scholarly journals Functional Metagenomics of a Biostimulated Petroleum-Contaminated Soil Reveals an Extraordinary Diversity of Extradiol Dioxygenases

2016 ◽  
Vol 82 (8) ◽  
pp. 2467-2478 ◽  
Author(s):  
Laura Terrón-González ◽  
Guadalupe Martín-Cabello ◽  
Manuel Ferrer ◽  
Eduardo Santero
Keyword(s):  
Contaminated Soil ◽  
Phylogenetic Analyses ◽  
Metagenomic Library ◽  
Type I ◽  
Type Ii ◽  
Extradiol Dioxygenase ◽  
Metagenomic Dna ◽  
Petroleum Contaminated Soil ◽  
Definition Of ◽  
Extradiol Dioxygenases

ABSTRACTA metagenomic library of a petroleum-contaminated soil was constructed in a fosmid vector that allowed heterologous expression of metagenomic DNA. The library, consisting of 6.5 Gb of metagenomic DNA, was screened for extradiol dioxygenase (Edo) activity using catechol and 2,3-dihydroxybiphenyl as the substrates. Fifty-eight independent clones encoding extradiol dioxygenase activity were identified. Forty-one different Edo-encoding genes were identified. The population of Edo genes was not dominated by a particular gene or by highly similar genes; rather, the genes had an even distribution and high diversity. Phylogenetic analyses revealed that most of the genes could not be ascribed to previously defined subfamilies of Edos. Rather, the Edo genes led to the definition of 10 new subfamilies of type I Edos. Phylogenetic analysis of type II enzymes defined 7 families, 2 of which harbored the type II Edos that were found in this work. Particularly striking was the diversity found in family I.3 Edos; 15 out of the 17 sequences assigned to this family belonged to 7 newly defined subfamilies. A strong bias was found that depended on the substrate used for the screening: catechol mainly led to the detection of Edos belonging to the I.2 family, while 2,3-dihydroxybiphenyl led to the detection of most other Edos. Members of the I.2 family showed a clear substrate preference for monocyclic substrates, while those from the I.3 family showed a broader substrate range and high activity toward 2,3-dihydroxybiphenyl. This metagenomic analysis has substantially increased our knowledge of the existing biodiversity of Edos.

Proposed Recommended Nutrient Densities for Moderately Malnourished Children

2009 ◽  
Vol 30 (3_suppl3) ◽  
pp. S267-S342 ◽  
Author(s):  
Michael H. Golden
Keyword(s):  
Dietary Intake ◽  
Severe Malnutrition ◽  
Type I ◽  
Type Ii ◽  
Healthy Individuals ◽  
Malnourished Children ◽  
Factorial Approach ◽  
Accelerated Growth ◽  
Moderate Malnutrition ◽  
Definition Of

Recommended Nutrient Intakes (RNIs) are set for healthy individuals living in clean environments. There are no generally accepted RNIs for those with moderate malnutrition, wasting, and stunting, who live in poor environments. Two sets of recommendations are made for the dietary intake of 30 essential nutrients in children with moderate malnutrition who require accelerated growth to regain normality: first, for those moderately malnourished children who will receive specially formulated foods and diets; and second, for those who are to take mixtures of locally available foods over a longer term to treat or prevent moderate stunting and wasting. Because of the change in definition of severe malnutrition, much of the older literature is pertinent to the moderately wasted or stunted child. A factorial approach has been used in deriving the recommendations for both functional, protective nutrients (type I) and growth nutrients (type II).

scholarly journals Phylogenetic and Structural Comparisons of the Three Types of Methyl Coenzyme M Reductase from Methanococcales and Methanobacteriales

2017 ◽  
Vol 199 (16) ◽  
Author(s):  
Tristan Wagner ◽  
Carl-Eric Wegner ◽  
Jörg Kahnt ◽  
Ulrich Ermler ◽  
Seigo Shima
Keyword(s):  
Active Site ◽  
Phylogenetic Analyses ◽  
Methanogenic Archaea ◽  
Methane Formation ◽  
Type I ◽  
Type Ii ◽  
Coenzyme M ◽  
Content Type ◽  
Type Iii ◽  
Methyl Coenzyme M Reductase

ABSTRACT The phylogenetically diverse family of methanogenic archaea universally use methyl coenzyme M reductase (MCR) for catalyzing the final methane-forming reaction step of the methanogenic energy metabolism. Some methanogens of the orders Methanobacteriales and Methanococcales contain two isoenzymes. Comprehensive phylogenetic analyses on the basis of all three subunits grouped MCRs from Methanobacteriales and Methanococcales into three distinct types: (i) MCRs from Methanobacteriales, (ii) MCRs from Methanobacteriales and Methanococcales, and (iii) MCRs from Methanococcales. The first and second types contain MCR isoenzymes I and II from Methanothermobacter marburgensis, respectively; therefore, they were designated MCR type I and type II and accordingly; the third one was designated MCR type III. For comparison with the known MCR type I and type II structures, we determined the structure of MCR type III from Methanotorris formicicus and Methanothermococcus thermolithotrophicus. As predicted, the three MCR types revealed highly similar overall structures and virtually identical active site architectures reflecting the chemically challenging mechanism of methane formation. Pronounced differences were found at the protein surface with respect to loop geometries and electrostatic properties, which also involve the entrance of the active-site funnel. In addition, the C-terminal end of the γ-subunit is prolonged by an extra helix after helix γ8 in MCR type II and type III, which is, however, differently arranged in the two MCR types. MCR types I, II, and III share most of the posttranslational modifications which appear to fine-tune the enzymatic catalysis. Interestingly, MCR type III lacks the methyl-cysteine but possesses in subunit α of M. formicicus a 6-hydroxy-tryptophan, which thus far has been found only in the α-amanitin toxin peptide but not in proteins. IMPORTANCE Methyl coenzyme M reductase (MCR) represents a prime target for the mitigation of methane releases. Phylogenetic analyses of MCRs suggested several distinct sequence clusters; those from Methanobacteriales and Methanococcales were subdivided into three types: MCR type I from Methanobacteriales, MCR type II from Methanobacteriales and Methanococcales, and the newly designated MCR type III exclusively from Methanococcales. We determined the first X-ray structures for an MCR type III. Detailed analyses revealed substantial differences between the three types only in the peripheral region. The subtle modifications identified and electrostatic profiles suggested enhanced substrate binding for MCR type III. In addition, MCR type III from Methanotorris formicicus contains 6-hydroxy-tryptophan, a new posttranslational modification that thus far has been found only in the α-amanitin toxin.

scholarly journals Transformations in Embryonic Motility in Chick: Kinematic Correlates of Type I and II Motility at E9 and E12

1999 ◽  
Vol 81 (4) ◽  
pp. 1486-1494 ◽  
Author(s):  
Nina S. Bradley
Keyword(s):  
Type I ◽  
Type Ii ◽  
In Ovo ◽  
Movement Experience ◽  
Age Related ◽  
Behavioral Studies ◽  
Kinematic Analyses ◽  
Underlying Mechanisms ◽  
Definition Of ◽  
Embryonic Motility

Transformations in embryonic motility in chick: kinematic correlates of type I and II motility at E9 and E12. Soon after hatching, chicks exhibit an array of adaptive, coordinated behaviors. Chick embryos also acquire nearly 18 days of movement experience, referred to as embryonic motility, before hatching. The chick expresses three forms of motility, types I, II, and III, and each emerges at a different stage of embryonic development. Although much is known about the mechanisms associated with motility at early embryonic stages and at the onset of hatching, the transformations in behavior and underlying mechanisms are not fully understood. Thus the purpose of this study was to determine how motility is modified during the first expected transformation, from type I to type II. It was hypothesized that kinematic features for motility at embryonic day 12 (E12) would differ significantly from features at E9 because type II motility emerges during E11. Embryos were video taped for extended intervals in ovo at E9 or E12 and entire sequences of motility were computer digitized for kinematic analyses. Results reported here indicate that several of the kinematic features characteristic of motility at E9 are also reliable features at E12. On the basis of these findings, a kinematic definition of type I motility is posed for use in subsequent behavioral studies. Several parameters distinguished motility at E12 from E9. The most notable difference between ages was the less regular timing of repetitive limb movements at E12, a finding consistent with recent reports suggesting early motility is an emergent product of a transient neural network rather than a specialized pattern generator. As predicted from established definitions for type II motility, startle-like movements were common at E12; however, they also were present in many kinematic plots at E9, suggesting the discreet age-dependent boundaries in the established definition for type II motility may require modification. Some age-related differences, such as increased intralimb coordination and excursion velocity, may be prerequisites for adaptive behavior after hatching.

scholarly journals Diversification of methanogens into hyperalkaline serpentinizing environments through adaptations to minimize oxidant limitation

2020 ◽  
Author(s):  
Elizabeth M. Fones ◽  
Daniel R. Colman ◽  
Emily A. Kraus ◽  
Ramunas Stepanauskas ◽  
Alexis S. Templeton ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Relative Abundance ◽  
Hydrogen Oxidation ◽  
Phylogenetic Analyses ◽  
Gene Content ◽  
Type I ◽  
Type Ii ◽  
Sultanate Of Oman ◽  
Methane Generation ◽  
Hydrogenotrophic Methanogens

AbstractMetagenome assembled genomes (MAGs) and single amplified genomes (SAGs) affiliated with two distinct Methanobacterium lineages were recovered from subsurface fracture waters of the Samail Ophiolite, Sultanate of Oman. Lineage Type I was abundant in waters with circumneutral pH, whereas lineage Type II was abundant in hydrogen rich, hyperalkaline waters. Type I encoded proteins to couple hydrogen oxidation to CO2 reduction, typical of hydrogenotrophic methanogens. Surprisingly, Type II, which branched from the Type I lineage, lacked homologs of two key oxidative [NiFe]-hydrogenases. These functions were presumably replaced by formate dehydrogenases that oxidize formate to yield reductant and cytoplasmic CO2 via a pathway that was unique among characterized Methanobacteria, allowing cells to overcome CO2/oxidant limitation in high pH waters. This prediction was supported by microcosm-based radiotracer experiments that showed significant biological methane generation from formate, but not bicarbonate, in waters where the Type II lineage was detected in highest relative abundance. Phylogenetic analyses and variability in gene content suggested that recent and ongoing diversification of the Type II lineage was enabled by gene transfer, loss, and transposition. These data indicate that selection imposed by CO2/oxidant availability drove recent methanogen diversification into hyperalkaline waters that are heavily impacted by serpentinization.

scholarly journals Classification of homogeneous bounded domains of lower dimension

1974 ◽  
Vol 53 ◽  
pp. 1-46 ◽  
Author(s):  
Soji Kaneyuki ◽  
Tadashi Tsuji
Keyword(s):  
The Other ◽  
Type I ◽  
Bounded Domains ◽  
Type Ii ◽  
Large Classes ◽  
Siegel Domains ◽  
Dual Cones ◽  
Definition Of ◽  
Lower Dimensional

The theory of classification of homogeneous bounded domains in the complex number space Cn has been developed mainly in the recent papers [10], [6], [3] and [7]. As a result, the classification is reduced to that of S-algebras due to Takeuchi [7] which correspond to irreducible Siegel domains of type I or type II (For the definition of irreducibility see § 1). On the other hand Pjateckii-Sapiro [5] found large classes of homogeneous Siegel domains obtained from classical self-dual cones. Even in lower-dimensional cases, however, there are still homogeneous Siegel domains which do not appear in his results.

scholarly journals Molecular Evolution of a Developmental Pathway: Phylogenetic Analyses of Transforming Growth Factor-β Family Ligands, Receptors and Smad Signal Transducers

Genetics ◽  
1999 ◽  
Vol 152 (2) ◽  
pp. 783-795 ◽  
Author(s):  
Stuart J Newfeld ◽  
Robert G Wisotzkey ◽  
Sudhir Kumar
Keyword(s):  
Growth Factor ◽  
Transforming Growth Factor ◽  
Genomic Sequence ◽  
Phylogenetic Analyses ◽  
Transforming Growth Factor Β ◽  
Type I ◽  
Type Ii ◽  
Intercellular Signaling ◽  
Signal Transducers ◽  
Transitional State

Abstract Intercellular signaling by transforming growth factor-β (TGF-β) proteins coordinates developmental decisions in many organisms. A receptor complex and Smad signal transducers are required for proper responses to TGF-β signals. We have taken a phylogenetic approach to understanding the developmental evolutionary history of TGF-β signaling pathways. We were interested in detecting evolutionary influences among the physically interacting multigene families encoding TGF-β ligands, receptors, and Smads. Our analyses included new ligands and Smads identified from genomic sequence as well as the newest published family members. From an evolutionary perspective we find that (1) TGF-β pathways do not predate the divergence of animals, plants, and fungi; (2) ligands of the TGF-β/activin subfamily likely originated after the divergence of nematodes and arthropods; (3) type I receptors from Caenorhabditis elegans are distinct from other receptors and may reflect an ancestral transitional state between type I and type II receptors; and (4) the Smad family appears to be evolving faster than, and independently of, ligands and receptors. From a developmental perspective we find (1) numerous phylogenetic associations not previously detected in each multigene family; (2) that there are unidentified pathway components that discriminate between type I and type II receptors; (3) that there are more Smads to be discovered in Drosophila and mammals; and (4) that the number of C-terminal serines is the best predictor of a Smad’s role in TGF-β signal transduction. We discuss these findings with respect to the coevolution of physically interacting genes.

X-ray Bragg reflexion, ‘spike’ reflexion and ultra-violet absorption topography of diamonds

1964 ◽  
Vol 281 (1386) ◽  
pp. 310-322 ◽  
Keyword(s):  
Ultra Violet ◽  
Perfect Crystal ◽  
Type I ◽  
Type Ii ◽  
High Definition ◽  
Characteristic Type ◽  
X Ray ◽  
The Matrix ◽  
Definition Of ◽  
Subsequent Diffusion

The relation between X-ray diffracting properties and ultra-violet absorption has been studied point by point on polished plates of diamond having thicknesses from 0-1 mm to more than 1 mm and edge lengths from 2 mm to more than 1 cm. Most specimens exhibit marked non-uniformity of ultra-violet absorption. The intensity of the ‘spike’ X-ray reflexions was found to be roughly proportional to ultra-violet absorption, point by point, a t least in the range of weak and moderate spike intensities. Hence it is concluded that the platelets responsible for the ‘spikes’ are also responsible for the characteristic type I absorptions. However, high values of spike intensity and ultra-violet absorption have only been observed in relatively perfect crystal regions with a low density of grown-in dislocations as determined by X-ray topography; and it is suggested that in imperfect regions containing many grown-in dislocations impurity precipitation in the form of platelets coherent with the matrix may have been inhibited or pre-empted by precipitation in some other way. Thus the absence of ‘ spikes ’ and characteristic type I absorptions may not necessarily imply absence of impurity. On the other hand, some regions of high ultra-violet transparency can be highly perfect; hence lattice imperfection is not necessarily associated with type II optical characteristics. A comparison of ‘spike’ intensity in equivalent cube directions, made on a specimen selected for the high definition of its ‘spike’ topograph features, showed that where platelet precipitation was present it had occurred equally on all cube planes. The sharpness of boundaries between regions of high and low ultra-violet absorption and the association of such boundaries with growth stratifications revealed by Bragg reflexion topographs suggest that they correspond to variations of concentration of grown-in impurity in the crystal, no detectable subsequent diffusion having taken place.

scholarly journals Definition of two agonist types at the mammalian cold-activated channel TRPM8

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Annelies Janssens ◽  
Maarten Gees ◽  
Balazs Istvan Toth ◽  
Debapriya Ghosh ◽  
Marie Mulier ◽  
...  
Keyword(s):  
Trp Channels ◽  
Function Analysis ◽  
Channel Gating ◽  
Allyl Isothiocyanate ◽  
Channel Structure ◽  
Trp Channel ◽  
Mustard Oil ◽  
Type I ◽  
Type Ii ◽  
Definition Of

Various TRP channels act as polymodal sensors of thermal and chemical stimuli, but the mechanisms whereby chemical ligands impact on TRP channel gating are poorly understood. Here we show that AITC (allyl isothiocyanate; mustard oil) and menthol represent two distinct types of ligands at the mammalian cold sensor TRPM8. Kinetic analysis of channel gating revealed that AITC acts by destabilizing the closed channel, whereas menthol stabilizes the open channel, relative to the transition state. Based on these differences, we classify agonists as either type I (menthol-like) or type II (AITC-like), and provide a kinetic model that faithfully reproduces their differential effects. We further demonstrate that type I and type II agonists have a distinct impact on TRPM8 currents and TRPM8-mediated calcium signals in excitable cells. These findings provide a theoretical framework for understanding the differential actions of TRP channel ligands, with important ramifications for TRP channel structure-function analysis and pharmacology.

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