under the TEM and SEM. Results showed several membrane anomalies and structural changes that were not observed in the control cells. Additionally, clay minerals appeared in some places attached to cell walls. Experiments showed that exchanging AMZ clay with KCl caused loss of antibacterial property. Among the exchangeable -and potentially toxic- ions we measured Al+3, Cu+2, Zn+2, Ba+2 and Co+2. Besides being toxic at high concentrations, these species affect the electrophoretic interactions between clay and bacteria surfaces. Additionally, the cation exchange neutralizes the clay surface charge thus modifying further the behavior of particles in suspension. Therefore, we evaluated the clay and bacteria zeta potential (ζ) as an index for possible electrostatic forces and modeled the total interactions using DLVO theory. We suspended the particles in water equilibrated with clay (leachate). Results show that at pH 4, the ζ of clays is -14 mV while it is -3mV for bacteria. The divalent ions and trivalent Aluminum, present in the AMZ leachate, compress the thickness of the double layer (hydration shell) thus decreasing electrostatic repulsion and allowing particles to come closer. The proximity of particles increases the probability of attractive forces to bind clays and cells. In summary, results indicate that a process other than simple chemical transfer from clay to bacteria is operating. The electrostatic attraction and physical proximity may enhance the toxic action of metals and interfere with the membrane properties or processes.

Propagating annular modes

NASA Astrophysics Data System (ADS)

Sheshadri, A.; Plumb, R. A.

2017-12-01

The leading "annular mode", defined as the dominant EOF of surface pressure or of zonal mean zonal wind variability, appears as a dipolar structure straddling the mean midlatitude jet and thus seems to describe north-south wobbling of the jet latitude. However, extratropical zonal wind anomalies frequently tend to migrate poleward. This behavior can be described by the first two EOFs, the first (AM1) being the dipolar structure, and the second (AM2) having a tripolar structure centered on the mean jet. Taken in isolation, AM1 thus describes a north-south wobbling of the jet position, while AM2 describes a strengthening and narrowing of the jet. However, despite the fact that they are spatially orthogonal, and their corresponding time series temporally orthogonal, AM1 and AM2 are not independent, but show significant lag-correlations which reveal the propagation. The EOFs are not modes of the underlying dynamical system governing the zonal flow evolution. The true modes can be estimated using principal oscillation pattern (POP) analysis. In the troposphere, the leading POPs manifest themselves as a pair of complex conjugate structures with conjugate eigenvalues thus, in reality, constituting a single, complex, mode that describes propagating anomalies. Even though the principal components associated with the two leading EOFs decay at different rates, each decays faster than the true mode. These facts have implications for eddy feedback and the susceptibility of the mode to external perturbations. If one interprets the annular modes as the modes of the system, then simple theory predicts that the response to steady forcing will usually be dominated by AM1 (with the longest time scale). However, such arguments should really be applied to the true modes. Experiments with a simplified GCM show that climate response to perturbations do not necessarily have AM1 structures. Implications of these results for stratosphere-troposphere interactions are explored. The POP structures are shown to be independent of any weighting (unlike the EOFs, the structures and time scales of which change substantially with pressure weighting), a fact that is particularly important for a deep system such as the troposphere and stratospere. The structure and time evolution of coupled modes of the troposphere-stratosphere system are studied.

A Mixed-Mode (I-II) Fracture Criterion for AS4/8552 Carbon/Epoxy Composite Laminate

NASA Astrophysics Data System (ADS)

Karnati, Sidharth Reddy

A majority of aerospace structures are subjected to bending and stretching loads that introduce peel and shear stresses between the plies of a composite laminate. These two stress components cause a combination of mode I and II fracture modes in the matrix layer of the composite laminate. The most common failure mode in laminated composites is delamination that affects the structural integrity of composite structures. Damage tolerant designs of structures require two types of materials data: mixed-mode (I-II) delamination fracture toughness that predicts failure and delamination growth rate that predicts the life of the structural component. This research focuses determining mixed-mode (I-II) fracture toughness under a combination of mode I and mode II stress states and then a fracture criterion for AS4/8552 composite laminate, which is widely used in general aviation. The AS4/8552 prepreg was supplied by Hexcel Corporation and autoclave fabricated into a 20-ply unidirectional laminate with an artificial delamination by a Fluorinated Ethylene Propylene (FEP) film at the mid-plane. Standard split beam specimens were prepared and tested in double cantilever beam (DCB) and end notched flexure modes to determine mode I (GIC) and II (GIIC) fracture toughnesses, respectively. The DCB specimens were also tested in a modified mixed-mode bending apparatus at GIIm /GT ratios of 0.18, 0.37, 0.57 and 0.78, where GT is total and GIIm is the mode II component of energy release rates. The measured fracture toughness, GC, was found to follow the locus a power law equation. The equation was validated for the present and literature experimental data.

Synthetic analogs of bacterial quorum sensors

DOEpatents

Iyer, Rashi [Los Alamos, NM; Ganguly, Kumkum [Los Alamos, NM; Silks, Louis A [Los Alamos, NM

2011-12-06

Bacterial quorum-sensing molecule analogs having the following structures: ##STR00001## and methods of reducing bacterial pathogenicity, comprising providing a biological system comprising pathogenic bacteria which produce natural quorum-sensing molecule; providing a synthetic bacterial quorum-sensing molecule having the above structures and introducing the synthetic quorum-sensing molecule into the biological system comprising pathogenic bacteria. Further is provided a method of targeted delivery of an antibiotic, comprising providing a synthetic quorum-sensing molecule; chemically linking the synthetic quorum-sensing molecule to an antibiotic to produce a quorum-sensing molecule-antibiotic conjugate; and introducing the conjugate into a biological system comprising pathogenic bacteria susceptible to the antibiotic.

Synthetic analogs of bacterial quorum sensors

DOEpatents

Iyer, Rashi S.; Ganguly, Kumkum; Silks, Louis A.

2013-01-08

Bacterial quorum-sensing molecule analogs having the following structures: ##STR00001## and methods of reducing bacterial pathogenicity, comprising providing a biological system comprising pathogenic bacteria which produce natural quorum-sensing molecule; providing a synthetic bacterial quorum-sensing molecule having the above structures and introducing the synthetic quorum-sensing molecule into the biological system comprising pathogenic bacteria. Further is provided a method of targeted delivery of an antibiotic, comprising providing a synthetic quorum-sensing molecule; chemically linking the synthetic quorum-sensing molecule to an antibiotic to produce a quorum-sensing molecule-antibiotic conjugate; and introducing the conjugate into a biological system comprising pathogenic bacteria susceptible to the antibiotic.

Expanding the Use of a Fluorogenic Method to Determine Activity and Mode of Action of Bacillus thuringiensis Bacteriocins Against Gram-Positive and Gram-Negative Bacteria

PubMed Central

de la Fuente-Salcido, Norma M.; Barboza-Corona, J. Eleazar; Espino Monzón, A. N.; Pacheco Cano, R. D.; Balagurusamy, N.; Bideshi, Dennis K.; Salcedo-Hernández, Rubén

2012-01-01

Previously we described a rapid fluorogenic method to measure the activity of five bacteriocins produced by Mexican strains of Bacillus thuringiensis against B. cereus 183. Here we standardize this method to efficiently determine the activity of bacteriocins against both Gram-positive and Gram-negative bacteria. It was determined that the crucial parameter required to obtain reproducible results was the number of cells used in the assay, that is, ~4 × 108 cell/mL and ~7 × 108 cell/mL, respectively, for target Gram-positive and Gram-negative bacteria. Comparative analyses of the fluorogenic and traditional well-diffusion assays showed correlation coefficients of 0.88 to 0.99 and 0.83 to 0.99, respectively, for Gram-positive and Gram-negative bacteria. The fluorogenic method demonstrated that the five bacteriocins of B. thuringiensis have bacteriolytic and bacteriostatic activities against all microorganisms tested, including clinically significant bacteria such as Listeria monocytogenes, Proteus vulgaris, and Shigella flexneri reported previously to be resistant to the antimicrobials as determined using the well-diffusion protocol. These results demonstrate that the fluorogenic assay is a more sensitive, reliable, and rapid method when compared with the well-diffusion method and can easily be adapted in screening protocols for bacteriocin production by other microorganisms. PMID:22919330

Autoimmunity: a decision theory model.

PubMed Central

Morris, J A

1987-01-01

Concepts from statistical decision theory were used to analyse the detection problem faced by the body's immune system in mounting immune responses to bacteria of the normal body flora. Given that these bacteria are potentially harmful, that there can be extensive cross reaction between bacterial antigens and host tissues, and that the decisions are made in uncertainty, there is a finite chance of error in immune response leading to autoimmune disease. A model of ageing in the immune system is proposed that is based on random decay in components of the decision process, leading to a steep age dependent increase in the probability of error. The age incidence of those autoimmune diseases which peak in early and middle life can be explained as the resultant of two processes: an exponentially falling curve of incidence of first contact with common bacteria, and a rapidly rising error function. Epidemiological data on the variation of incidence with social class, sibship order, climate and culture can be used to predict the likely site of carriage and mode of spread of the causative bacteria. Furthermore, those autoimmune diseases precipitated by common viral respiratory tract infections might represent reactions to nasopharyngeal bacterial overgrowth, and this theory can be tested using monoclonal antibodies to search the bacterial isolates for cross reacting antigens. If this model is correct then prevention of autoimmune disease by early exposure to low doses of bacteria might be possible. PMID:3818985

2.4 GHz CMOS power amplifier with mode-locking structure to enhance gain.

PubMed

Lee, Changhyun; Park, Changkun

2014-01-01

We propose a mode-locking method optimized for the cascode structure of an RF CMOS power amplifier. To maximize the advantage of the typical mode-locking method in the cascode structure, the input of the cross-coupled transistor is modified from that of a typical mode-locking structure. To prove the feasibility of the proposed structure, we designed a 2.4 GHz CMOS power amplifier with a 0.18 μm RFCMOS process for polar transmitter applications. The measured power added efficiency is 34.9%, while the saturated output power is 23.32 dBm. The designed chip size is 1.4 × 0.6 mm(2).

2.4 GHz CMOS Power Amplifier with Mode-Locking Structure to Enhance Gain

PubMed Central

2014-01-01

We propose a mode-locking method optimized for the cascode structure of an RF CMOS power amplifier. To maximize the advantage of the typical mode-locking method in the cascode structure, the input of the cross-coupled transistor is modified from that of a typical mode-locking structure. To prove the feasibility of the proposed structure, we designed a 2.4 GHz CMOS power amplifier with a 0.18 μm RFCMOS process for polar transmitter applications. The measured power added efficiency is 34.9%, while the saturated output power is 23.32 dBm. The designed chip size is 1.4 × 0.6 mm2. PMID:25045755

Alcohol sensor based on single-mode-multimode-single-mode fiber structure

NASA Astrophysics Data System (ADS)

Mefina Yulias, R.; Hatta, A. M.; Sekartedjo, Sekartedjo

2016-11-01

Alcohol sensor based on Single-mode -Multimode-Single-mode (SMS) fiber structure is being proposed to sense alcohol concentration in alcohol-water mixtures. This proposed sensor uses refractive index sensing as its sensing principle. Fabricated SMS fiber structure had 40 m of multimode length. With power input -6 dBm and wavelength 1550 nm, the proposed sensor showed good response with sensitivity 1,983 dB per % v/v with measurement range 05 % v/v and measurement span 0,5% v/v.

Bacterial signaling ecology and potential applications during aquatic biofilm construction.

PubMed

Vega, Leticia M; Alvarez, Pedro J; McLean, Robert J C

2014-07-01

In their natural environment, bacteria and other microorganisms typically grow as surface-adherent biofilm communities. Cell signal processes, including quorum signaling, are now recognized as being intimately involved in the development and function of biofilms. In contrast to their planktonic (unattached) counterparts, bacteria within biofilms are notoriously resistant to many traditional antimicrobial agents and so represent a major challenge in industry and medicine. Although biofilms impact many human activities, they actually represent an ancient mode of bacterial growth as shown in the fossil record. Consequently, many aquatic organisms have evolved strategies involving signal manipulation to control or co-exist with biofilms. Here, we review the chemical ecology of biofilms and propose mechanisms whereby signal manipulation can be used to promote or control biofilms.

The essential features and modes of bacterial polar growth.

PubMed

Cameron, Todd A; Zupan, John R; Zambryski, Patricia C

2015-06-01

Polar growth represents a surprising departure from the canonical dispersed cell growth model. However, we know relatively little of the underlying mechanisms governing polar growth or the requisite suite of factors that direct polar growth. Underscoring how classic doctrine can be turned on its head, the peptidoglycan layer of polar-growing bacteria features unusual crosslinks and in some species the quintessential cell division proteins FtsA and FtsZ are recruited to the growing poles. Remarkably, numerous medically important pathogens utilize polar growth, accentuating the need for intensive research in this area. Here we review models of polar growth in bacteria based on recent research in the Actinomycetales and Rhizobiales, with emphasis on Mycobacterium and Agrobacterium species. Copyright © 2015 Elsevier Ltd. All rights reserved.

Comparative activity of pradofloxacin against anaerobic bacteria isolated from dogs and cats.

PubMed

Silley, Peter; Stephan, Bernd; Greife, Heinrich A; Pridmore, Andrew

2007-11-01

To compare the intrinsic activity of pradofloxacin, a new fluoroquinolone developed for use in veterinary medicine, with other fluoroquinolones, against anaerobic bacteria isolated from dogs and cats. One hundred and forty-one anaerobes were isolated from dogs and cats and comparative MICs of pradofloxacin, marbofloxacin, enrofloxacin, difloxacin and ibafloxacin were determined according to standardized agar dilution methodology. Pradofloxacin exerted the greatest antibacterial activity followed by marbofloxacin, enrofloxacin, difloxacin and ibafloxacin. Based on the distinctly lower MIC(50), MIC(90) and mode MIC values, pradofloxacin exhibited a higher in vitro activity than any of the comparator fluoroquinolones. Pradofloxacin, a novel third-generation fluoroquinolone, has broad-spectrum anti-anaerobe activity and offers utility as single-drug therapy for mixed aerobic/anaerobic infections.

Animal Viruses, Bacteria, and Cancer: A Brief Commentary

PubMed Central

Efird, Jimmy T.; Davies, Stephen W.; O’Neal, Wesley T.; Anderson, Ethan J.

2014-01-01

Animal viruses and bacteria are ubiquitous in the environment. However, little is known about their mode of transmission and etiologic role in human cancers, especially among high-risk groups (e.g., farmers, veterinarians, poultry plant workers, pet owners, and infants). Many factors may affect the survival, transmissibility, and carcinogenicity of these agents, depending on the animal-host environment, hygiene practices, climate, travel, herd immunity, and cultural differences in food consumption and preparation. Seasonal variations in immune function also may increase host susceptibility at certain times of the year. The lack of objective measures, inconsistent study designs, and sources of epidemiologic bias (e.g., residual confounding, recall bias, and non-randomized patient selection) are some of the factors that complicate a clear understanding of this subject. PMID:24592380

THE EFFECT OF STREPTOMYCIN AND PENICILLIN ON THE INFLAMMATORY PROCESS IN IRRADIATED ANIMALS (in Russian)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sosova, V.F.

The importance of the mode of intreduction, the number of administrations and the dose of the antibiotic (penicillin and streptomycin) in the treatment of infectious inflammation in irradiated rabbits (800 r) was studied. In the treatment of skin inflammatory foci, caused by the infection with B. coli, intramuscular administration of streptomycin was ineffective. The introduction of the antibiotic into the focus of inflammation reduced the number of microbes, the effect depending upon the quantity of bacteria in the tissus of the focus and on the dose of the antibiotic. In a number of instances upon introduction of streptomycin into themore » focus there developed very rapidly (in 24 hours) resistant forms of bacteria. (auth)« less

A really useful pathogen, Agrobacterium tumefaciens.

PubMed

Yuan, Ze-Chun; Williams, Mary

2012-10-01

Bacteria of the genus Agrobacterium are very useful and unusual plant pathogens. Through a rare inter-kingdom DNA transfer, the bacteria move some of their genes into their host's genome, thereby inducing the host cells to proliferate and produce opines, nutrients sources for the pathogen. Agrobacterium's ability to transfer DNA makes can be adapted to introduce other genes, such as those encoding useful traits, into plant genomes. The development of Agrobacterium as a tool to transform plants is a landmark event in modern plant biology. This lecture provides an introduction to Agrobacterium tumefaciens and related species, focusing on their modes of pathogenicity, their usefulness as tools for plant transformation, and their use as a model for the study of plant-pathogen interactions.

Bacterial community structures in air conditioners installed in Japanese residential buildings.

PubMed

Hatayama, Kouta; Oikawa, Yurika; Ito, Hiroyuki

2018-01-01

The bacterial community structures in four Japanese split-type air conditioners were analyzed using a next-generation sequencer. A variety of bacteria were detected in the air filter of an air conditioner installed on the first floor. In the evaporator of this air conditioner, bacteria belonging to the genus Methylobacterium, or the family of Sphingomonadaceae, were predominantly detected. On the other hand, the majority of bacteria detected in the air filters and evaporators of air conditioners installed on the fifth and twelfth floors belonged to the family Enterobacteriaceae. The source of bacteria belonging to the family Enterobacteriaceae may have been aerosols generated by toilet flushing in the buildings. Our results suggested the possibility that the bacterial contamination in the air conditioners was affected by the floor level on which they were installed. The air conditioner installed on the lower floor, near the ground, may have been contaminated by a variety of outdoor bacteria, whereas the air conditioners installed on floors more distant from the ground may have been less contaminated by outdoor bacteria. However, these suppositions may apply only to the specific split-type air conditioners that we analyzed, because our sample size was small.

Early Interactions of Rhizobium leguminosarum bv. phaseoli and Bean Roots: Specificity in the Process of Adsorption and Its Requirement of Ca(sup2+) and Mg(sup2+) Ions

PubMed Central

Lodeiro, A. R.; Lagares, A.; Martinez, E. N.; Favelukes, G.

1995-01-01

Roots of Phaseolus vulgaris L. were incubated with dilute suspensions (1 x 10(sup3) to 3 x 10(sup3) bacteria ml(sup-1)) of an antibiotic-resistant indicator strain of Rhizobium leguminosarum bv. phaseoli in mineral medium and washed four times by a standardized procedure prior to quantitation of adsorption (G. Caetano-Anolles and G. Favelukes, Appl. Environ. Microbiol. 52:371-376, 1986). The population of rhizobia remaining adsorbed on roots after washing was homogeneous, as indicated by the first-order course of its desorption by hydrodynamic shear. Rhizobia were maximally active for adsorption in the early stationary phase of growth. The process leading to adsorption was rapid, without an initial lag, and slowed down after 1 h. Adsorption of the indicator strain at 10(sup3) bacteria ml(sup-1) was inhibited to different extents in the presence of 10(sup3) to 10(sup8) antibiotic-sensitive competitor rhizobia ml(sup-1). After a steep rise above 10(sup4) bacteria ml(sup-1), inhibition by heterologous competitors in the concentration range of 10(sup5) to 10(sup7) bacteria ml(sup-1) was markedly less than by homologous strains, while at 10(sup8) bacteria ml(sup-1) it approached the high level of inhibition by the latter. At 10(sup7) bacteria ml(sup-1), all of the heterologous strains tested were consistently less inhibitory than homologous competitors (P < 0.001). These differences in competitive behavior indicate that in the process of adsorption of R. leguminosarum bv. phaseoli to its host bean roots, different modes of adsorption occur and that some of these modes are specific for the microsymbiont (as previously reported for the alfalfa system [G. Caetano-Anolles and G. Favelukes, Appl. Environ. Microbiol. 52:377-381, 1986]). Moreover, whereas the nonspecific process occurred either in the absence or in the presence of Ca(sup2+) and Mg(sup2+) ions, expression of specificity was totally dependent on the presence of those cations. R. leguminosarum bv. phaseoli bacteria adsorbed in the presence of Ca(sup2+) and Mg(sup2+) were more resistant to desorption by shear forces than were rhizobia adsorbed in their absence. These results indicate that (i) symbiotic specificity in the P. vulgaris-R. leguminosarum bv. phaseoli system is expressed already during the early process of rhizobial adsorption to roots, (ii) Ca(sup2+) and Mg(sup2+) ions are required by R. leguminosarum bv. phaseoli for that specificity, and (iii) those cations cause tighter binding of rhizobia to roots. PMID:16535005

EH 11n modes E type in the disk and washer accelerating structure

NASA Astrophysics Data System (ADS)

Andreev, V. G.; Belugin, V. M.; Daikovsky, A. G.; Esin, S. K.; Kravchuk, L. V.; Paramonov, V. V.; Ryabov, A. D.

1983-01-01

The disk and washer accelerating structure has a great deal to do with high-beta structures progress. The frequencies and electromagnetic fields for modes, which have a different number of azimuthal variations, are calculated to determined the dispersion properties and other characteristics of parasitic modes in a disc and washer accelerating structure. The main attention was given to the accelerating structure of the linear accelerator of the Institute for Nuclear Research (INR) of the USSR Academy of Sciences. Modification of a structure for PIGMI accelerator (LANL, USA) is considered briefly.

Nonlinear Evolution of Counter-Propagating Whistler Mode Waves Excited by Anisotropic Electrons Within the Equatorial Source Region: 1-D PIC Simulations

NASA Astrophysics Data System (ADS)

Chen, Huayue; Gao, Xinliang; Lu, Quanming; Sun, Jicheng; Wang, Shui

2018-02-01

Nonlinear physical processes related to whistler mode waves are attracting more and more attention for their significant role in reshaping whistler mode spectra in the Earth's magnetosphere. Using a 1-D particle-in-cell simulation model, we have investigated the nonlinear evolution of parallel counter-propagating whistler mode waves excited by anisotropic electrons within the equatorial source region. In our simulations, after the linear phase of whistler mode instability, the strong electrostatic standing structures along the background magnetic field will be formed, resulting from the coupling between excited counter-propagating whistler mode waves. The wave numbers of electrostatic standing structures are about twice those of whistler mode waves generated by anisotropic hot electrons. Moreover, these electrostatic standing structures can further be coupled with either parallel or antiparallel propagating whistler mode waves to excite high-k modes in this plasma system. Compared with excited whistler mode waves, these high-k modes typically have 3 times wave number, same frequency, and about 2 orders of magnitude smaller amplitude. Our study may provide a fresh view on the evolution of whistler mode waves within their equatorial source regions in the Earth's magnetosphere.

One-way mode transmission in one-dimensional phononic crystal plates

NASA Astrophysics Data System (ADS)

Zhu, Xuefeng; Zou, Xinye; Liang, Bin; Cheng, Jianchun

2010-12-01

We investigate theoretically the band structures of one-dimensional phononic crystal (PC) plates with both antisymmetric and symmetric structures, and show how unidirectional transmission behavior can be obtained for either antisymmetric waves (A modes) or symmetric waves (S modes) by exploiting mode conversion and selection in the linear plate systems. The theoretical approach is illustrated for one PC plate example where unidirectional transmission behavior is obtained in certain frequency bands. Employing harmonic frequency analysis, we numerically demonstrate the one-way mode transmission for the PC plate with finite superlattice by calculating the steady-state displacement fields under A modes source (or S modes source) in forward and backward direction, respectively. The results show that the incident waves from A modes source (or S modes source) are transformed into S modes waves (or A modes waves) after passing through the superlattice in the forward direction and the Lamb wave rejections in the backward direction are striking with a power extinction ratio of more than 1000. The present structure can be easily extended to two-dimensional PC plate and efficiently encourage practical studies of experimental realization which is believed to have much significance for one-way Lamb wave mode transmission.

Label-Free Biological and Chemical Sensing Using Whispering Gallery Mode Optical Resonators: Past, Present, and Future

PubMed Central

Su, Judith

2017-01-01

Sensitive and rapid label-free biological and chemical sensors are needed for a wide variety of applications including early disease diagnosis and prognosis, the monitoring of food and water quality, as well as the detection of bacteria and viruses for public health concerns and chemical threat sensing. Whispering gallery mode optical resonator based sensing is a rapidly developing field due to the high sensitivity and speed of these devices as well as their label-free nature. Here, we describe the history of whispering gallery mode optical resonator sensors, the principles behind detection, the latest developments in the fields of biological and chemical sensing, current challenges toward widespread adoption of these devices, and an outlook for the future. In addition, we evaluate the performance capabilities of these sensors across three key parameters: sensitivity, selectivity, and speed. PMID:28282881

Urease Inhibition in the Presence of N-(n-Butyl)thiophosphoric Triamide, a Suicide Substrate: Structure and Kinetics.

PubMed

Mazzei, Luca; Cianci, Michele; Contaldo, Umberto; Musiani, Francesco; Ciurli, Stefano

2017-10-10

The nickel-dependent enzyme urease is a virulence factor for a large number of pathogenic and antibiotic-resistant bacteria, as well as a negative factor for the efficiency of soil nitrogen fertilization for crop production. The use of urease inhibitors to offset these effects requires knowledge, at a molecular level, of their mode of action. The 1.28 Å resolution structure of the enzyme-inhibitor complex obtained upon incubation of Sporosarcina pasteurii urease with N-(n-butyl)thiophosphoric triamide (NBPT), a molecule largely utilized in agriculture, reveals the presence of the monoamidothiophosphoric acid (MATP) moiety, obtained upon enzymatic hydrolysis of the diamide derivative of NBPT (NBPD) to yield n-butyl amine. MATP is bound to the two Ni(II) ions in the active site of urease using a μ 2 -bridging O atom and terminally bound O and NH 2 groups, with the S atom of the thiophosphoric amide pointing away from the metal center. The mobile flap modulating the size of the active site cavity is found in the closed conformation. Docking calculations suggest that the interaction between urease in the open flap conformation and NBPD involves a role for the conserved αArg339 in capturing and orienting the inhibitor prior to flap closure. Calorimetric and spectrophotometric determinations of the kinetic parameters of this inhibition indicate the occurrence of a reversible slow inhibition mode of action, characterized, for both bacterial and plant ureases, by a very small value of the dissociation constant of the urease-MATP complex. No need to convert NBPT to its oxo derivative NBPTO, as previously proposed, is necessary for urease inhibition.

Structural Analysis of the Hg(II)-Regulatory Protein Tn501 MerR from Pseudomonas aeruginosa

PubMed Central

Wang, Dan; Huang, Shanqing; Liu, Pingying; Liu, Xichun; He, Yafeng; Chen, Weizhong; Hu, Qingyuan; Wei, Tianbiao; Gan, Jianhua; Ma, Jing; Chen, Hao

2016-01-01

The metalloprotein MerR is a mercury(II)-dependent transcriptional repressor-activator that responds to mercury(II) with extraordinary sensitivity and selectivity. It’s widely distributed in both Gram-negative and Gram-positive bacteria but with barely detectable sequence identities between the two sources. To provide structural basis for the considerable biochemical and biophysical experiments previously performed on Tn501 and Tn21 MerR from Gram-negative bacteria, we analyzed the crystal structure of mercury(II)-bound Tn501 MerR. The structure in the metal-binding domain provides Tn501 MerR with a high affinity for mercury(II) and the ability to distinguish mercury(II) from other metals with its unique planar trigonal coordination geometry, which is adopted by both Gram-negative and Gram-positive bacteria. The mercury(II) coordination state in the C-terminal metal-binding domain is transmitted through the allosteric network across the dimer interface to the N-terminal DNA-binding domain. Together with the previous mutagenesis analyses, the present data indicate that the residues in the allosteric pathway have a central role in maintaining the functions of Tn501 MerR. In addition, the complex structure exhibits significant differences in tertiary and quaternary structural arrangements compared to those of Bacillus MerR from Gram-positive bacteria, which probably enable them to function with specific promoter DNA with different spacers between −35 and −10 elements. PMID:27641146

Coevolutionary diversification creates nested-modular structure in phage–bacteria interaction networks

PubMed Central

Beckett, Stephen J.; Williams, Hywel T. P.

2013-01-01

Phage and their bacterial hosts are the most diverse and abundant biological entities in the oceans, where their interactions have a major impact on marine ecology and ecosystem function. The structure of interaction networks for natural phage–bacteria communities offers insight into their coevolutionary origin. At small phylogenetic scales, observed communities typically show a nested structure, in which both hosts and phages can be ranked by their range of resistance and infectivity, respectively. A qualitatively different multi-scale structure is seen at larger phylogenetic scales; a natural assemblage sampled from the Atlantic Ocean displays large-scale modularity and local nestedness within each module. Here, we show that such ‘nested-modular’ interaction networks can be produced by a simple model of host–phage coevolution in which infection depends on genetic matching. Negative frequency-dependent selection causes diversification of hosts (to escape phages) and phages (to track their evolving hosts). This creates a diverse community of bacteria and phage, maintained by kill-the-winner ecological dynamics. When the resulting communities are visualized as bipartite networks of who infects whom, they show the nested-modular structure characteristic of the Atlantic sample. The statistical significance and strength of this observation varies depending on whether the interaction networks take into account the density of the interacting strains, with implications for interpretation of interaction networks constructed by different methods. Our results suggest that the apparently complex community structures associated with marine bacteria and phage may arise from relatively simple coevolutionary origins. PMID:24516719

Spatial variation in the bacterial and denitrifying bacterial community in a biofilter treating subsurface agricultural drainage.

PubMed

Andrus, J Malia; Porter, Matthew D; Rodríguez, Luis F; Kuehlhorn, Timothy; Cooke, Richard A C; Zhang, Yuanhui; Kent, Angela D; Zilles, Julie L

2014-02-01

Denitrifying biofilters can remove agricultural nitrates from subsurface drainage, reducing nitrate pollution that contributes to coastal hypoxic zones. The performance and reliability of natural and engineered systems dependent upon microbially mediated processes, such as the denitrifying biofilters, can be affected by the spatial structure of their microbial communities. Furthermore, our understanding of the relationship between microbial community composition and function is influenced by the spatial distribution of samples.In this study we characterized the spatial structure of bacterial communities in a denitrifying biofilter in central Illinois. Bacterial communities were assessed using automated ribosomal intergenic spacer analysis for bacteria and terminal restriction fragment length polymorphism of nosZ for denitrifying bacteria.Non-metric multidimensional scaling and analysis of similarity (ANOSIM) analyses indicated that bacteria showed statistically significant spatial structure by depth and transect,while denitrifying bacteria did not exhibit significant spatial structure. For determination of spatial patterns, we developed a package of automated functions for the R statistical environment that allows directional analysis of microbial community composition data using either ANOSIM or Mantel statistics.Applying this package to the biofilter data, the flow path correlation range for the bacterial community was 6.4 m at the shallower, periodically in undated depth and 10.7 m at the deeper, continually submerged depth. These spatial structures suggest a strong influence of hydrology on the microbial community composition in these denitrifying biofilters. Understanding such spatial structure can also guide optimal sample collection strategies for microbial community analyses.

75 FR 36423 - Government-Owned Inventions; Availability for Licensing

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-25

... tested for antimicrobial activity against drug resistant bacteria, methicillin- resistant Staphylococcus.... Advantages: Structurally distinct antimicrobial compounds. Attack newly validated antibacterial targeted... GTPase activity. Inhibit drug-susceptible and drug-resistant bacteria. Development Status: [[Page 36424...

Self-Similarity of Plasmon Edge Modes on Koch Fractal Antennas.

PubMed

Bellido, Edson P; Bernasconi, Gabriel D; Rossouw, David; Butet, Jérémy; Martin, Olivier J F; Botton, Gianluigi A

2017-11-28

We investigate the plasmonic behavior of Koch snowflake fractal geometries and their possible application as broadband optical antennas. Lithographically defined planar silver Koch fractal antennas were fabricated and characterized with high spatial and spectral resolution using electron energy loss spectroscopy. The experimental data are supported by numerical calculations carried out with a surface integral equation method. Multiple surface plasmon edge modes supported by the fractal structures have been imaged and analyzed. Furthermore, by isolating and reproducing self-similar features in long silver strip antennas, the edge modes present in the Koch snowflake fractals are identified. We demonstrate that the fractal response can be obtained by the sum of basic self-similar segments called characteristic edge units. Interestingly, the plasmon edge modes follow a fractal-scaling rule that depends on these self-similar segments formed in the structure after a fractal iteration. As the size of a fractal structure is reduced, coupling of the modes in the characteristic edge units becomes relevant, and the symmetry of the fractal affects the formation of hybrid modes. This analysis can be utilized not only to understand the edge modes in other planar structures but also in the design and fabrication of fractal structures for nanophotonic applications.

Giant amplification in degenerate band edge slow-wave structures interacting with an electron beam

DOE Office of Scientific and Technical Information (OSTI.GOV)

Othman, Mohamed A. K.; Veysi, Mehdi; Capolino, Filippo

2016-03-15

We propose a new amplification regime based on a synchronous operation of four degenerate electromagnetic (EM) modes in a slow-wave structure and the electron beam, referred to as super synchronization. These four EM modes arise in a Fabry-Pérot cavity when degenerate band edge (DBE) condition is satisfied. The modes interact constructively with the electron beam resulting in superior amplification. In particular, much larger gains are achieved for smaller beam currents compared to conventional structures based on synchronization with only a single EM mode. We demonstrate giant gain scaling with respect to the length of the slow-wave structure compared to conventionalmore » Pierce type single mode traveling wave tube amplifiers. We construct a coupled transmission line model for a loaded waveguide slow-wave structure exhibiting a DBE, and investigate the phenomenon of giant gain via super synchronization using the Pierce model generalized to multimode interaction.« less

A novel optical waveguide LP01/LP02 mode converter

NASA Astrophysics Data System (ADS)

Shen, Dongya; Wang, Changhui; Ma, Chuan; Mellah, Hakim; Zhang, Xiupu; Yuan, Hong; Ren, Wenping

2018-07-01

A novel optical waveguide LP01 /LP02 mode converter is proposed using combination of bicone structure based on the coupled-mode theory. It is composed of a cladding, a tapered core and combined bicone structure. It is found that this mode converter can have operating bandwidth of 1350-1700 nm, i.e. 350 nm, with a conversion efficiency of ∼90% (∼0.5 dB) and low crosstalk from other modes

Molecular mechanics of Staphylococcus aureus adhesin, CNA, and the inhibition of bacterial adhesion by stretching collagen

PubMed Central

Madani, Ali; Garakani, Kiavash

2017-01-01

Bacterial adhesion to collagen, the most abundant protein in humans, is a critical step in the initiation and persistence of numerous bacterial infections. In this study, we explore the collagen binding mechanism of the multi-modular cell wall anchored collagen adhesin (CNA) in Staphylococcus aureus and examine how applied mechanical forces can modulate adhesion ability. The common structural-functional elements and domain organization of CNA are present across over 50 genera of bacteria. Through the use of molecular dynamics models and normal mode analysis, we shed light on the CNA’s structural and conformational dynamics and its interactions with collagen that lead to collagen binding. Our results suggest that the linker region, CNA165-173, acts as a hinge exhibiting bending, extensional, and torsional modes of structural flexibility and its residues are key in the interaction of the CNA-collagen complex. Steered molecular dynamics simulations were conducted with umbrella sampling. During the course of these simulations, the ‘locking’ latch from the CNA N2 domain was dissociated from its groove in the CNA N1 domain, implying the importance of the latch for effective ligand binding. Finally, we observed that the binding efficiency of the CNA N1-N2 domains to collagen decreases greatly with increasing tensile force application to the collagen peptides. Thus, CNA and similar adhesins might preferentially bind to sites in which collagen fibers are cleaved, such as in wounded, injured, or inflamed tissues, or in which the collagenous tissue is less mature. As alternative techniques for control of bacterial infection are in-demand due to the rise of bacterial antibiotic resistance, results from our computational studies with respect to the mechanoregulation of the collagen binding site may inspire new therapeutics and engineering solutions by mechanically preventing colonization and/or further pathogenesis. PMID:28665944

Analyses and tests of the B-1 aircraft structural mode control system

NASA Technical Reports Server (NTRS)

Wykes, J. H.; Byar, T. R.; Macmiller, C. J.; Greek, D. C.

1980-01-01

Analyses and flight tests of the B-1 structural mode control system (SMCS) are presented. Improvements in the total dynamic response of a flexible aircraft and the benefits to ride qualities, handling qualities, crew efficiency, and reduced dynamic loads on the primary structures, were investigated. The effectiveness and the performance of the SMCS, which uses small aerodynamic surfaces at the vehicle nose to provide damping to the structural modes, were evaluated.

Spillover stabilization and decentralized modal control of large space structures

NASA Technical Reports Server (NTRS)

Czajkowski, Eva A.; Preumont, Andre

1987-01-01

The stabilization of the neglected dynamics of the higher modes of vibration in large space structures is studied, and the influence of the structure of the plant noise intensity matrix of the Kalman-Bucy filter on the stability margin of the residual modes is shown. An optimization procedure uses information on the residual modes to minimize spillover of known residual modes while preserving robustness with respect to the unknown dynamics, and the optimum plant noise intensity matrix is selected to maximize the stability margins of the residual modes and to properly place the observer poles. Examples for both centralized and decentralized control are considered.

Mode of Infection of Metarhizium spp. Fungus and Their Potential as Biological Control Agents

PubMed Central

Aw, Kimberly Moon San; Hue, Seow Mun

2017-01-01

Chemical insecticides have been commonly used to control agricultural pests, termites, and biological vectors such as mosquitoes and ticks. However, the harmful impacts of toxic chemical insecticides on the environment, the development of resistance in pests and vectors towards chemical insecticides, and public concern have driven extensive research for alternatives, especially biological control agents such as fungus and bacteria. In this review, the mode of infection of Metarhizium fungus on both terrestrial and aquatic insect larvae and how these interactions have been widely employed will be outlined. The potential uses of Metarhizium anisopliae and Metarhizium acridum biological control agents and molecular approaches to increase their virulence will be discussed. PMID:29371548

Analysis of complex elastic structures by a Rayleigh-Ritz component modes method using Lagrange multipliers. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Klein, L. R.

1974-01-01

The free vibrations of elastic structures of arbitrary complexity were analyzed in terms of their component modes. The method was based upon the use of the normal unconstrained modes of the components in a Rayleigh-Ritz analysis. The continuity conditions were enforced by means of Lagrange Multipliers. Examples of the structures considered are: (1) beams with nonuniform properties; (2) airplane structures with high or low aspect ratio lifting surface components; (3) the oblique wing airplane; and (4) plate structures. The method was also applied to the analysis of modal damping of linear elastic structures. Convergence of the method versus the number of modes per component and/or the number of components is discussed and compared to more conventional approaches, ad-hoc methods, and experimental results.

Improved Numerical Calculation of the Single-Mode-No-Core-Single-Mode Fiber Structure Using the Fields Far from Cutoff Approximation

PubMed Central

Yang, Xianchao; Xu, Degang; Rong, Feng; Zhao, Junfa; Yao, Jianquan

2017-01-01

Multimode interferometers based on the single-mode-no-core-single-mode fiber (SNCS) structure have been widely investigated as functional devices and sensors. However, the theoretical support for the sensing mechanism is still imperfect, especially for the cladding refractive index response. In this paper, a modified model of no-core fiber (NCF) based on far from cut-off approximation is proposed to investigate the spectrum characteristic and sensing mechanism of the SNCS structure. Guided-mode propagation analysis (MPA) is used to analyze the self-image effect and spectrum response to the cladding refractive index and temperature. Verified by experiments, the performance of the SNCS structure can be estimated specifically and easily by the proposed method. PMID:28961174

A symmetry measure for damage detection with mode shapes

NASA Astrophysics Data System (ADS)

Chen, Justin G.; Büyüköztürk, Oral

2017-11-01

This paper introduces a feature for detecting damage or changes in structures, the continuous symmetry measure, which can quantify the amount of a particular rotational, mirror, or translational symmetry in a mode shape of a structure. Many structures in the built environment have geometries that are either symmetric or almost symmetric, however damage typically occurs in a local manner causing asymmetric changes in the structure's geometry or material properties, and alters its mode shapes. The continuous symmetry measure can quantify these changes in symmetry as a novel indicator of damage for data-based structural health monitoring approaches. This paper describes the concept as a basis for detecting changes in mode shapes and detecting structural damage. Application of the method is demonstrated in various structures with different symmetrical properties: a pipe cross-section with a finite element model and experimental study, the NASA 8-bay truss model, and the simulated IASC-ASCE structural health monitoring benchmark structure. The applicability and limitations of the feature in applying it to structures of varying geometries is discussed.

Total synthesis of teixobactin

NASA Astrophysics Data System (ADS)

Jin, Kang; Sam, Iek Hou; Po, Kathy Hiu Laam; Lin, Du'an; Ghazvini Zadeh, Ebrahim H.; Chen, Sheng; Yuan, Yu; Li, Xuechen

2016-08-01

To cope with the global bacterial multidrug resistance, scientific communities have devoted significant efforts to develop novel antibiotics, particularly those with new modes of actions. Teixobactin, recently isolated from uncultured bacteria, is considered as a promising first-in-class drug candidate for clinical development. Herein, we report its total synthesis by a highly convergent Ser ligation approach and this strategy allows us to prepare several analogues of the natural product.

Waves in a plane graphene - dielectric waveguide structure

NASA Astrophysics Data System (ADS)

Evseev, Dmitry A.; Eliseeva, Svetlana V.; Sementsov, Dmitry I.

2017-10-01

The features of the guided TE modes propagation have been investigated on the basis of computer simulations in a planar structure consisting of a set of alternating layers of dielectric and graphene. Within the framework of the effective medium approximation, the dispersion relations have been received for symmetric and antisymmetric waveguide modes, determined by the frequency range of their existence. The wave field distribution by structure, frequency dependences of the constants of propagation and transverse components of the wave vectors, as well as group and phase velocities of waveguide modes have been obtained, the effect of the graphene part in a structure on the waveguide mode behavior has been shown.

Does Initial Leaf Chemistry Affect the Contribution of Insects, Fungi, and Bacteria to Leaf Breakdown in a Lowland Tropical Stream?

NASA Astrophysics Data System (ADS)

Ardon, M.; Pringle, C. M.

2005-05-01

We examined effects of initial leaf chemistry of six common riparian species on the relative contribution of fungi, bacteria, and invertebrates to leaf breakdown in a lowland stream in Costa Rica. We hypothesized that fungi and bacteria would contribute more to the breakdown of species with low concentrations of secondary (tannins and phenolics) and structural (cellulose and lignin) compounds, while invertebrates would be more important in the processing of species with high concentrations of secondary and structural compounds. We incubated single species leaf bags of six common riparian species, representing a range in secondary and structural compounds, in a third-order stream at La Selva Biological Station, Costa Rica. We measured leaf chemistry during the breakdown process. We determined fungal biomass using ergosterol methods, bacteria using DAPI counts, and invertebrate biomass using length-weight regressions. We then used biomass estimates for each group to determine their contribution to the overall breakdown process. Breakdown rates ranged from very fast (Trema integerima, k = 0.23 day-1) to slow (Zygia longifolia , k = 0.011 day-1). While analyses are still under way, preliminary results support our initial hypothesis that fungi contribute more to the break down of leaves from tree species with low concentrations of secondary and structural compounds.

Grazers structure the bacterial and algal diversity of aquatic metacommunities.

PubMed

Birtel, Julia; Matthews, Blake

2016-12-01

Consumers can have strong effects on the biotic and abiotic dynamics of spatially-structured ecosystems. In metacommunities, dispersing consumers can alter local assembly dynamics either directly through trophic interactions or indirectly by modifying local environmental conditions. In aquatic systems, very little is known about how key grazers, such as Daphnia, structure the microbial diversity of metacommunities and influence bacterial-mediated ecosystem functions. In an outdoor mesocosm experiment with replicate metacommunities (two 300 L mesocosms), we tested how the presence and absence of Daphnia and the initial density of the microbial community (manipulated via dilution) influenced the diversity and community structure of algae and bacteria, and several ecosystem properties (e.g., pH, dissolved substances) and functions (e.g., enzyme activity, respiration). We found that Daphnia strongly affected the local and regional diversity of both phytoplankton and bacteria, the taxonomic composition of bacterial communities, the biomass of algae, and ecosystem metabolism (i.e., respiration). Diluting the microbial inoculum (0.2-5 μm size fraction) to the metacommunities increased local phytoplankton diversity, decreased bacteria beta-diversity, and changed the relative abundance of bacterial classes. Changes in the rank abundance of different bacterial groups exhibited phylogenetic signal, implying that closely related bacteria species might share similar responses to the presence of Daphnia. © 2016 by the Ecological Society of America.

Surprising Alteration of Antibacterial Activity of 5″-Modified Neomycin against Resistant Bacteria

PubMed Central

Zhang, Jianjun; Chiang, Fang-I; Wu, Long; Czyryca, Przemyslaw Greg; Li, Ding; Chang, Cheng-Wei Tom

2009-01-01

A facile synthetic protocol for the production of neomycin B derivatives with various modifications at the 5″ position has been developed. Structural activity relationship (SAR) against aminoglycoside resistant bacteria equipped with various aminoglycoside-modifying enzymes (AME's) was investigated. Enzymatic and molecular modeling studies reveal that the superb substrate promiscuity of AME's allows the resistant bacteria to cope with diverse structural modifications despite the observation that several derivatives show enhanced antibacterial activity than the parent neomycin. Surprisingly, when testing synthetic neomycin derivatives against other human pathogens, two leads exhibit prominent activity against both Methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE) that are known to exert high level of resistance against clinically used aminoglycosides. These findings can be extremely useful in developing new aminoglycoside antibiotics against resistant bacteria. Our result also suggests that new biological and antimicrobial activities can be obtained by chemical modifications of old drugs. PMID:19012394

Scaling of mode shapes from operational modal analysis using harmonic forces

NASA Astrophysics Data System (ADS)

Brandt, A.; Berardengo, M.; Manzoni, S.; Cigada, A.

2017-10-01

This paper presents a new method for scaling mode shapes obtained by means of operational modal analysis. The method is capable of scaling mode shapes on any structure, also structures with closely coupled modes, and the method can be used in the presence of ambient vibration from traffic or wind loads, etc. Harmonic excitation can be relatively easily accomplished by using general-purpose actuators, also for force levels necessary for driving large structures such as bridges and highrise buildings. The signal processing necessary for mode shape scaling by the proposed method is simple and the method can easily be implemented in most measurement systems capable of generating a sine wave output. The tests necessary to scale the modes are short compared to typical operational modal analysis test time. The proposed method is thus easy to apply and inexpensive relative to some other methods for scaling mode shapes that are available in literature. Although it is not necessary per se, we propose to excite the structure at, or close to, the eigenfrequencies of the modes to be scaled, since this provides better signal-to-noise ratio in the response sensors, thus permitting the use of smaller actuators. An extensive experimental activity on a real structure was carried out and the results reported demonstrate the feasibility and accuracy of the proposed method. Since the method utilizes harmonic excitation for the mode shape scaling, we propose to call the method OMAH.

Single-mode annular chirally-coupled core fibers for fiber lasers

NASA Astrophysics Data System (ADS)

Zhang, Haitao; Hao, He; He, Linlu; Gong, Mali

2018-03-01

Chirally-coupled core (CCC) fiber can transmit single fundamental mode and effectively suppresses higher-order mode (HOM) propagation, thus improve the beam quality. However, the manufacture of CCC fiber is complicated due to its small side core. To decrease the manufacture difficulty in China, a novel fiber structure is presented, defined as annular chirally-coupled core (ACCC) fiber, replacing the small side core by a larger side annulus. In this paper, we designed the fiber parameters of this new structure, and demonstrated that the new structure has a similar property of single mode with traditional CCC fiber. Helical coordinate system was introduced into the finite element method (FEM) to analyze the mode field in the fiber, and the beam propagation method (BPM) was employed to analyze the influence of the fiber parameters on the mode loss. Based on the result above, the fiber structure was optimized for efficient single-mode transmission, in which the core diameter is 35 μm with beam quality M2 value of 1.04 and an optical to optical conversion efficiency of 84%. In this fiber, fundamental mode propagates in an acceptable loss, while the HOMs decay rapidly.

Ancient acquisition of "alginate utilization loci" by human gut microbiota.

PubMed

Mathieu, Sophie; Touvrey-Loiodice, Mélanie; Poulet, Laurent; Drouillard, Sophie; Vincentelli, Renaud; Henrissat, Bernard; Skjåk-Bræk, Gudmund; Helbert, William

2018-05-23

In bacteria from the phylum Bacteroidetes, the genes coding for enzymes involved in polysaccharide degradation are often colocalized and coregulated in so-called "polysaccharide utilization loci" (PULs). PULs dedicated to the degradation of marine polysaccharides (e.g. laminaran, ulvan, alginate and porphyran) have been characterized in marine bacteria. Interestingly, the gut microbiome of Japanese individuals acquired, by lateral transfer from marine bacteria, the genes involved in the breakdown of porphyran, the cell wall polysaccharide of the red seaweed used in maki. Sequence similarity analyses predict that the human gut microbiome also encodes enzymes for the degradation of alginate, the main cell wall polysaccharide of brown algae. We undertook the functional characterization of diverse polysaccharide lyases from family PL17, frequently found in marine bacteria as well as those of human gut bacteria. We demonstrate here that this family is polyspecific. Our phylogenetic analysis of family PL17 reveals that all alginate lyases, which have all the same specificity and mode of action, cluster together in a very distinct subfamily. The alginate lyases found in human gut bacteria group together in a single clade which is rooted deeply in the PL17 tree. These enzymes were found in PULs containing PL6 enzymes, which also clustered together in the phylogenetic tree of PL6. Together, biochemical and bioinformatics analyses suggest that acquisition of this system appears ancient and, because only traces of two successful transfers were detected upon inspection of PL6 and PL17 families, the pace of acquisition of marine polysaccharide degradation system is probably very slow.

Impact of gut microbiota on neurological diseases: Diet composition and novel treatments.

PubMed

Larroya-García, Ana; Navas-Carrillo, Diana; Orenes-Piñero, Esteban

2018-06-05

Gut microbiota has significant effects on the structure and function of the enteric and central nervous system including human behaviour and brain regulation. Herein, we analyze the role of this intestinal ecosystem, the effects of dietary changes and the administration of nutritional supplements, such as probiotics, prebiotics, or fecal transplantation in neuropsychiatric disorders. Numerous factors have been highlighted to influence gut microbiota composition, including genetics, health status, mode of birth delivery and environment. However, diet composition and nutritional status has been repeatedly shown to be one of the most critical modifiable factors of this ecosystem. A comprehensively analysis of the microbiome-intestine-brain axis has been performed, including the impact of intestinal bacteria in alterations in the nervous, immune and endocrine systems and their metabolites. Finally, we discuss the latest literature examining the effects of diet composition, nutritional status and microbiota alterations in several neuropsychiatric disorders, such as autism, anxiety, depression, Alzheimer's disease and anorexia nervosa.

Microfossils in Carbonaceous Meteorites

NASA Technical Reports Server (NTRS)

Hoover, Richard B.

2009-01-01

Microfossils of large filamentous trichomic prokaryotes have been detected during in-situ investigations of carbonaceous meteorites. This research has been carried out using the Field Emission Scanning Electron Microscope (FESEM) to examine freshly fractured interior surfaces of the meteorites. The images obtained reveal that many of these remains are embedded in the meteorite rock matrix. Energy Dispersive X-Ray Spectroscopy (EDS) studies establish that the filamentous microstructures have elemental compositions consistent with the meteorite matrix, but are often encased within carbon-rich electron transparent sheath-like structures infilled with magnesium sulfate. This is consistent with the taphonomic modes of fossilization of cyanobacteria and sulphur bacteria, since the life habits and processes of these microorganisms frequently result in distinctive chemical biosignatures associated with the properties of their cell-walls, trichomes, and the extracellular polymeric substances (EPS) of the sheath. In this paper the evidence for biogenicity presented includes detailed morphological and morphometric data consistent with known characteristics of uniseriate and multiseriate cyanobacteria. Evidence for indigeneity includes the embedded nature of the fossils and elemental compositions inconsistent with modern biocontaminants.

FTIR spectroscopic study of biofilms formed by the rhizobacterium Azospirillum brasilense Sp245 and its mutant Azospirillum brasilense Sp245.1610

NASA Astrophysics Data System (ADS)

Tugarova, Anna V.; Scheludko, Andrei V.; Dyatlova, Yulia A.; Filip'echeva, Yulia A.; Kamnev, Alexander A.

2017-07-01

Biofilms are spatially and metabolically structured communities of microorganisms, representing a mode of their existence which is ubiquitous in nature, with cells localised within an extracellular biopolymeric matrix, attached to each other, at an interface. For plant-growth-promoting rhizobacteria (PGPR), the formation of biofilms is of special importance due to their primary localisation at the surface of plant root systems. In this work, FTIR spectroscopy was used, for the first time for bacteria of the genus Azospirillum, to comparatively study 6-day-mature biofilms formed on the surface of ZnSe discs by the rhizobacterium Azospirillum brasilense Sp245 and its mutant A. brasilense Sp245.1610. The mutant strain, having an Omegon Km insertion in the gene of lipid metabolism fabG1 on the plasmid AZOBR_p1, as compared to the wild-type strain Sp245 (see http://dx.doi.org/10.1134/S1022795413110112)

Dynamic allostery of protein alpha helical coiled-coils

PubMed Central

Hawkins, Rhoda J; McLeish, Tom C.B

2005-01-01

Alpha helical coiled-coils appear in many important allosteric proteins such as the dynein molecular motor and bacteria chemotaxis transmembrane receptors. As a mechanism for transmitting the information of ligand binding to a distant site across an allosteric protein, an alternative to conformational change in the mean static structure is an induced change in the pattern of the internal dynamics of the protein. We explore how ligand binding may change the intramolecular vibrational free energy of a coiled-coil, using parameterized coarse-grained models, treating the case of dynein in detail. The models predict that coupling of slide, bend and twist modes of the coiled-coil transmits an allosteric free energy of ∼2kBT, consistent with experimental results. A further prediction is a quantitative increase in the effective stiffness of the coiled-coil without any change in inherent flexibility of the individual helices. The model provides a possible and experimentally testable mechanism for transmission of information through the alpha helical coiled-coil of dynein. PMID:16849225

Molecular structure and vibrational spectroscopic studies of prothionamide by density functional theory

NASA Astrophysics Data System (ADS)

Yilmaz, A.; Bolukbasi, O.

2016-01-01

Prothionamide (PTH) is the secondary drug used against Mycobacterium tuberculosis bacteria and leprosy. The aim of this work was to investigate the potential energy surface map, anharmonic and harmonic vibrational spectra, NBO analysis and ELF (Electron Localization Function) of the title compound using DFT approach with the B3LYP (Becke, three-parameter, Lee-Yang-Parr) exchange-correlation functional with the 6-31G++(d, p) and the Z3POLX basis sets were employed. In the experimental part of this study, FT-Mid IR, FT-Far IR and FT-Raman spectra of the molecule were recorded in the regions 4000-450 cm-1, 700-30 cm-1 and 4000-100 cm-1 respectively in the solid phase. The comparison between calculated and experimental vibrational spectra (infrared and Raman spectra) and assignments of fundamental vibrational modes were characterized by total energy distribution (TED). Theoretical spectra were seen to be in good agreement with those of the experimental ones.

Ozonation of trimethoprim in aqueous solution: identification of reaction products and their toxicity.

PubMed

Kuang, Jiangmeng; Huang, Jun; Wang, Bin; Cao, Qiming; Deng, Shubo; Yu, Gang

2013-05-15

This work aimed to better understand the ozonation process of a typical antibiotic pharmaceutical, trimethoprim in aqueous solution. The parent compound was almost completely degraded with ozone dose up to 3.5 mg/L with no mineralization. Twenty one degradation products were identified using an electrospray quadrupole time-of-flight mass spectrometer. Several ozonation pathways were proposed including hydroxylation, demethylation, carbonylation, deamination and methylene group cleavage. Two species of luminescent bacteria Photobacterium phosphoreum and Vibrio qinghaiensis were selected to assess the toxicity of ozonation products. For P. phosphoreum, higher level of toxicity was observed compared to the parent compound, but a negligible toxicity change was observed for V. qinghaiensis, indicating different modes of action for the same water sample. This was further confirmed by quantitative structure-active relationship analysis. This work proves the dominant role of ozone rather than hydroxyl radicals in the reaction and the potential risk after ozonation. Copyright © 2013 Elsevier Ltd. All rights reserved.

Novel small molecule inhibitors targeting the "switch region" of bacterial RNAP: structure-based optimization of a virtual screening hit.

PubMed

Sahner, J Henning; Groh, Matthias; Negri, Matthias; Haupenthal, Jörg; Hartmann, Rolf W

2013-07-01

Rising resistance against current antibiotics necessitates the development of antibacterial agents with alternative targets. The "switch region" of RNA polymerase (RNAP), addressed by the myxopyronins, could be such a novel target site. Based on a hit candidate discovered by virtual screening, a small library of 5-phenyl-3-ureidothiophene-2-carboxylic acids was synthesized resulting in compounds with increased RNAP inhibition. Hansch analysis revealed π (lipophilicity constant) and σ (Hammet substituent constant) of the substituents at the 5-phenyl moiety to be crucial for activity. The binding mode was proven by the targeted introduction of a moiety mimicking the enecarbamate side chain of myxopyronin into the hit compound, accompanied by enhanced RNAP inhibitory potency. The new compounds displayed good antibacterial activities against Gram positive bacteria and Gram negative Escherichia coli TolC and a reduced resistance frequency compared to the established antibiotic rifampicin. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

Identification of KasA as the cellular target of an anti-tubercular scaffold

PubMed Central

Abrahams, Katherine A.; Chung, Chun-wa; Ghidelli-Disse, Sonja; Rullas, Joaquín; Rebollo-López, María José; Gurcha, Sudagar S.; Cox, Jonathan A. G.; Mendoza, Alfonso; Jiménez-Navarro, Elena; Martínez-Martínez, María Santos; Neu, Margarete; Shillings, Anthony; Homes, Paul; Argyrou, Argyrides; Casanueva, Ruth; Loman, Nicholas J.; Moynihan, Patrick J.; Lelièvre, Joël; Selenski, Carolyn; Axtman, Matthew; Kremer, Laurent; Bantscheff, Marcus; Angulo-Barturen, Iñigo; Izquierdo, Mónica Cacho; Cammack, Nicholas C.; Drewes, Gerard; Ballell, Lluis; Barros, David; Besra, Gurdyal S.; Bates, Robert H.

2016-01-01

Phenotypic screens for bactericidal compounds are starting to yield promising hits against tuberculosis. In this regard, whole-genome sequencing of spontaneous resistant mutants generated against an indazole sulfonamide (GSK3011724A) identifies several specific single-nucleotide polymorphisms in the essential Mycobacterium tuberculosis β-ketoacyl synthase (kas) A gene. Here, this genomic-based target assignment is confirmed by biochemical assays, chemical proteomics and structural resolution of a KasA-GSK3011724A complex by X-ray crystallography. Finally, M. tuberculosis GSK3011724A-resistant mutants increase the in vitro minimum inhibitory concentration and the in vivo 99% effective dose in mice, establishing in vitro and in vivo target engagement. Surprisingly, the lack of target engagement of the related β-ketoacyl synthases (FabH and KasB) suggests a different mode of inhibition when compared with other Kas inhibitors of fatty acid biosynthesis in bacteria. These results clearly identify KasA as the biological target of GSK3011724A and validate this enzyme for further drug discovery efforts against tuberculosis. PMID:27581223

ModeRNA server: an online tool for modeling RNA 3D structures.

PubMed

Rother, Magdalena; Milanowska, Kaja; Puton, Tomasz; Jeleniewicz, Jaroslaw; Rother, Kristian; Bujnicki, Janusz M

2011-09-01

The diverse functional roles of non-coding RNA molecules are determined by their underlying structure. ModeRNA server is an online tool for RNA 3D structure modeling by the comparative approach, based on a template RNA structure and a user-defined target-template sequence alignment. It offers an option to search for potential templates, given the target sequence. The server also provides tools for analyzing, editing and formatting of RNA structure files. It facilitates the use of the ModeRNA software and offers new options in comparison to the standalone program. ModeRNA server was implemented using the Python language and the Django web framework. It is freely available at http://iimcb.genesilico.pl/modernaserver. iamb@genesilico.pl.

Structural adaptations of octaheme nitrite reductases from haloalkaliphilic Thioalkalivibrio bacteria to alkaline pH and high salinity.

PubMed

Popinako, Anna; Antonov, Mikhail; Tikhonov, Alexey; Tikhonova, Tamara; Popov, Vladimir

2017-01-01

Bacteria Tv. nitratireducens and Tv. paradoxus from soda lakes grow optimally in sodium carbonate/NaCl brines at pH range from 9.5 to 10 and salinity from 0.5 to 1.5 M Na+. Octaheme nitrite reductases (ONRs) from haloalkaliphilic bacteria of genus Thioalkalivibrio are stable and active in a wide range of pH (up to 11) and salinity (up to 1 M NaCl). To establish adaptation mechanisms of ONRs from haloalkaliphilic bacteria a comparative analysis of amino acid sequences and structures of ONRs from haloalkaliphilic bacteria and their homologues from non-halophilic neutrophilic bacteria was performed. The following adaptation strategies were observed: (1) strategies specific for halophilic and alkaliphilic proteins (an increase in the number of aspartate and glutamate residues and a decrease in the number of lysine residues on the protein surface), (2) strategies specific for halophilic proteins (an increase in the arginine content and a decrease in the number of hydrophobic residues on the solvent-accessible protein surface), (3) strategies specific for alkaliphilic proteins (an increase in the area of intersubunit hydrophobic contacts). Unique adaptation mechanism inherent in the ONRs from bacteria of genus Thioalkalivibrio was revealed (an increase in the core in the number of tryptophan and phenylalanine residues, and an increase in the number of small side chain residues, such as alanine and valine, in the core).

Confirmation of putative stormwater impact on water quality at a Florida beach by microbial source tracking methods and structure of indicator organism populations.

PubMed

Brownell, M J; Harwood, V J; Kurz, R C; McQuaig, S M; Lukasik, J; Scott, T M

2007-08-01

The effect of a stormwater conveyance system on indicator bacteria levels at a Florida beach was assessed using microbial source tracking methods, and by investigating indicator bacteria population structure in water and sediments. During a rain event, regulatory standards for both fecal coliforms and Enterococcus spp. were exceeded, contrasting with significantly lower levels under dry conditions. Indicator bacteria levels were high in sediments under all conditions. The involvement of human sewage in the contamination was investigated using polymerase chain reaction (PCR) assays for the esp gene of Enterococcus faecium and for the conserved T antigen of human polyomaviruses, all of which were negative. BOX-PCR subtyping of Escherichia coli and Enterococcus showed higher population diversity during the rain event; and higher population similarity during dry conditions, suggesting that without fresh inputs, only a subset of the population survives the selective pressure of the secondary habitat. These data indicate that high indicator bacteria levels were attributable to a stormwater system that acted as a reservoir and conduit, flushing high levels of indicator bacteria to the beach during a rain event. Such environmental reservoirs of indicator bacteria further complicate the already questionable relationship between indicator organisms and human pathogens, and call for a better understanding of the ecology, fate and persistence of indicator bacteria.

Analysis of magnetite crystals and inclusion bodies inside magnetotactic bacteria from different environmental locations

NASA Astrophysics Data System (ADS)

Oestreicher, Z.; Lower, B.; Lower, S.; Bazylinski, D. A.

2011-12-01

Biomineralization occurs throughout the living world; a few common examples include iron oxide in chiton teeth, calcium carbonate in mollusk shells, calcium phosphate in animal bones and teeth, silica in diatom shells, and magnetite crystals inside the cells of magnetotactic bacteria. Biologically controlled mineralization is characterized by biominerals that have species-specific properties such as: preferential crystallographic orientation, consistent particle size, highly ordered spatial locations, and well-defined composition and structure. It is well known that magnetotactic bacteria synthesize crystals of magnetite inside of their cells, but how they mineralize the magnetite is poorly understood. Magnetosomes have a species-specific morphology that is due to specific proteins involved in the mineralization process. In addition to magnetite crystals, magnetotactic bacteria also produce inclusion bodies or granules that contain different elements, such as phosphorus, calcium, and sulfur. In this study we used the transmission electron microscope to analyze the structure of magnetite crystals and inclusion bodies from different species of magnetotactic bacteria in order to determine the composition of the inclusion bodies and to ascertain whether or not the magnetite crystals contain elements other than iron and oxygen. Using energy dispersive spectroscopy we found that different bacteria from different environments possess inclusion bodies that contain different elements such as phosphorus, calcium, barium, magnesium, and sulfur. These differences may reflect the conditions of the environment in which the bacteria inhabit.

Observations of fluorescent and biological aerosol at a high-altitude site in central France

NASA Astrophysics Data System (ADS)

Gabey, A. M.; Vaitilingom, M.; Freney, E.; Boulon, J.; Sellegri, K.; Gallagher, M. W.; Crawford, I. P.; Robinson, N. H.; Stanley, W. R.; Kaye, P. H.

2013-08-01

Total bacteria, fungal spore and yeast counts were compared with ultraviolet-light-induced fluorescence (UV-LIF) measurements of ambient aerosol at the summit of the Puy de Dôme (PdD) mountain in central France (1465 m a.s.l), which represents a background elevated site. Bacteria, fungal spores and yeast were enumerated by epifluorescence microscopy (EFM) and found to number 2.2 to 23 L-1 and 0.8 to 2 L-1, respectively. Bacteria counts on two successive nights were an order of magnitude larger than in the intervening day. A wide issue bioaerosol spectrometer, version 3 (WIBS-3) was used to perform UV-LIF measurements on ambient aerosol sized 0.8 to 20 μm. Mean total number concentration was 270 L-1 (σ = 66 L-1), found predominantly in a size mode at 2 μm for most of the campaign. Total concentration (fluorescent + non-fluorescent aerosol) peaked at 500 L-1 with a size mode at 1 μm because of a change in air mass origin lasting around 48 h. The WIBS-3 features two excitation and fluorescence detection wavelengths corresponding to different biological molecules, although non-biological interferents also contribute. The mean fluorescent particle concentration after short-wave (280 nm; associated with tryptophan) excitation was 12 L-1 (σ = 6 L-1), and did not vary much throughout the campaign. In contrast, the mean concentration of particles fluorescent after long-wave (370 nm; associated with NADH) excitation was 95 L-1 (σ = 25 L-1), and a nightly rise and subsequent fall of up to 100 L-1 formed a strong diurnal cycle in the latter. The two fluorescent populations exhibited size modes at 3 μm and 2 to 3 μm, respectively. A hierarchical agglomerative cluster analysis algorithm was applied to the data and used to extract different particle factors. A cluster concentration time series representative of bacteria was identified. This was found to exhibit a diurnal cycle with a maximum peak appearing during the day. Analysis of organic mass spectra recorded using an aerosol mass spectrometer (AMS; Aerodyne Inc.) suggests that aerosol reaching the site at night was more aged than that during the day, indicative of sampling the residual layer at night. Supplementary meteorological data and previous work also show that PdD lies in the residual layer/free troposphere at night, and this is thought to cause the observed diurnal cycles in organic-type and fluorescent aerosol particles. Based on the observed disparity between bacteria and fluorescent particle concentrations, fluorescent non-PBA is likely to be important in the WIBS-3 data and the surprisingly high fluorescent concentration in the residual layer/free troposphere raises questions about a ubiquitous background in continental air during the summer.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Podoskin, A. A., E-mail: podoskin@mail.ioffe.ru; Shashkin, I. S.; Slipchenko, S. O.

A model describing the operation of a completely optical cell, based on the competition of lasing of Fabry-Perot cavity modes and the high-Q closed mode in high-power semiconductor lasers is proposed. Based on rate equations, the conditions of lasing switching between Fabry-Perot modes for ground and excited lasing levels and the closed mode are considered in the case of increasing internal optical loss under conditions of high current pump levels. The optical-cell operation conditions in the mode of a high-power laser radiation switch (reversible mode-structure switching) and in the mode of a memory cell with bistable irreversible lasing switching betweenmore » mode structures with various Q-factors are considered.« less

Elimination of the asymmetric modes in a Ka-band super overmoded coaxial Cerenkov oscillator

NASA Astrophysics Data System (ADS)

Bai, Zhen; Zhang, Jun; Zhong, Huihuang; Zhao, Xuelong; Yang, Fuxiang

2017-12-01

The issue of asymmetric modes output of a Ka-band super overmoded coaxial Cerenkov oscillator is analyzed in this paper. Due to serious passband overlapping in a super overmoded coaxial slow wave structure (SWS), the asymmetric competition mode EH11 can hardly be suppressed thoroughly by the methods adopted in moderately overmoded devices, especially in the startup of oscillation. If the output structures reflect the asymmetric modes, the asymmetric mode competition in SWS will be aggravated and the normal operation state will be destroyed. In order to solve this problem, a taper waveguide is inserted at a specific position to achieve the destructive interference of the reflected TM11, and a special support structure is designed to avoid reflection of TE11. With these methods, asymmetric mode competition can be successfully eliminated, and the oscillator is capable of achieving a steady fundamental mode operation performance.

Sound Power Estimation for Beam and Plate Structures Using Polyvinylidene Fluoride Films as Sensors

PubMed Central

Mao, Qibo; Zhong, Haibing

2017-01-01

The theory for calculation and/or measurement of sound power based on the classical velocity-based radiation mode (V-mode) approach is well established for planar structures. However, the current V-mode theory is limited in scope in that it can only be applied to conventional motion sensors (i.e., accelerometers). In this study, in order to estimate the sound power of vibrating beam and plate structure by using polyvinylidene fluoride (PVDF) films as sensors, a PVDF-based radiation mode (C-mode) approach concept is introduced to determine the sound power radiation from the output signals of PVDF films of the vibrating structure. The proposed method is a hybrid of vibration measurement and numerical calculation of C-modes. The proposed C-mode approach has the following advantages: (1) compared to conventional motion sensors, the PVDF films are lightweight, flexible, and low-cost; (2) there is no need for special measuring environments, since the proposed method does not require the measurement of sound fields; (3) In low frequency range (typically with dimensionless frequency kl < 4), the radiation efficiencies of the C-modes fall off very rapidly with increasing mode order, furthermore, the shapes of the C-modes remain almost unchanged, which means that the computation load can be significantly reduced due to the fact only the first few dominant C-modes are involved in the low frequency range. Numerical simulations and experimental investigations were carried out to verify the accuracy and efficiency of the proposed method. PMID:28509870

Structure, Biology, and Therapeutic Application of Toxin-Antitoxin Systems in Pathogenic Bacteria.

PubMed

Lee, Ki-Young; Lee, Bong-Jin

2016-10-22

Bacterial toxin-antitoxin (TA) systems have received increasing attention for their diverse identities, structures, and functional implications in cell cycle arrest and survival against environmental stresses such as nutrient deficiency, antibiotic treatments, and immune system attacks. In this review, we describe the biological functions and the auto-regulatory mechanisms of six different types of TA systems, among which the type II TA system has been most extensively studied. The functions of type II toxins include mRNA/tRNA cleavage, gyrase/ribosome poison, and protein phosphorylation, which can be neutralized by their cognate antitoxins. We mainly explore the similar but divergent structures of type II TA proteins from 12 important pathogenic bacteria, including various aspects of protein-protein interactions. Accumulating knowledge about the structure-function correlation of TA systems from pathogenic bacteria has facilitated a novel strategy to develop antibiotic drugs that target specific pathogens. These molecules could increase the intrinsic activity of the toxin by artificially interfering with the intermolecular network of the TA systems.

Shrink-Induced Superhydrophobic and Antibacterial Surfaces in Consumer Plastics

PubMed Central

Freschauf, Lauren R.; McLane, Jolie; Sharma, Himanshu; Khine, Michelle

2012-01-01

Structurally modified superhydrophobic surfaces have become particularly desirable as stable antibacterial surfaces. Because their self-cleaning and water resistant properties prohibit bacteria growth, structurally modified superhydrophobic surfaces obviate bacterial resistance common with chemical agents, and therefore a robust and stable means to prevent bacteria growth is possible. In this study, we present a rapid fabrication method for creating such superhydrophobic surfaces in consumer hard plastic materials with resulting antibacterial effects. To replace complex fabrication materials and techniques, the initial mold is made with commodity shrink-wrap film and is compatible with large plastic roll-to-roll manufacturing and scale-up techniques. This method involves a purely structural modification free of chemical additives leading to its inherent consistency over time and successive recasting from the same molds. Finally, antibacterial properties are demonstrated in polystyrene (PS), polycarbonate (PC), and polyethylene (PE) by demonstrating the prevention of gram-negative Escherichia coli (E. coli) bacteria growth on our structured plastic surfaces. PMID:22916100

The impact of long-term hydrocarbon exposure on the structure, activity, and biogeochemical functioning of microbial mats.

PubMed

Aubé, Johanne; Senin, Pavel; Pringault, Olivier; Bonin, Patricia; Deflandre, Bruno; Bouchez, Olivier; Bru, Noëlle; Biritxinaga-Etchart, Edurne; Klopp, Christophe; Guyoneaud, Rémy; Goñi-Urriza, Marisol

2016-10-15

Photosynthetic microbial mats are metabolically structured systems driven by solar light. They are ubiquitous and can grow in hydrocarbon-polluted sites. Our aim is to determine the impact of chronic hydrocarbon contamination on the structure, activity, and functioning of a microbial mat. We compared it to an uncontaminated mat harboring similar geochemical characteristics. The mats were sampled in spring and fall for 2years. Seasonal variations were observed for the reference mat: sulfur cycle-related bacteria dominated spring samples, while Cyanobacteria dominated in autumn. The contaminated mat showed minor seasonal variation; a progressive increase of Cyanobacteria was noticed, indicating a perturbation of the classical seasonal behavior. Hydrocarbon content was the main factor explaining the differences in the microbial community structure; however, hydrocarbonoclastic bacteria were among rare or transient Operational Taxonomic Units (OTUs) in the contaminated mat. We suggest that in long-term contaminated systems, hydrocarbonoclastic bacteria cannot be considered a sentinel of contamination. Copyright © 2016 Elsevier Ltd. All rights reserved.

Escherichia coli Cell Surface Perturbation and Disruption Induced by Antimicrobial Peptides BP100 and pepR*

PubMed Central

Alves, Carla S.; Melo, Manuel N.; Franquelim, Henri G.; Ferre, Rafael; Planas, Marta; Feliu, Lidia; Bardají, Eduard; Kowalczyk, Wioleta; Andreu, David; Santos, Nuno C.; Fernandes, Miguel X.; Castanho, Miguel A. R. B.

2010-01-01

The potential of antimicrobial peptides (AMPs) as an alternative to conventional therapies is well recognized. Insights into the biological and biophysical properties of AMPs are thus key to understanding their mode of action. In this study, the mechanisms adopted by two AMPs in disrupting the Gram-negative Escherichia coli bacterial envelope were explored. BP100 is a short cecropin A-melittin hybrid peptide known to inhibit the growth of phytopathogenic Gram-negative bacteria. pepR, on the other hand, is a novel AMP derived from the dengue virus capsid protein. Both BP100 and pepR were found to inhibit the growth of E. coli at micromolar concentrations. Zeta potential measurements of E. coli incubated with increasing peptide concentrations allowed for the establishment of a correlation between the minimal inhibitory concentration (MIC) of each AMP and membrane surface charge neutralization. While a neutralization-mediated killing mechanism adopted by either AMP is not necessarily implied, the hypothesis that surface neutralization occurs close to MIC values was confirmed. Atomic force microscopy (AFM) was then employed to visualize the structural effect of the interaction of each AMP with the E. coli cell envelope. At their MICs, BP100 and pepR progressively destroyed the bacterial envelope, with extensive damage already occurring 2 h after peptide addition to the bacteria. A similar effect was observed for each AMP in the concentration-dependent studies. At peptide concentrations below MIC values, only minor disruptions of the bacterial surface occurred. PMID:20566635

Removal of airborne microorganisms emitted from a wastewater treatment oxidation ditch by adsorption on activated carbon.

PubMed

Li, Lin; Gao, Min; Liu, Junxin; Guo, Xuesong

2011-01-01

Bioaerosol emissions from wastewater and wastewater treatment processes are a significant subgroup of atmospheric aerosols. Most previous work has focused on the evaluation of their biological risks. In this study, however, the adsorption method was applied to reduce airborne microorganisms generated from a pilot scale wastewater treatment facility with oxidation ditch. Results showed adsorption on granule activated carbon (GAC) was an efficient method for the purification of airborne microorganisms. The GAC itself had a maximum adsorption capacity of 2217 CFU/g for airborne bacteria and 225 CFU/g for fungi with a flow rate of 1.50 m3/hr. Over 85% of airborne bacteria and fungi emitted from the oxidation ditch were adsorbed within 80 hr of continuous operation mode. Most of them had a particle size of 0.65-4.7 microm. Those airborne microorganisms with small particle size were apt to be adsorbed. The SEM/EDAX, BET and Boehm's titration methods were applied to analyse the physicochemical characteristics of the GAC. Relationships between GAC surface characteristics and its adsorption performance demonstrated that porous structure, large surface area, and hydrophobicity rendered GAC an effective absorber of airborne microorganisms. Two regenerate methods, ultraviolet irradiation and high pressure vapor, were compared for the regeneration of used activated carbon. High pressure vapor was an effective technique as it totally destroyed the microorganisms adhered to the activated carbon. Microscopic observation was also carried out to investigate original and used adsorbents.

Static biofilm removal around ultrasonic tips in vitro.

PubMed

Thurnheer, Thomas; Rohrer, Elodie; Belibasakis, Georgios N; Attin, Thomas; Schmidlin, Patrick R

2014-09-01

This study aims to investigate the biofilm removal capacity of two ultrasonic tips under standardized conditions using a multi-species biofilm model. Six-species biofilms were grown on hydroxyapatite discs for 64.5 h and were treated for 15 s with a standardized load of 40 g with a piezoelectric or magnetostrictive device. Tips were applied either with the tip end or with the side facing downwards. Detached bacteria were determined in the supernatant and colony-forming units (CFUs) counted after 72 h of incubation. Untreated specimens served as controls. Moreover, the biofilms remaining on the hydroxyapatite surface after treatment were stained using the Live/Dead stain, and the pattern of their detachment was assessed by confocal laser scanning microscopy (CLSM). As compared to the untreated control, it was found that only a side application of the magnetostrictive device was able to remove efficiently the biofilm. In contrast, its tip application as well as both applications of the piezoelectric device removed significantly less bacteria from the biofilm structure. These findings were corroborated by CLSM observation. Both ultrasonic tips under investigations led to bacterial detachment, but the action mode as well as the tip configuration and adaptation appeared to be influenced by the biofilm removal effectiveness. Biofilm removal remains a main goal of ultrasonic debridement. This should be reflected in respective laboratory investigations. The presented combination of methods applied on a multi-species biofilm model in vitro allows the evaluation of the effectiveness of different ultrasonic scaler applications.

Advances in MRSA drug discovery: where are we and where do we need to be?

PubMed Central

Kurosu, Michio; Siricilla, Shajila; Mitachi, Katsuhiko

2013-01-01

Introduction Methicillin-resistant Staphylococcus aureus (MRSA) have been on the increase during the past decade, due to the steady growth of the elderly and immunocompromised patients, and the emergence of multi-drug-resistant (MDR) bacterial strains. Although, only a limited number of anti-MRSA drugs are available, a number of different combination antimicrobial drug regimens have been used to treat serious MRSA infections. Thus, addition of several new antistaphylococcal drugs into clinical practice should broaden therapeutic options. Because MRSA is one of the most common and problematic bacteria associated with increasing antimicrobial resistance, continuous efforts on discovery of lead compounds as well as development of alternative therapies and faster diagnostics to ensure effective antistaphylococcal therapy are required. Areas covered This article summarizes the FDA approved drugs to treat MRSA infections, the drugs in clinical trials, and the drug leads for MRSA and related Gram-positive bacterial infections. In addition, the mode of action of antistaphylococcal molecules and resistant mechanisms of some molecules are briefly discussed. Expert opinion The number of pipeline drugs presently undergoing clinical trials is not particularly encouraging. There are limited and rather expensive therapeutic options for the infections by MRSA in the critically ill. This review article provides an update on antistaphylococcal drugs in clinical trials and antibacterial molecules effective against Gram-positive bacteria including MRSA. The structural and biological information of antibacterials summarized here are very useful for designing drug leads to develop into new anti-MRSA drugs. PMID:23829425

Complementary structure for designer localized surface plasmons

NASA Astrophysics Data System (ADS)

Gao, Zhen; Gao, Fei; Zhang, Youming; Zhang, Baile

2015-11-01

Magnetic localized surface plasmons (LSPs) supported on metallic structures corrugated by very long and curved grooves have been recently proposed and demonstrated on an extremely thin metallic spiral structure (MSS) in the microwave regime. However, the mode profile for the magnetic LSPs was demonstrated by measuring only the electric field, not the magnetic field. Here, based on Babinet's principle, we propose a Babinet-inverted, or complementary MSS whose electric/magnetic mode profiles match the magnetic/electric mode profiles of MSS. This complementarity of mode profiles allows mapping the magnetic field distribution of magnetic LSP mode profile on MSS by measuring the electric field distribution of the corresponding mode on complementary MSS. Experiment at microwave frequencies also demonstrate the use of complementary MSS in sensing refractive-index change in the environment.

Asymmetric transmission and reflection spectra of FBG in single-multi-single mode fiber structure.

PubMed

Chai, Quan; Liu, Yanlei; Zhang, Jianzhong; Yang, Jun; Chen, Yujin; Yuan, Libo; Peng, Gang-Ding

2015-05-04

We give a comprehensive theoretical analysis and simulation of a FBG in single-multi-single mode fiber structure (FBG-in-SMS), based on the coupled mode analysis and the mode interference analysis. This enables us to explain the experimental observations, its asymmetric transmission and reflection spectra with the similar temperature responses near the spectral range of Bragg wavelengths. The transmission spectrum shift during FBG written-in process is observed and discussed. The analysis results are useful in the design of the SMS structure based sensors and filters.

Broad Specificity Efflux pumps and Their Role in Multidrug Resistance of Gram Negative Bacteria

PubMed Central

Nikaido, Hiroshi; Pagès, Jean-Marie

2013-01-01

Antibiotic resistance mechanisms reported in Gram-negative bacteria are producing a worldwide health problem. The continuous dissemination of «multi-drug resistant» (MDR) bacteria drastically reduces the efficacy of our antibiotic “arsenal” and consequently increases the frequency of therapeutic failure. In MDR bacteria, the over-expression of efflux pumps that expel structurally-unrelated drugs contributes to the reduced susceptibility by decreasing the intracellular concentration of antibiotics. During the last decade, several clinical data indicate an increasing involvement of efflux pumps in the emergence and dissemination of resistant Gram-negative bacteria. It is necessary to clearly define the molecular, functional and genetic bases of the efflux pump in order to understand the translocation of antibiotic molecules through the efflux transporter. The recent investigation on the efflux pump AcrB at its structural and physiological level, including the identification of drug affinity sites and kinetic parameters for various antibiotics, may open the way to rationally develop an improved new generation of antibacterial agents as well as efflux inhibitors in order to efficiently combat efflux-based resistance mechanisms. PMID:21707670

Goldstone-like phonon modes in a (111)-strained perovskite

NASA Astrophysics Data System (ADS)

Marthinsen, A.; Griffin, S. M.; Moreau, M.; Grande, T.; Tybell, T.; Selbach, S. M.

2018-01-01

Goldstone modes are massless particles resulting from spontaneous symmetry breaking. Although such modes are found in elementary particle physics as well as in condensed-matter systems like superfluid helium, superconductors, and magnons, structural Goldstone modes are rare. Epitaxial strain in thin films can induce structures and properties not accessible in bulk and has been intensively studied for (001)-oriented perovskite oxides. Here we predict Goldstone-like phonon modes in (111)-strained SrMn O3 by first-principles calculations. Under compressive strain the coupling between two in-plane rotational instabilities gives rise to a Mexican hat-shaped energy surface characteristic of a Goldstone mode. Conversely, large tensile strain induces in-plane polar instabilities with no directional preference, giving rise to a continuous polar ground state. Such phonon modes with U (1) symmetry could emulate structural condensed-matter Higgs modes. The mass of this Higgs boson, given by the shape of the Mexican hat energy surface, can be tuned by strain through proper choice of substrate.

Determination of the structural damping coefficients of six full-scale helicopter rotor blades of different materials and methods of construction

NASA Technical Reports Server (NTRS)

Gibson, Frederick W

1956-01-01

Results of an experimental investigation of the structural damping of six full-scale helicopter rotor blades, made to determine the variation of structural damping with materials and methods of construction, are presented. The damping of the blades was determined for the first three flapwise bending modes, first chordwise bending mode, and first torsion mode. The contribution of structural damping to the total damping of the blades is discussed for several aerodynamic conditions in order to point out situations where structural damping is significant.

Engineering self-assembled bioreactors from protein microcompartments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Savage, David

2016-10-12

The goals of this research are to understand how organisms such as bacteria segregate certain metabolic processes inside of specific structures, or “microcompartments,” in the cell and apply this knowledge to develop novel engineered microcompartments for use in nanotechnology and metabolic engineering. For example, in some bacteria, self-assembling protein microcompartments called carboxysomes encapsulate the enzymes involved in carbon fixation, enabling the cell to utilize carbon dioxide more effectively than if the enzymes were free in the cell. The proposed research will determine how structures such as carboxysomes assemble and function in bacteria and develop a means for creating novel, syntheticmore » microcompartments for optimizing production of specific energy-rich compounds.« less

Label-Free in Situ Discrimination of Live and Dead Bacteria by Surface-Enhanced Raman Scattering.

PubMed

Zhou, Haibo; Yang, Danting; Ivleva, Natalia P; Mircescu, Nicoleta E; Schubert, Sören; Niessner, Reinhard; Wieser, Andreas; Haisch, Christoph

2015-07-07

Techniques to distinguish between live and dead bacteria in a quantitative manner are in high demand in numerous fields including medical care, food safety, and public security as well as basic science research. This work demonstrates new nanostructures (silver nanoparticles coating bacteria structure, Bacteria@AgNPs) and their utility for rapid counting of live and dead bacteria by surface-enhanced Raman scattering (SERS). We found that suspensions containing Gram-negative organisms as well as AgNPs give strong SERS signals of live bacteria when generated selectively on the particle surface. However, almost no SERS signals can be detected from Bacteria@AgNPs suspensions containing dead bacteria. We demonstrate successful quantification of different percentages of dead bacteria both in bulk liquid and on glass surfaces by using SERS mapping on a single cell basis. Furthermore, different chemicals have been used to elucidate the mechanism involved in this observation. Finally, we used the Bacteria@AgNPs method to detect antibiotic resistance of E. coli strains against several antibiotics used in human medicine.

Highly damped quasinormal modes and the small scale structure of quantum corrected black hole exteriors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Babb, James; Kunstatter, Gabor; Daghigh, Ramin

2011-10-15

Quasinormal modes provide valuable information about the structure of spacetime outside a black hole. There is also a conjectured relationship between the highly damped quasinormal modes and the semiclassical spectrum of the horizon area/entropy. In this paper, we show that for spacetimes characterized by more than one scale, the 'infinitely damped' modes in principle probe the structure of spacetime outside the horizon at the shortest length scales. We demonstrate this with the calculation of the highly damped quasinormal modes of the nonsingular, single-horizon, quantum corrected black hole derived in [A. Peltola and G. Kunstatter, Phys. Rev. D 79, 061501 (2009);more » ].« less

Structure, Function, and Assembly of Adhesive Organelles by Uropathogenic Bacteria

PubMed Central

Chahales, Peter; Thanassi, David G.

2015-01-01

Bacteria assemble a wide range of adhesive proteins, termed adhesins, to mediate binding to receptors and colonization of surfaces. For pathogenic bacteria, adhesins are critical for early stages of infection, allowing the bacteria to initiate contact with host cells, colonize different tissues, and establish a foothold within the host. The adhesins expressed by a pathogen are also critical for bacterial-bacterial interactions and the formation of bacterial communities such as biofilms. The ability to adhere to host tissues is particularly important for bacteria that colonize sites such as the urinary tract, where the flow of urine functions to maintain sterility by washing away non-adherent pathogens. Adhesins vary from monomeric proteins that are directly anchored to the bacterial surface to polymeric, hairlike fibers that extend out from the cell surface. These latter fibers are termed pili or fimbriae, and were among the first identified virulence factors of uropathogenic Escherichia coli. Studies since then have identified a range of both pilus and non-pilus adhesins that contribute to bacterial colonization of the urinary tract, and have revealed molecular details of the structures, assembly pathways, and functions of these adhesive organelles. In this review, we describe the different types of adhesins expressed by both Gram-negative and Gram-positive uropathogens, what is known about their structures, how they are assembled on the bacterial surface, and the functions of specific adhesins in the pathogenesis of urinary tract infections. PMID:26542038

Characterization of Epiphytic Bacterial Communities from Grapes, Leaves, Bark and Soil of Grapevine Plants Grown, and Their Relations

PubMed Central

Martins, Guilherme; Lauga, Béatrice; Miot-Sertier, Cécile; Mercier, Anne; Lonvaud, Aline; Soulas, Marie-Louise; Soulas, Guy; Masneuf-Pomarède, Isabelle

2013-01-01

Despite its importance in plant health and crop quality, the diversity of epiphytic bacteria on grape berries and other plant parts, like leaves and bark, remains poorly described, as does the role of telluric bacteria in plant colonization. In this study, we compare the bacterial community size and structure in vineyard soils, as well as on grapevine bark, leaves and berries. Analyses of culturable bacteria revealed differences in the size and structure of the populations in each ecosystem. The highest bacteria population counts and the greatest diversity of genera were found in soil samples, followed by bark, grapes and leaves. The identification of isolates revealed that some genera – Pseudomonas, Curtobacterium, and Bacillus – were present in all ecosystems, but in different amounts, while others were ecosystem-specific. About 50% of the genera were common to soil and bark, but absent from leaves and grapes. The opposite was also observed: grape and leaf samples presented 50% of genera in common that were absent from trunk and soil. The bacterial community structure analyzed by T-RFLP indicated similarities between the profiles of leaves and grapes, on the one hand, and bark and soil, on the other, reflecting the number of shared T-RFs. The results suggest an interaction between telluric bacterial communities and the epiphytic bacteria present on the different grapevine parts. PMID:24023666

Clavulanic acid production estimation based on color and structural features of Streptomyces clavuligerus bacteria using self-organizing map and genetic algorithm.

PubMed

Nurmohamadi, Maryam; Pourghassem, Hossein

2014-05-01

The utilization of antibiotics produced by Clavulanic acid (CA) is an increasing need in medicine and industry. Usually, the CA is created from the fermentation of Streptomycen Clavuligerus (SC) bacteria. Analysis of visual and morphological features of SC bacteria is an appropriate measure to estimate the growth of CA. In this paper, an automatic and fast CA production level estimation algorithm based on visual and structural features of SC bacteria instead of statistical methods and experimental evaluation by microbiologist is proposed. In this algorithm, structural features such as the number of newborn branches, thickness of hyphal and bacterial density and also color features such as acceptance color levels are extracted from the SC bacteria. Moreover, PH and biomass of the medium provided by microbiologists are considered as specified features. The level of CA production is estimated by using a new application of Self-Organizing Map (SOM), and a hybrid model of genetic algorithm with back propagation network (GA-BPN). The proposed algorithm is evaluated on four carbonic resources including malt, starch, wheat flour and glycerol that had used as different mediums of bacterial growth. Then, the obtained results are compared and evaluated with observation of specialist. Finally, the Relative Error (RE) for the SOM and GA-BPN are achieved 14.97% and 16.63%, respectively. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Theory of the mode stabilization mechanism in concave-micromirror-capped vertical-cavity surface-emitting lasers

NASA Astrophysics Data System (ADS)

Park, Si-Hyun; Park, Yeonsang; Jeon, Heonsu

2003-08-01

We have investigated theoretically the transverse mode stabilization mechanism in oxide-confined concave-micromirror-capped vertical-cavity surface-emitting lasers (CMC-VCSELs) as reported by Park et al. [Appl. Phys. Lett. 80, 183 (2002)]. From detailed numerical calculations on a model CMC-VCSEL structure, we found that mode discrimination factors appear to be periodic in the micromirror layer thickness with a periodicity of λ/2. We also found that there are two possible concave micromirror structures for the fundamental transverse mode laser operation. These structures can be grouped according to the thickness of the concave micromirror layer: whether it is an integer or a half-integer multiple of λ/2. The optimal micromirror curvature radius differs accordingly for each case. In an optimally designed CMC-VCSEL model structure, the fundamental transverse mode can be favored as much as 4, 8, and 13 times more strongly than the first, second, and third excited modes, respectively.

Using multi-ring structure for suppression of mode competition in stable single-longitudinal-mode erbium fiber laser

NASA Astrophysics Data System (ADS)

Yeh, Chien-Hung; Huang, Tzu-Jung; Yang, Zi-Qing; Chow, Chi-Wai

2017-12-01

In this demonstration, a stable and tunable single-longitudinal-mode (SLM) erbium-doped fiber (EDF) laser with multiple-ring configuration is proposed and investigated. The proposed compound-ring structure can create different free spectrum ranges (FSRs) to result in the mode-filter effect based on the Vernier effect for suppressing the other modes. Additionally, the output stabilization of power and wavelength in the proposed EDF multiple-ring laser are also discussed.

Structural and immunomodulatory differences among lactobacilli exopolysaccharides isolated from intestines of mice with experimentally induced inflammatory bowel disease.

PubMed

Górska, Sabina; Sandstrőm, Corine; Wojas-Turek, Justyna; Rossowska, Joanna; Pajtasz-Piasecka, Elżbieta; Brzozowska, Ewa; Gamian, Andrzej

2016-11-21

Characteristic changes in the microbiota biostructure and a decreased tolerance to intestinal bacteria have been associated with inflammatory bowel disease (IBD). However, few studies have examined the constituents of the intestinal microbiota, including the surface molecules of the bacteria, in healthy and IBD subsets. Here, we compare the chemical structures and immunomodulatory properties of the exopolysaccharides (EPS) of lactobacilli isolated from mice with induced IBD (IBD "+") versus those of healthy mice (IBD "-"). Classical structural analyses were performed using nuclear magnetic resonance spectroscopy and mass spectrometry. Immunomodulatory properties were assessed by stimulation of dendritic cells derived from mouse bone marrow or human peripheral mononuclear blood cells. Our results revealed that EPS produced by IBD "+" species are structurally different from those isolated from IBD "-". Moreover, the structurally different EPS generate different immune responses by dendritic cells. We speculate that resident strains could, upon gut inflammation, switch to producing EPS with specific motifs that are absent from lactobacilli IBD "-", and/or that bacteria with a particular EPS structure might inhabit the inflamed intestinal mucosa. This study may shed light on the role of EPS in IBD and help the development of a specific probiotic therapy for this disease.

Fourier transform-infrared spectroscopic methods for microbial ecology: analysis of bacteria, bacteria-polymer mixtures and biofilms

NASA Technical Reports Server (NTRS)

Nichols, P. D.; Henson, J. M.; Guckert, J. B.; Nivens, D. E.; White, D. C.

1985-01-01

Fourier transform-infrared (FT-IR) spectroscopy has been used to rapidly and nondestructively analyze bacteria, bacteria-polymer mixtures, digester samples and microbial biofilms. Diffuse reflectance FT-IR (DRIFT) analysis of freeze-dried, powdered samples offered a means of obtaining structural information. The bacteria examined were divided into two groups. The first group was characterized by a dominant amide I band and the second group of organisms displayed an additional strong carbonyl stretch at approximately 1740 cm-1. The differences illustrated by the subtraction spectra obtained for microbes of the two groups suggest that FT-IR spectroscopy can be utilized to recognize differences in microbial community structure. Calculation of specific band ratios has enabled the composition of bacteria and extracellular or intracellular storage product polymer mixtures to be determined for bacteria-gum arabic (amide I/carbohydrate C-O approximately 1150 cm-1) and bacteria-poly-beta-hydroxybutyrate (amide I/carbonyl approximately 1740 cm-1). The key band ratios correlate with the compositions of the material and provide useful information for the application of FT-IR spectroscopy to environmental biofilm samples and for distinguishing bacteria grown under differing nutrient conditions. DRIFT spectra have been obtained for biofilms produced by Vibrio natriegens on stainless steel disks. Between 48 and 144 h, an increase in bands at approximately 1440 and 1090 cm-1 was seen in FT-IR spectra of the V. natriegens biofilm. DRIFT spectra of mixed culture effluents of anaerobic digesters show differences induced by shifts in input feedstocks. The use of flow-through attenuated total reflectance has permitted in situ real-time changes in biofilm formation to be monitored and provides a powerful tool for understanding the interactions within adherent microbial consortia.

On Three-dimensional Structures in Relativistic Hydrodynamic Jets

NASA Astrophysics Data System (ADS)

Hardee, Philip E.

2000-04-01

The appearance of wavelike helical structures on steady relativistic jets is studied using a normal mode analysis of the linearized fluid equations. Helical structures produced by the normal modes scale relative to the resonant (most unstable) wavelength and not with the absolute wavelength. The resonant wavelength of the normal modes can be less than the jet radius even on highly relativistic jets. High-pressure regions helically twisted around the jet beam may be confined close to the jet surface, penetrate deeply into the jet interior, or be confined to the jet interior. The high-pressure regions range from thin and ribbon-like to thick and tubelike depending on the mode and wavelength. The wave speeds can be significantly different at different wavelengths but are less than the flow speed. The highest wave speed for the jets studied has a Lorentz factor somewhat more than half that of the underlying flow speed. A maximum pressure fluctuation criterion found through comparison between theory and a set of relativistic axisymmetric jet simulations is applied to estimate the maximum amplitudes of the helical, elliptical, and triangular normal modes. Transverse velocity fluctuations for these asymmetric modes are up to twice the amplitude of those associated with the axisymmetric pinch mode. The maximum amplitude of jet distortions and the accompanying velocity fluctuations at, for example, the resonant wavelength decreases as the Lorentz factor increases. Long-wavelength helical surface mode and shorter wavelength helical first body mode generated structures should be the most significant. Emission from high-pressure regions as they twist around the jet beam can vary significantly as a result of angular variation in the flow direction associated with normal mode structures if they are viewed at about the beaming angle θ=1/γ. Variation in the Doppler boost factor can lead to brightness asymmetries by factors up to 6 as long-wavelength helical structure produced by the helical surface mode winds around the jet. Higher order surface modes and first body modes produce less variation. Angular variation in the flow direction associated with the helical mode appears consistent with precessing jet models that have been proposed to explain the variability in 3C 273 and BL Lac object AO 0235+164. In particular, cyclic angular variation in the flow direction produced by the normal modes could produce the activity seen in BL Lac object OJ 287. Jet precession provides a mechanism for triggering the helical modes on multiple length scales, e.g., the galactic superluminal GRO J1655-40.

CRISPR-based herd immunity can limit phage epidemics in bacterial populations

PubMed Central

Geyrhofer, Lukas; Barton, Nicholas H

2018-01-01

Herd immunity, a process in which resistant individuals limit the spread of a pathogen among susceptible hosts has been extensively studied in eukaryotes. Even though bacteria have evolved multiple immune systems against their phage pathogens, herd immunity in bacteria remains unexplored. Here we experimentally demonstrate that herd immunity arises during phage epidemics in structured and unstructured Escherichia coli populations consisting of differing frequencies of susceptible and resistant cells harboring CRISPR immunity. In addition, we develop a mathematical model that quantifies how herd immunity is affected by spatial population structure, bacterial growth rate, and phage replication rate. Using our model we infer a general epidemiological rule describing the relative speed of an epidemic in partially resistant spatially structured populations. Our experimental and theoretical findings indicate that herd immunity may be important in bacterial communities, allowing for stable coexistence of bacteria and their phages and the maintenance of polymorphism in bacterial immunity. PMID:29521625

PARADIGM: The Partnership for Advancing Interdisciplinary Global Modeling - Year 4 Annual Report

DTIC Science & Technology

2005-01-01

Microbial Foodweb - Microzooplankton and Bacteria Defining and/or generating functional groups of phytoplankton and biogeochemical functions and their...Peninsula (Karner et al. 2001; Church et al. 2003). Archaea are structurally similar to bacteria (they are both prokaryotes) but are genetically distinct...With the Bacteria and Eukarya, the Archaea form the three fundamental domains of life. They may be numerically dominant in a large part of all ocean

Perchlorate reduction by hydrogen autotrophic bacteria and microbial community analysis using high-throughput sequencing.

PubMed

Wan, Dongjin; Liu, Yongde; Niu, Zhenhua; Xiao, Shuhu; Li, Daorong

2016-02-01

Hydrogen autotrophic reduction of perchlorate have advantages of high removal efficiency and harmless to drinking water. But so far the reported information about the microbial community structure was comparatively limited, changes in the biodiversity and the dominant bacteria during acclimation process required detailed study. In this study, perchlorate-reducing hydrogen autotrophic bacteria were acclimated by hydrogen aeration from activated sludge. For the first time, high-throughput sequencing was applied to analyze changes in biodiversity and the dominant bacteria during acclimation process. The Michaelis-Menten model described the perchlorate reduction kinetics well. Model parameters q(max) and K(s) were 2.521-3.245 (mg ClO4(-)/gVSS h) and 5.44-8.23 (mg/l), respectively. Microbial perchlorate reduction occurred across at pH range 5.0-11.0; removal was highest at pH 9.0. The enriched mixed bacteria could use perchlorate, nitrate and sulfate as electron accepter, and the sequence of preference was: NO3(-) > ClO4(-) > SO4(2-). Compared to the feed culture, biodiversity decreased greatly during acclimation process, the microbial community structure gradually stabilized after 9 acclimation cycles. The Thauera genus related to Rhodocyclales was the dominated perchlorate reducing bacteria (PRB) in the mixed culture.

Dynamic Motion and Communication in the Streptococcal C1 Phage Lysin, PlyC

PubMed Central

Reboul, Cyril F.; Cowieson, Nathan P.; Costa, Mauricio G. S.; Kass, Itamar; Jackson, Colin; Perahia, David; Buckle, Ashley M.; McGowan, Sheena

2015-01-01

The growing problem of antibiotic resistance underlies the critical need to develop new treatments to prevent and control resistant bacterial infection. Exogenous application of bacteriophage lysins results in rapid and specific destruction of Gram-positive bacteria and therefore lysins represent novel antibacterial agents. The PlyC phage lysin is the most potent lysin characterized to date and can rapidly lyse Group A, C and E streptococci. Previously, we have determined the X-ray crystal structure of PlyC, revealing a complicated and unique arrangement of nine proteins. The scaffold features a multimeric cell-wall docking assembly bound to two catalytic domains that communicate and work synergistically. However, the crystal structure appeared to be auto-inhibited and raised important questions as to the mechanism underlying its extreme potency. Here we use small angle X-ray scattering (SAXS) and reveal that the conformational ensemble of PlyC in solution is different to that in the crystal structure. We also investigated the flexibility of the enzyme using both normal mode (NM) analysis and molecular dynamics (MD) simulations. Consistent with our SAXS data, MD simulations show rotational dynamics of both catalytic domains, and implicate inter-domain communication in achieving a substrate-ready conformation required for enzyme function. Our studies therefore provide insights into how the domains in the PlyC holoenzyme may act together to achieve its extraordinary potency. PMID:26470022

Covalent docking of selected boron-based serine beta-lactamase inhibitors

NASA Astrophysics Data System (ADS)

Sgrignani, Jacopo; Novati, Beatrice; Colombo, Giorgio; Grazioso, Giovanni

2015-05-01

AmpC β-lactamase is a hydrolytic enzyme conferring resistance to β-lactam antibiotics in multiple Gram-negative bacteria. Therefore, identification of non-β-lactam compounds able to inhibit the enzyme is crucial for the development of novel antibacterial therapies. In general, AmpC inhibitors have to engage the highly solvent-exposed catalytic site of the enzyme. Therefore, understanding the implications of ligand-protein induced-fit and water-mediated interactions behind the inhibitor-enzyme recognition process is fundamental for undertaking structure-based drug design process. Here, we focus on boronic acids, a promising class of beta-lactamase covalent inhibitors. First, we optimized a docking protocol able to reproduce the experimentally determined binding mode of AmpC inhibitors bearing a boronic group. This goal was pursued (1) performing rigid and flexible docking calculations aiming to establish the role of the side chain conformations; and (2) investigating the role of specific water molecules in shaping the enzyme active site and mediating ligand protein interactions. Our calculations showed that some water molecules, conserved in the majority of the considered X-ray structures, are needed to correctly predict the binding pose of known covalent AmpC inhibitors. On this basis, we formalized our findings in a docking and scoring protocol that could be useful for the structure-based design of new boronic acid AmpC inhibitors.

Exploring the binding mechanisms of diaminopimelic acid analogs to meso-diaminopimelate dehydrogenase by molecular modeling.

PubMed

Wang, Huiqun; Kellogg, Glen E; Xu, Ping; Zhang, Yan

2018-06-02

Meso-Diaminopimelic acid (meso-2,6-diamino-heptanedioic acid, DAP) is an important component of the cell wall of many bacteria. Meso-diaminopimelate dehydrogenase (m-Ddh) is a critical enzyme in the process of converting tetrahydrodipicolinate to DAP. Here, we are proposing that DAP analogs targeting m-Ddh may be considered as potential antibiotics. Four DAP analogs without significant structural change from DAP have been obtained and their inhibitory potencies against m-Ddh from the P. gingivalis strain W83 show significant differences from that of DAP. However, their inhibitory mechanisms as for how simple structural change influences the inhibitory potency remain unknown. Therefore, we employed molecular modeling methods to obtain insight into the inhibitory mechanisms of DAP and analogs with m-Ddh. The predicted binding mode of DAP was highly consistent with the experimental structural data and disclosed the important roles played by the binding pocket residues. According to our predictions, the isoxazoline ring of compounds 1 and 2 and the double bonds in compounds 3 and 4 had distinct influences on these compounds' binding to m-Ddh. This enriched understanding of the inhibitory mechanisms of DAP and these four analogs to m-Ddh has provided new and relevant information for future rational development of potent inhibitors targeting m-Ddh. Copyright © 2018. Published by Elsevier Inc.

Inactivation of TEM-1 by avibactam (NXL-104): insights from quantum mechanics/molecular mechanics metadynamics simulations.

PubMed

Sgrignani, Jacopo; Grazioso, Giovanni; De Amici, Marco; Colombo, Giorgio

2014-08-12

The fast and constant development of drug-resistant bacteria represents a serious medical emergence. To overcome this problem, the development of drugs with new structures and modes of action is urgently needed. In this context, avibactam represents a promising, innovative inhibitor of beta-lactamases with a novel molecular structure compared to previously developed inhibitors, showing a promising inhibitory activity toward a significant number of beta-lactamase enzymes. In this work, we studied, at the atomistic level, the mechanisms of formation of the covalent complex between avibactam and TEM-1, an experimentally well-characterized class A beta-lactamase, using classical and quantum mechanics/molecular mechanics (QM/MM) simulations combined with metadynamics. Our simulations provide a detailed structural and energetic picture of the molecular steps leading to the formation of the avibactam/TEM-1 covalent adduct. In particular, they support a mechanism in which the rate-determining step is the water-assisted Glu166 deprotonation by Ser70. In this mechanistic framework, the predicted activation energy is in good agreement with experimental kinetic measurements. Additionally, our simulations highlight the important role of Lys73 in assisting the Ser70 and Ser130 deprotonations. While based on the specific case of the avibactam/TEM-1, the simple protocol we present here can be immediately extended and applied to the study of covalent complex formation in different enzyme-inhibitor pairs.

Defining the Mode of Action of Tetramic Acid Antibacterials Derived from Pseudomonas aeruginosa Quorum Sensing Signals

PubMed Central

Lowery, Colin A.; Park, Junguk; Gloeckner, Christian; Meijler, Michael M.; Mueller, Ryan S.; Boshoff, Helena I.; Ulrich, Ricky L.; Barry, Clifton E.; Bartlett, Douglas H.; Kravchenko, Vladimir V.; Kaufmann, Gunnar F.; Janda, Kim D.

2009-01-01

In Nature, bacteria rarely exist as single, isolated entities, but rather as communities comprised of many other species including higher host organisms. To survive in these competitive environments, microorganisms have developed elaborate tactics such as the formation of biofilms and the production of antimicrobial toxins. Recently, it was discovered that the Gram-negative bacterium Pseudomonas aeruginosa, an opportunistic human pathogen, produces an antibiotic, 3-(1-hydroxydecylidene)-5-(2-hydroxyethyl)pyrrolidine-2,4-dione (C12-TA), derived from one of its quorum sensing molecules. Here, we present a comprehensive study of the expanded spectrum of C12-TA antibacterial activity against microbial competitors encountered by P. aeruginosa in Nature as well as significant human pathogens. The mechanism of action of C12-TA was also elucidated and C12-TA was found to dissipate both the membrane potential and pH gradient of Gram-positive bacteria, correlating well with cell death. Notably, in stark contrast to its parent molecule 3-oxo-dodecanoyl homoserine lactone (3-oxo-C12-HSL), neither activation of cellular stress pathways nor cytotoxicity was observed in human cells treated with C12-TA. Our results suggest that the QS machinery of P. aeruginosa has evolved for a dual-function, both to signal others of the same species, and also to defend against both host immunity and competing bacteria. Because of the broad-spectrum antibacterial activity, established mode of action, lack of rapid resistance development, and tolerance by human cells, the C12-TA scaffold may also serve as a new lead compound for the development of antimicrobial therapeutics. PMID:19807189

Electrochemical Detection of E. coli O157:H7 in Water after Electrocatalytic and Ultraviolet Treatments Using a Polyguanine-Labeled Secondary Bead Sensor.

PubMed

Beeman, Michael G; Nze, Ugochukwu C; Sant, Himanshu J; Malik, Hammad; Mohanty, Swomitra; Gale, Bruce K; Carlson, Krista

2018-05-10

The availability of clean drinking water is a significant problem worldwide. Many technologies exist for purifying drinking water, however, many of these methods require chemicals or use simple methods, such as boiling and filtering, which may or may not be effective in removing waterborne pathogens. Present methods for detecting pathogens in point-of-use (POU) sterilized water are typically time prohibitive or have limited ability differentiating between active and inactive cells. This work describes a rapid electrochemical sensor to differentially detect the presence of active Escherichia coli (E. coli) O157:H7 in samples that have been partially or completely sterilized using a new POU electrocatalytic water purification technology based on superradicals generated by defect laden titania (TiO₂) nanotubes. The sensor was also used to detect pathogens sterilized by UV-C radiation for a comparison of different modes of cell death. The sensor utilizes immunomagnetic bead separation to isolate active bacteria by forming a sandwich assay comprised of antibody functionalized secondary magnetic beads, E. coli O157:H7, and polyguanine (polyG) oligonucleotide functionalized secondary polystyrene beads as an electrochemical tag. The assay is formed by the attachment of antibodies to active receptors on the membrane of E. coli , allowing the sensor to differentially detect viable cells. Ultravioloet (UV)-C radiation and an electrocatalytic reactor (ER) with integrated defect-laden titania nanotubes were used to examine the sensors’ performance in detecting sterilized cells under different modes of cell death. Plate counts and flow cytometry were used to quantify disinfection efficacy and cell damage. It was found that the ER treatments shredded the bacteria into multiple fragments, while UV-C treatments inactivated the bacteria but left the cell membrane mostly intact.

Optimization of cyanophycin production in recombinant strains of Pseudomonas putida and Ralstonia eutropha employing elementary mode analysis and statistical experimental design.

PubMed

Diniz, Simone Cardoso; Voss, Ingo; Steinbüchel, Alexander

2006-03-05

Elementary mode analysis was applied to simulate conditions for cyanophycin (CGP) biosynthesis and to optimize its production in bacteria. The conclusions from these simulations were confirmed by experiments with recombinant strains of the wild types and polyhydroxyalkanoate (PHA)-negative mutants of Ralstonia eutropha and Pseudomonas putida expressing CGP synthetase genes (cphA) of Synechocystis sp. strain PCC6308 or Anabaena sp. strain PCC7120. In particular, the effects of suitable precursor substrates and of oxygen supply as well as of the capability to accumulate PHA in addition to CGP biosynthesis were investigated. Since CGP consists of the amino acids aspartate and arginine, the tricarboxylic acid cycle (TCC), which provides intermediates for biosynthesis of these amino acids, seems to be important. Excretion of intermediates of the TCC upon cultivation at restricted oxygen supply and conversion of fumarate mainly to malate and to only little succinate in the absence of oxygen indicated that TCC intermediates for arginine and aspartate biosynthesis were provided by the oxidative or reductive parts of the TCC, respectively. The following important conclusions were made from the experiments and the simulations: (i) external arginine additionally supplied to the medium, (ii) oxygen limitation, and (iii) absence of PHA accumulation exerted positive effects on CGP accumulation. These conclusions were utilized to obtain CGP contents in the cells of as high as 17.9% (w x w(-1)) during cultivation of the investigated bacteria at the 30-L scale using mineral salts medium. Such high CGP contents were previously not obtained with these bacteria at a 30-L scale, even if complex media were used.

Studies in tilt rotor VTOL aircraft aeroelasticity, volume 2. Ph.D. Thesis - Case Western Reserve Univ.

NASA Technical Reports Server (NTRS)

Kvaternik, R. G.

1973-01-01

Two methods for natural mode vibration analysis are discussed. The first consists of a direct approach based on a finite element representation of the complete structure as an entity. The mass and stiffness matrices for the complete structure are assembled by properly combining the mass and stiffness matrices of the individual elements into which the structure has been divided. The second approach is that of component mode synthesis. This method is based on the concept of synthesizing the natural modes of the complete structure from modes of conveniently difined substructures, or components, into which the structure has been partitioned. In this way the expedient of reducing the system degrees of freedom, and thus the size of the eigenvalue problem, can be introduced by partial modal synthesis.

Structural and Functional Characterization of Aerobactin Synthetase IucA from a Hypervirulent Pathotype of Klebsiella pneumoniae

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bailey, Daniel C.; Drake, Eric J.; Grant, Thomas D.

Iron is a vital mineral nutrient required by virtually all life forms to prosper; pathogenic bacteria are no exception. Despite the abundance of iron within the human host, highly regulated iron physiology can result in exceedingly low levels of iron bioavailable to prospective invading bacteria. To combat this scarcity of iron, many pathogenic bacteria have acquired specific and efficient iron acquisition systems, which allow them to thrive in iron-deficient host environments. One of the more prominent bacterial iron acquisition systems involves the synthesis, secretion, and reuptake of small-molecule iron chelators known as siderophores. Aerobactin, a citrate-hydroxamate siderophore originally isolated nearlymore » 50 years ago, is produced by a number of pathogenic Gram-negative bacteria. Aerobactin has recently been demonstrated to play a pivotal role in mediating the enhanced virulence of a particularly invasive pathotype of Klebsiella pneumoniae (hvKP). Toward further understanding of this key virulence factor, we report the structural and functional characterization of aerobactin synthetase IucA from a strain of hvKP. The X-ray crystal structures of unliganded and ATP-bound forms of IucA were solved, forming the foundation of our structural analysis. Small angle X-ray scattering (SAXS) data suggest that, unlike its closest structurally characterized homologues, IucA adopts a tetrameric assembly in solution. Finally, we employed activity assays to investigate the substrate specificity and determine the apparent steady-state kinetic parameters of IucA.« less

Jumping Genes: The Transposable DNAs of Bacteria.

ERIC Educational Resources Information Center

Berg, Claire M.; Berg, Douglas E.

1984-01-01

Transposons are transposable elements that carry genes for antibiotic resistance. Provides background information on the structure and organization of these "jumping genes" in bacteria. Also describes the use of transposons in tagging genes and lists pertinent references and resource materials. (DH)

Dynamic Dispersal of Surface Layer Biofilm Induced by Nanosized TiO2 Based on Surface Plasmon Resonance and Waveguide.

PubMed

Zhang, Peng; Guo, Jin-Song; Yan, Peng; Chen, You-Peng; Wang, Wei; Dai, You-Zhi; Fang, Fang; Wang, Gui-Xue; Shen, Yu

2018-05-01

Pollutant degradation is present mainly in the surface layer of biofilms, and the surface layer is the most vulnerable to impairment by toxic pollutants. In this work, the effects of nanosized TiO 2 (n-TiO 2 ) on the average thicknesses of Bacillus subtilis biofilm and on bacterial attachment on different surfaces were investigated. The binding mechanism of n-TiO 2 to the cell surface was also probed. The results revealed that n-TiO 2 caused biofilm dispersal and the thicknesses decreased by 2.0 to 2.6 μm after several hours of exposure. The attachment abilities of bacteria with extracellular polymeric substances (EPS) on hydrophilic surfaces were significantly reduced by 31% and 81% under 10 and 100 mg/liter of n-TiO 2 , respectively, whereas those of bacteria without EPS were significantly reduced by 43% and 87%, respectively. The attachment abilities of bacteria with and without EPS on hydrophobic surfaces were significantly reduced by 50% and 56%, respectively, under 100 mg/liter of n-TiO 2 The results demonstrated that biofilm dispersal can be attributed to the changes in the cell surface structure and the reduction of microbial attachment ability. IMPORTANCE Nanoparticles can penetrate into the outer layer of biofilm in a relatively short period and can bind onto EPS and bacterial surfaces. The current work probed the effects of nanosized TiO 2 (n-TiO 2 ) on biofilm thickness, bacterial migration, and surface properties of the cell in the early stage using the surface plasmon resonance waveguide mode. The results demonstrated that n-TiO 2 decreased the adhesive ability of both cell and EPS and induced bacterial migration and biofilm detachment in several hours. The decreased adhesive ability of microbes and EPS worked against microbial aggregation, reducing the effluent quality in the biological wastewater treatment process. Copyright © 2018 American Society for Microbiology.

Cupiennin 1a exhibits a remarkably broad, non-stereospecific cytolytic activity on bacteria, protozoan parasites, insects, and human cancer cells.

PubMed

Kuhn-Nentwig, Lucia; Willems, Jean; Seebeck, Thomas; Shalaby, Tarek; Kaiser, Marcel; Nentwig, Wolfgang

2011-01-01

Cupiennin 1a, a cytolytic peptide isolated from the venom of the spider Cupiennius salei, exhibits broad membranolytic activity towards bacteria, trypanosomes, and plasmodia, as well as human blood and cancer cells. In analysing the cytolytic activity of synthesised all-D: - and all-L: -cupiennin 1a towards pro- and eukaryotic cells, a stereospecific mode of membrane destruction could be excluded. The importance of negatively charged sialic acids on the outer leaflet of erythrocytes for the binding and haemolytic activity of L: -cupiennin 1a was demonstrated. Reducing the overall negative charges of erythrocytes by partially removing their sialic acids or by protecting them with tri- or pentalysine results in reduced haemolytic activity of the peptide.

Bactericidal catechins damage the lipid bilayer.

PubMed

Ikigai, H; Nakae, T; Hara, Y; Shimamura, T

1993-04-08

The mode of antibacterial action of, the green tea (Camellia sinensis) extracts, (-)-epigallocatechin gallate (EGCg) and (-)-epicatechin (EC) was investigated. Strong bactericidal EGCg caused leakage of 5,6-carboxyfluorescein from phosphatidylcholine liposomes (PC), but EC with very weak bactericidal activity caused little damage to the membrane. Phosphatidylserine and dicetyl phosphate partially protected the membrane from EGCg-mediated damage when reconstituted into the liposome membrane with PC. EGCg, but not EC, caused strong aggregation and NPN-fluorescence quenching of PC-liposomes and these actions were markedly lowered in the presence of negatively charged lipids. These results show that bactericidal catechins primarily act on and damage bacterial membranes. The observation that Gram-negative bacteria are more resistant to bactericidal catechins than Gram-positive bacteria can be explained to some extent by the presence of negatively charged lipopolysaccharide.

Study of electromechanical and mechanical properties of bacteria using force microscopy

NASA Astrophysics Data System (ADS)

Reukov, Vladimir; Thompson, Gary; Nikiforov, Maxim; Guo, Senli; Ovchinnikov, Oleg; Jesse, Stephen; Kalinin, Sergei; Vertegel, Alexey

2010-03-01

The application of scanning probe microscopy (SPM) to biological systems has evolved over the past decade into a multimodal and spectroscopic instrument that provides multiple information channels at each spatial pixel acquired. Recently, functional recognition imaging based on differing electromechanical properties between Gram negative and Gram positive bacteria was achieved using artificial neural network analysis of band excitation piezoresponse force microscopy (BEPFM) data. The immediate goal of this project was to study mechanical and electromechanical properties of bacterial systems physiologically-relevant solutions using Band-width Excitation Piezoresponce Force Microscopy (BE PFM) in combination with Force Mapping. Electromechanical imaging in physiological environments will improve the versatility of functional recognition imaging and open the way for application of the rapid BEPFM line mode method to other living cell systems.

Physiology of the Inactivation of Vegetative Bacteria by Thermal Treatments: Mode of Action, Influence of Environmental Factors and Inactivation Kinetics

PubMed Central

Condón, Santiago; Mañas, Pilar

2017-01-01

Heat has been used extensively in the food industry as a preservation method, especially due to its ability to inactivate microorganisms present in foods. However, many aspects regarding the mechanisms of bacterial inactivation by heat and the factors affecting this process are still not fully understood. The purpose of this review is to offer a general overview of the most important aspects of the physiology of the inactivation or survival of microorganisms, particularly vegetative bacteria, submitted to heat treatments. This could help improve the design of current heat processes methods in order to apply milder and/or more effective treatments that could fulfill consumer requirements for fresh-like foods while maintaining the advantages of traditional heat treatments. PMID:29189748

Phylogenetic assessment of heterotrophic bacteria from a water distribution system using 16S rDNA sequencing.

PubMed

Tokajian, Sima T; Hashwa, Fuad A; Hancock, Ian C; Zalloua, Pierre A

2005-04-01

Determination of a heterotrophic plate count (HPC) for drinking-water samples alone is not enough to assess possible health hazards associated with sudden changes in the bacterial count. Speciation is very crucial to determine whether the population includes pathogens and (or) opportunistic pathogens. Most of the isolates recovered from drinking water samples could not be allocated to a specific phylogenetic branch based on the use of conventional diagnostic methods. The present study had to use phylogenetic analysis, which was simplified by determining and using the first 500-bp sequence of the 16S rDNA, to successfully identify the type and species of bacteria found in the samples. Gram-positive bacteria alpha-, beta-, and gamma-Proteobacteria were found to be the major groups representing the heterotrophic bacteria in drinking water. The study also revealed that the presence of sphingomonads in drinking water supplies may be much more common than has been reported so far and thus further studies are merited. The intermittent mode of supply, mainly characterized by water stagnation and flow interruption associated possibly with biofilm detachment, raised the possibility that the studied bacterial populations in such systems represented organisms coming from 2 different niches, the biofilm and the water column.

Autotrophic and heterotrophic acquisition of carbon and nitrogen by a mixotrophic chrysophyte established through stable isotope analysis.

PubMed

Terrado, Ramon; Pasulka, Alexis L; Lie, Alle A-Y; Orphan, Victoria J; Heidelberg, Karla B; Caron, David A

2017-09-01

Collectively, phagotrophic algae (mixotrophs) form a functional continuum of nutritional modes between autotrophy and heterotrophy, but the specific physiological benefits of mixotrophic nutrition differ among taxa. Ochromonas spp. are ubiquitous chrysophytes that exhibit high nutritional flexibility, although most species generally fall towards the heterotrophic end of the mixotrophy spectrum. We assessed the sources of carbon and nitrogen in Ochromonas sp. strain BG-1 growing mixotrophically via short-term stable isotope probing. An axenic culture was grown in the presence of either heat-killed bacteria enriched with 15 N and 13 C, or unlabeled heat-killed bacteria and labeled inorganic substrates ( 13 C-bicarbonate and 15 N-ammonium). The alga exhibited high growth rates (up to 2 divisions per day) only until heat-killed bacteria were depleted. NanoSIMS and bulk IRMS isotope analyses revealed that Ochromonas obtained 84-99% of its carbon and 88-95% of its nitrogen from consumed bacteria. The chrysophyte assimilated inorganic 13 C-carbon and 15 N-nitrogen when bacterial abundances were very low, but autotrophic (photosynthetic) activity was insufficient to support net population growth of the alga. Our use of nanoSIMS represents its first application towards the study of a mixotrophic alga, enabling a better understanding and quantitative assessment of carbon and nutrient acquisition by this species.

Bioleaching of arsenic in contaminated soil using metal-reducing bacteria

NASA Astrophysics Data System (ADS)

Lee, So-Ra; Lee, Jong-Un; Chon, Hyo-Taek

2014-05-01

A study on the extraction of arsenic in the contaminated soil collected from an old smelting site in Korea was carried out using metal-reducing bacteria. Two types of batch-type experiments, biostimulation and bioaugmentation, were conducted for 28 days under anaerobic conditions. The biostimulation experiments were performed through activation of indigenous bacteria by supply with glucose or lactate as a carbon source. The contaminated, autoclaved soil was inoculated with metal-reducing bacteria, Shewanella oneidensis MR-1 and S. algae BrY, in the bioaugmentation experiments. The results indicated that the maximum concentration of the extracted As was 11.2 mg/L at 4 days from the onset of the experiment when 20 mM glucose was supplied and the extraction efficiency of As ranged 60~63% in the biostimulation experiments. In the case of bioaugmentation, the highest dissolved As concentration was 24.4 mg/L at 2 days, though it dramatically decreased over time through re-adsorption onto soil particles. After both treatments, mode of As occurrence in the soil appeared to be changed to readily extractable fractions. This novel technique of bioleaching may be practically applied for remediation of As-contaminated soil after determination of optimum operational conditions such as operation time and proper carbon source and its concentration.

ModeRNA: a tool for comparative modeling of RNA 3D structure

PubMed Central

Rother, Magdalena; Rother, Kristian; Puton, Tomasz; Bujnicki, Janusz M.

2011-01-01

RNA is a large group of functionally important biomacromolecules. In striking analogy to proteins, the function of RNA depends on its structure and dynamics, which in turn is encoded in the linear sequence. However, while there are numerous methods for computational prediction of protein three-dimensional (3D) structure from sequence, with comparative modeling being the most reliable approach, there are very few such methods for RNA. Here, we present ModeRNA, a software tool for comparative modeling of RNA 3D structures. As an input, ModeRNA requires a 3D structure of a template RNA molecule, and a sequence alignment between the target to be modeled and the template. It must be emphasized that a good alignment is required for successful modeling, and for large and complex RNA molecules the development of a good alignment usually requires manual adjustments of the input data based on previous expertise of the respective RNA family. ModeRNA can model post-transcriptional modifications, a functionally important feature analogous to post-translational modifications in proteins. ModeRNA can also model DNA structures or use them as templates. It is equipped with many functions for merging fragments of different nucleic acid structures into a single model and analyzing their geometry. Windows and UNIX implementations of ModeRNA with comprehensive documentation and a tutorial are freely available. PMID:21300639

Edge-localized mode avoidance and pedestal structure in I-mode plasmas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Walk, J. R., E-mail: jrwalk@psfc.mit.edu; Hughes, J. W.; Hubbard, A. E.

I-mode is a high-performance tokamak regime characterized by the formation of a temperature pedestal and enhanced energy confinement, without an accompanying density pedestal or drop in particle and impurity transport. I-mode operation appears to have naturally occurring suppression of large Edge-Localized Modes (ELMs) in addition to its highly favorable scalings of pedestal structure and overall performance. Extensive study of the ELMy H-mode has led to the development of the EPED model, which utilizes calculations of coupled peeling-ballooning MHD modes and kinetic-ballooning mode (KBM) stability limits to predict the pedestal structure preceding an ELM crash. We apply similar tools to themore » structure and ELM stability of I-mode pedestals. Analysis of I-mode discharges prepared with high-resolution pedestal data from the most recent C-Mod campaign reveals favorable pedestal scalings for extrapolation to large machines—pedestal temperature scales strongly with power per particle P{sub net}/n{sup ¯}{sub e}, and likewise pedestal pressure scales as the net heating power (consistent with weak degradation of confinement with heating power). Matched discharges in current, field, and shaping demonstrate the decoupling of energy and particle transport in I-mode, increasing fueling to span nearly a factor of two in density while maintaining matched temperature pedestals with consistent levels of P{sub net}/n{sup ¯}{sub e}. This is consistent with targets for increased performance in I-mode, elevating pedestal β{sub p} and global performance with matched increases in density and heating power. MHD calculations using the ELITE code indicate that I-mode pedestals are strongly stable to edge peeling-ballooning instabilities. Likewise, numerical modeling of the KBM turbulence onset, as well as scalings of the pedestal width with poloidal beta, indicates that I-mode pedestals are not limited by KBM turbulence—both features identified with the trigger for large ELMs, consistent with the observed suppression of large ELMs in I-mode.« less

Edge-localized mode avoidance and pedestal structure in I-mode plasmasa)

NASA Astrophysics Data System (ADS)

Walk, J. R.; Hughes, J. W.; Hubbard, A. E.; Terry, J. L.; Whyte, D. G.; White, A. E.; Baek, S. G.; Reinke, M. L.; Theiler, C.; Churchill, R. M.; Rice, J. E.; Snyder, P. B.; Osborne, T.; Dominguez, A.; Cziegler, I.

2014-05-01

I-mode is a high-performance tokamak regime characterized by the formation of a temperature pedestal and enhanced energy confinement, without an accompanying density pedestal or drop in particle and impurity transport. I-mode operation appears to have naturally occurring suppression of large Edge-Localized Modes (ELMs) in addition to its highly favorable scalings of pedestal structure and overall performance. Extensive study of the ELMy H-mode has led to the development of the EPED model, which utilizes calculations of coupled peeling-ballooning MHD modes and kinetic-ballooning mode (KBM) stability limits to predict the pedestal structure preceding an ELM crash. We apply similar tools to the structure and ELM stability of I-mode pedestals. Analysis of I-mode discharges prepared with high-resolution pedestal data from the most recent C-Mod campaign reveals favorable pedestal scalings for extrapolation to large machines—pedestal temperature scales strongly with power per particle Pnet/n ¯e, and likewise pedestal pressure scales as the net heating power (consistent with weak degradation of confinement with heating power). Matched discharges in current, field, and shaping demonstrate the decoupling of energy and particle transport in I-mode, increasing fueling to span nearly a factor of two in density while maintaining matched temperature pedestals with consistent levels of Pnet/n ¯e. This is consistent with targets for increased performance in I-mode, elevating pedestal βp and global performance with matched increases in density and heating power. MHD calculations using the ELITE code indicate that I-mode pedestals are strongly stable to edge peeling-ballooning instabilities. Likewise, numerical modeling of the KBM turbulence onset, as well as scalings of the pedestal width with poloidal beta, indicates that I-mode pedestals are not limited by KBM turbulence—both features identified with the trigger for large ELMs, consistent with the observed suppression of large ELMs in I-mode.

An Acoustic Plate Mode Sensor for Biowarfare Toxins, Phase II

DTIC Science & Technology

1997-10-01

Biological agents -- such as bacteria , bacterial toxins and viruses -- must be detected rapidly to allow their neutralization or the quick treatment of...Results were comparable. 16 * r Cyclic voltammetry (CV) studies indicate that the monolayers made with the thiodialkyne, D1, which have been photolyzed...Microprocessor system development is ahead of schedule. Preliminary biosensor data is offered using Y. Pestis. The data indi- cates marginal detection

Kinetic scale structure of low-frequency waves and fluctuations

NASA Astrophysics Data System (ADS)

Lopez Herrera, R. A.; Figueroa-Vinas, A.; Araneda, J. A.; Yoon, P. H.

2017-12-01

The dissipation of solar wind turbulence at kinetic scales is believed to be important for heating the corona and accelerating the wind. Linear Vlasov kinetic theory is a useful tool in identifying various wave modes, including kinetic Alfvén, fast magnetosonic/whistler, ion-acoustic (or kinetic slow mode), and their possible roles in the dissipation. However, kinetic mode structure near the vicinity of ion cyclotron modes is not clearly understood. The present poster aims to further elucidate the structure of these low-frequency waves by introducing discrete particle effects through hybrid simulations and Klimontovich formalism of spontaneous emission theory. The theory and simulation of spontaneously emitted low-frequency fluctuations are employed to identify and distinguish the detailed mode structures associated with ion Bernstein versus quasi modes. The spontaneous emission theory and simulation also confirm the findings of Vlasov theory in that the kinetic Alfvén wave can be defined over a wide range of frequencies, including the proton cyclotron frequency and its harmonics, especially for high beta plasmas. This implies that these low-frequency modes may play predominant roles even in the fully kinetic description of kinetic scale turbulence and dissipation despite the fact that cyclotron harmonic and Bernstein modes may also play important roles in wave-particle interactions.

Biofilm formation enhances Helicobacter pylori survivability in vegetables.

PubMed

Ng, Chow Goon; Loke, Mun Fai; Goh, Khean Lee; Vadivelu, Jamuna; Ho, Bow

2017-04-01

To date, the exact route and mode of transmission of Helicobacter pylori remains elusive. The detection of H. pylori in food using molecular approaches has led us to postulate that the gastric pathogen may survive in the extragastric environment for an extended period. In this study, we show that H. pylori prolongs its survival by forming biofilm and micro-colonies on vegetables. The biofilm forming capability of H. pylori is both strain and vegetable dependent. H. pylori strains were classified into high and low biofilm formers based on their highest relative biofilm units (BU). High biofilm formers survived longer on vegetables compared to low biofilm formers. The bacteria survived better on cabbage compared to other vegetables tested. In addition, images captured on scanning electron and confocal laser scanning microscopes revealed that the bacteria were able to form biofilm and reside as micro-colonies on vegetable surfaces, strengthening the notion of possible survival of H. pylori on vegetables for an extended period of time. Taken together, the ability of H. pylori to form biofilm on vegetables (a common food source for human) potentially plays an important role in its survival, serving as a mode of transmission of H. pylori in the extragastric environment. Copyright © 2016 Elsevier Ltd. All rights reserved.

Reconstruction of the Fatty Acid Biosynthetic Pathway of Exiguobacterium antarcticum B7 Based on Genomic and Bibliomic Data.

PubMed

Kawasaki, Regiane; Baraúna, Rafael A; Silva, Artur; Carepo, Marta S P; Oliveira, Rui; Marques, Rodolfo; Ramos, Rommel T J; Schneider, Maria P C

2016-01-01

Exiguobacterium antarcticum B7 is extremophile Gram-positive bacteria able to survive in cold environments. A key factor to understanding cold adaptation processes is related to the modification of fatty acids composing the cell membranes of psychrotrophic bacteria. In our study we show the in silico reconstruction of the fatty acid biosynthesis pathway of E. antarcticum B7. To build the stoichiometric model, a semiautomatic procedure was applied, which integrates genome information using KEGG and RAST/SEED. Constraint-based methods, namely, Flux Balance Analysis (FBA) and elementary modes (EM), were applied. FBA was implemented in the sense of hexadecenoic acid production maximization. To evaluate the influence of the gene expression in the fluxome analysis, FBA was also calculated using the log2⁡FC values obtained in the transcriptome analysis at 0°C and 37°C. The fatty acid biosynthesis pathway showed a total of 13 elementary flux modes, four of which showed routes for the production of hexadecenoic acid. The reconstructed pathway demonstrated the capacity of E. antarcticum B7 to de novo produce fatty acid molecules. Under the influence of the transcriptome, the fluxome was altered, promoting the production of short-chain fatty acids. The calculated models contribute to better understanding of the bacterial adaptation at cold environments.

The diagram of phase-field crystal structures: an influence of model parameters in a two-mode approximation

NASA Astrophysics Data System (ADS)

Ankudinov, V.; Galenko, P. K.

2017-04-01

Effect of phase-field crystal model (PFC-model) parameters on the structure diagram is analyzed. The PFC-model is taken in a two-mode approximation and the construction of structure diagram follows from the free energy minimization and Maxwell thermodynamic rule. The diagram of structure’s coexistence for three dimensional crystal structures [Body-Centered-Cubic (BCC), Face-Centered-Cubic (FCC) and homogeneous structures] are constructed. An influence of the model parameters, including the stability parameters, are discussed. A question about the structure diagram construction using the two-mode PFC-model with the application to real materials is established.

Reflection of a TE-polarised Gaussian beam from a layered structure under conditions of resonance excitation of waveguide modes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sokolov, V I; Marusin, N V; Molchanova, S I

2014-11-30

The problem of reflection of a TE-polarised Gaussian light beam from a layered structure under conditions of resonance excitation of waveguide modes using a total internal reflection prism is considered. Using the spectral approach we have derived the analytic expressions for the mode propagation lengths, widths and depths of m-lines (sharp and narrow dips in the angular dependence of the specular reflection coefficient), depending on the structure parameters. It is shown that in the case of weak coupling, when the propagation lengths l{sub m} of the waveguide modes are mainly determined by the extinction coefficient in the film, the depthmore » of m-lines grows with the mode number m. In the case of strong coupling, when l{sub m} is determined mainly by the radiation of modes into the prism, the depth of m-lines decreases with increasing m. The change in the TE-polarised Gaussian beam shape after its reflection from the layered structure is studied, which is determined by the energy transfer from the incident beam into waveguide modes that propagate along the structure by the distance l{sub m}, are radiated in the direction of specular reflection and interfere with a part of the beam reflected from the working face of the prism. It is shown that this interference can lead to the field intensity oscillations near m-lines. The analysis of different methods for determining the parameters of thin-film structures is presented, including the measurement of mode angles θ{sub m} and the reflected beam shape. The methods are based on simultaneous excitation of a few waveguide modes in the film with a strongly focused monochromatic Gaussian beam, the waist width of which is much smaller than the propagation length of the modes. As an example of using these methods, the refractive index and the thickness of silicon monoxide film on silica substrate at the wavelength 633 nm are determined. (fibre and integrated-optical structures)« less

A review on comparative mechanistic studies of antimicrobial peptides against archaea.

PubMed

Varnava, Kyriakos G; Ronimus, Ron S; Sarojini, Vijayalekshmi

2017-11-01

Archaea was until recently considered as a third domain of life in addition to bacteria and eukarya but recent studies support the existence of only two superphyla (bacteria and archaea). The fundamental differences between archaeal, bacterial, and eukaryal cells are probably the main reasons for the comparatively lower susceptibility of archaeal strains to current antimicrobial agents. The possible emerging pathogenicity of archaea and the role of archaeal methanogens in methane emissions, a potent greenhouse gas, has led many researchers to examine the sensitivity patterns of archaea and make attempts to find agents that have significant anti-archaeal activity. Even though antimicrobial peptides (AMPs) are well known with several published reviews concerning their mode of action against bacteria and eukarya, to our knowledge, to date no reviews are available that focus on the action of these peptides against archaea. Herein, we present a review on all the peptides that have been tested against archaea. In addition, in an attempt to shed more light on possible future work that needs to be performed we have included a brief overview of the chemical characteristics, spectrum of activity, and the known mechanism of action of each of these peptides against bacteria and/or fungi. We also discuss the nature of and key physiological differences between Archaea, Bacteria, and Eukarya that are relevant to the development of anti-archaeal peptides. Despite our relatively limited knowledge about archaea, available data suggest that AMPs have an even broader spectrum of activity than currently recognized. © 2017 Wiley Periodicals, Inc.

Synergistic Antibacterial Effects of Chitosan-Caffeic Acid Conjugate against Antibiotic-Resistant Acne-Related Bacteria.

PubMed

Kim, Ji-Hoon; Yu, Daeung; Eom, Sung-Hwan; Kim, Song-Hee; Oh, Junghwan; Jung, Won-Kyo; Kim, Young-Mog

2017-06-08

The object of this study was to discover an alternative therapeutic agent with fewer side effects against acne vulgaris, one of the most common skin diseases. Acne vulgaris is often associated with acne-related bacteria such as Propionibacterium acnes , Staphylococcus epidermidis , Staphylococcus aureus , and Pseudomonas aeruginosa . Some of these bacteria exhibit a resistance against commercial antibiotics that have been used in the treatment of acne vulgaris (tetracycline, erythromycin, and lincomycin). In the current study, we tested in vitro antibacterial effect of chitosan-phytochemical conjugates on acne-related bacteria. Three chitosan-phytochemical conjugates used in this study exhibited stronger antibacterial activity than that of chitosan (unmodified control). Chitosan-caffeic acid conjugate (CCA) showed the highest antibacterial effect on acne-related bacteria along with minimum inhibitory concentration (MIC; 8 to 256 μg/mL). Additionally, the MIC values of antibiotics against antibiotic-resistant P. acnes and P. aeruginosa strains were dramatically reduced in combination with CCA, suggesting that CCA would restore the antibacterial activity of the antibiotics. The analysis of fractional inhibitory concentration (FIC) indices clearly revealed a synergistic antibacterial effect of CCA with antibiotics. Thus, the median sum of FIC (∑FIC) values against the antibiotic-resistant bacterial strains ranged from 0.375 to 0.533 in the combination mode of CCA and antibiotics. The results of the present study suggested a potential possibility of chitosan-phytochemical conjugates in the control of infections related to acne vulgaris.

Characterization of CCN and IN activity of bacterial isolates collected in Atlanta, GA

NASA Astrophysics Data System (ADS)

Purdue, Sara; Waters, Samantha; Karthikeyan, Smruthi; Konstantinidis, Kostas; Nenes, Athanasios

2016-04-01

Characterization of CCN activity of bacteria, other than a few select types such as Pseudomonas syringae, is limited, especially when looked at in conjunction with corresponding IN activity. The link between these two points is especially important for bacteria as those that have high CCN activity are likely to form an aqueous phase required for immersion freezing. Given the high ice nucleation temperature of bacterial cells, especially in immersion mode, it is important to characterize the CCN and IN activity of many different bacterial strains. To this effect, we developed a droplet freezing assay (DFA) which consists of an aluminum cold plate, cooled by a continuous flow of an ethylene glycol-water mixture, in order to observe immersion freezing of the collected bacteria. Here, we present the initial results on the CCN and IN activities of bacterial samples we have collected in Atlanta, GA. Bacterial strains were collected and isolated from rainwater samples taken from different storms throughout the year. We then characterized the CCN activity of each strain using a DMT Continuous Flow Streamwise Thermal Gradient CCN Counter by exposing the aerosolized bacteria to supersaturations ranging from 0.05% to 0.6%. Additionally, using our new DFA, we characterized the IN activity of each bacterial strain at temperatures ranging from -20oC to 0oC. The combined CCN and IN activity gives us valuable information on how some uncharacterized bacteria contribute to warm and mixed-phase cloud formation in the atmosphere.

Peri-Elastodynamic Simulations of Guided Ultrasonic Waves in Plate-Like Structure with Surface Mounted PZT.

PubMed

Patra, Subir; Ahmed, Hossain; Banerjee, Sourav

2018-01-18

Peridynamic based elastodynamic computation tool named Peri-elastodynamics is proposed herein to simulate the three-dimensional (3D) Lamb wave modes in materials for the first time. Peri-elastodynamics is a nonlocal meshless approach which is a scale-independent generalized technique to visualize the acoustic and ultrasonic waves in plate-like structure, micro-electro-mechanical systems (MEMS) and nanodevices for their respective characterization. In this article, the characteristics of the fundamental Lamb wave modes are simulated in a sample plate-like structure. Lamb wave modes are generated using a surface mounted piezoelectric (PZT) transducer which is actuated from the top surface. The proposed generalized Peri-elastodynamics method is not only capable of simulating two dimensional (2D) in plane wave under plane strain condition formulated previously but also capable of accurately simulating the out of plane Symmetric and Antisymmetric Lamb wave modes in plate like structures in 3D. For structural health monitoring (SHM) of plate-like structures and nondestructive evaluation (NDE) of MEMS devices, it is necessary to simulate the 3D wave-damage interaction scenarios and visualize the different wave features due to damages. Hence, in addition, to simulating the guided ultrasonic wave modes in pristine material, Lamb waves were also simulated in a damaged plate. The accuracy of the proposed technique is verified by comparing the modes generated in the plate and the mode shapes across the thickness of the plate with theoretical wave analysis.

Surface electromagnetic waves in Fibonacci superlattices: Theoretical and experimental results

NASA Astrophysics Data System (ADS)

El Hassouani, Y.; Aynaou, H.; El Boudouti, E. H.; Djafari-Rouhani, B.; Akjouj, A.; Velasco, V. R.

2006-07-01

We study theoretically and experimentally the existence and behavior of the localized surface modes in one-dimensional (1D) quasiperiodic photonic band gap structures. These structures are made of segments and loops arranged according to a Fibonacci sequence. The experiments are carried out by using coaxial cables in the frequency region of a few tens of MHz. We consider 1D periodic structures (superlattice) where each cell is a well-defined Fibonacci generation. In these structures, we generalize a theoretical rule on the surface modes, namely when one considers two semi-infinite superlattices obtained by the cleavage of an infinite superlattice, it exists exactly one surface mode in each gap. This mode is localized on the surface either of one or the other semi-infinite superlattice. We discuss the existence of various types of surface modes and their spatial localization. The experimental observation of these modes is carried out by measuring the transmission through a guide along which a finite superlattice (i.e., constituted of a finite number of quasiperiodic cells) is grafted vertically. The surface modes appear as maxima of the transmission spectrum. These experiments are in good agreement with the theoretical model based on the formalism of the Green function.

Biogeography and environmental conditions shape bacteriophage-bacteria networks across the human microbiome

PubMed Central

Hannigan, Geoffrey D.; Duhaime, Melissa B.; Koutra, Danai

2018-01-01

Viruses and bacteria are critical components of the human microbiome and play important roles in health and disease. Most previous work has relied on studying bacteria and viruses independently, thereby reducing them to two separate communities. Such approaches are unable to capture how these microbial communities interact, such as through processes that maintain community robustness or allow phage-host populations to co-evolve. We implemented a network-based analytical approach to describe phage-bacteria network diversity throughout the human body. We built these community networks using a machine learning algorithm to predict which phages could infect which bacteria in a given microbiome. Our algorithm was applied to paired viral and bacterial metagenomic sequence sets from three previously published human cohorts. We organized the predicted interactions into networks that allowed us to evaluate phage-bacteria connectedness across the human body. We observed evidence that gut and skin network structures were person-specific and not conserved among cohabitating family members. High-fat diets appeared to be associated with less connected networks. Network structure differed between skin sites, with those exposed to the external environment being less connected and likely more susceptible to network degradation by microbial extinction events. This study quantified and contrasted the diversity of virome-microbiome networks across the human body and illustrated how environmental factors may influence phage-bacteria interactive dynamics. This work provides a baseline for future studies to better understand system perturbations, such as disease states, through ecological networks. PMID:29668682