Comparison of 16S rRNA gene sequences of genus Methanobrevibacter

BACKGROUND: The phylogeny of the genus Methanobrevibacter was established almost 25 years ago on the basis of the similarities of the 16S rRNA oligonucleotide catalogs. Since then, many 16S rRNA gene sequences of newly isolated strains or clones representing the genus Methanobrevibacter have been deposited. We tried to reorganize the 16S rRNA gene sequences of this genus and revise the taxonomic affiliation of the isolates and clones representing the genus Methanobrevibacter. RESULTS: The phylogenetic analysis of the genus based on 786 bp aligned region from fifty-four representative sequences of the 120 available sequences for the genus revealed seven multi-member groups namely, Ruminantium, Smithii, Woesei, Curvatus, Arboriphilicus, Filiformis, and the Termite gut symbionts along with three separate lineages represented by Mbr. wolinii, Mbr. acididurans, and termite gut flagellate symbiont LHD12. The cophenetic correlation coefficient, a test for the ultrametric properties of the 16S rRNA gene sequences used for the tree was found to be 0.913 indicating the high degree of goodness of fit of the tree topology. A significant relationship was found between the 16S rRNA sequence similarity (S) and the extent of DNA hybridization (D) for the genus with the correlation coefficient (r) for logD and logS, and for [ln(-lnD) and ln(-lnS)] being 0.73 and 0.796 respectively. Our analysis revealed that for this genus, when S = 0.984, D would be <70% at least 99% of the times, and with 70% D as the species "cutoff", any 16S rRNA gene sequence showing <98% sequence similarity can be considered as a separate species. In addition, we deduced group specific signature positions that have remained conserved in evolution of the genus. CONCLUSIONS: A very significant relationship between D and S was found to exist for the genus Methanobrevibacter, implying that it is possible to predict D from S with a known precision for the genus. We propose to include the termite gut flagellate symbiont LHD12, the methanogenic endosymbionts of the ciliate Nyctotherus ovalis, and rat feces isolate RT reported earlier, as separate species of the genus Methanobrevibacter

Lactobacillus plantarum (VR1) isolated from an Ayurvedic medicine (Kutajarista) ameliorates in vitro cellular damage caused by Aeromonas veronii

<p>Abstract</p> <p>Background</p> <p><it>Lactobacillus plantarum </it>is considered as a safe and effective probiotic microorganism. Among various sources of isolation, traditionally fermented foods are considered to be rich in <it>Lactobacillus </it>spp., which can be exploited for their probiotic attribute. Antibacterial property of <it>L. plantarum </it>has been demonstrated against various enteric pathogens in both <it>in vitro </it>and <it>in vivo </it>systems. This study was aimed at characterizing <it>L. plantarum </it>isolated from Kutajarista, an ayurvedic fermented biomedicine, and assessing its antagonistic property against a common enteropathogen <it>Aeromonas veronii</it>.</p> <p>Results</p> <p>We report the isolation of <it>L. plantarum </it>(VR1) from Kutajarista, and efficacy of its cell free supernatant (CFS) in amelioration of cytotoxicity caused by <it>Aeromonas veronii</it>. On the part of probiotic attributes, VR1 was tolerant to pH 2, 0.3% bile salts and simulated gastric juice. Additionally, VR1 also exhibited adhesive property to human intestinal HT-29 cell line. Furthermore, CFS of VR1 was antibacterial to enteric pathogens like <it>Pseudomonas aeruginosa, Staphylococcus aureus, Escherichia coli</it>, <it>Aeromonas veronii </it>and clinical isolates of <it>P. aeruginosa </it>and <it>E. coli</it>. Detailed study regarding the effect of VR1 CFS on <it>A. veronii </it>cytotoxicity showed a significant decrease in vacuole formation and detrimental cellular changes in Vero cells. On the other hand, <it>A. veronii </it>CFS caused disruption of tight junction proteins ZO-1 and actin in MDCK cell line, which was prevented by pre-incubation with CFS of VR1.</p> <p>Conclusions</p> <p>This is the first study to report isolation of <it>L. plantarum </it>(VR1) from Kutajarista and characterisation for its probiotic attributes. Our study demonstrates the antagonistic property of VR1 to <it>A. veronii </it>and effect of VR1 CFS in reduction of cellular damage caused by <it>A. veronii </it>in both Vero and MDCK cell lines.</p

Au-Ag template stripped pattern for scanning probe investigations of DNA arrays produced by Dip Pen Nanolithography

We report on DNA arrays produced by Dip Pen Nanolithography (DPN) on a novel Au-Ag micro patterned template stripped surface. DNA arrays have been investigated by atomic force microscopy (AFM) and scanning tunnelling microscopy (STM) showing that the patterned template stripped substrate enables easy retrieval of the DPN-functionalized zone with a standard optical microscope permitting a multi-instrument and multi-technique local detection and analysis. Moreover the smooth surface of the Au squares (abput 5-10 angstrom roughness) allows to be sensitive to the hybridization of the oligonucleotide array with label-free target DNA. Our Au-Ag substrates, combining the retrieving capabilities of the patterned surface with the smoothness of the template stripped technique, are candidates for the investigation of DPN nanostructures and for the development of label free detection methods for DNA nanoarrays based on the use of scanning probes.Comment: Langmuir (accepted

Improvement in the Electrical Properties of Nickel-Plated Steel Using Graphitic Carbon Coatings

Thin layers of highly conductive graphitic carbon are deposited onto nickel‐plated steel substrates using a direct photothermal chemical vapor deposition (PTCVD) technique. The coated nickel‐plated steel substrates improve electrical properties (sheet resistance and interfacial contact resistance [ICR]) compared with pristine nickel‐plated steel, which makes it a cost‐effective alternative to stainless steel for steel producers to use in high‐end electrical applications such as energy storage and microelectronics. The coated nickel‐plated steel is found to have ≈10% reduction in sheet resistance and 200 times reduction in ICR (under compression at 140 N cm−2), compared with pristine nickel‐plated steel. ICR is also three times lower than that of a benchmark gold‐coated stainless steel equivalent at the same pressure

Ethno-veterinary medicinal uses of garlic (Allium sativum) by livestock rearers

426-435Garlic (Allium sativum) is used as an important ingredient in the traditional veterinary ethno-medicine since long time among the farmers. The knowledge of the use of garlic individually or additively with other ingredients is scattered in different regions as well as literature. The study was undertaken during 2018-19 to screen the ITKs available in the different sources in which the use of garlic is predominant in ethno-veterinary practices and validate these ITKs with the experts. The validation of ITK was done with 30 experts having the experience in veterinary and ITK practices for their relevance in scientific scenario. The responses of experts for validation were taken on 3-point validity continuum. Out of 46 formulations of garlic with other herbal additives, 56.52% were claimed to have the score above 120 out of 150, showing their wider applicability and validity in ethno-veterinary practice. Ethno-veterinary use of garlic was found for curing cough, cold, fever, urinary problems like oliguria & anuria, bloat, foot and mouth disease, pleuropneumonia, otalgia, dog bite, snake bite, trembling, respiratory system disorder like pleuritis and pneumonia, yoke gall, bone fracture, flatulence, wounds and gangrene. Due to allicin and other sulfur compounds, garlic has antibiotic, antibacterial and antimycotic properties. Ready availability of garlic in every household can be a cost effective first aid or emergency prescription to the livestock rearers who have no immediate access to modern veterinary facilities

Tissue Microenvironments Define and Get Reinforced by Macrophage Phenotypes in Homeostasis or during Inflammation, Repair and Fibrosis

Current macrophage phenotype classifications are based on distinct in vitro culture conditions that do not adequately mirror complex tissue environments. In vivo monocyte progenitors populate all tissues for immune surveillance which supports the maintenance of homeostasis as well as regaining homeostasis after injury. Here we propose to classify macrophage phenotypes according to prototypical tissue environments, e.g. as they occur during homeostasis as well as during the different phases of (dermal) wound healing. In tissue necrosis and/or infection, damage- and/or pathogen-associated molecular patterns induce proinflammatory macrophages by Toll-like receptors or inflammasomes. Such classically activated macrophages contribute to further tissue inflammation and damage. Apoptotic cells and antiinflammatory cytokines dominate in postinflammatory tissues which induce macrophages to produce more antiinflammatory mediators. Similarly, tumor-associated macrophages also confer immunosuppression in tumor stroma. Insufficient parenchymal healing despite abundant growth factors pushes macrophages to gain a profibrotic phenotype and promote fibrocyte recruitment which both enforce tissue scarring. Ischemic scars are largely devoid of cytokines and growth factors so that fibrolytic macrophages that predominantly secrete proteases digest the excess extracellular matrix. Together, macrophages stabilize their surrounding tissue microenvironments by adapting different phenotypes as feed-forward mechanisms to maintain tissue homeostasis or regain it following injury. Furthermore, macrophage heterogeneity in healthy or injured tissues mirrors spatial and temporal differences in microenvironments during the various stages of tissue injury and repair. Copyright (C) 2012 S. Karger AG, Base

Validation of ethno-veterinary medicinal practices of onion (Allium cepa L.)

775-783Onion (Allium cepa) is an important medicinal herb apart from its culinary uses. It has wide array of uses in ethnoveterinary medicine since long time. The study was conducted to review, document and validate the ethno-veterinary practices in which onion is a dominant constituent. The validation of the ethno-veterinary practices was done with 30 experts from the relevant scientific field. The responses of experts for validation were taken on a three-point validity continuum. Among the 58 combinations of ingredients, 27.58% scored above 120 and 55.17% were scored ranging 100 to 120 out of 150, showing their wider applicability and validity in ethno-veterinary practices. The results showed that onions have a wide array of uses in ethno-veterinary practices, ranging from treating gastro-intestinal problems like tympany, indigestion and bloat to proven insecticidal anti-parasitic, repellant and antiseptic actions with different dosage and formulations. Onion is effective on various diseases due to unique combination of different compounds including fructans, flavonoids and organosulfur compounds. Validated practices of onion in ethno-veterinary medicine may be useful particularly among poor or remote livestock rearers who can neither afford nor may access expensive or distant conventional healthcare options

Gas barrier polymer nanocomposite films prepared by graphene oxide encapsulated polystyrene microparticles

The dispersion and orientation of two-dimensional (2D) inorganic nanoplatelets in polymers are technical challenges faced in polymer nanocomposite manufacturing. This work demonstrates an effective way to facilitate the dispersion and orientation of graphene oxide (GO) nanoplatelets in a polymer matrix through encapsulating the polymer within a nanoplatelet shell. Briefly, few-layered GO nanoplatelets encapsulated polystyrene (PS) microparticles were synthesized by a Pickering suspension polymerization method. The synthesis conditions, morphologies, and barrier properties of the GO encapsulated PS spheres and the melt-compressed films are characterized. The addition of salt induces flocculation of GO onto the surface of the styrene monomer droplet, resulting in the formation of a multilayered GO shell as well as the sedimenting of the PS/GO particles during polymerization. The obtained GO encapsulated PS microspheres were purified, dried, and melt-compressed to form composite films. The oxygen permeability (expressed as transmission rate) of the PS/GO composite film containing 2 wt % GO was 526.02 ± 55.78 cm3 m–2 24 h–1—a reduction of 96% relative to the PS control film and 34% lower than the solution mixed PS/GO composite film. This indicates that the encapsulated PS spheres act as an effective carrier to facilitate the dispersion of GO. The orientation was realized by the following melt-compression process, which creates tortuous pathways hindering the permeation of gases through the PS matrix

The 'K' selected oligophilic bacteria: a key to uncultured diversity?

Molecular techniques have made it increasingly clear that a large proportion of bacterial diversity in natural habitats is uncultured and therefore unexplored. We suggest and give evidence in support of a hypothesis that a large proportion, if not all, of the uncultured diversity from a variety of aquatic and terrestrial habitats are oligophilic (oligotrophic) bacteria. Oligophilic bacteria grow only on dilute nutrient media and form small or microscopic colonies. A technique to cultivate and isolate the moderately oligophilic bacteria was developed and 90 cultures isolated, The twelve bacterial cultures characterized showed high growth yield coefficients and carbon conversion efficiencies at low substrate concentrations and progressively decreased with increasing substrate concentrations. Most of the growth yields were substantially higher than those reported in the literature and lie near the theoretical maximum. Slow growth rates and high yields indicate that they are 'K' selected species. 16S rDNA partial sequence analysis of the isolates indicates that it is a novel as well as diverse group