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PubMed1997

Mixture toxicity of nitrobenzene and trinitrobenzene using the marine bacterium Vibrio harveyi as the test organism.

Vibrio harveyi, a bioluminescent marine bacterium, was used to evaluate combined or mixture toxicity of two organic compounds, nitrobenzene and trinitrobenzene. An estimated median effective concentration (EC50) and confidence interval were determined for each chemical. These chemicals at their EC50 were evaluated in combination and an additive index method was used to determine a numerical toxicology value. Combinations at 20% intervals of the EC50 were performed using isopleths. The isopleths employed were the isobole plot and the isobologram. Bioluminescent change was also determined and graphed for evaluation of toxicity. Statistical evaluation of isopleths and the additive index method were employed by incorporating confidence intervals. Bioluminescent change and isopleths suggest that mixtures of nitrobenzene and trinitrobenzene are additive, while the additive index method is suggestive of synergism. Statistical evaluation between mixtures and single values, using the z test, was in some cases different at the 5% level. These data suggest that interaction of combinations should be evaluated and described by multiple methodologies. Evaluation of these data suggests, in part, that one mixture is statistically different for antagonism. This study supports the use of bioluminescent microbial toxicity tests with various evaluative methodologies for the determination of mixture interactions.

Drug Interactions↗

PubMed2001

Crystal structure of sensory rhodopsin II at 2.4 angstroms: insights into color tuning and transducer interaction.

We report an atomic-resolution structure for a sensory member of the microbial rhodopsin family, the phototaxis receptor sensory rhodopsin II (NpSRII), which mediates blue-light avoidance by the haloarchaeon Natronobacterium pharaonis. The 2.4 angstrom structure reveals features responsible for the 70- to 80-nanometer blue shift of its absorption maximum relative to those of haloarchaeal transport rhodopsins, as well as structural differences due to its sensory, as opposed to transport, function. Multiple factors appear to account for the spectral tuning difference with respect to bacteriorhodopsin: (i) repositioning of the guanidinium group of arginine 72, a residue that interacts with the counterion to the retinylidene protonated Schiff base; (ii) rearrangement of the protein near the retinal ring; and (iii) changes in tilt and slant of the retinal polyene chain. Inspection of the surface topography reveals an exposed polar residue, tyrosine 199, not present in bacteriorhodopsin, in the middle of the membrane bilayer. We propose that this residue interacts with the adjacent helices of the cognate NpSRII transducer NpHtrII.

Archaeal Proteins↗

PubMed2002

Signal integration following Toll-like receptor triggering.

Innate immune cells sense infectious danger through recognition of pathogen-associated molecular patterns (PAMP). Toll-like receptors (TLRs) play a pivotal role in the recognition of PAMP. Although various TLRs with distinct ligand specificities are expressed almost completely and contemporaneously by innate immune cells, and although central key signal transduction pathways of TLRs are shared, the innate response pattern is not uniform. Innate immune cells organize their response dependent on spatial and temporal requirements and mount a pathogen-specific and microbial-adopted reaction. Thus, after triggering of TLRs, complex signaling interactions take place that control and shape the reactivity patterns of innate immune cells. Here we discuss the central signaling pathways of TLRs and their interconnection with other signaling pathways, with emphasis on Janus kinases/signal transducers and activators of transcription JAK/STAT)-dependent intracellular signals. Cis and trans acting signal convergence mechanisms and mutual influence of TLR and cytokine signaling pathways determine the response profile. Hence, in innate immune cells, integration and processing of microbial-dependent and immunologic signals is achieved within individual cells to ascertain an appropriate immune response. Knowledge of these complex mechanisms will help to clarify the critical events during initiation of infection, which in turn may lead to new strategies to control and overcome infectious disease.

Animals↗

PubMed2004

Assessing the use of delta(13)C natural abundance in separation of root and microbial respiration in a Danish beech (Fagus sylvatica L.) forest.

Our understanding of forest biosphere-atmosphere interactions is fundamental for predicting forest ecosystem responses to climatic changes. Currently, however, our knowledge is incomplete partly due to inability to separate the major components of soil CO(2) effluxes, viz. root respiration, microbial decomposition of soil organic matter and microbial decomposition of litter material. In this study we examined whether the delta(13)C characteristics of solid organic matter and respired CO(2) from different soil-C components and root respiration in a Danish beech forest were useful to provide information on the root respiration contribution to total CO(2) effluxes. The delta(13)C isotopic analyses of CO(2) were performed using a FinniganMAT Delta(PLUS) isotope-ratio mass spectrometer coupled in continuous flow mode to a trace gas preparation-concentration unit (PreCon). Gas samples in 2-mL crimp seal vials were analysed in a fully automatic mode with an experimental standard error +/-0.11 per thousand. We observed that the CO(2) derived from root-free mineral soil horizons (A, B(W)) was more enriched in (13)C (delta(13)C range -21.6 to -21.2 per thousand ) compared with CO(2) derived from root-free humus layers (delta(13)C range -23.6 to -23.4 per thousand ). The CO(2) evolved from root respiration in isolated young beech plants revealed a value intermediate between those for the soil humus and mineral horizons, delta(13)C(root) = -22.2 per thousand, but was associated with great variability (SE +/- 1.0 per thousand ) due to plant-specific differences. delta(13)C of CO(2) from in situ below-ground respiration averaged -22.8 per thousand, intermediate between the values for the humus layer and root respiration, but variability was great (SE +/- 0.4 per thousand ) due to pronounced spatial patterns. Overall, we were unable to statistically separate the CO(2) of root respiration vs. soil organic matter decomposition based solely on delta(13)C signatures, yet the trend in the data suggests that root respiration contributed approximately 43% to total respiration. The vertical gradient in delta(13)C, however, might be a useful tool in partitioning respiration in different soil layers. The experiment also showed an unexpected (13)C-enrichment of CO(2) (>3.5 per thousand ) compared with the total-C signatures in the individual soil-C components. This may suggest that analyses of bulk samples are not representative for the C-pools actively undergoing decomposition.

Biomass↗

PubMed2026

Integrative machine learning models to unravel gut microbial dysbiosis and functional disruption in polycystic ovary syndrome.

OBJECTIVE: To study gut microbial diversity and metabolic pathway disruptions in women with PolyCystic Ovary Syndrome (PCOS) compared with healthy controls, and to evaluate the diagnostic potential of microbiome-driven machine learning models. DESIGN: Case-controlled metagenomic data analysis SUBJECTS: Gut metagenomic data from women diagnosed with PCOS and age-matched healthy female controls EXPOSURE: Presence of PCOS MAIN OUTCOME MEASURES: The primary outcome measures will include gut microbial alpha and beta diversity indices, microbial taxon abundance, functional pathway profiles, predicted metabolite levels, microbe-functional pathway-metabolite interaction networks, and the diagnostic accuracy of microbiome-based machine learning models. RESULTS: Alpha and beta diversity analyses revealed marked gut microbial dysbiosis in women with PCOS, despite comparable species richness to healthy controls. Differential abundance analysis identified 41 significantly altered microbial species, including enrichment of proinflammatory taxa, such as Bacteroides vulgatus and Ruminococcus gnavus, and depletion of beneficial commensals, including Roseburia hominis and Prevotella copri. These compositional shifts indicate a proinflammatory microbial community structure in PCOS. Functional profiling demonstrated the upregulation of pathways involved in nucleotide turnover, lipid and carbohydrate metabolism, and neurotransmitter synthesis, potentially contributing to metabolic and neuroendocrine disruption. Network analysis revealed fragmented and unstable microbial-metabolite associations in PCOS compared with cohesive networks in controls. Microbiome-based machine learning models achieved a diagnostic accuracy of 84.25% (area under the curve 0.93), underscoring their predictive potential. CONCLUSION: The gut microbiome in PCOS is characterized by a proinflammatory community structure and disrupted metabolic pathways. These findings demonstrate the diagnostic potential of microbiome-based models and underscore the gut microbiome as a promising target for therapeutic interventions in the management of PCOS.

Polycystic Ovary Syndrome↗

PubMed2025

Effects of a novel Paraburkholderia phage IPK on the phenanthrene degradation efficiency of the PAH-degrading strain Paraburkholderia caledonica Bk.

Phages are a major cause of bacterial mortality, affecting bacterial diversity and ecosystem functioning. However, the impact of phage-host interactions in contaminated environments and their role in pollutant biodegradation have largely been overlooked. We isolated and characterized a novel phage that infects the PAH-degrading bacterium Paraburkholderia caledonica Bk from a polycyclic aromatic hydrocarbon (PAH)-contaminated soil and investigated the effect of different multiplicity of infection (MOI) ratios on the degradation efficiency of phenanthrene. The phage IPK is a temperate phage with a wide pH and temperature tolerance and a burst size of 80  PFU ml⁻1. The phage was classified as a member of the Caudoviricetes and is related to Pseudomonas and Burkholderia phages. However, its low intergenomic similarity indicates that it is a new species. Three auxiliary metabolic genes (AMGs) related to amino acid metabolism and to bacterial growth regulation were identified in the phage genome. The highest multiplicity of infection (MOI 10) showed a rapid recovery of the host density and greater phenanthrene degradation than MOIs ranging from 0.01 to 1. This work highlights the important role of phage-host interactions in modulating the efficiency of pollutant degradation, which could be a key for improving the establishment of inoculants in bioremediation processes.

Phenanthrenes↗

PubMed1998

Structure of human salivary histatin 5 in aqueous and nonaqueous solutions.

The solution structure of human salivary histatin 5 (D-S-H-A-K-R-H-H-G-Y-K-R-K-F-H-E-K-H-H-S-H-R-G-Y) was examined in water (pH 3.8) and dimethyl sulfoxide solutions using 500 MHz homo- and heteronuclear two-dimensional (2D) nmr. The resonance assignment of peptide backbone and side-chain protons was accomplished by 2D total correlated spectroscopy and nuclear Overhauser effect (NOE) spectroscopy. The high JNH-C alpha H values (> or = 7.4 Hz), absence of any characteristic NH-NH (i, i + 1) or C alpha H-C beta H (i, i + 3) NOE connectivities, high d delta/dT values (> or = 0.004 ppm K-1) and the fast 1H/2H amide exchange suggest that histatin 5 molecules remain unstructured in aqueous solution at pH 3.8. In contrast, histatin 5 prefers largely alpha-helical conformation in dimethyl sulfoxide solution as evident from the JNH-C alpha H values (< or = 6.4 Hz), slow 1H/2H exchange, low d delta/dT values (< or = 0.003 ppm K-1) observed for amide resonances of residues 6-24, and the characteristic NH-NH (i, i + 1) and C alpha H-C beta H (i, i + 3) NOE connectivities. All backbone amide 15N-1H connectivities fall within 6 ppm on the 15N scale in the 2D heteronuclear single quantum correlated spectrum, and the restrained structure calculations using DIANA suggest the prevalence of alpha-helical conformations stabilized by 19 (5-->1) intramolecular backbone amide hydrogen bonds in polar aprotic medium such as dimethyl sulfoxide. The interside-chain hydrogen bonding and salt-bridge type interactions that normally stabilize the helical structure of linear peptides in aqueous solutions are not observed. Histatin 5, unlike other naturally occurring antimicrobial polypeptides such as magainins, defensins, and tachyplesins, does not adopt amphiphilic structure, precluding its insertion into microbial membranes and formation of ion channels across membranes. Electrostatic (ionic type) and hydrogen bonding interactions of the positively charged and polar residues with the head groups of microbial membranes or with a membrane-bound receptor could be the initial step involved in the mechanism of antimicrobial activity of histatins.

Amino Acid Sequence↗

PubMed2003

Application of 16S rDNA-DGGE to examine the microbial ecology associated with a social wasp Vespula germanica.

Invertebrates host numerous bacteria, with interactions ranging from pathogenesis to symbiosis. While certain symbiotic relationships have been well studied, little is known about the dynamics of these bacterial communities. Denaturing gradient gel electrophoresis (DGGE) was used to examine the bacterial microflora associated with the eusocial wasp Vespula germanica. DGGE profiles of larval guts revealed a variable microflora, suggesting that V. germanica is not dependent on a particular suite of mutualists. The variation in profiles was not related to season, nest size or macrohabitat. Sequences corresponding to Lactococcus, Lactobacillus, a novel Leuconostoc and two Rickettsiella grylli strains were obtained. DGGE proved to be a useful technique for characterizing the wasp microflora. Given the importance of microbial communities to invertebrates, there is much to be gained from the application of such techniques.

Animals↗

PubMed1996

A hitchhiker's guide to antisense and nonantisense biochemical pathways.

Antisense pharmaceutical research has sought to provide drugs that would yield effective therapies for diseases resulting from the production of deleterious proteins. The original concept was straightforward: eliminate production of unwanted proteins, such as oncogenic proteins, by blocking the function of their mRNAs; and block their mRNAs by adding "antisense" nucleic acids that bind them through complementary base pairing. However, it has proven difficult to develop clinically useful antisense strategies. Conventional antisense nucleic acids are large, highly charged, complex molecules that interact with a wide variety of unintended cellular and microbial components, often causing "nonantisense effects." It is now clear that a broad knowledge of nucleic acid biochemistry will be needed to optimize antisense molecules for use in patients. The efficacy of naturally occurring antisense molecules and the success of antisense agricultural strategies prove that antisense approaches can be powerful and specific. Pharmaceutical antisense research can be expected to yield many valuable products once sufficient information about antisense mechanisms has been gathered and applied. This article explains the biochemical events that give rise to both antisense and nonantisense effects and provides guidelines for designing and evaluating antisense experiments.

Animals↗

PubMed2006

Immunobiology of human NKG2D and its ligands.

The NKG2D-DAP10 receptor complex activates natural killer (NK) cells and costimulates effector T cell subsets upon engagement of ligands that can be conditionally expressed under physiologically harmful conditions such as microbial infections and malignancies. These characteristics have given rise to the widely embraced concept of immunorecognition of "induced or damaged self," complementing the "missing self" paradigm that is represented by MHC class I allotypes and their interactions with inhibitory receptors on NK cells. However, this notion may only be partially sustainable, as various patterns of constitutive tissue distributions have become apparent among members of one NKG2D ligand family. This review summarizes the biological properties of NKG2D and its ligands and discusses the interactions and regulation of these molecules with emphasis of their significance in microbial infections, tumor immunology, and autoimmune disease.

Autoimmune Diseases↗

PubMed1995

Molecular evolution in bacteria.

Recent advances in microbiology and molecular biology have a unifying influence on our understanding of genetic diversity/similarity and evolutionary relationships in microorganisms. This article attempts to unify information from diverse areas such as microbiology, molecular biology, microbial physiology, clay crystal genes, metals-microbe-clay interactions and bacterial DNA restriction-modification systems (R-M) as they may apply to molecular evolution of bacteria. The possibility is discussed that the first informational molecules may have been catalytic RNA (micro-assembler) not DNA (now the master copy) and these first micro-assemblers may have been precursors of ribosomes.

Adenosine Triphosphate↗

PubMed1989

Physical methods for characterization of microbial surfaces.

There are different concepts for explaining the adsorption of microorganisms to solid surfaces: the DLVO theory and the surface free energy. Basic aspects of both theories are discussed. Established methods for determining the surface properties of microbial cells are reviewed: Electrophoretic mobility, colloid titration, electrostatic interaction chromatography, bacterial adherence to hydrocarbons, partitioning in an aqueous two-phase system, hydrophobic interaction chromatography, contact angle measurement and X-ray photoelectron spectroscopy. They are discussed and classified according to their potential for the correlation of cell surface characteristics and adsorption behavior.

Adsorption↗

PubMed1994

Binding and internalization of microorganisms by integrin receptors.

Many microbial pathogens bind host-cell integrin receptors. These interactions are promoted either by a host protein binding the microorganism or by a surface-localized ligand encoded by the pathogen. Attachment facilitates extracellular adhesion of the microorganism or internalization by the host cell.

Amino Acid Sequence↗

PubMed2006

Involvement of DNA mismatch repair in stationary-phase mutagenesis during prolonged starvation of Pseudomonas putida.

One of the popular ideas is that decline in methyl-directed mismatch repair (MMR) in carbon-starved bacteria might facilitate occurrence of stationary-phase mutations. We compared the frequency of accumulation of stationary-phase mutations in carbon-starved Pseudomonas putida wild-type and MMR-defective strains and found that knockout of MMR system increased significantly emergence of base substitutions in starving P. putida. At the same time, the appearance of 1-bp deletion mutations was less affected by MMR in this bacterium. The spectrum of base substitution mutations which occurred in starving populations of P. putida wild-type strain was distinct from mutation spectrum identified in MMR-defective strains. The spectrum of base substitutions differed also in this case when mutants emerged in starved populations of MutS or MutL-defective strains were comparatively analyzed. Based on our results we suppose that other mechanisms than malfunctioning of MMR system in resting cells might be considered to explain the accumulation of stationary-phase mutations in P. putida. To further characterize populations of P. putida starved on selective plates, we stained bacteria with LIVE/DEAD kit in situ on agar plates. We found that although the overall number of colony forming units (CFU) did not decline in long-term-starved populations, these populations were very heterogeneous on the plates and contained many dead cells. Our results imply that slow growth of subpopulation of cells at the expenses of dead cells on selective plates might be important for the generation of stationary-phase mutations in P. putida. Additionally, the different survival patterns of P. putida on the same selective plates hint that competitive interactions taking place under conditions of prolonged starvation of microbial populations on semi-solid surfaces might be more complicated than previously assumed.

Base Pair Mismatch↗

PubMed2004

Non-exhaustive extraction techniques (NEETs) for the prediction of naphthalene mineralisation in soil.

Non-exhaustive extraction techniques (NEETs) have been shown to measure the putatively bioavailable fraction of hydrophobic compounds in soil. To date, these studies have only considered bioavailability in a single soil type. In this study, naphthalene was amended into five different soil types and mineralisation, bacterial biosensor response and the number of indigenous microbial naphthalene degraders were determined. Two NEETs were used to extract the naphthalene from soil; hydroxypropyl-beta-cyclodextrin (HPCD) and XAD-4. The HPCD extractable fraction correlated closely (R2 = 0.917) with the portion that was mineralised, but the XAD-4 extract did not (R2 = 0.044). HPCD may be ideal for the rapid assessment of the fraction of a hydrophobic organic contaminant that is available for biodegradation. A NEET that complements environmental microbial analysis will enhance our understanding of soil pollution interactions and equip us better in designing risk assessment models that integrate biological parameters. This application, although refined for soil samples, should be transferable to other environmental matrices.

Bacteriological Techniques↗

PubMed1999

The classification, recognition and significance of polyagglutination in transfusion medicine.

Polyagglutination, although an uncommon phenomenon in transfusion medicine, is becoming increasingly recognized as a potential pitfall in correct ABO typing and can hinder the rapid allocation of accurately crossmatched blood products. Polyagglutination refers to erythrocytes which demonstrate agglutination with the majority of adult sera upon initial ABO crossmatch testing. Most types of polyagglutination involve alteration of red cell surface antigens through microbial enzymatic activity in patients with sepsis, and subsequent interaction of these newly exposed 'cryptantigens' with naturally occuring IgM antibody which is present in most adult sera. Less common variants include essential inborn variations in red cell development, and have been associated with myelodysplastic syndromes, congenital anemias, and various leukemias; it has been suggested that patients shown to possess these types of polyagglutination may benefit from increased hematologic surveillance. Recognition of polyagglutination in these settings is important to allow successful resolution of ABO typing discrepancies and permit efficient administration of appropriate blood products to these patients, who are often quite ill. The classification and method of laboratory recognition of polyagglutination is reviewed.

Adult↗

PubMed2001

Microbial leaching of metals from sulfide minerals.

Microorganisms are important in metal recovery from ores, particularly sulfide ores. Copper, zinc, gold, etc. can be recovered from sulfide ores by microbial leaching. Mineral solubilization is achieved both by 'direct (contact) leaching' by bacteria and by 'indirect leaching' by ferric iron (Fe(3+)) that is regenerated from ferrous iron (Fe(2+)) by bacterial oxidation. Thiobacillus ferrooxidans is the most studied organism in microbial leaching, but other iron- or sulfide/sulfur-oxidizing bacteria as well as archaea are potential microbial agents for metal leaching at high temperature or low pH environment. Oxidation of iron or sulfur can be selectively controlled leading to solubilization of desired metals leaving undesired metals (e.g., Fe) behind. Microbial contribution is obvious even in electrochemistry of galvanic interactions between minerals.

Journal Article↗

PubMed1999

Early events in host-pathogen interactions.

Research focused on early events in host-pathogen interactions has provided new insights into fundamental aspects of microbial pathogenicity and plant responses. Considerable progress has been made in understanding regulation of the delivery of pathogenicity determinants from bacteria into plant cells, signal cascades involved in fungal pathogenicity, the co-ordinating role of the plant cytoskeleton in plant defence and calcium flux as a primary signalling function during the hypersensitive reaction.

Bacteria↗

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