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At least 757 records · Page 42Linked to original sources
PubMed2002

Comparison of extracellular enzyme activities and community composition of attached and free-living bacteria in porous medium columns.

Free-living and surface-associated microbial communities in sand-packed columns perfused with groundwater were compared by examination of compositional and functional characteristics. The composition of the microbial communities was assessed by bulk DNA extraction, PCR amplification of 16S ribosomal DNA fragments, separation of these fragments by denaturing gradient gel electrophoresis, and sequence analysis. Community function was assessed by measurement of beta-glucosidase and aminopeptidase extracellular enzyme activities. Free-living populations in the aqueous phase exhibited a greater diversity of phylotypes than populations associated with the solid phase. The attached bacterial community displayed significantly greater beta-glucosidase and aminopeptidase enzyme activities per volume of porous medium than those of the free-living community. On a per-cell basis, the attached community had a significantly higher cell-specific aminopeptidase enzyme activity (1.07 x 10(-7) nmol cell(-1) h(-1)) than the free-living community (5.02 x 10(-8) nmol cell(-1) h(-1)). Conversely, the free-living community had a significantly higher cell-specific beta-glucosidase activity (1.92 x 10(-6) nmol cell(-1) h(-1)) than the surface-associated community (6.08 x 10(-7) nmol cell(-1) h(-1)). The compositional and functional differences observed between these two communities may reflect different roles for these distinct but interacting communities in the decomposition of natural organic matter or biodegradation of xenobiotics in aquifers.

Aminopeptidases↗
PubMed2005

Functions of the Yersinia effector proteins in inhibiting host immune responses.

The invasion strategies used by Yersinia species involve the 'hijacking' of host cellular signaling pathways, often involving microbial gene products that mimic the functions of the cellular proteins. Yersinia uses a type III secretion system to inject these microbial gene products, referred to as Yersinia effector proteins, into the host cytosol. Yersinia effector proteins can inhibit the host immune system through a diverse array of mechanisms including inhibition of the inflammatory response by interfering with cytokine production, inhibition of phagocytosis by disrupting the actin cytoskeleton, induction of apoptosis in macrophages and through the formation of novel signaling complexes.

Bacterial Outer Membrane Proteins↗
PubMed2006

Reciprocal gut microbiota transplants from zebrafish and mice to germ-free recipients reveal host habitat selection.

The gut microbiotas of zebrafish and mice share six bacterial divisions, although the specific bacteria within these divisions differ. To test how factors specific to host gut habitat shape microbial community structure, we performed reciprocal transplantations of these microbiotas into germ-free zebrafish and mouse recipients. The results reveal that communities are assembled in predictable ways. The transplanted community resembles its community of origin in terms of the lineages present, but the relative abundance of the lineages changes to resemble the normal gut microbial community composition of the recipient host. Thus, differences in community structure between zebrafish and mice arise in part from distinct selective pressures imposed within the gut habitat of each host. Nonetheless, vertebrate responses to microbial colonization of the gut are ancient: Functional genomic studies disclosed shared host responses to their compositionally distinct microbial communities and distinct microbial species that elicit conserved responses.

Animals↗
PubMed2005

Phenotypic and functional profiling of human proinflammatory type-1 and anti-inflammatory type-2 macrophages in response to microbial antigens and IFN-gamma- and CD40L-mediated costimulation.

Macrophages (Mphi) comprise a heterogeneous population of cells with various immune and homeostatic functions. Recently, we have described type-1 and type-2 human monocyte-derived Mphi subsets. Although both support outgrowth of intracellular mycobacteria, Mphi-1 secretes interleukin (IL)-23/IL-12 and supports T helper cell type 1 (Th1) responses, whereas Mphi-2 fails to produce IL-23/IL-12, predominantly secretes IL-10, and inhibits Th1 function. Here, we further describe the phenotypic and functional profiles of Mphi-1 and Mphi-2 in response to microbial antigens and interferon-gamma (IFN-gamma) and CD40L as costimulatory T cell back-talk signals. Activated IL-23(+)/IL-12(+) Mphi-1 secreted IL-1beta, IL-18, IL-6, and tumor necrosis factor-alpha (TNF-alpha), as well as IL-8, monocyte chemoattractant protein-1 (MCP-1), IFN-inducible protein 10 (IP-10), Mphi inflammatory protein-1beta (MIP-1beta), regulated on activation, normal T expressed and secreted (RANTES), Mphi-derived chemokine (MDC), and (low levels of) pulmonary and activation-regulated chemokine and thymus and activation-regulated chemokine (TARC), corroborating their proinflammatory function. Regardless of the stimulus, Mphi-2 maintained their IL-10(+) signature cytokine profile and produced no or relatively low levels of IL-12p40, IL-1beta, IL-6, TNF-alpha, MDC, or TARC. It is remarkable that Mphi-2 secreted high levels of IL-8, MCP-1, IP-10, MIP-1beta, and RANTES, suggesting an active role for these cells in regulating cellular immunity and homeostasis. Mphi-1 and Mphi-2 expressed similar levels of Toll-like receptor and dendritic cell-specific intercellular adhesion molecule-3-grabbing nonintegrin as microbial pattern recognition receptors. Mphi-2, unlike Mphi-1 but like other nonclassical Mphi described previously, expressed CD163 and down-modulated human leukocyte antigen and costimulatory molecules specifically upon activation. These findings demonstrate how Mphi-1/Mphi-2 polarization can differentially skew the host response toward pro- or anti-inflammatory immune responses, respectively. This is likely to be relevant for host-pathogen interactions in chronic bacterial infections and provides a model for dissecting pro- and anti-inflammatory cascades.

Antigens, Bacterial↗
PubMed2002

Functional properties of oat globulin modified by a calcium-independent microbial transglutaminase.

Oat globulin was modified by a calcium-independent microbial transglutaminase (TG). The TG-polymerized protein had higher solubility than the control at acidic pH and had improved water- and fat-binding properties. Incubation of 10% (w/v) oat globulin dispersions in the presence of TG at 37 degrees C led to the formation of a well-developed viscoelastic gel network with a microstructure characterized by thick strands and large clusters. The TG-induced gels had higher modulus values, lower loss tangent values, and lower frequency dependency than the heat-induced gels. The TG-induced gel system has the characteristics of classical polymer gel with permanent "chemical" cross-links, whereas the heat-denatured system has the characteristics of a temporary "physical" gel with breakable cross-links. Fourier transform infrared spectroscopy showed marked shift and intensity changes in several major bands, suggesting pronounced changes in protein conformation during TG-induced gelation. Aggregation of protein molecules was also indicated by the progressive increases in two infrared bands (1679-1682 and 1622-1625 cm(-)(1)) associated with the formation of intermolecular beta-sheets and strands. Results suggest that new food polymers with unique functionality can be produced from oat globulin treated with TG and that elastic gels can be formed near neutral pH, instead of the alkaline pH required for thermally induced oat globulin gels.

Avena↗
PubMed1985

Microbial toxins and diarrhoeal diseases: introduction and overview.

Without question, diarrhoeal diseases constitute one of the greatest causes of morbidity and death on a global scale. To an increasingly recognized extent, they are caused by an expanding array of microbial products or "toxins'. The symposium focuses on microbial products that alter normal bowel function either by augmenting secretory pathways or by selectively destroying mucosal cells or pathways, thus leading to an imbalance in the concert of normal absorptive function that results in diarrhoea. An understanding of normal intestinal physiology is thus the key to unraveling the specific actions of microbial toxins. In many instances, the microbial toxins are themselves providing unique pharmacological tools with which to dissect normal intestinal function. Specifically, families of enterotoxins are reviewed that appear to cause secretion through the recognized second messengers of cyclic AMP and cyclic GMP as well as cyclic nucleotide-independent and calcium-dependent pathways. Potential "third messengers' such as the protein kinases, through which one or more of the second messengers may act, are also considered. We examine cytotoxins that alter the orchestrated function of specialized regions of intact intestinal mucosa by selectively impeding or killing certain cells, so leading to small intestinal or colonic pathology and contributing to diarrhoea. We also consider a wide range of recognized bacterial and parasitic agents and their enterotoxic products. In some instances, these toxins may strikingly resemble our own endogenous humoral regulators or hormones. At this point, the possible roles of viruses or other transmissible genome products in this area await further clarification. Finally, we examine pharmacological and immunological approaches to attacking the toxins themselves or the deranged physiology they cause, in order to approach the control of the potentially devastating diseases of diarrhoea.

Acute Disease↗
PubMed2003

Contributions of microbial biofilms to ecosystem processes in stream mesocosms.

In many aquatic ecosystems, most microbes live in matrix-enclosed biofilms and contribute substantially to energy flow and nutrient cycling. Little is known, however, about the coupling of structure and dynamics of these biofilms to ecosystem function. Here we show that microbial biofilms changed the physical and chemical microhabitat and contributed to ecosystem processes in 30-m-long stream mesocosms. Biofilm growth increased hydrodynamic transient storage-streamwater detained in quiescent zones, which is a major physical template for ecological processes in streams-by 300% and the retention of suspended particles by 120%. In addition, by enhancing the relative uptake of organic molecules of lower bioavailability, the interplay of biofilm microarchitecture and mass transfer changed their downstream linkage. As living zones of transient storage, biofilms bring hydrodynamic retention and biochemical processing into close spatial proximity and influence biogeochemical processes and patterns in streams. Thus, biofilms are highly efficient and successful ecological communities that may also contribute to the influence that headwater streams have on rivers, estuaries and even oceans through longitudinal linkages of local biogeochemical and hydrodynamic processes.

Arabinose↗
PubMed1996

Comparison between irradiated and thermally pasteurized liquid egg white on functional, physical, and microbiological properties.

A comparative study was undertaken to determine the effect of irradiation and thermal pasteurization on the functional, physical, and microbiological properties of liquid egg white (LEW). The LEW was irradiated or thermally pasteurized then stored at 4 C for 3 mo. Both treatments destroyed the inoculum, Salmonella typhimurium. The microbial growth rate was slower in the irradiated LEW than in the thermally pasteurized treatment. Irradiated samples had 47% lower foam drainage and more stable viscosity than samples that were thermally pasteurized. Volume of angel food cake prepared with irradiated or pasteurized LEW decreased 48 and 57%, respectively, after 90 d. Color did not differ between treatments. Ionizing radiation is an alternative processing method that inhibits microbial growth and helps maintain functionality of LEW.

Animals↗
PubMed2006

Patterns and mechanisms of genetic and phenotypic differentiation in marine microbes.

Microbes in the ocean dominate biogeochemical processes and are far more diverse than anticipated. Thus, in order to understand the ocean system, we need to delineate microbial populations with predictable ecological functions. Recent observations suggest that ocean communities comprise diverse groups of bacteria organized into genotypic (and phenotypic) clusters of closely related organisms. Although such patterns are similar to metazoan communities, the underlying mechanisms for microbial communities may differ substantially. Indeed, the potential among ocean microbes for vast population sizes, extensive migration and both homologous and illegitimate genetic recombinations, which are uncoupled from reproduction, challenges classical population models primarily developed for sexually reproducing animals. We examine possible mechanisms leading to the formation of genotypic clusters and consider alternative population genetic models for differentiation at individual loci as well as gene content at the level of whole genomes. We further suggest that ocean bacteria follow at least two different adaptive strategies, which constrain rates and bounds of evolutionary processes: the 'opportunitroph', exploiting spatially and temporally variable resources; and the passive oligotroph, efficiently using low nutrient concentrations. These ecological lifestyle differences may represent a fundamental divide with major consequences for growth and predation rates, genome evolution and population diversity, as emergent properties driving the division of labour within microbial communities.

Adaptation, Biological↗
PubMed1998

Microbial relatives of seed storage proteins: conservation of motifs in a functionally diverse superfamily of enzymes

Plant storage proteins comprise a major part of the human diet. Sequence analysis has revealed that these proteins probably share a common ancestor with a fungal oxalate decarboxylase and/or related bacterial genes. Additionally, all these proteins share a central core sequence with several other functionally diverse enzymes and binding proteins, many of which are associated with synthesis of the extracellular matrix during sporulation/encystment. A possible prokaryotic relative of this sequence is a bacterial protein (SASP) known to bind to DNA and thereby protect spores from extreme environmental conditions. This ability to maintain cell viability during periods of dehydration in spores and seeds may relate to absolute conservation of residues involved in structure determination.

Journal Article↗
PubMed2004

Progress curve analysis for enzyme and microbial kinetic reactions using explicit solutions based on the Lambert W function.

We present a simple method for estimating kinetic parameters from progress curve analysis of biologically catalyzed reactions that reduce to forms analogous to the Michaelis-Menten equation. Specifically, the Lambert W function is used to obtain explicit, closed-form solutions to differential rate expressions that describe the dynamics of substrate depletion. The explicit nature of the new solutions greatly simplifies nonlinear estimation of the kinetic parameters since numerical techniques such as the Runge-Kutta and Newton-Raphson methods used to solve the differential and integral forms of the kinetic equations, respectively, are replaced with a simple algebraic expression. The applicability of this approach for estimating Vmax and Km in the Michaelis-Menten equation was verified using a combination of simulated and experimental progress curve data. For simulated data, final estimates of Vmax and Km were close to the actual values of 1 microM/h and 1 microM, respectively, while the standard errors for these parameter estimates were proportional to the error level in the simulated data sets. The method was also applied to hydrogen depletion experiments by mixed cultures of bacteria in activated sludge resulting in Vmax and Km estimates of 6.531 microM/h and 2.136 microM, respectively. The algebraic nature of this solution, coupled with its relatively high accuracy, makes it an attractive candidate for kinetic parameter estimation from progress curve data.

Algorithms↗
PubMed2006

Effects of the antibiotic ciprofloxacin on stream microbial communities and detritivorous macroinvertebrates.

Microbial communities play an important role in stream ecosystem processes, such as breakdown of senescent leaf litter, and as a primary nutritional source for detritivorous macroinvertebrates. Antibiotics may affect stream microbial communities and associated ecosystem processes, especially because recent stream and river monitoring programs have indicated the presence of antibiotics downstream of wastewater treatment plants. In the current study, effects of chronic exposure to the fluoroquinolone antibiotic ciprofloxacin (Cipro) were examined on stream microbial community-level physiological profiles and growth indices of detritivorous amphipods (Gammarus spp.) and caddisflies (Lepidostoma liba). Microcosm experiments were conducted using stream sediments and water, senesced leaf material (Acer saccharum), and macroinvertebrates. A shift in function of leaf-associated microbial communities (based on carbon source utilization) was observed for samples exposed to 100 microg/L of Cipro for 12 d compared to control and treatments exposed to 1 and 10 microg/L of Cipro. This was attributable to carbohydrate substrates, which had 2.7- to 3.5-fold lower microbial respiration than the lower concentrations and control (p < 0.001). For detritivores, Gammarus spp. condition index did not differ among control, 0.1, and 1.0 microg/L treatments after 30-d exposures (p > 0.05). Similarly, L. liba growth rate did not vary among control, 10, and 100 microg/L treatments after 45-d exposures (p > 0.05). These results suggest that Cipro may affect leaf-associated microbial communities, but at concentrations four orders of magnitude above those detected in streams. However, effects of the antibiotic on growth and condition of detritivores were not observed. Future work should focus on identifying specific changes in stream microbial communities as a result of Cipro exposure and impacts on other aquatic species.

Animals↗
PubMed2007

The future prospects of microbial cellulose in biomedical applications.

Microbial cellulose has proven to be a remarkably versatile biomaterial and can be used in wide variety of applied scientific endeavors, such as paper products, electronics, acoustics, and biomedical devices. In fact, biomedical devices recently have gained a significant amount of attention because of an increased interest in tissue-engineered products for both wound care and the regeneration of damaged or diseased organs. Due to its unique nanostructure and properties, microbial cellulose is a natural candidate for numerous medical and tissue-engineered applications. For example, a microbial cellulose membrane has been successfully used as a wound-healing device for severely damaged skin and as a small-diameter blood vessel replacement. The nonwoven ribbons of microbial cellulose microfibrils closely resemble the structure of native extracellular matrices, suggesting that it could function as a scaffold for the production of many tissue-engineered constructs. In addition, microbial cellulose membranes, having a unique nanostructure, could have many other uses in wound healing and regenerative medicine, such as guided tissue regeneration (GTR), periodontal treatments, or as a replacement for dura mater (a membrane that surrounds brain tissue). In effect, microbial cellulose could function as a scaffold material for the regeneration of a wide variety of tissues, showing that it could eventually become an excellent platform technology for medicine. If microbial cellulose can be successfully mass produced, it will eventually become a vital biomaterial and will be used in the creation of a wide variety of medical devices and consumer products.

Acetobacter↗
PubMed2004

Fetal cardiac dysfunction in preterm premature rupture of membranes.

BACKGROUND: Preterm premature rupture of membranes (PROM) is associated with one-third of preterm births. In about 50% of preterm PROM cases, the fetuses will elicit a fetal inflammatory response syndrome (FIRS). FIRS is associated with the impending onset of preterm labor, periventricular leukomalacia, neonatal sepsis, and long-term handicap, including the development of bronchopulmonary dysplasia and cerebral palsy. The fetal myocardium is a potential target organ of proinflammatory cytokines released during FIRS. The objective of this study was to determine whether preterm PROM is associated with functional changes in the fetal heart, as determined by fetal echocardiography. METHODS: A retrospective study was conducted to assess the diastolic function of fetuses with preterm PROM with documented microbial invasion of the amniotic cavity (n = 25), preterm PROM without microbial invasion of the amniotic cavity (n = 42), and fetuses from normal pregnancies (control group = 150). Pregnancies with multiple gestation, fetal distress, fetuses that were small for gestational age, and major congenital anomalies were excluded. Fetal echocardiography studies were performed with two-dimensional ultrasound, color Doppler imaging and pulsed Doppler ultrasound. Non-parametric statistics were used for comparisons. A p value of < 0.05 was considered significant. RESULTS: The prevalence of positive amniotic fluid cultures for micro-organisms in patients with preterm PROM was 35.8% (24/67). Ureaplasma urealyticum was the most frequent isolate, either alone (41.7%; 10/24) or with other micro-organisms (29.2%; 7/24). Fetuses with preterm PROM had a higher delta early diastolic filling/atrial contraction (E/A) peak velocity ratio, a higher delta E/A velocity-time integral (VTI) ratio, a lower delta A peak velocity, a lower delta A VTI, and a lower A VTI/total VTI ratio in the mitral valve compared to those with uncomplicated pregnancies. The delta E/A peak velocity ratio was significantly higher and the delta A VTI significantly lower in fetuses with preterm PROM and microbial invasion of the amniotic cavity than in those with preterm PROM without microbial invasion of the amniotic cavity. CONCLUSIONS: Preterm PROM is associated with changes in fetal cardiac function consistent with increased left ventricular compliance. These observations were also noted in fetuses with microbial invasion of the amniotic cavity. Our findings suggest that fetal cardiac function is altered in preterm PROM and, in particular, in cases with intra-amniotic infection.

Echocardiography↗
PubMed2026

A voyage of reprogrammable metabolic bioengineering reshapes plant defense: from editing tools to synthetic systems.

Metabolic bioengineering has emerged as a transformative approach for reshaping plant defense by targeting intrinsic biosynthetic pathways to enhance immunity in modern agriculture. Moving beyond proof-of-concept metabolomics to broad-spectrum programmable pathway engineering addresses gaps in plant rational design and optimizes resilience in response to diverse environmental cues. This review aims to comprehensively highlight the transition of innovative approaches to phenolics, alkaloids, flavonoids, terpenoids, and benzoxazinoids, inferring adaptive reprogramming that mediates the growth-defense balance and functions as molecular sentinels in plants. Furthermore, decoding the volatile metabolome reveals a dynamic signaling interface that influences defense responses and stress-induced plant-microbe interactions, with the shikimate, jasmonate, and salicylate pathways functioning as central hubs for microbial deterrence and priming immune memory. Recent developments in multi-scalar genome-editing strategies, including CRISPR-driven combinatorial edits, enzyme orthogonalization, fluxomics, and spatially resolved multi-omics, reconfigure central and specialized metabolic fluxes toward improved defense function and regulation. Additionally, emerging tools, such as WUSCHEL2 and BABY BOOM transcriptional modules, and artificial engineering strategies integrating deep learning model-driven predictions facilitate rapid development of synthetic genetic circuits and support a predictive engineering of plants. Moreover, Mass spectrometry imaging (MSI) in spatial metabolomics enables to obtain structures and locations of unidentified endogenous metabolites within cells and tissues. Overall, this review emphasizes a diverse array of primary and secondary metabolites, spanning molecular concepts to recent advances in plant immune mechanisms. It also illustrates new frontiers in programmable metabolic engineering that accelerate the understanding of plant-microbe-metabolite cross-talks, offering strategies to improve plant resistance and advance sustainable agricultural solutions.

metabolic bioengineering↗
PubMed2004

Utility of environmental primers targeting ancient enzymes: methylotroph detection in Lake Washington.

Methods have been explored for detection of methylotrophs in natural samples, using environmental primers based on genes involved in the tetrahydromethanopterin (H4MPT)-linked C1 transfer pathway. The underlying hypotheses were that the H4MPT-linked pathway is an ancient methylotrophy pathway, based on gene divergence, and that primers targeting more divergent genes will detect a broader variety of methylotrophs compared to the variety uncovered using probes and primers targeting highly conserved genes. Three groups of novel primer sets were developed targeting mch, mtdB, and fae, key genes in the H4MPT-linked pathway, and these were used to assess the variety of microorganisms possessing these genes in sediments from Lake Washington in Seattle, WA. Environmental clone libraries were constructed for each of the genes and were analyzed by RFLP, and representatives of different RFLP groups were sequenced and subjected to phylogenetic analysis. A combination of all three sets of novel primers allowed detection of the two previously characterized groups of methylotrophs in the site: methanotrophs of the (alpha- and the gamma-proteobacterial groups, belonghg to genera Methylosinus, Methylocystis, Methylomonas, Methylobacter, Methylomicrobium, and Methylococcus. In addition to the genes belonging to known methanotroph populations, novel genes were identified, suggesting existence of previously undetected microbial groups possessing C1 transfer functions in this site. These included sequences clustering with the well-characterized methylotrophic phyla, Methylobacterium, Hyphomicrobium, and Xanthobacter. In addition, sequences divergent from those known for any groups of methylotrophs or methanogens were obtained, suggesting the presence of a yet unidentified microbial group possessing this H4MPT-linked C1 transfer pathway.

Bacteria↗