structurally distinct types: Topics by Science.gov

Sample records for structurally distinct types

Taxometric Analysis as a General Strategy for Distinguishing Categorical from Dimensional Latent Structure

ERIC Educational Resources Information Center

McGrath, Robert E.; Walters, Glenn D.

2012-01-01

Statistical analyses investigating latent structure can be divided into those that estimate structural model parameters and those that detect the structural model type. The most basic distinction among structure types is between categorical (discrete) and dimensional (continuous) models. It is a common, and potentially misleading, practice to…
Cerebral vascular amyloid seeds drive amyloid β-protein fibril assembly with a distinct anti-parallel structure

PubMed Central

Xu, Feng; Fu, Ziao; Dass, Sharmila; Kotarba, AnnMarie E.; Davis, Judianne; Smith, Steven O.; Van Nostrand, William E.

2016-01-01

Cerebrovascular accumulation of amyloid β-protein (Aβ), a condition known as cerebral amyloid angiopathy (CAA), is a common pathological feature of patients with Alzheimer's disease. Familial Aβ mutations, such as Dutch-E22Q and Iowa-D23N, can cause severe cerebrovascular accumulation of amyloid that serves as a potent driver of vascular cognitive impairment and dementia. The distinctive features of vascular amyloid that underlie its unique pathological properties remain unknown. Here, we use transgenic mouse models producing CAA mutants (Tg-SwDI) or overproducing human wild-type Aβ (Tg2576) to demonstrate that CAA-mutant vascular amyloid influences wild-type Aβ deposition in brain. We also show isolated microvascular amyloid seeds from Tg-SwDI mice drive assembly of human wild-type Aβ into distinct anti-parallel β-sheet fibrils. These findings indicate that cerebrovascular amyloid can serve as an effective scaffold to promote rapid assembly and strong deposition of Aβ into a unique structure that likely contributes to its distinctive pathology. PMID:27869115
Bacterial Biofilms as Complex Communities

NASA Astrophysics Data System (ADS)

Vlamakis, Hera

2010-03-01

Many microbial populations form surface-associated multicellular communities known as biofilms. These multicellular communities are encased in a self-produced extracellular matrix composed of polysaccharides and proteins. Division of labor is a key feature of these communities and different cells serve distinct functions. We have found that in biofilms of the bacterium Bacillus subtilis, different cell types including matrix-producing and sporulating cells coexist and localize to distinct regions within the structured community. We were interested in understanding how these different cell types arise. Using fluorescence reporters under the control of promoters that are specific for distinct cell types we were able to follow the dynamics of differentiation throughout biofilm development. We found that a series of extracellular signals leads to differentiation of distinct cell types during biofilm formation. In addition, we found that extracellular matrix functions as a differentiation signal for timely sporulation within a biofilm and mutants unable to produce matrix were delayed in sporulation. Our results indicate that within a biofilm, cell-cell signaling is directional in that one cell type produces a signal that is sensed by another distinct cell type. Furthermore, once differentiated, cells become resistant to the action of other signaling molecules making it possible to maintain distinct cell populations over prolonged periods.
Call types of Bigg's killer whales (Orcinus orca) in western Alaska: Using vocal dialects to assess population structure

NASA Astrophysics Data System (ADS)

Sharpe, Deborah Lynn

Apex predators are important indicators of ecosystem health, but little is known about the population structure of Bigg's killer whales ( Orcinus orca; i.e. 'transient' ecotype) in western Alaska. Currently, all Bigg's killer whales in western Alaska are ascribed to a single broad stock for management under the US Marine Mammal Protection Act. However, recent nuclear microsatellite and mitochondrial DNA analyses indicate that this stock is likely comprised of genetically distinct sub-populations. In accordance with what is known about killer whale vocal dialects in other locations, I sought to evaluate Bigg's killer whale population structure by examining the spatial distribution of group-specific call types in western Alaska. Digital audio recordings were collected from 33 encounters with Bigg's killer whales throughout the Aleutian and Pribilof Islands in the summers of 2001-2007 and 2009-2010. Recorded calls were perceptually classified into discrete types and then quantitatively described using 12 structural and time-frequency measures. Resulting call categories were objectively validated using a random forest approach. A total of 36 call types and subtypes were identified across the entire study area, and regional patterns of call type usage revealed three distinct dialects, each of which corresponding to proposed genetic delineations. I suggest that at least three acoustically and genetically distinct subpopulations are present in western Alaska, and put forth an initial catalog for this area describing the regional vocal repertoires of Bigg's killer whale call types.
Characterization and structural analysis of wild type and a non-abscission mutant at the development funiculus (Def) locus in Pisum sativum L.

PubMed

Ayeh, Kwadwo Owusu; Lee, YeonKyeong; Ambrose, Mike J; Hvoslef-Eide, Anne Kathrine

2009-06-23

In pea seeds (Pisum sativum L.), the Def locus defines an abscission event where the seed separates from the funicle through the intervening hilum region at maturity. A spontaneous mutation at this locus results in the seed failing to abscise from the funicle as occurs in wild type peas. In this work, structural differences between wild type peas that developed a distinct abscission zone (AZ) between the funicle and the seed coat and non-abscission def mutant were characterized. A clear abscission event was observed in wild type pea seeds that were associated with a distinct double palisade layers at the junction between the seed coat and funicle. Generally, mature seeds fully developed an AZ, which was not present in young wild type seeds. The AZ was formed exactly below the counter palisade layer. In contrast, the palisade layers at the junction of the seed coat and funicle were completely absent in the def mutant pea seeds and the cells in this region were seen to be extensions of surrounding parenchymatous cells. The Def wild type developed a distinct AZ associated with palisade layer and counterpalisade layer at the junction of the seed coat and funicle while the def mutant pea seed showed non-abscission and an absence of the double palisade layers in the same region. We conclude that the presence of the double palisade layer in the hilum of the wild type pea seeds plays an important structural role in AZ formation by delimiting the specific region between the seed coat and the funicle and may play a structural role in the AZ formation and subsequent detachment of the seed from the funicle.
Microbial Community and Functional Structure Significantly Varied among Distinct Types of Paddy Soils But Responded Differently along Gradients of Soil Depth Layers

PubMed Central

Bai, Ren; Wang, Jun-Tao; Deng, Ye; He, Ji-Zheng; Feng, Kai; Zhang, Li-Mei

2017-01-01

Paddy rice fields occupy broad agricultural area in China and cover diverse soil types. Microbial community in paddy soils is of great interest since many microorganisms are involved in soil functional processes. In the present study, Illumina Mi-Seq sequencing and functional gene array (GeoChip 4.2) techniques were combined to investigate soil microbial communities and functional gene patterns across the three soil types including an Inceptisol (Binhai), an Oxisol (Leizhou), and an Ultisol (Taoyuan) along four profile depths (up to 70 cm in depth) in mesocosm incubation columns. Detrended correspondence analysis revealed that distinctly differentiation in microbial community existed among soil types and profile depths, while the manifest variance in functional structure was only observed among soil types and two rice growth stages, but not across profile depths. Along the profile depth within each soil type, Acidobacteria, Chloroflexi, and Firmicutes increased whereas Cyanobacteria, β-proteobacteria, and Verrucomicrobia declined, suggesting their specific ecophysiological properties. Compared to bacterial community, the archaeal community showed a more contrasting pattern with the predominant groups within phyla Euryarchaeota, Thaumarchaeota, and Crenarchaeota largely varying among soil types and depths. Phylogenetic molecular ecological network (pMEN) analysis further indicated that the pattern of bacterial and archaeal communities interactions changed with soil depth and the highest modularity of microbial community occurred in top soils, implying a relatively higher system resistance to environmental change compared to communities in deeper soil layers. Meanwhile, microbial communities had higher connectivity in deeper soils in comparison with upper soils, suggesting less microbial interaction in surface soils. Structure equation models were developed and the models indicated that pH was the most representative characteristics of soil type and identified as the key driver in shaping both bacterial and archaeal community structure, but did not directly affect microbial functional structure. The distinctive pattern of microbial taxonomic and functional composition along soil profiles implied functional redundancy within these paddy soils. PMID:28611747
Microbial Community and Functional Structure Significantly Varied among Distinct Types of Paddy Soils But Responded Differently along Gradients of Soil Depth Layers.

PubMed

Bai, Ren; Wang, Jun-Tao; Deng, Ye; He, Ji-Zheng; Feng, Kai; Zhang, Li-Mei

2017-01-01

Paddy rice fields occupy broad agricultural area in China and cover diverse soil types. Microbial community in paddy soils is of great interest since many microorganisms are involved in soil functional processes. In the present study, Illumina Mi-Seq sequencing and functional gene array (GeoChip 4.2) techniques were combined to investigate soil microbial communities and functional gene patterns across the three soil types including an Inceptisol (Binhai), an Oxisol (Leizhou), and an Ultisol (Taoyuan) along four profile depths (up to 70 cm in depth) in mesocosm incubation columns. Detrended correspondence analysis revealed that distinctly differentiation in microbial community existed among soil types and profile depths, while the manifest variance in functional structure was only observed among soil types and two rice growth stages, but not across profile depths. Along the profile depth within each soil type, Acidobacteria , Chloroflexi , and Firmicutes increased whereas Cyanobacteria , β -proteobacteria , and Verrucomicrobia declined, suggesting their specific ecophysiological properties. Compared to bacterial community, the archaeal community showed a more contrasting pattern with the predominant groups within phyla Euryarchaeota , Thaumarchaeota , and Crenarchaeota largely varying among soil types and depths. Phylogenetic molecular ecological network (pMEN) analysis further indicated that the pattern of bacterial and archaeal communities interactions changed with soil depth and the highest modularity of microbial community occurred in top soils, implying a relatively higher system resistance to environmental change compared to communities in deeper soil layers. Meanwhile, microbial communities had higher connectivity in deeper soils in comparison with upper soils, suggesting less microbial interaction in surface soils. Structure equation models were developed and the models indicated that pH was the most representative characteristics of soil type and identified as the key driver in shaping both bacterial and archaeal community structure, but did not directly affect microbial functional structure. The distinctive pattern of microbial taxonomic and functional composition along soil profiles implied functional redundancy within these paddy soils.
Defined types of cortical interneurone structure space and spike timing in the hippocampus

PubMed Central

Somogyi, Peter; Klausberger, Thomas

2005-01-01

The cerebral cortex encodes, stores and combines information about the internal and external environment in rhythmic activity of multiple frequency ranges. Neurones of the cortex can be defined, recognized and compared on the comprehensive application of the following measures: (i) brain area- and cell domain-specific distribution of input and output synapses, (ii) expression of molecules involved in cell signalling, (iii) membrane and synaptic properties reflecting the expression of membrane proteins, (iv) temporal structure of firing in vivo, resulting from (i)–(iii). Spatial and temporal measures of neurones in the network reflect an indivisible unity of evolutionary design, i.e. neurones do not have separate structure or function. The blueprint of this design is most easily accessible in the CA1 area of the hippocampus, where a relatively uniform population of pyramidal cells and their inputs follow an instantly recognizable laminated pattern and act within stereotyped network activity patterns. Reviewing the cell types and their spatio-temporal interactions, we suggest that CA1 pyramidal cells are supported by at least 16 distinct types of GABAergic neurone. During a given behaviour-contingent network oscillation, interneurones of a given type exhibit similar firing patterns. During different network oscillations representing two distinct brain states, interneurones of the same class show different firing patterns modulating their postsynaptic target-domain in a brain-state-dependent manner. These results suggest roles for specific interneurone types in structuring the activity of pyramidal cells via their respective target domains, and accurately timing and synchronizing pyramidal cell discharge, rather than providing generalized inhibition. Finally, interneurones belonging to different classes may fire preferentially at distinct time points during a given oscillation. As different interneurones innervate distinct domains of the pyramidal cells, the different compartments will receive GABAergic input differentiated in time. Such a dynamic, spatio-temporal, GABAergic control, which evolves distinct patterns during different brain states, is ideally suited to regulating the input integration of individual pyramidal cells contributing to the formation of cell assemblies and representations in the hippocampus and, probably, throughout the cerebral cortex. PMID:15539390
Evidence of segregated spawning in a single marine fish stock: Sympatric divergence of ecotypes in icelandic cod?

USGS Publications Warehouse

Grabowski, T.B.; Thorsteinsson, Vilhjalmur; McAdam, B.J.; Marteinsdottir, G.

2011-01-01

There is increasing recognition of intraspecific diversity and population structure within marine fish species, yet there is little direct evidence of the isolating mechanisms that maintain it or documentation of its ecological extent. We analyzed depth and temperature histories collected by electronic data storage tags retrieved from 104 Atlantic cod at liberty ???1 year to evaluate a possible isolating mechanisms maintaining population structure within the Icelandic cod stock. This stock consists of two distinct behavioral types, resident coastal cod and migratory frontal cod, each occurring within two geographically distinct populations. Despite being captured together on the same spawning grounds, we show the behavioral types seem reproductively isolated by fine-scale differences in spawning habitat selection, primarily depth. Additionally, the different groups occupied distinct seasonal thermal and bathymetric niches that generally demonstrated low levels of overlap throughout the year. Our results indicate that isolating mechanisms, such as differential habitat selection during spawning, might contribute to maintaining diversity and fine-scale population structure in broadcast-spawning marine fishes.
The first Fe-based Na+-ion cathode with two distinct types of polyanions: Fe 3P 5SiO 19

DOE PAGES

Kan, W. H.; Huq, A.; Manthiram, A.

2015-05-15

We report the synthesis, structure, and electrochemistry of the first Na +-ion cathode with two distinct types of polyanions: Fe 3P 5SiO 19. The Fe-based cathode has a reversible capacity of ca. 70 mAh g -1; ca. 1.7 Na + ions per formula can be inserted/extracted at an average voltage of 2.5 V versus Na +/Na.
Structural and functional dissection reveals distinct roles of Ca2+-binding sites in the giant adhesin SiiE of Salmonella enterica

PubMed Central

Klingl, Stefan; Sandmann, Achim; Taccardi, Nicola; Sticht, Heinrich; Muller, Yves A.; Hensel, Michael

2017-01-01

The giant non-fimbrial adhesin SiiE of Salmonella enterica mediates the first contact to the apical site of epithelial cells and enables subsequent invasion. SiiE is a 595 kDa protein composed of 53 repetitive bacterial immunoglobulin (BIg) domains and the only known substrate of the SPI4-encoded type 1 secretion system (T1SS). The crystal structure of BIg50-52 of SiiE revealed two distinct Ca2+-binding sites per BIg domain formed by conserved aspartate or glutamate residues. In a mutational analysis Ca2+-binding sites were disrupted by aspartate to serine exchange at various positions in the BIg domains of SiiE. Amounts of secreted SiiE diminish with a decreasing number of intact Ca2+-binding sites. BIg domains of SiiE contain distinct Ca2+-binding sites, with type I sites being similar to other T1SS-secreted proteins and type II sites newly identified in SiiE. We functionally and structurally dissected the roles of type I and type II Ca2+-binding sites in SiiE, as well as the importance of Ca2+-binding sites in various positions of SiiE. Type I Ca2+-binding sites were critical for efficient secretion of SiiE and a decreasing number of type I sites correlated with reduced secretion. Type II sites were less important for secretion, stability and surface expression of SiiE, however integrity of type II sites in the C-terminal portion was required for the function of SiiE in mediating adhesion and invasion. PMID:28558023
Differentiating Left- and Right-Handed Carbon Nanotubes by DNA.

PubMed

Ao, Geyou; Streit, Jason K; Fagan, Jeffrey A; Zheng, Ming

2016-12-28

New structural characteristics emerge when solid-state crystals are constructed in lower dimensions. This is exemplified by single-wall carbon nanotubes, which exhibit a degree of freedom in handedness and a multitude of helicities that give rise to three distinct types of electronic structures: metals, quasi-metals, and semiconductors. Here we report the use of intrinsically chiral single-stranded DNA to achieve simultaneous handedness and helicity control for all three types of nanotubes. We apply polymer aqueous two-phase systems to select special DNA-wrapped carbon nanotubes, each of which we argue must have an ordered DNA structure that binds to a nanotube of defined handedness and helicity and resembles a well-folded biomacromolecule with innate stereoselectivity. We have screened over 300 short single-stranded DNA sequences with palindrome symmetry, leading to the selection of more than 20 distinct carbon nanotube structures that have defined helicity and handedness and cover the entire chiral angle range and all three electronic types. The mechanism of handedness selection is illustrated by a DNA sequence that adopts two distinct folds on a pair of (6,5) nanotube enantiomers, rendering them large differences in fluorescence intensity and chemical reactivity. This result establishes a first example of functionally distinguishable left- and right-handed carbon nanotubes. Taken together, our work demonstrates highly efficient enantiomer differentiation by DNA and offers a first comprehensive solution to achieve simultaneous handedness and helicity control for all three electronic types of carbon nanotubes.
Differentiating Left- and Right-handed Carbon Nanotubes by DNA

NASA Astrophysics Data System (ADS)

Zheng, Ming

New structural characteristics emerge when solid-state crystals are constructed in lower dimensions. This is exemplified by single-wall carbon nanotubes, which exhibit a degree of freedom in handedness, and a multitude of helicity that gives rise to three distinct types of electronic structures - metals, quasi-metals, and semiconductors. Here, we report the use of intrinsically chiral single-stranded DNA to achieve simultaneous handedness and helicity control for all three types of nanotubes. We apply polymer aqueous two-phase systems to select special DNA-wrapped carbon nanotubes, each of which we argue must have an ordered DNA structure bound to a nanotube of defined handedness and helicity, resembling a well-folded biomacromolecule with innate stereo-selectivity. We have screened over 300 short single-stranded DNA sequences with palindrome symmetry, leading to the selection of more than 20 distinct carbon nanotube structures that have defined helicity and handedness and cover the entire chiral angle range and all three electronic types. The mechanism of handedness selection is illustrated by a DNA sequence that adopts two distinct folds on a pair of (6,5) nanotube enantiomers, respectively, rendering them large differences in fluorescence intensity and chemical reactivity. This result establishes a first example of functionally distinguishable left- and right-handed carbon nanotubes. Taken together, our work demonstrates highly efficient enantiomer differentiation by DNA, and offers a first comprehensive solution to achieve simultaneous handedness and helicity control for all three electronic types of carbon nanotubes. .
Growth of equilibrium structures built from a large number of distinct component types.

PubMed

Hedges, Lester O; Mannige, Ranjan V; Whitelam, Stephen

2014-09-14

We use simple analytic arguments and lattice-based computer simulations to study the growth of structures made from a large number of distinct component types. Components possess 'designed' interactions, chosen to stabilize an equilibrium target structure in which each component type has a defined spatial position, as well as 'undesigned' interactions that allow components to bind in a compositionally-disordered way. We find that high-fidelity growth of the equilibrium target structure can happen in the presence of substantial attractive undesigned interactions, as long as the energy scale of the set of designed interactions is chosen appropriately. This observation may help explain why equilibrium DNA 'brick' structures self-assemble even if undesigned interactions are not suppressed [Ke et al. Science, 338, 1177, (2012)]. We also find that high-fidelity growth of the target structure is most probable when designed interactions are drawn from a distribution that is as narrow as possible. We use this result to suggest how to choose complementary DNA sequences in order to maximize the fidelity of multicomponent self-assembly mediated by DNA. We also comment on the prospect of growing macroscopic structures in this manner.
Identification of O-rich structures on platinum(111)-supported ultrathin iron oxide films

DOE PAGES

Merte, Lindsay R.; Bai, Yunhai; Zeuthen, Helene; ...

2016-01-06

Using high-resolution scanning tunneling microscopy (STM) we have studied the oxidation of ultrathin FeO films grown on Pt(111). At the initial stage of the FeO film oxidation by atomic oxygen exposure, we identified three distinct types of line defects, all of which form boundaries between FeO domains of opposite orientation. Two types of line defects appearing bright ( type-i) and dark ( type-ii) in the STM images at typical scanning parameters are “metallic”, whereas the third line defect exhibits nonmetallic behavior ( type-iii). Atomic-scale structure models of these line defects are proposed, with type-i defects exhibiting 4-fold coordinated Fe atoms,more » type-ii exhibiting 2-fold coordinated O atoms, and type-iii exhibiting tetrahedrally-coordinated Fe atoms. In addition, FeO 2 trilayer islands are formed upon oxidation, which appear at FCC-type domains of the moiré structure. At high scanning bias, distinct protrusions on the trilayer islands are observed over surface O ions, which are assigned to H adatoms. The experimental data are supported by density functional theory (DFT) calculations, in which bare and hydroxylated FeO 2 trilayer islands are compared. Finally, we compare the formation of O-rich features on continuous FeO films using atomic oxygen with the oxidation of Pt(111)-supported FeO islands accomplished by O 2 exposure.« less
Three types of ependymal cells with intracellular calcium oscillation are characterized by distinct cilia beating properties.

PubMed

Liu, Tongyu; Jin, Xingjian; Prasad, Rahul M; Sari, Youssef; Nauli, Surya M

2014-09-01

Ependymal cells are multiciliated epithelial cells that line the ventricles in the adult brain. Abnormal function or structure of ependymal cilia has been associated with various neurological deficits. For the first time, we report three distinct ependymal cell types, I, II, and III, based on their unique ciliary beating frequency and beating angle. These ependymal cells have specific localizations within the third ventricle of the mouse brain. Furthermore, neither ependymal cell types nor their localizations are altered by aging. Our high-speed fluorescence imaging analysis reveals that these ependymal cells have an intracellular pacing calcium oscillation property. Our study further shows that alcohol can significantly repress the amplitude of calcium oscillation and the frequency of ciliary beating, resulting in an overall decrease in volume replacement by the cilia. Furthermore, the pharmacological agent cilostazol could differentially increase cilia beating frequency in type II, but not in type I or type III, ependymal cells. In summary, we provide the first evidence of three distinct types of ependymal cells with calcium oscillation properties. © 2014 Wiley Periodicals, Inc.
Collagen fibrils in functionally distinct tendons have differing structural responses to tendon rupture and fatigue loading.

PubMed

Herod, Tyler W; Chambers, Neil C; Veres, Samuel P

2016-09-15

In this study we investigate relationships between the nanoscale structure of collagen fibrils and the macroscale functional response of collagenous tissues. To do so, we study two functionally distinct classes of tendons, positional tendons and energy storing tendons, using a bovine forelimb model. Molecular-level assessment using differential scanning calorimetry (DSC), functional crosslink assessment using hydrothermal isometric tension (HIT) analysis, and ultrastructural assessment using scanning electron microscopy (SEM) were used to study undamaged, ruptured, and cyclically loaded samples from the two tendon types. HIT indicated differences in both crosslink type and crosslink density, with flexor tendons having more thermally stable crosslinks than the extensor tendons (higher TFmax of >90 vs. 75.1±2.7°C), and greater total crosslink density than the extensor tendons (higher t1/2 of 11.5±1.9 vs. 3.5±1.0h after NaBH4 treatment). Despite having a lower crosslink density than flexor tendons, extensor tendons were significantly stronger (37.6±8.1 vs. 23.1±7.7MPa) and tougher (14.3±3.6 vs. 6.8±3.4MJ/m(3)). SEM showed that collagen fibrils in the tougher, stronger extensor tendons were able to undergo remarkable levels of plastic deformation in the form of discrete plasticity, while those in the flexor tendons were not able to plastically deform. When cyclically loaded, collagen fibrils in extensor tendons accumulated fatigue damage rapidly in the form of kink bands, while those in flexor tendons did not accumulate significant fatigue damage. The results demonstrate that collagen fibrils in functionally distinct tendons respond differently to mechanical loading, and suggests that fibrillar collagens may be subject to a strength vs. fatigue resistance tradeoff. Collagen fibrils-nanoscale biological cables-are the fundamental load-bearing elements of all structural human tissues. While all collagen fibrils share common features, such as being composed of a precise quarter-staggered polymeric arrangement of triple-helical collagen molecules, their structure can vary significantly between tissue types, and even between different anatomical structures of the same tissue type. To understand normal function, homeostasis, and disease of collagenous tissues requires detailed knowledge of collagen fibril structure-function. Using anatomically proximate but structurally distinct tendons, we show that collagen fibrils in functionally distinct tendons have differing susceptibilities to damage under both tensile overload and cyclic fatigue loading. Our results suggest that the structure of collagen fibrils may lead to a strength versus fatigue resistance tradeoff, where high strength is gained at the expense of fatigue resistance, and vice versa. Copyright © 2016 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.
Impact of inhomogeneity on SH-type wave propagation in an initially stressed composite structure

NASA Astrophysics Data System (ADS)

Saha, S.; Chattopadhyay, A.; Singh, A. K.

2018-02-01

The present analysis has been made on the influence of distinct form of inhomogeneity in a composite structure comprised of double superficial layers lying over a half-space, on the phase velocity of SH-type wave propagating through it. Propagation of SH-type wave in the said structure has been examined in four distinct cases of inhomogeneity viz. when inhomogeneity in double superficial layer is due to exponential variation in density only (Case I); when inhomogeneity in double superficial layers is due to exponential variation in rigidity only (Case II); when inhomogeneity in double superficial layer is due to exponential variation in rigidity, density and initial stress (Case III) and when inhomogeneity in double superficial layer is due to linear variation in rigidity, density and initial stress (Case IV). Closed-form expression of dispersion relation has been accomplished for all four aforementioned cases through extensive application of Debye asymptotic analysis. Deduced dispersion relations for all the cases are found in well-agreement to the classical Love-wave equation. Numerical computation has been carried out to graphically demonstrate the effect of inhomogeneity parameters, initial stress parameters as well as width ratio associated with double superficial layers in the composite structure for each of the four aforesaid cases on dispersion curve. Meticulous examination of distinct cases of inhomogeneity and initial stress in context of considered problem has been carried out with detailed analysis in a comparative approach.
Comparing Curriculum Types: 'Powerful Knowledge' and '21st Century Learning'

ERIC Educational Resources Information Center

McPhail, Graham; Rata, Elizabeth

2016-01-01

This paper theorises a curriculum model containing four features. We use these features as criteria to analyse and evaluate two distinctive curriculum design types: '21st Century Learning' and 'Powerful Knowledge'. The four features are: (i) the underpinning theory of knowledge in each curriculum design type; (ii) the knowledge structures used to…
Detergent-dependent separation of postsynaptic density, membrane rafts and other subsynaptic structures from the synaptic plasma membrane of rat forebrain.

PubMed

Zhao, LiYing; Sakagami, Hiroyuki; Suzuki, Tatsuo

2014-10-01

We systematically investigated the purification process of post-synaptic density (PSD) and post-synaptic membrane rafts (PSRs) from the rat forebrain synaptic plasma membranes by examining the components and the structures of the materials obtained after the treatment of synaptic plasma membranes with TX-100, n-octyl β-d-glucoside (OG) or 3-([3-cholamidopropyl]dimethylammonio)-2-hydroxy-1-propanesulfonate (CHAPSO). These three detergents exhibited distinct separation profiles for the synaptic subdomains. Type I and type II PSD proteins displayed mutually exclusive distribution. After TX-100 treatment, type I PSD was recovered in two fractions: a pellet and an insoluble fraction 8, which contained partially broken PSD-PSR complexes. Conventional PSD was suggested to be a mixture of these two PSD pools and did not contain type II PSD. An association of type I PSD with PSRs was identified in the TX-100 treatment, and those with type II PSD in the OG and CHAPSO treatments. An association of GABA receptors with gephyrin was easily dissociated. OG at a high concentration solubilized the type I PSD proteins. CHAPSO treatment resulted in a variety of distinct fractions, which contained certain novel structures. Two different pools of GluA, either PSD or possibly raft-associated, were identified in the OG and CHAPSO treatments. These results are useful in advancing our understanding of the structural organization of synapses at the molecular level. We systematically investigated the purification process of post-synaptic density (PSD) and synaptic membrane rafts by examining the structures obtained after treatment of the SPMs with TX-100, n-octyl β-d-glucoside or CHAPSO. Differential distribution of type I and type II PSD, synaptic membrane rafts, and other novel subdomains in the SPM give clues to understand the structural organization of synapses at the molecular level. © 2014 International Society for Neurochemistry.

Overview of the creative genome: effects of genome structure and sequence on the generation of variation and evolution.

PubMed

Caporale, Lynn Helena

2012-09-01

This overview of a special issue of Annals of the New York Academy of Sciences discusses uneven distribution of distinct types of variation across the genome, the dependence of specific types of variation upon distinct classes of DNA sequences and/or the induction of specific proteins, the circumstances in which distinct variation-generating systems are activated, and the implications of this work for our understanding of evolution and of cancer. Also discussed is the value of non text-based computational methods for analyzing information carried by DNA, early insights into organizational frameworks that affect genome behavior, and implications of this work for comparative genomics. © 2012 New York Academy of Sciences.
Diverse Supramolecular Nanofiber Networks Assembled by Functional Low-Complexity Domains.

PubMed

An, Bolin; Wang, Xinyu; Cui, Mengkui; Gui, Xinrui; Mao, Xiuhai; Liu, Yan; Li, Ke; Chu, Cenfeng; Pu, Jiahua; Ren, Susu; Wang, Yanyi; Zhong, Guisheng; Lu, Timothy K; Liu, Cong; Zhong, Chao

2017-07-25

Self-assembling supramolecular nanofibers, common in the natural world, are of fundamental interest and technical importance to both nanotechnology and materials science. Despite important advances, synthetic nanofibers still lack the structural and functional diversity of biological molecules, and the controlled assembly of one type of molecule into a variety of fibrous structures with wide-ranging functional attributes remains challenging. Here, we harness the low-complexity (LC) sequence domain of fused in sarcoma (FUS) protein, an essential cellular nuclear protein with slow kinetics of amyloid fiber assembly, to construct random copolymer-like, multiblock, and self-sorted supramolecular fibrous networks with distinct structural features and fluorescent functionalities. We demonstrate the utilities of these networks in the templated, spatially controlled assembly of ligand-decorated gold nanoparticles, quantum dots, nanorods, DNA origami, and hybrid structures. Owing to the distinguishable nanoarchitectures of these nanofibers, this assembly is structure-dependent. By coupling a modular genetic strategy with kinetically controlled complex supramolecular self-assembly, we demonstrate that a single type of protein molecule can be used to engineer diverse one-dimensional supramolecular nanostructures with distinct functionalities.
Structure of Adeno-Associated Virus Type 4

PubMed Central

Padron, Eric; Bowman, Valorie; Kaludov, Nikola; Govindasamy, Lakshmanan; Levy, Hazel; Nick, Phillip; McKenna, Robert; Muzyczka, Nicholas; Chiorini, John A.; Baker, Timothy S.; Agbandje-McKenna, Mavis

2005-01-01

Adeno-associated virus (AAV) is a member of the Parvoviridae, belonging to the Dependovirus genus. Currently, several distinct isolates of AAV are in development for use in human gene therapy applications due to their ability to transduce different target cells. The need to manipulate AAV capsids for specific tissue delivery has generated interest in understanding their capsid structures. The structure of AAV type 4 (AAV4), one of the most antigenically distinct serotypes, was determined to 13-Å resolution by cryo-electron microscopy and image reconstruction. A pseudoatomic model was built for the AAV4 capsid by use of a structure-based sequence alignment of its major capsid protein, VP3, with that of AAV2, to which AAV4 is 58% identical and constrained by its reconstructed density envelope. The model showed variations in the surface loops that may account for the differences in receptor binding and antigenicity between AAV2 and AAV4. The AAV4 capsid surface topology also shows an unpredicted structural similarity to that of Aleutian mink disease virus and human parvovirus B19, autonomous members of the genus, despite limited sequence homology. PMID:15795290
Discovery of the Kinematic Alignment of Early-type Galaxies in the Virgo Cluster

NASA Astrophysics Data System (ADS)

Kim, Suk; Jeong, Hyunjin; Lee, Jaehyun; Lee, Youngdae; Joo, Seok-Joo; Kim, Hak-Sub; Rey, Soo-Chang

2018-06-01

Using the kinematic position angles (PAkin), an accurate indicator for the spin axis of a galaxy, obtained from the ATLAS3D integral-field-unit (IFU) spectroscopic data, we discovered that 57 Virgo early-type galaxies tend to prefer the specific PAkin values of 20° and 100°, suggesting that they are kinematically aligned with each other. These kinematic alignment angles are further associated with the directions of the two distinct axes of the Virgo cluster extending east–west and north–south, strongly suggesting that the two distinct axes are the filamentary structures within the cluster as a trace of infall patterns of galaxies. Given that the spin axis of a massive early-type galaxy does not change easily even in clusters from the hydrodynamic simulations, Virgo early-type galaxies are likely to fall into the cluster along the filamentary structures while maintaining their angular momentum. This implies that many early-type galaxies in clusters are formed in filaments via major mergers before subsequently falling into the cluster. Investigating the kinematic alignment in other clusters will allow us to understand the formation of galaxy clusters and early-type galaxies.
Some Structural Characteristics of Music Television Videos.

ERIC Educational Resources Information Center

Fry, Donald L.; Fry, Virginia H.

1987-01-01

Indicates, by analyzing two types of montage structures, that music television is a hybrid form of television programing displaying visual characteristics of both television commercials and drama. Argues that this amalgam of different characteristics gives music television its distinctive look and power as a promotional tool for the record…
Worse cardiac remodeling in response to pressure overload in type 2 diabetes mellitus.

PubMed

Gonçalves, N; Gomes-Ferreira, C; Moura, C; Roncon-Albuquerque, R; Leite-Moreira, A F; Falcão-Pires, I

2016-08-15

Diabetic cardiomyopathy is characterized by cardiac structural and functional abnormalities. Additionally, chronic pressure overload conditions are highly prevalent amongst diabetic population and this association leads to a more severe myocardial impairment. The differences in myocardial pathophysiology between type 1 and type 2 diabetes mellitus (DM) still remain to be clarified. Thus, we aimed to investigate biventricular structural and functional changes promoted by the two types of DM and the impact of concomitant chronic pressure overload. Wistar rats were injected with streptozotocin (Type 1 DM, T1DM) or fed with a hypercaloric diet (Type 2 DM, T2DM). Pressure overload was imposed in DM animals by aortic constriction and after 5weeks of DM the cardiac function and structure were evaluated. Both types of DM promoted hypertrophy, increased fibrosis and advanced glycation end-products deposition, in the two ventricles. Interestingly, the induced myocardial alterations were distinct. While T1DM stimulated a pronounced hypertrophy and extracellular matrix remodeling, T2DM induced functional impairment. The negative impact of the association of DM with aortic constriction was more pronounced in T2DM, promoting impaired function and increased stiffness, particularly in the right ventricle. Our study demonstrated that the two types of diabetes induce distinct cardiac alterations per se or when combined with chronic pressure overload. T1DM promoted a more extensive remodeling in cardiac structure while T2DM significantly impaired ventricular function. The impact of pressure overload was more notorious in T2DM as observed by worse myocardial remodeling, suggesting a higher susceptibility to the deleterious effects of chronic pressure overload, namely hypertension, among this diabetic population. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.
Differential progression of structural and functional alterations in distinct retinal ganglion cell types in a mouse model of glaucoma.

PubMed

Della Santina, Luca; Inman, Denise M; Lupien, Caroline B; Horner, Philip J; Wong, Rachel O L

2013-10-30

Intraocular pressure (IOP) elevation is a principal risk factor for glaucoma. Using a microbead injection technique to chronically raise IOP for 15 or 30 d in mice, we identified the early changes in visual response properties of different types of retinal ganglion cells (RGCs) and correlated these changes with neuronal morphology before cell death. Microbead-injected eyes showed reduced optokinetic tracking as well as cell death. In such eyes, multielectrode array recordings revealed that four RGC types show diverse alterations in their light responses upon IOP elevation. OFF-transient RGCs exhibited a more rapid decline in both structural and functional organizations compared with other RGCs. In contrast, although the light-evoked responses of OFF-sustained RGCs were perturbed, the dendritic arbor of this cell type remained intact. ON-transient and ON-sustained RGCs had normal functional receptive field sizes but their spontaneous and light-evoked firing rates were reduced. ON- and OFF-sustained RGCs lost excitatory synapses across an otherwise structurally normal dendritic arbor. Together, our observations indicate that there are changes in spontaneous activity and light-evoked responses in RGCs before detectable dendritic loss. However, when dendrites retract, we found corresponding changes in receptive field center size. Importantly, the effects of IOP elevation are not uniformly manifested in the structure and function of diverse RGC populations, nor are distinct RGC types perturbed within the same time-frame by such a challenge.
The Influence of Culture on Agroecosystem Structure: A Comparison of the Spatial Patterns of Homegardens of Different Ethnic Groups in Thailand and Vietnam.

PubMed

Timsuksai, Pijika; Rambo, A Terry

2016-01-01

Different ethnic groups have evolved distinctive cultural models which guide their interactions with the environment, including their agroecosystems. Although it is probable that variations in the structures of homegardens among separate ethnic groups reflect differences in the cultural models of the farmers, empirical support for this assumption is limited. In this paper the modal horizontal structural patterns of the homegardens of 8 ethnic groups in Northeast Thailand and Vietnam are described. Six of these groups (5 speaking Tai languages and 1 speaking Vietnamese) live in close proximity to each other in separate villages in Northeast Thailand, and 2 of the groups (one Tai-speaking and one Vietnamese-speaking) live in different parts of Vietnam. Detailed information on the horizontal structure of homegardens was collected from samples of households belonging to each group. Although each ethnic group has a somewhat distinctive modal structure, the groups cluster into 2 different types. The Tai speaking Cao Lan, Kalaeng, Lao, Nyaw, and Yoy make up Type I while both of the Vietnamese groups, along with the Tai speaking Phu Thai, belong to Type II. Type I gardens have predominantly organic shapes, indeterminate boundaries, polycentric planting patterns, and multi-species composition within planting areas. Type II homegardens have geometric shapes, sharp boundaries, lineal planting patterns, and mono-species composition of planting areas. That the homegardens of most of the Tai ethnic groups share a relatively similar horizontal structural pattern that is quite different from the pattern shared by both of the Vietnamese groups suggests that the spatial layout of homegardens is strongly influenced by their different cultural models.
The Influence of Culture on Agroecosystem Structure: A Comparison of the Spatial Patterns of Homegardens of Different Ethnic Groups in Thailand and Vietnam

PubMed Central

2016-01-01

Different ethnic groups have evolved distinctive cultural models which guide their interactions with the environment, including their agroecosystems. Although it is probable that variations in the structures of homegardens among separate ethnic groups reflect differences in the cultural models of the farmers, empirical support for this assumption is limited. In this paper the modal horizontal structural patterns of the homegardens of 8 ethnic groups in Northeast Thailand and Vietnam are described. Six of these groups (5 speaking Tai languages and 1 speaking Vietnamese) live in close proximity to each other in separate villages in Northeast Thailand, and 2 of the groups (one Tai-speaking and one Vietnamese-speaking) live in different parts of Vietnam. Detailed information on the horizontal structure of homegardens was collected from samples of households belonging to each group. Although each ethnic group has a somewhat distinctive modal structure, the groups cluster into 2 different types. The Tai speaking Cao Lan, Kalaeng, Lao, Nyaw, and Yoy make up Type I while both of the Vietnamese groups, along with the Tai speaking Phu Thai, belong to Type II. Type I gardens have predominantly organic shapes, indeterminate boundaries, polycentric planting patterns, and multi-species composition within planting areas. Type II homegardens have geometric shapes, sharp boundaries, lineal planting patterns, and mono-species composition of planting areas. That the homegardens of most of the Tai ethnic groups share a relatively similar horizontal structural pattern that is quite different from the pattern shared by both of the Vietnamese groups suggests that the spatial layout of homegardens is strongly influenced by their different cultural models. PMID:26752564
Characterization of Cell Surface and EPS Remodeling of Azospirillum brasilense Chemotaxis-like 1 Signal Transduction Pathway mutants by Atomic Force Microscopy

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

Billings, Amanda N; Siuti, Piro; Bible, Amber

2011-01-01

To compete in complex microbial communities, bacteria must quickly sense environmental changes and adjust cellular functions for optimal growth. Chemotaxis-like signal transduction pathways are implicated in the modulation of multiple cellular responses, including motility, EPS production, and cell-to-cell interactions. Recently, the Che1 chemotaxis-like pathway from Azospirillum brasilense was shown to modulate flocculation. In A. brasilense, cell surface properties, including EPS production, are thought to play a direct role in promoting flocculation. Using atomic force microscopy (AFM), we have detected distinct changes in the surface morphology of flocculating A. brasilense Che1 mutant strains that are absent in the wild type strain.more » Whereas the wild type strain produces a smooth mucosal extracellular matrix, the flocculating Che1 mutant strains produce distinctive extracellular fibril structures. Further analyses using flocculation inhibition and lectin-binding assays suggest that the composition of EPS components in the extracellular matrix differs between the cheA1 and cheY1 mutants, despite an apparent similarity in the macroscopic floc structures. Collectively, these data indicate that mutations in the Che1 pathway that result in increased flocculation are correlated with distinctive changes in the extracellular matrix structure produced by the mutants, including likely changes in the EPS structure and/or composition.« less
Variations in Both-Addends-Unknown Problems

ERIC Educational Resources Information Center

Champagne, Zachary M.; Schoen, Robert; Riddell, Claire M.

2014-01-01

Early elementary school students are expected to solve twelve distinct types of word problems. A math researcher and two teachers pose a structure for thinking about one problem type that has not been studied as closely as the other eleven. In this article, the authors share some of their discoveries with regard to the variety of…
Linking structural features from mitochondrial and bacterial F-type ATP synthases to their distinct mechanisms of ATPase inhibition.

PubMed

Krah, Alexander

2015-10-01

ATP synthases are molecular motors, which synthesize ATP, the ubiquitous energy source in all living cells. They use an electrochemical gradient to drive a rotation in the membrane embedded Fo domain, namely the c-ring, causing a conformational change in the soluble F1 domain which leads to the catalytic event. In the opposite fashion, they can also hydrolyse ATP to maintain the ion gradient across the membrane. To prevent wasteful ATP hydrolysis, bacteria and mammals have developed peculiar mechanistic features in addition to a common one, namely MgADP inhibition. Here I discuss the distinct ATPase inhibition mechanism in mitochondrial (IF1) and bacterial (subunits ε and ζ) F-type ATP synthases, based on available structural, biophysical and biochemical data. Copyright © 2015 Elsevier Ltd. All rights reserved.
Generation of a Multicomponent Library of Disulfide Donor-Acceptor Architectures Using Dynamic Combinatorial Chemistry

PubMed Central

Drożdż, Wojciech; Kołodziejski, Michał; Markiewicz, Grzegorz; Jenczak, Anna; Stefankiewicz, Artur R.

2015-01-01

We describe here the generation of new donor-acceptor disulfide architectures obtained in aqueous solution at physiological pH. The application of a dynamic combinatorial chemistry approach allowed us to generate a large number of new disulfide macrocyclic architectures together with a new type of [2]catenanes consisting of four distinct components. Up to fifteen types of structurally-distinct dynamic architectures have been generated through one-pot disulfide exchange reactions between four thiol-functionalized aqueous components. The distribution of disulfide products formed was found to be strongly dependent on the structural features of the thiol components employed. This work not only constitutes a success in the synthesis of topologically- and morphologically-complex targets, but it may also open new horizons for the use of this methodology in the construction of molecular machines. PMID:26193265
Generation of a Multicomponent Library of Disulfide Donor-Acceptor Architectures Using Dynamic Combinatorial Chemistry.

PubMed

Drożdż, Wojciech; Kołodziejski, Michał; Markiewicz, Grzegorz; Jenczak, Anna; Stefankiewicz, Artur R

2015-07-17

We describe here the generation of new donor-acceptor disulfide architectures obtained in aqueous solution at physiological pH. The application of a dynamic combinatorial chemistry approach allowed us to generate a large number of new disulfide macrocyclic architectures together with a new type of [2]catenanes consisting of four distinct components. Up to fifteen types of structurally-distinct dynamic architectures have been generated through one-pot disulfide exchange reactions between four thiol-functionalized aqueous components. The distribution of disulfide products formed was found to be strongly dependent on the structural features of the thiol components employed. This work not only constitutes a success in the synthesis of topologically- and morphologically-complex targets, but it may also open new horizons for the use of this methodology in the construction of molecular machines.
Three Types of Cortical L5 Neurons that Differ in Brain-Wide Connectivity and Function

PubMed Central

Kim, Euiseok J.; Juavinett, Ashley L.; Kyubwa, Espoir M.; Jacobs, Matthew W.; Callaway, Edward M.

2015-01-01

SUMMARY Cortical layer 5 (L5) pyramidal neurons integrate inputs from many sources and distribute outputs to cortical and subcortical structures. Previous studies demonstrate two L5 pyramid types: cortico-cortical (CC) and cortico-subcortical (CS). We characterize connectivity and function of these cell types in mouse primary visual cortex and reveal a new subtype. Unlike previously described L5 CC and CS neurons, this new subtype does not project to striatum [cortico-cortical, non-striatal (CC-NS)] and has distinct morphology, physiology and visual responses. Monosynaptic rabies tracing reveals that CC neurons preferentially receive input from higher visual areas, while CS neurons receive more input from structures implicated in top-down modulation of brain states. CS neurons are also more direction-selective and prefer faster stimuli than CC neurons. These differences suggest distinct roles as specialized output channels, with CS neurons integrating information and generating responses more relevant to movement control and CC neurons being more important in visual perception. PMID:26671462
Three Types of Cortical Layer 5 Neurons That Differ in Brain-wide Connectivity and Function.

PubMed

Kim, Euiseok J; Juavinett, Ashley L; Kyubwa, Espoir M; Jacobs, Matthew W; Callaway, Edward M

2015-12-16

Cortical layer 5 (L5) pyramidal neurons integrate inputs from many sources and distribute outputs to cortical and subcortical structures. Previous studies demonstrate two L5 pyramid types: cortico-cortical (CC) and cortico-subcortical (CS). We characterize connectivity and function of these cell types in mouse primary visual cortex and reveal a new subtype. Unlike previously described L5 CC and CS neurons, this new subtype does not project to striatum [cortico-cortical, non-striatal (CC-NS)] and has distinct morphology, physiology, and visual responses. Monosynaptic rabies tracing reveals that CC neurons preferentially receive input from higher visual areas, while CS neurons receive more input from structures implicated in top-down modulation of brain states. CS neurons are also more direction-selective and prefer faster stimuli than CC neurons. These differences suggest distinct roles as specialized output channels, with CS neurons integrating information and generating responses more relevant to movement control and CC neurons being more important in visual perception. Copyright © 2015 Elsevier Inc. All rights reserved.
Four alpha ganglion cell types in mouse retina: Function, structure, and molecular signatures

PubMed Central

Sanes, Joshua R.

2017-01-01

The retina communicates with the brain using ≥30 parallel channels, each carried by axons of distinct types of retinal ganglion cells. In every mammalian retina one finds so-called "alpha" ganglion cells (αRGCs), identified by their large cell bodies, stout axons, wide and mono-stratified dendritic fields, and high levels of neurofilament protein. In the mouse, three αRGC types have been described based on responses to light steps: On-sustained, Off-sustained, and Off-transient. Here we employed a transgenic mouse line that labels αRGCs in the live retina, allowing systematic targeted recordings. We characterize the three known types and identify a fourth, with On-transient responses. All four αRGC types share basic aspects of visual signaling, including a large receptive field center, a weak antagonistic surround, and absence of any direction selectivity. They also share a distinctive waveform of the action potential, faster than that of other RGC types. Morphologically, they differ in the level of dendritic stratification within the IPL, which accounts for their response properties. Molecularly, each type has a distinct signature. A comparison across mammals suggests a common theme, in which four large-bodied ganglion cell types split the visual signal into four channels arranged symmetrically with respect to polarity and kinetics. PMID:28753612
Crystal Structure of Streptococcus pyogenes Cas1 and Its Interaction with Csn2 in the Type II CRISPR-Cas System.

PubMed

Ka, Donghyun; Lee, Hasup; Jung, Yi-Deun; Kim, Kyunggon; Seok, Chaok; Suh, Nayoung; Bae, Euiyoung

2016-01-05

CRISPRs and Cas proteins constitute an RNA-guided microbial immune system against invading nucleic acids. Cas1 is a universal Cas protein found in all three types of CRISPR-Cas systems, and its role is implicated in new spacer acquisition during CRISPR-mediated adaptive immunity. Here, we report the crystal structure of Streptococcus pyogenes Cas1 (SpCas1) in a type II CRISPR-Cas system and characterize its interaction with S. pyogenes Csn2 (SpCsn2). The SpCas1 structure reveals a unique conformational state distinct from type I Cas1 structures, resulting in a more extensive dimerization interface, a more globular overall structure, and a disruption of potential metal-binding sites for catalysis. We demonstrate that SpCas1 directly interacts with SpCsn2, and identify the binding interface and key residues for Cas complex formation. These results provide structural information for a type II Cas1 protein, and lay a foundation for studying multiprotein Cas complexes functioning in type II CRISPR-Cas systems. Copyright © 2016 Elsevier Ltd. All rights reserved.
Cognitive Emotion Regulation Strategies in Anxiety and Depression Understood as Types of Personality.

PubMed

Domaradzka, Ewa; Fajkowska, Małgorzata

2018-01-01

The identification of distinctive and overlapping features of anxiety and depression remains an important scientific problem. Currently, the literature does not allow to determine stable similarities and differences in the use of cognitive emotion regulation strategies (CERS) in anxiety and depression, especially concerning the adaptive strategies. Consequently, the aim of this study was to identify the overlapping and distinctive patterns of CERS use in the recently proposed types of anxiety and depression in a general population. In this dimensional approach, types of anxiety and depression are considered as personality types and distinguished based on their specific structural composition and functional role (reactive or regulative) in stimulation processing. 1,632 participants from a representative sample completed the Anxiety and Depression Questionnaire (measuring the Arousal and Apprehension Types of anxiety and the Valence and Anhedonic Types of depression) and the Cognitive Emotion Regulation Questionnaire. Regression analyses were conducted with the affective types as predictors. The co-occurrence of the types was accounted for in order to examine their independent relationships with the CERS. We found that reactive arousal anxiety was not related to any strategies, while regulative apprehension anxiety primarily predicted the use of rumination, which is presumably related to the type's cognitive structural components. The strategy specific to reactive valence depression was other-blame (as predicted by the high negative affect in its structure), and the regulative, most structurally complex anhedonic depression predicted the use of the largest number of strategies, including the adaptive ones. The relationships between the types of depression and self-blame and refocus on planning were moderated by sex but the effects were small. These findings fit into the current trend of exploring the shared and specific features of anxiety and depression, which might facilitate their differentiation by identifying CERS that are characteristic for the specific types. This information can be used for supporting diagnosis and targeting selected strategies in therapy both in clinical and non-clinical populations.
Understanding Cultivar-Specificity and Soil Determinants of the Cannabis Microbiome

DOE PAGES

Winston, Max E.; Hampton-Marcell, Jarrad; Zarraonaindia, Iratxe; ...

2014-06-16

Understanding microbial partnerships with the medicinally and economically important crop Cannabis has the potential to affect agricultural practice by improving plant fitness and production yield. Furthermore, Cannabis presents an interesting model to explore plant-microbiome interactions as it produces numerous secondary metabolic compounds. Here we present the first description of the endorhiza-, rhizosphere-, and bulk soil-associated microbiome of five distinct Cannabis cultivars. Bacterial communities of the endorhiza showed significant cultivar-specificity. When controlling cultivar and soil type the microbial community structure was significantly different between plant cultivars, soil types, and between the endorhiza, rhizosphere and soil. In conclusion, the influence of soilmore » type, plant cultivar and sample type differentiation on the microbial community structure provides support for a previously published two-tier selection model, whereby community composition across sample types is determined mainly by soil type, while community structure within endorhiza samples is determined mainly by host cultivar.« less

Understanding Cultivar-Specificity and Soil Determinants of the Cannabis Microbiome

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

Winston, Max E.; Hampton-Marcell, Jarrad; Zarraonaindia, Iratxe

Understanding microbial partnerships with the medicinally and economically important crop Cannabis has the potential to affect agricultural practice by improving plant fitness and production yield. Furthermore, Cannabis presents an interesting model to explore plant-microbiome interactions as it produces numerous secondary metabolic compounds. Here we present the first description of the endorhiza-, rhizosphere-, and bulk soil-associated microbiome of five distinct Cannabis cultivars. Bacterial communities of the endorhiza showed significant cultivar-specificity. When controlling cultivar and soil type the microbial community structure was significantly different between plant cultivars, soil types, and between the endorhiza, rhizosphere and soil. In conclusion, the influence of soilmore » type, plant cultivar and sample type differentiation on the microbial community structure provides support for a previously published two-tier selection model, whereby community composition across sample types is determined mainly by soil type, while community structure within endorhiza samples is determined mainly by host cultivar.« less
Theoretical model to explain the problem-solving process in physics

NASA Astrophysics Data System (ADS)

Lopez, Carlos

2011-03-01

This work reports a theoretical model developed with the aim to explain the mental mechanisms of knowledge building during the problem-solving process in physics using a hybrid approach of assimilation- formation of concepts. The model has been termed conceptual chains and represents graphic diagrams of conceptual dependency, which have yielded information about the background knowledge required during the learning process, as well as about the formation of diverse structures that correspond to distinct forms of networking concepts Additionally, the conceptual constructs of the model have been classified according to five types of knowledge. Evidence was found about the influence of these structures, as well as of the distinct types of knowledge about the degree of difficulty of the problems. I want to be grateful to Laureate International Universities, Baltimore M.D., USA, for the financing granted for the accomplishment of this work.
Stories and Gossip in English: The Macro-Structure of Casual Talk.

ERIC Educational Resources Information Center

Slade, Diana

1997-01-01

A discussion of two text-types commonly occurring in casual conversation, stories and gossip, (1) details four kinds of stories told in casual talk, (2) demonstrates that gossip is a culturally-determined process with a distinctive structure, and (3) considers implications for teaching English-as-a- Second-Language. Analysis is based on over three…
Contesting the science/ethics distinction in the review of clinical research

PubMed Central

Dawson, Angus J; Yentis, Steve M

2007-01-01

Recent policy in relation to clinical research proposals in the UK has distinguished between two types of review: scientific and ethical. This distinction has been formally enshrined in the recent changes to research ethics committee (REC) structure and operating procedures, introduced as the UK response to the EU Directive on clinical trials. Recent reviews and recommendations have confirmed the place of the distinction and the separate review processes. However, serious reservations can be mounted about the science/ethics distinction and the policy of separate review that has been built upon it. We argue here that, first, the science/ethics distinction is incoherent, and, second, that RECs should not only be permitted to consider a study's science, but that they have anobligation do so. PMID:17329389
Distinct and overlapping fMRI activation networks for processing of novel identities and locations of objects.

PubMed

Pihlajamäki, Maija; Tanila, Heikki; Könönen, Mervi; Hänninen, Tuomo; Aronen, Hannu J; Soininen, Hilkka

2005-10-01

The ventral visual stream processes information about the identity of objects ('what'), whereas the dorsal stream processes the spatial locations of objects ('where'). There is a corresponding, although disputed, distinction for the ventrolateral and dorsolateral prefrontal areas. Furthermore, there seems to be a distinction between the anterior and posterior medial temporal lobe (MTL) structures in the processing of novel items and new spatial arrangements, respectively. Functional differentiation of the intermediary mid-line cortical and temporal neocortical structures that communicate with the occipitotemporal, occipitoparietal, prefrontal, and MTL structures, however, is unclear. Therefore, in the present functional magnetic resonance imaging (fMRI) study, we examined whether the distinction among the MTL structures extends to these closely connected cortical areas. The most striking difference in the fMRI responses during visual presentation of changes in either items or their locations was the bilateral activation of the temporal lobe and ventrolateral prefrontal cortical areas for novel object identification in contrast to wide parietal and dorsolateral prefrontal activation for the novel locations of objects. An anterior-posterior distinction of fMRI responses similar to the MTL was observed in the cingulate/retrosplenial, and superior and middle temporal cortices. In addition to the distinct areas of activation, certain frontal, parietal, and temporo-occipital areas responded to both object and spatial novelty, suggesting a common attentional network for both types of changes in the visual environment. These findings offer new insights to the functional roles and intrinsic specialization of the cingulate/retrosplenial, and lateral temporal cortical areas in visuospatial cognition.
Emergence of a few distinct structures from a single formal structure type during high-throughput screening for stable compounds: The case of RbCuS and RbCuSe

NASA Astrophysics Data System (ADS)

Trimarchi, Giancarlo; Zhang, Xiuwen; DeVries Vermeer, Michael J.; Cantwell, Jacqueline; Poeppelmeier, Kenneth R.; Zunger, Alex

2015-10-01

Theoretical sorting of stable and synthesizable "missing compounds" from those that are unstable is a crucial step in the discovery of previously unknown functional materials. This active research area often involves high-throughput (HT) examination of the total energy of a given compound in a list of candidate formal structure types (FSTs), searching for those with the lowest energy within that list. While it is well appreciated that local relaxation methods based on a fixed list of structure types can lead to inaccurate geometries, this approach is widely used in HT studies because it produces answers faster than global optimization methods (that vary lattice vectors and atomic positions without local restrictions). We find, however, a different failure mode of the HT protocol: specific crystallographic classes of formal structure types each correspond to a series of chemically distinct "daughter structure types" (DSTs) that have the same space group but possess totally different local bonding configurations, including coordination types. Failure to include such DSTs in the fixed list of examined candidate structures used in contemporary high-throughput approaches can lead to qualitative misidentification of the stable bonding pattern, not just quantitative inaccuracies. In this work, we (i) clarify the understanding of the general DST-FST relationship, thus improving current discovery HT approaches, (ii) illustrate this failure mode for RbCuS and RbCuSe (the latter being a yet unreported compound and is predicted here) by developing a synthesis method and accelerated crystal-structure determination, and (iii) apply the genetic-algorithm-based global space-group optimization (GSGO) approach which is not vulnerable to the failure mode of HT searches of fixed lists, demonstrating a correct identification of the stable DST. The broad impact of items (i)-(iii) lies in the demonstrated predictive ability of a more comprehensive search strategy than what is currently used—use HT calculations as the preliminary broad screening followed by unbiased GSGO of the final candidates.
Terrorism, Wars, Nuclear Holocaust.

ERIC Educational Resources Information Center

Kende, Istvan

1986-01-01

Presents a brief survey of the political and structural violence which pervades contemporary life. Attempts to demonstrate the ancient dictum that violence breeds more violence. Draws distinctions between different types of political violence and explores the political nature of nuclear deterrence. (JDH)
Visual projection neurons in the Drosophila lobula link feature detection to distinct behavioral programs

PubMed Central

Wu, Ming; Nern, Aljoscha; Williamson, W Ryan; Morimoto, Mai M; Reiser, Michael B; Card, Gwyneth M; Rubin, Gerald M

2016-01-01

Visual projection neurons (VPNs) provide an anatomical connection between early visual processing and higher brain regions. Here we characterize lobula columnar (LC) cells, a class of Drosophila VPNs that project to distinct central brain structures called optic glomeruli. We anatomically describe 22 different LC types and show that, for several types, optogenetic activation in freely moving flies evokes specific behaviors. The activation phenotypes of two LC types closely resemble natural avoidance behaviors triggered by a visual loom. In vivo two-photon calcium imaging reveals that these LC types respond to looming stimuli, while another type does not, but instead responds to the motion of a small object. Activation of LC neurons on only one side of the brain can result in attractive or aversive turning behaviors depending on the cell type. Our results indicate that LC neurons convey information on the presence and location of visual features relevant for specific behaviors. DOI: http://dx.doi.org/10.7554/eLife.21022.001 PMID:28029094
The Structural Enzymology of Iterative Aromatic Polyketide Synthases: A Critical Comparison with Fatty Acid Synthases.

PubMed

Tsai, Shiou-Chuan Sheryl

2018-06-20

Polyketides are a large family of structurally complex natural products including compounds with important bioactivities. Polyketides are biosynthesized by polyketide synthases (PKSs), multienzyme complexes derived evolutionarily from fatty acid synthases (FASs). The focus of this review is to critically compare the properties of FASs with iterative aromatic PKSs, including type II PKSs and fungal type I nonreducing PKSs whose chemical logic is distinct from that of modular PKSs. This review focuses on structural and enzymological studies that reveal both similarities and striking differences between FASs and aromatic PKSs. The potential application of FAS and aromatic PKS structures for bioengineering future drugs and biofuels is highlighted.
Molecular evolution of miraculin-like proteins in soybean Kunitz super-family.

PubMed

Selvakumar, Purushotham; Gahloth, Deepankar; Tomar, Prabhat Pratap Singh; Sharma, Nidhi; Sharma, Ashwani Kumar

2011-12-01

Miraculin-like proteins (MLPs) belong to soybean Kunitz super-family and have been characterized from many plant families like Rutaceae, Solanaceae, Rubiaceae, etc. Many of them possess trypsin inhibitory activity and are involved in plant defense. MLPs exhibit significant sequence identity (~30-95%) to native miraculin protein, also belonging to Kunitz super-family compared with a typical Kunitz family member (~30%). The sequence and structure-function comparison of MLPs with that of a classical Kunitz inhibitor have demonstrated that MLPs have evolved to form a distinct group within Kunitz super-family. Sequence analysis of new genes along with available MLP sequences in the literature revealed three major groups for these proteins. A significant feature of Rutaceae MLP type 2 sequences is the presence of phosphorylation motif. Subtle changes are seen in putative reactive loop residues among different MLPs suggesting altered specificities to specific proteases. In phylogenetic analysis, Rutaceae MLP type 1 and type 2 proteins clustered together on separate branches, whereas native miraculin along with other MLPs formed distinct clusters. Site-specific positive Darwinian selection was observed at many sites in both the groups of Rutaceae MLP sequences with most of the residues undergoing positive selection located in loop regions. The results demonstrate the sequence and thereby the structure-function divergence of MLPs as a distinct group within soybean Kunitz super-family due to biotic and abiotic stresses of local environment.
The population structure of Vibrio cholerae from the Chandigarh Region of Northern India.

PubMed

Abd El Ghany, Moataz; Chander, Jagadish; Mutreja, Ankur; Rashid, Mamoon; Hill-Cawthorne, Grant A; Ali, Shahjahan; Naeem, Raeece; Thomson, Nicholas R; Dougan, Gordon; Pain, Arnab

2014-07-01

Cholera infection continues to be a threat to global public health. The current cholera pandemic associated with Vibrio cholerae El Tor has now been ongoing for over half a century. Thirty-eight V. cholerae El Tor isolates associated with a cholera outbreak in 2009 from the Chandigarh region of India were characterised by a combination of microbiology, molecular typing and whole-genome sequencing. The genomic analysis indicated that two clones of V. cholera circulated in the region and caused disease during this time. These clones fell into two distinct sub-clades that map independently onto wave 3 of the phylogenetic tree of seventh pandemic V. cholerae El Tor. Sequence analyses of the cholera toxin gene, the Vibrio seventh Pandemic Island II (VSPII) and SXT element correlated with this phylogenetic position of the two clades on the El Tor tree. The clade 2 isolates, characterized by a drug-resistant profile and the expression of a distinct cholera toxin, are closely related to the recent V. cholerae isolated elsewhere, including Haiti, but fell on a distinct branch of the tree, showing they were independent outbreaks. Multi-Locus Sequence Typing (MLST) distinguishes two sequence types among the 38 isolates, that did not correspond to the clades defined by whole-genome sequencing. Multi-Locus Variable-length tandem-nucleotide repeat Analysis (MLVA) identified 16 distinct clusters. The use of whole-genome sequencing enabled the identification of two clones of V. cholerae that circulated during the 2009 Chandigarh outbreak. These clones harboured a similar structure of ICEVchHai1 but differed mainly in the structure of CTX phage and VSPII. The limited capacity of MLST and MLVA to discriminate between the clones that circulated in the 2009 Chandigarh outbreak highlights the value of whole-genome sequencing as a route to the identification of further genetic markers to subtype V. cholerae isolates.
The Staphylococcus aureus Two-Component System AgrAC Displays Four Distinct Genomic Arrangements That Delineate Genomic Virulence Factor Signatures

PubMed Central

Choudhary, Kumari S.; Mih, Nathan; Monk, Jonathan; Kavvas, Erol; Yurkovich, James T.; Sakoulas, George; Palsson, Bernhard O.

2018-01-01

Two-component systems (TCSs) consist of a histidine kinase and a response regulator. Here, we evaluated the conservation of the AgrAC TCS among 149 completely sequenced Staphylococcus aureus strains. It is composed of four genes: agrBDCA. We found that: (i) AgrAC system (agr) was found in all but one of the 149 strains, (ii) the agr positive strains were further classified into four agr types based on AgrD protein sequences, (iii) the four agr types not only specified the chromosomal arrangement of the agr genes but also the sequence divergence of AgrC histidine kinase protein, which confers signal specificity, (iv) the sequence divergence was reflected in distinct structural properties especially in the transmembrane region and second extracellular binding domain, and (v) there was a strong correlation between the agr type and the virulence genomic profile of the organism. Taken together, these results demonstrate that bioinformatic analysis of the agr locus leads to a classification system that correlates with the presence of virulence factors and protein structural properties. PMID:29887846
Phylogenetic and structural comparisons of the three types of methyl-coenzyme M reductase from Methanococcales and Methanobacteriales.

PubMed

Wagner, Tristan; Wegner, Carl-Eric; Kahnt, Jörg; Ermler, Ulrich; Shima, Seigo

2017-05-30

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, Methanococcales and Methanopyrales into three distinct types: (1) MCRs from Methanobacteriales, (2) MCRs from Methanobacteriales and Methanococcales and (3) MCRs from Methanococcales. The first and second types contain MCR isoenzyme I and II from Methanothermobacter marburgensis , respectively; therefore, they were designated as MCR type I and type II and accordingly, the third one was designated as 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 a virtually identical active site architecture 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 post-translational 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 has been, so far, only found 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 MCR 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 only revealed substantial differences between the three types in the peripheral region. Identified subtle modifications 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 post-translational modification that was, so far, only found in the α-amanitin toxin. Copyright © 2017 American Society for Microbiology.
Extending Miles & Snow's strategy choice typology to the German hospital sector.

PubMed

Helmig, Bernd; Hinz, Vera; Ingerfurth, Stefan

2014-12-01

Hospitals' strategy choices represent highly relevant factors that affect organizational performance and survival. This study assesses the differences among hospitals' strategic choices. This strategy definition and assessment reflects the typology proposed by Miles and Snow, who distinguish four strategy types: defender, analyzer, prospector, and reactor. Synthesis of empirical evidence from previous studies that have applied Miles and Snow's typology in the hospital sector using various methodological approaches and measures provides hints for industry-specific patterns and avenues for further research. Taking an extended view of strategic choice, the authors conduct an empirical survey of a sample of 178 German hospitals. The authors apply a multi-item measure of the Miles and Snow strategy types in the hospital sector and identify hybrid strategy types that deviate from the four strategy types defined by Miles and Snow. Overall, seven distinct strategy types emerge from this analysis. There exist three distinct hybrid types in particular. Strategy choice is systematically related to hospital size and teaching status but not to ownership and location. The significant variance in performance for the seven different strategy types justifies the distinction between them. The results support the idea of industry-specific strategy choices. Policy makers should analyze the structural context in which hospitals operate and intervene through political and regulatory means. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.
Nondeterministic self-assembly of two tile types on a lattice.

PubMed

Tesoro, S; Ahnert, S E

2016-04-01

Self-assembly is ubiquitous in nature, particularly in biology, where it underlies the formation of protein quaternary structure and protein aggregation. Quaternary structure assembles deterministically and performs a wide range of important functions in the cell, whereas protein aggregation is the hallmark of a number of diseases and represents a nondeterministic self-assembly process. Here we build on previous work on a lattice model of deterministic self-assembly to investigate nondeterministic self-assembly of single lattice tiles and mixtures of two tiles at varying relative concentrations. Despite limiting the simplicity of the model to two interface types, which results in 13 topologically distinct single tiles and 106 topologically distinct sets of two tiles, we observe a wide variety of concentration-dependent behaviors. Several two-tile sets display critical behaviors in the form of a sharp transition from bound to unbound structures as the relative concentration of one tile to another increases. Other sets exhibit gradual monotonic changes in structural density, or nonmonotonic changes, while again others show no concentration dependence at all. We catalog this extensive range of behaviors and present a model that provides a reasonably good estimate of the critical concentrations for a subset of the critical transitions. In addition, we show that the structures resulting from these tile sets are fractal, with one of two different fractal dimensions.
Functions, Compositions, and Evolution of the Two Types of Carboxysomes: Polyhedral Microcompartments That Facilitate CO2 Fixation in Cyanobacteria and Some Proteobacteria

PubMed Central

Rae, Benjamin D.; Long, Benedict M.; Badger, Murray R.

2013-01-01

SUMMARY Cyanobacteria are the globally dominant photoautotrophic lineage. Their success is dependent on a set of adaptations collectively termed the CO2-concentrating mechanism (CCM). The purpose of the CCM is to support effective CO2 fixation by enhancing the chemical conditions in the vicinity of the primary CO2-fixing enzyme, d-ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), to promote the carboxylase reaction and suppress the oxygenase reaction. In cyanobacteria and some proteobacteria, this is achieved by encapsulation of RubisCO within carboxysomes, which are examples of a group of proteinaceous bodies called bacterial microcompartments. Carboxysomes encapsulate the CO2-fixing enzyme within the selectively permeable protein shell and simultaneously encapsulate a carbonic anhydrase enzyme for CO2 supply from a cytoplasmic bicarbonate pool. These bodies appear to have arisen twice and undergone a process of convergent evolution. While the gross structures of all known carboxysomes are ostensibly very similar, with shared gross features such as a selectively permeable shell layer, each type of carboxysome encapsulates a phyletically distinct form of RubisCO enzyme. Furthermore, the specific proteins forming structures such as the protein shell or the inner RubisCO matrix are not identical between carboxysome types. Each type has evolutionarily distinct forms of the same proteins, as well as proteins that are entirely unrelated to one another. In light of recent developments in the study of carboxysome structure and function, we present this review to summarize the knowledge of the structure and function of both types of carboxysome. We also endeavor to cast light on differing evolutionary trajectories which may have led to the differences observed in extant carboxysomes. PMID:24006469
Tree Regeneration Under Different Land-Use Mosaics in the Brazilian Amazon's "Arc of Deforestation".

PubMed

Do Vale, Igor; Miranda, Izildinha Souza; Mitja, Danielle; Grimaldi, Michel; Nelson, Bruce Walker; Desjardins, Thierry; Costa, Luiz Gonzaga Silva

2015-08-01

We studied the tree-regeneration patterns in three distinct agricultural settlements in the Eastern Amazon to test the influence of land-use mosaics. The following questions are addressed: are the floristic structure and composition of regenerating trees affected by the various land-use types applied in the agricultural settlements? Do tree-regeneration patterns respond similarly to distinct land-use mosaics? Is there a relationship between tree regeneration and soil characteristics among the land-use types? The regeneration was inventoried at 45 sampling points in each settlement. At each sampling point, fourteen soil variables were analyzed. Nine different land-use types were considered. The floristic structure and composition of the settlements showed differences in the density of individuals and species and high species heterogeneity among the land-use types. The maximum Jaccard similarity coefficient found between land-use types was only 29%. Shade-tolerant species were the most diverse functional group in most land-use types, including pasture and annual crops, ranging from 91% of the number of species in the conserved and exploited forests of Travessão 338-S to 53% in the invaded pastures of Maçaranduba. The land-use types influenced significantly the floristic structure and composition of regenerating trees in two agricultural settlements, but not in third the settlement, which had greater forest cover. This finding demonstrates that the composition of each land-use mosaic, established by different management approaches, affects regeneration patterns. Tree regeneration was related to soil characteristics in all mosaics. Preparation of the area by burning was most likely the determining factor in the differences in soil characteristics between forests and agricultural areas.
Bayesian phylogeny of sucrose transporters: ancient origins, differential expansion and convergent evolution in monocots and dicots

PubMed Central

Peng, Duo; Gu, Xi; Xue, Liang-Jiao; Leebens-Mack, James H.; Tsai, Chung-Jui

2014-01-01

Sucrose transporters (SUTs) are essential for the export and efficient movement of sucrose from source leaves to sink organs in plants. The angiosperm SUT family was previously classified into three or four distinct groups, Types I, II (subgroup IIB), and III, with dicot-specific Type I and monocot-specific Type IIB functioning in phloem loading. To shed light on the underlying drivers of SUT evolution, Bayesian phylogenetic inference was undertaken using 41 sequenced plant genomes, including seven basal lineages at key evolutionary junctures. Our analysis supports four phylogenetically and structurally distinct SUT subfamilies, originating from two ancient groups (AG1 and AG2) that diverged early during terrestrial colonization. In both AG1 and AG2, multiple intron acquisition events in the progenitor vascular plant established the gene structures of modern SUTs. Tonoplastic Type III and plasmalemmal Type II represent evolutionarily conserved descendants of AG1 and AG2, respectively. Type I and Type IIB were previously thought to evolve after the dicot-monocot split. We show, however, that divergence of Type I from Type III SUT predated basal angiosperms, likely associated with evolution of vascular cambium and phloem transport. Type I SUT was subsequently lost in monocots along with vascular cambium, and independent evolution of Type IIB coincided with modified monocot vasculature. Both Type I and Type IIB underwent lineage-specific expansion. In multiple unrelated taxa, the newly-derived SUTs exhibit biased expression in reproductive tissues, suggesting a functional link between phloem loading and reproductive fitness. Convergent evolution of Type I and Type IIB for SUT function in phloem loading and reproductive organs supports the idea that differential vascular development in dicots and monocots is a strong driver for SUT family evolution in angiosperms. PMID:25429293
Sidescan backscatter variations of cold seeps on the Hikurangi Margin (New Zealand): indications for different stages in seep development

NASA Astrophysics Data System (ADS)

Dumke, Ines; Klaucke, Ingo; Berndt, Christian; Bialas, Jörg

2014-06-01

Cold seeps on the Hikurangi Margin off New Zealand exhibit various seabed morphologies producing different intensity patterns in sidescan backscatter images. Acoustic backscatter characteristics of 25 investigated seep sites fall into four distinct types characterised by variations in backscatter intensity, distribution and inferred structural heights. The types reflect different carbonate morphologies including up to 20-m-high structures (type 1), low-relief crusts (type 2), scattered blocks (type 3) and carbonate-free sites (type 4). Each seep corresponds to a single type; intermediates were not observed. This correlates well with published data on seep fauna at each site, with the four types representing three different faunal habitats of successive stages of seep development. Backscatter signatures in sidescan sonar images of cold seeps may therefore serve as a convenient proxy for variations in faunal habitats.
Compositional structure of the asteroid belt

NASA Technical Reports Server (NTRS)

Gradie, J.; Tedesco, E.

1982-01-01

A variety of observations, mainly albedos derived from 10 and 20 micron radiometry and eight-filter broadband spectrophotometry, were used to show that the asteroid belt is highly structured in composition. The bias-corrected distribution from 1.8 to 5.2 A.U. of the previously defined compositional types C,S,E,R, and M, plus type D and the newly described types F and P, are reported on. In terms of the relative abundances of the types discussed, the asteroid belt appears to be composed of at least six major compositionally distinct regions. The inferred composition of the asteroids in each semimajor axis region is consistent with the theory that the asteroids accreted from the solar nebula at or near their present location.

Temperature and density anti-correlations in solar wind fluctuations

NASA Technical Reports Server (NTRS)

Zank, G. P.; Matthaeus, W. H.; Klein, L. W.

1990-01-01

Recent theoretical investigations of low Mach number flows, that describe two distinct approaches by fluids to the incompressible regime are summarized. The first includes the effects of relatively strong density and temperature fluctuations (Type I), while the second places fluctuations in mechanical pressure, density, and temperature on an equal footing (Type II). In the latter case, the relations between density and pressure are recovered, whereas the former case yields departures from incompressible behavior in that density and temperature fluctuations are predicted to be anti-correlated. It is suggested that nearly incompressible fluids can be classified as either Type I or II, and it is shown that the well-known pressure-balanced structures represent a subclass of static solutions within this classification. Two examples from Voyager data illustrate the potential for observing these distinct nearly incompressible dynamical ordering in the solar wind.
Unique organization and unprecedented diversity of the Bacteroides (Pseudobacteroides) cellulosolvens cellulosome system

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

Zhivin, Olga; Dassa, Bareket; Moraïs, Sarah

The organization of the B. cellulosolvens cellulosome is unique compared to previously described cellulosome systems. In contrast to all other known cellulosomes, the cohesin types are reversed for all scaffoldins i.e., the type II cohesins are located on the enzyme-integrating primary scaffoldin, whereas the type I cohesins are located on the anchoring scaffoldins. Many of the type II dockerin-bearing ORFs include X60 modules, which are known to stabilize type II cohesin–dockerin interactions. In the present work, we focused on revealing the architectural arrangement of cellulosome structure in this bacterium by examining numerous interactions between the various cohesin and dockerin modules.more » In total, we cloned and expressed 43 representative cohesins and 27 dockerins. The results revealed various possible architectures of cell-anchored and cell-free cellulosomes, which serve to assemble distinctive cellulosome types via three distinct cohesin–dockerin specificities: type I, type II, and a novel-type designated R (distinct from type III interactions, predominant in ruminococcal cellulosomes). The results of this study provide novel insight into the architecture and function of the most intricate and extensive cellulosomal system known today, thereby extending significantly our overall knowledge base of cellulosome systems and their components. The robust cellulosome system of B. cellulosolvens, with its unique binding specificities and reversal of cohesin–dockerin types, has served to amend our view of the cellulosome paradigm. Revealing new cellulosomal interactions and arrangements is critical for designing high-efficiency artificial cellulosomes for conversion of plant-derived cellulosic biomass towards improved production of biofuels.« less
Unique organization and unprecedented diversity of the Bacteroides (Pseudobacteroides) cellulosolvens cellulosome system

DOE PAGES

Zhivin, Olga; Dassa, Bareket; Moraïs, Sarah; ...

2017-09-07

The organization of the B. cellulosolvens cellulosome is unique compared to previously described cellulosome systems. In contrast to all other known cellulosomes, the cohesin types are reversed for all scaffoldins i.e., the type II cohesins are located on the enzyme-integrating primary scaffoldin, whereas the type I cohesins are located on the anchoring scaffoldins. Many of the type II dockerin-bearing ORFs include X60 modules, which are known to stabilize type II cohesin–dockerin interactions. In the present work, we focused on revealing the architectural arrangement of cellulosome structure in this bacterium by examining numerous interactions between the various cohesin and dockerin modules.more » In total, we cloned and expressed 43 representative cohesins and 27 dockerins. The results revealed various possible architectures of cell-anchored and cell-free cellulosomes, which serve to assemble distinctive cellulosome types via three distinct cohesin–dockerin specificities: type I, type II, and a novel-type designated R (distinct from type III interactions, predominant in ruminococcal cellulosomes). The results of this study provide novel insight into the architecture and function of the most intricate and extensive cellulosomal system known today, thereby extending significantly our overall knowledge base of cellulosome systems and their components. The robust cellulosome system of B. cellulosolvens, with its unique binding specificities and reversal of cohesin–dockerin types, has served to amend our view of the cellulosome paradigm. Revealing new cellulosomal interactions and arrangements is critical for designing high-efficiency artificial cellulosomes for conversion of plant-derived cellulosic biomass towards improved production of biofuels.« less
Cocaine-Induced Structural Plasticity in Input Regions to Distinct Cell Types in Nucleus Accumbens.

PubMed

Barrientos, Cindy; Knowland, Daniel; Wu, Mingche M J; Lilascharoen, Varoth; Huang, Kee Wui; Malenka, Robert C; Lim, Byung Kook

2018-05-09

The nucleus accumbens (NAc) is a brain region implicated in pathological motivated behaviors such as drug addiction and is composed predominantly of two discrete populations of neurons, dopamine receptor-1- and dopamine receptor-2-expressing medium spiny neurons (D1-MSNs and D2-MSNs, respectively). It is unclear whether these populations receive inputs from different brain areas and whether input regions to these cell types undergo distinct structural adaptations in response to the administration of addictive drugs such as cocaine. Using a modified rabies virus-mediated tracing method, we created a comprehensive brain-wide monosynaptic input map to NAc D1- and D2-MSNs. Next, we analyzed nearly 2000 dendrites and 125,000 spines of neurons across four input regions (the prelimbic cortex, medial orbitofrontal cortex, basolateral amygdala, and ventral hippocampus) at four separate time points during cocaine administration and withdrawal to examine changes in spine density in response to repeated intraperitoneal cocaine injection in mice. D1- and D2-MSNs display overall similar input profiles, with the exception that D1-MSNs receive significantly more input from the medial orbitofrontal cortex. We found that neurons in distinct brain areas projecting to D1- and D2-MSNs display different adaptations in dendritic spine density at different stages of cocaine administration and withdrawal. While NAc D1- and D2-MSNs receive input from similar brain structures, cocaine-induced spine density changes in input regions are quite distinct and dynamic. While previous studies have focused on input-specific postsynaptic changes within NAc MSNs in response to cocaine, these findings emphasize the dramatic changes that occur in the afferent input regions as well. Published by Elsevier Inc.
Stomatal cell wall composition: distinctive structural patterns associated with different phylogenetic groups

PubMed Central

Shtein, Ilana; Shelef, Yaniv; Marom, Ziv; Zelinger, Einat; Schwartz, Amnon; Popper, Zoë A.; Bar-On, Benny

2017-01-01

Background and Aims Stomatal morphology and function have remained largely conserved throughout ∼400 million years of plant evolution. However, plant cell wall composition has evolved and changed. Here stomatal cell wall composition was investigated in different vascular plant groups in attempt to understand their possible effect on stomatal function. Methods A renewed look at stomatal cell walls was attempted utilizing digitalized polar microscopy, confocal microscopy, histology and a numerical finite-elements simulation. The six species of vascular plants chosen for this study cover a broad structural, ecophysiological and evolutionary spectrum: ferns (Asplenium nidus and Platycerium bifurcatum) and angiosperms (Arabidopsis thaliana and Commelina erecta) with kidney-shaped stomata, and grasses (angiosperms, family Poaceae) with dumbbell-shaped stomata (Sorghum bicolor and Triticum aestivum). Key Results Three distinct patterns of cellulose crystallinity in stomatal cell walls were observed: Type I (kidney-shaped stomata, ferns), Type II (kidney-shaped stomata, angiosperms) and Type III (dumbbell-shaped stomata, grasses). The different stomatal cell wall attributes investigated (cellulose crystallinity, pectins, lignin, phenolics) exhibited taxon-specific patterns, with reciprocal substitution of structural elements in the end-walls of kidney-shaped stomata. According to a numerical bio-mechanical model, the end walls of kidney-shaped stomata develop the highest stresses during opening. Conclusions The data presented demonstrate for the first time the existence of distinct spatial patterns of varying cellulose crystallinity in guard cell walls. It is also highly intriguing that in angiosperms crystalline cellulose appears to have replaced lignin that occurs in the stomatal end-walls of ferns serving a similar wall strengthening function. Such taxon-specific spatial patterns of cell wall components could imply different biomechanical functions, which in turn could be a consequence of differences in environmental selection along the course of plant evolution. PMID:28158449
The Cultural Evolution of Structured Languages in an Open-Ended, Continuous World

ERIC Educational Resources Information Center

Carr, Jon W.; Smith, Kenny; Cornish, Hannah; Kirby, Simon

2017-01-01

Language maps signals onto meanings through the use of two distinct types of structure. First, the space of meanings is discretized into categories that are shared by all users of the language. Second, the signals employed by the language are compositional: The meaning of the whole is a function of its parts and the way in which those parts are…
Post-natal molecular adaptations in anteromedial and posterolateral bundles of the ovine anterior cruciate ligament: one structure with two parts or two distinct ligaments?

PubMed

Huebner, Kyla D; O'Brien, Etienne J O; Heard, Bryan J; Chung, May; Achari, Yamini; Shrive, Nigel G; Frank, Cyril B

2012-01-01

The human anterior cruciate ligament (ACL) is a composite structure of two anatomically distinct bundles: an anteromedial (AM) and posterolateral (PL) bundles. Tendons are often used as autografts for surgical reconstruction of ACL following severe injury. However, despite successful surgical reconstruction, some people experience re-rupture and later development of osteoarthritis. Understanding the structure and molecular makeup of normal ACL is essential for its optimal replacement. Reportedly the two bundles display different tensions throughout joint motion and may be fundamentally different. This study assessed the similarities and differences in ultrastructure and molecular composition of the AM and PL bundles to test the hypothesis that the two bundles of the ACL develop unique characteristics with maturation. ACLs from nine mature and six immature sheep were compared. The bundles were examined for mRNA and protein levels of collagen types I, III, V, and VI, and two proteoglycans. The fibril diameter composition of the two bundles was examined with transmission electron microscopy. Maturation does alter the molecular and structural composition of the two bundles of ACL. Although the PL band appears to mature slower than the AM band, no significant differences were detected between the bundles in the mature animals. We thus reject our hypothesis that the two ACL bundles are distinct. The two anatomically distinct bundles of the sheep ACL can be considered as two parts of one structure at maturity and material that would result in a structure of similar functionality can be used to replace each ACL bundle in the sheep.
Native structure of a type IV secretion system core complex essential for Legionella pathogenesis.

PubMed

Kubori, Tomoko; Koike, Masafumi; Bui, Xuan Thanh; Higaki, Saori; Aizawa, Shin-Ichi; Nagai, Hiroki

2014-08-12

Bacterial type IV secretion systems are evolutionarily related to conjugation systems and play a pivotal role in infection by delivering numerous virulence factors into host cells. Using transmission electron microscopy, we report the native molecular structure of the core complex of the Dot/Icm type IV secretion system encoded by Legionella pneumophila, an intracellular human pathogen. The biochemically isolated core complex, composed of at least five proteins--DotC, DotD, DotF, DotG, and DotH--has a ring-shaped structure. Intriguingly, morphologically distinct premature complexes are formed in the absence of DotG or DotF. Our data suggest that DotG forms a central channel spanning inner and outer membranes. DotF, a component dispensable for type IV secretion, plays a role in efficient embedment of DotG into the functional core complex. These results highlight a common scheme for the biogenesis of transport machinery.
The Rock Elm meteorite impact structure, Wisconsin: Geology and shock-metamorphic effects in quartz

USGS Publications Warehouse

French, B.M.; Cordua, W.S.; Plescia, J.B.

2004-01-01

The Rock Elm structure in southwest Wisconsin is an anomalous circular area of highly deformed rocks, ???6.5 km in diameter, located in a region of virtually horizontal undeformed sedimentary rocks. Shock-produced planar microstructures (PMs) have been identified in quartz grains in several lithologies associated with the structure: sandstones, quartzite pebbles, and breccia. Two distinct types of PMs are present: P1 features, which appear identical to planar fractures (PFs or cleavage), and P2 features, which are interpreted as possible incipient planar deformation features (PDFs). The latter are uniquely produced by the shock waves associated with meteorite impact events. Both types of PMs are oriented parallel to specific crystallographic planes in the quartz, most commonly to c(0001), ??112??2, and r/z101??1. The association of unusual, structurally deformed strata with distinct shock-produced microdeformation features in their quartz-bearing rocks establishes Rock Elm as a meteorite impact structure and supports the view that the presence of multiple parallel cleavages in quartz may be used independently as a criterion for meteorite impact. Preliminary paleontological studies indicate a minimum age of Middle Ordovician for the Rock Elm structure. A similar age estimate (450-400 Ma) is obtained independently by combining the results of studies of the general morphology of complex impact structures with estimated rates of sedimentation for the region. Such methods may be applicable to dating other old and deeply eroded impact structures formed in sedimentary target rocks.
Branchial Cilia and Sperm Flagella Recruit Distinct Axonemal Components

PubMed Central

Konno, Alu; Shiba, Kogiku; Cai, Chunhua; Inaba, Kazuo

2015-01-01

Eukaryotic cilia and flagella have highly conserved 9 + 2 structures. They are functionally diverged to play cell-type-specific roles even in a multicellular organism. Although their structural components are therefore believed to be common, few studies have investigated the molecular diversity of the protein components of the cilia and flagella in a single organism. Here we carried out a proteomic analysis and compared protein components between branchial cilia and sperm flagella in a marine invertebrate chordate, Ciona intestinalis. Distinct feature of protein recruitment in branchial cilia and sperm flagella has been clarified; (1) Isoforms of α- and β-tubulins as well as those of actins are distinctly used in branchial cilia or sperm flagella. (2) Structural components, such as dynein docking complex, tektins and an outer dense fiber protein, are used differently by the cilia and flagella. (3) Sperm flagella are specialized for the cAMP- and Ca2+-dependent regulation of outer arm dynein and for energy metabolism by glycolytic enzymes. Our present study clearly demonstrates that flagellar or ciliary proteins are properly recruited according to their function and stability, despite their apparent structural resemblance and conservation. PMID:25962172
Ultrastructure of the filiform papillae on the tongue of the hamster.

PubMed Central

Fernandez, B; Suarez, I; Zapata, A

1978-01-01

The fine structure of the filiform papillae on the hamster tongue is described level by level from the basal layer to the surface. We did not observe two distinct types of cells with different morphology or components which could be held responsible for the production of two different types of keratin as have been described in other animals, but rather a uniformity of cell structures in each layer and only the so-called "smooth" type of keratin. However, keratin granules were more abundant in the anterior part of the papilla. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 Fig. 5 Fig. 6 Fig. 7 Fig. 8 Fig. 9 Fig. 10 PMID:689988
Rigid polyurethane foam – kenaf core composites for structural applications

USDA-ARS?s Scientific Manuscript database

Kenaf (Hibiscus cannabinus L.) is a fast growing summer annual crop with numerous commercial applications (fibers, biofuels, bioremediation, paper pulp, building materials, cover crops, and livestock forages). The stalks of the kenaf plants contain two distinct fiber types, bast and core fibers. The...
Architecture and biogenesis of plus-strand RNA virus replication factories

PubMed Central

Paul, David; Bartenschlager, Ralf

2013-01-01

Plus-strand RNA virus replication occurs in tight association with cytoplasmic host cell membranes. Both, viral and cellular factors cooperatively generate distinct organelle-like structures, designated viral replication factories. This compartmentalization allows coordination of the different steps of the viral replication cycle, highly efficient genome replication and protection of the viral RNA from cellular defense mechanisms. Electron tomography studies conducted during the last couple of years revealed the three dimensional structure of numerous plus-strand RNA virus replication compartments and highlight morphological analogies between different virus families. Based on the morphology of virus-induced membrane rearrangements, we propose two separate subclasses: the invaginated vesicle/spherule type and the double membrane vesicle type. This review discusses common themes and distinct differences in the architecture of plus-strand RNA virus-induced membrane alterations and summarizes recent progress that has been made in understanding the complex interplay between viral and co-opted cellular factors in biogenesis and maintenance of plus-strand RNA virus replication factories. PMID:24175228
Single Amino Acid Alteration between Valine and Isoleucine Determines the Distinct Pyrabactin Selectivity by PYL1 and PYL2*

PubMed Central

Yuan, Xiaoqiu; Yin, Ping; Hao, Qi; Yan, Chuangye; Wang, Jiawei; Yan, Nieng

2010-01-01

Abscisic acid (ABA) is one of the most important phytohormones in plant. PYL proteins were identified to be ABA receptors in Arabidopsis thaliana. Despite the remarkably high degree of sequence similarity, PYL1 and PYL2 exhibit distinct responses toward pyrabactin, an ABA agonist. PYL1 inhibits protein phosphatase type 2C upon binding of pyrabactin. In contrast, PYL2 appears relatively insensitive to this compound. The crystal structure of pyrabactin-bound PYL1 revealed that most of the PYL1 residues involved in pyrabactin binding are conserved, hence failing to explain the selectivity of pyrabactin for PYL1 over PYL2. To understand the molecular basis of pyrabactin selectivity, we determined the crystal structure of PYL2 in complex with pyrabactin at 1.64 Å resolution. Structural comparison and biochemical analyses demonstrated that one single amino acid alteration between a corresponding valine and isoleucine determines the distinct pyrabactin selectivity by PYL1 and PYL2. These characterizations provide an important clue to dissecting the redundancy of PYL proteins. PMID:20630864
Spatial genetic and morphologic structure of wolves and coyotes in relation to environmental heterogeneity in a Canis hybrid zone.

PubMed

Benson, John F; Patterson, Brent R; Wheeldon, Tyler J

2012-12-01

Eastern wolves have hybridized extensively with coyotes and gray wolves and are listed as a 'species of special concern' in Canada. However, a distinct population of eastern wolves has been identified in Algonquin Provincial Park (APP) in Ontario. Previous studies of the diverse Canis hybrid zone adjacent to APP have not linked genetic analysis with field data to investigate genotype-specific morphology or determine how resident animals of different ancestry are distributed across the landscape in relation to heterogeneous environmental conditions. Accordingly, we studied resident wolves and coyotes in and adjacent to APP to identify distinct Canis types, clarify the extent of the APP eastern wolf population beyond the park boundaries and investigate fine-scale spatial genetic structure and landscape-genotype associations in the hybrid zone. We documented three genetically distinct Canis types within the APP region that also differed morphologically, corresponding to putative gray wolves, eastern wolves and coyotes. We also documented a substantial number of hybrid individuals (36%) that were admixed between 2 or 3 of the Canis types. Breeding eastern wolves were less common outside of APP, but occurred in some unprotected areas where they were sympatric with a diverse combination of coyotes, gray wolves and hybrids. We found significant spatial genetic structure and identified a steep cline extending west from APP where the dominant genotype shifted abruptly from eastern wolves to coyotes and hybrids. The genotypic pattern to the south and northwest was a more complex mosaic of alternating genotypes. We modelled genetic ancestry in response to prey availability and human disturbance and found that individuals with greater wolf ancestry occupied areas of higher moose density and fewer roads. Our results clarify the structure of the Canis hybrid zone adjacent to APP and provide unique insight into environmental conditions influencing hybridization dynamics between wolves and coyotes. © 2012 Blackwell Publishing Ltd.
Chromosomal structures and repetitive sequences divergence in Cucumis species revealed by comparative cytogenetic mapping.

PubMed

Zhang, Yunxia; Cheng, Chunyan; Li, Ji; Yang, Shuqiong; Wang, Yunzhu; Li, Ziang; Chen, Jinfeng; Lou, Qunfeng

2015-09-25

Differentiation and copy number of repetitive sequences affect directly chromosome structure which contributes to reproductive isolation and speciation. Comparative cytogenetic mapping has been verified an efficient tool to elucidate the differentiation and distribution of repetitive sequences in genome. In present study, the distinct chromosomal structures of five Cucumis species were revealed through genomic in situ hybridization (GISH) technique and comparative cytogenetic mapping of major satellite repeats. Chromosome structures of five Cucumis species were investigated using GISH and comparative mapping of specific satellites. Southern hybridization was employed to study the proliferation of satellites, whose structural characteristics were helpful for analyzing chromosome evolution. Preferential distribution of repetitive DNAs at the subtelomeric regions was found in C. sativus, C hystrix and C. metuliferus, while majority was positioned at the pericentromeric heterochromatin regions in C. melo and C. anguria. Further, comparative GISH (cGISH) through using genomic DNA of other species as probes revealed high homology of repeats between C. sativus and C. hystrix. Specific satellites including 45S rDNA, Type I/II, Type III, Type IV, CentM and telomeric repeat were then comparatively mapped in these species. Type I/II and Type IV produced bright signals at the subtelomeric regions of C. sativus and C. hystrix simultaneously, which might explain the significance of their amplification in the divergence of Cucumis subgenus from the ancient ancestor. Unique positioning of Type III and CentM only at the centromeric domains of C. sativus and C. melo, respectively, combining with unique southern bands, revealed rapid evolutionary patterns of centromeric DNA in Cucumis. Obvious interstitial telomeric repeats were observed in chromosomes 1 and 2 of C. sativus, which might provide evidence of the fusion hypothesis of chromosome evolution from x = 12 to x = 7 in Cucumis species. Besides, the significant correlation was found between gene density along chromosome and GISH band intensity in C. sativus and C. melo. In summary, comparative cytogenetic mapping of major satellites and GISH revealed the distinct differentiation of chromosome structure during species formation. The evolution of repetitive sequences was the main force for the divergence of Cucumis species from common ancestor.
Fine-tuning the extent and dynamics of binding cleft opening as a potential general regulatory mechanism in parvulin-type peptidyl prolyl isomerases

NASA Astrophysics Data System (ADS)

Czajlik, András; Kovács, Bertalan; Permi, Perttu; Gáspári, Zoltán

2017-03-01

Parvulins or rotamases form a distinct group within peptidyl prolyl cis-trans isomerases. Their exact mode of action as well as the role of conserved residues in the family are still not unambiguously resolved. Using backbone S2 order parameters and NOEs as restraints, we have generated dynamic structural ensembles of three distinct parvulins, SaPrsA, TbPin1 and CsPinA. The resulting ensembles are in good agreement with the experimental data but reveal important differences between the three enzymes. The largest difference can be attributed to the extent of the opening of the substrate binding cleft, along which motional mode the three molecules occupy distinct regions. Comparison with a wide range of other available parvulin structures highlights structural divergence along the bottom of the binding cleft acting as a hinge during the opening-closing motion. In the prototype WW-domain containing parvulin, Pin1, this region is also important in forming contacts with the WW domain known to modulate enzymatic activity of the catalytic domain. We hypothesize that modulation of the extent and dynamics of the identified ‘breathing motion’ might be one of the factors responsible for functional differences in the distinct parvulin subfamilies.
Structural geology practice and learning, from the perspective of cognitive science

NASA Astrophysics Data System (ADS)

Shipley, Thomas F.; Tikoff, Basil; Ormand, Carol; Manduca, Cathy

2013-09-01

Spatial ability is required by practitioners and students of structural geology and so, considering spatial skills in the context of cognitive science has the potential to improve structural geology teaching and practice. Spatial thinking skills may be organized using three dichotomies, which can be linked to structural geology practice. First, a distinction is made between separating (attending to part of a whole) and combining (linking together aspects of the whole). While everyone has a basic ability to separate and combine, experts attend to differences guided by experiences of rock properties in context. Second, a distinction is made between seeing the relations among multiple objects as separate items or the relations within a single object with multiple parts. Experts can flexibly consider relations among or between objects to optimally reason about different types of spatial problems. Third, a distinction is made between reasoning about stationary and moving objects. Experts recognize static configurations that encode a movement history, and create mental models of the processes that led to the static state. The observations and inferences made by a geologist leading a field trip are compared with the corresponding observations and inferences made by a cognitive psychologist interested in spatial learning. The presented framework provides a vocabulary for discussing spatial skills both within and between the fields of structural geology and cognitive psychology.
Giant landslide deposits in northwest Argentina

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

Fauque, L.; Strecker, M.R.; Bloom, A.L.

1985-01-01

Giant Quaternary landslide deposits occur along mountain fronts in the structural transition zone between the high-angle reverse-fault-bounded Sierras Pampeanas and the low-angle thrust belt of the Sierras Subandinas. There are two modes of occurrence: (1) chaotic masses without distinct geometry, and (2) masses with distinct lobate geometry similar to glacial moraines. Type (1) deposits occur where the moving rock mass followed a narrow valley and blocked the drainage. Many of these caused subsequent formation of lakes and changed the sedimentation processes on pediments at the mountain fronts. In type (2) deposits, lateral and frontal ridges are up to 10 mmore » higher than the interior parts; in some places pressure ridges within the lobes are well preserved. Type (2) deposits show reverse grading and were deposited on relatively smooth pediments or alluvial fans. The lobate geometry strongly suggests that type (2) deposits are a product of flowage and are debris stream or sturzstrom deposits (sense of Heim, 1932 and Hsu, 1975). All investigated deposits occur in areas of demonstrated Quaternary faulting and are interpreted as the result of tectonic movements, although structural inhomogeneities in the source area may have been a significant factor for some of the landslides. No datable materials have yet been found associated with the deposits.« less
MutSα's Multi-Domain Allosteric Response to Three DNA Damage Types Revealed by Machine Learning

NASA Astrophysics Data System (ADS)

Melvin, Ryan L.; Thompson, William G.; Godwin, Ryan C.; Gmeiner, William H.; Salsbury, Freddie R.

2017-03-01

MutSalpha is a key component in the mismatch repair (MMR) pathway. This protein is responsible for initiating the signaling pathways for DNA repair or cell death. Herein we investigate this heterodimer’s post-recognition, post-binding response to three types of DNA damage involving cytotoxic, anti-cancer agents - carboplatin, cisplatin, and FdU. Through a combination of supervised and unsupervised machine learning techniques along with more traditional structural and kinetic analysis applied to all-atom molecular dynamics (MD) calculations, we predict that MutSalpha has a distinct response to each of the three damage types. Via a binary classification tree (a supervised machine learning technique), we identify key hydrogen bond motifs unique to each type of damage and suggest residues for experimental mutation studies. Through a combination of a recently developed clustering (unsupervised learning) algorithm, RMSF calculations, PCA, and correlated motions we predict that each type of damage causes MutS↵to explore a specific region of conformation space. Detailed analysis suggests a short range effect for carboplatin - primarily altering the structures and kinetics of residues within 10 angstroms of the damaged DNA - and distinct longer-range effects for cisplatin and FdU. In our simulations, we also observe that a key phenylalanine residue - known to stack with a mismatched or unmatched bases in MMR - stacks with the base complementary to the damaged base in 88.61% of MD frames containing carboplatinated DNA. Similarly, this Phe71 stacks with the base complementary to damage in 91.73% of frames with cisplatinated DNA. This residue, however, stacks with the damaged base itself in 62.18% of trajectory frames with FdU-substituted DNA and has no stacking interaction at all in 30.72% of these frames. Each drug investigated here induces a unique perturbation in the MutS↵complex, indicating the possibility of a distinct signaling event and specific repair or death pathway (or set of pathways) for a given type of damage.

Classification of epilepsy types through global network analysis of scalp electroencephalograms

NASA Astrophysics Data System (ADS)

Lee, Uncheol; Kim, Seunghwan; Jung, Ki-Young

2006-04-01

Epilepsy is a dynamic disease in which self-organization and emergent structures occur dynamically at multiple levels of neuronal integration. Therefore, the transient relationship within multichannel electroencephalograms (EEGs) is crucial for understanding epileptic processes. In this paper, we show that the global relationship within multichannel EEGs provides us with more useful information in classifying two different epilepsy types than pairwise relationships such as cross correlation. To demonstrate this, we determine the global network structure within channels of the scalp EEG based on the minimum spanning tree method. The topological dissimilarity of the network structures from different types of temporal lobe epilepsy is described in the form of the divergence rate and is computed for 11 patients with left (LTLE) and right temporal lobe epilepsy (RTLE). We find that patients with LTLE and RTLE exhibit different large scale network structures, which emerge at the epoch immediately before the seizure onset, not in the preceding epochs. Our results suggest that patients with the two different epilepsy types display distinct large scale dynamical networks with characteristic epileptic network structures.
STRUCTURE OF THE VIBRIO CHOLERAE TYPE IVB PILUS AND STABILITY COMPARISON WITH THE NEISSERIA GONORRHOEAE TYPE IVA PILUS

PubMed Central

Li, Juliana; Egelman, Edward H.; Craig, Lisa

2012-01-01

Type IV pili are multifunctional filaments displayed on many bacterial pathogens. Members of the Type IVa pilus subclass are found on a diverse group of human pathogens whereas Type IVb pili are almost exclusively on enteric bacteria. The Type IVa and IVb subclasses are distinguished by differences in the pilin subunits, including the fold of the globular domain. To understand the implications of the distinct pilin folds we compared the stabilities of pilin subunits and pilus filaments for the Type IVa GC pilus from Neisseria gonorrhoeae and the Type IVb toxin-coregulated pilus (TCP) from Vibrio cholerae. We show that while recombinant TCP pilin is more stable than GC pilin, the GC pili are more resistant than TCP to proteolysis, heat and chemical denaturation, remaining intact in 8 M urea. To understand these differences we determined the TCP structure by electron microscopy and 3D image reconstruction. TCP have a similar architecture to GC pili, with subunits arranged in a right-handed one-start helix and related by an 8.4 Å axial rise and a 96.8° azimuthal rotation. However, the TCP subunits are not as tightly packed as GC pilins and the distinct Type IVb pilin fold exposes a segment of the α-helical core of TCP. Hydrophobic interactions dominate for both pilus subtypes, but base-stacking by aromatic residues conserved among the Type IVa pilins may contribute to GC pilus stability. The extraordinary stability of GC pili may represent an adaptation of the Type IVa pili to harsh environments and the need to retract against external forces. PMID:22361030
Expert Systems and Command, Control, and Communication System Acquisition

DTIC Science & Technology

1989-03-01

Systems and Command, Control, and Communicaton System Acquisition 12 Personal Author(s) James E. Minnema 13a Type of Report 13b Time Covered 14 Date...isolated strategic planning, unstructured problems, the author feels that this category should also include problems involving the integration of...distinct operational or management control, and structured or semi-structured problem efforts. The reason for this is that integration of a number of
Structural organization of process zones in upland watersheds of central Nevada and its influence on basin connectivity, dynamics, and wet meadow complexes

Treesearch

Jerry R. Miller; Mark L. Lord; Lionel F. Villarroel; Dru Germanoski; Jeanne C. Chambers

2012-01-01

The drainage network within upland watersheds in central Nevada can be subdivided into distinct zones each dominated by a unique set of processes on the basis of valley form, the geological materials that comprise the valley floor, and the presence or absence of surficial channels. On hillslopes, the type and structure (frequency, length, and spatial arrangement) of...
Two distinct β-sheet structures in Italian-mutant amyloid-beta fibrils: a potential link to different clinical phenotypes.

PubMed

Hubin, Ellen; Deroo, Stéphanie; Schierle, Gabriele Kaminksi; Kaminski, Clemens; Serpell, Louise; Subramaniam, Vinod; van Nuland, Nico; Broersen, Kerensa; Raussens, Vincent; Sarroukh, Rabia

2015-12-01

Most Alzheimer's disease (AD) cases are late-onset and characterized by the aggregation and deposition of the amyloid-beta (Aβ) peptide in extracellular plaques in the brain. However, a few rare and hereditary Aβ mutations, such as the Italian Glu22-to-Lys (E22K) mutation, guarantee the development of early-onset familial AD. This type of AD is associated with a younger age at disease onset, increased β-amyloid accumulation, and Aβ deposition in cerebral blood vessel walls, giving rise to cerebral amyloid angiopathy (CAA). It remains largely unknown how the Italian mutation results in the clinical phenotype that is characteristic of CAA. We therefore investigated how this single point mutation may affect the aggregation of Aβ1-42 in vitro and structurally characterized the resulting fibrils using a biophysical approach. This paper reports that wild-type and Italian-mutant Aβ both form fibrils characterized by the cross-β architecture, but with distinct β-sheet organizations, resulting in differences in thioflavin T fluorescence and solvent accessibility. E22K Aβ1-42 oligomers and fibrils both display an antiparallel β-sheet structure, in comparison with the parallel β-sheet structure of wild-type fibrils, characteristic of most amyloid fibrils described in the literature. Moreover, we demonstrate structural plasticity for Italian-mutant Aβ fibrils in a pH-dependent manner, in terms of their underlying β-sheet arrangement. These findings are of interest in the ongoing debate that (1) antiparallel β-sheet structure might represent a signature for toxicity, which could explain the higher toxicity reported for the Italian mutant, and that (2) fibril polymorphism might underlie differences in disease pathology and clinical manifestation.
Foot Type Biomechanics Part 1: Structure and Function of the Asymptomatic Foot

PubMed Central

Hillstrom, Howard J.; Song, Jinsup; Kraszewski, Andrew P.; Hafer, Jocelyn F.; Mootanah, Rajshree; Dufour, Alyssa B.; PT, Betty (Shingpui) Chow; Deland, Jonathan T.

2012-01-01

Background Differences in foot structure are thought to be associated with differences in foot function during movement. Many foot pathologies are of a biomechanical nature and often associated with foot type. Fundamental to the understanding of foot pathomechanics is the question: do different foot types have distinctly different structure and function? Aim To determine if objective measures of foot structure and function differ between planus, rectus and cavus foot types in asymptomatic individuals. Methods Sixty-one asymptomatic healthy adults between 18 and 77 years old, that had the same foot type bilaterally (44 planus feet, 54 rectus feet, and 24 cavus feet), were recruited. Structural and functional measurements were taken using custom equipment, an emed-x plantar pressure measuring device, a GaitMatII gait pattern measurement system, and a goniometer. Generalized Estimation Equation modeling was employed to determine if each dependent variable of foot structure and function was significantly different across foot type while accounting for potential dependencies between sides. Post hoc testing was performed to assess pairwise comparisons. Results Several measures of foot structure (malleolar valgus index and arch height index) were significantly different between foot types. Gait pattern parameters were invariant across foot types. Peak pressure, maximum force, pressure-time-integral, force-time-integral and contact area were significantly different in several medial forefoot and arch locations between foot types. Planus feet exhibited significantly different center of pressure excursion indices compared to rectus and cavus feet. Conclusions Planus, rectus and cavus feet exhibited significantly different measures of foot structure and function. PMID:23107625
Foot type biomechanics part 1: structure and function of the asymptomatic foot.

PubMed

Hillstrom, Howard J; Song, Jinsup; Kraszewski, Andrew P; Hafer, Jocelyn F; Mootanah, Rajshree; Dufour, Alyssa B; Chow, Betty Shingpui; Deland, Jonathan T

2013-03-01

Differences in foot structure are thought to be associated with differences in foot function during movement. Many foot pathologies are of a biomechanical nature and often associated with foot type. Fundamental to the understanding of foot pathomechanics is the question: do different foot types have distinctly different structure and function? To determine if objective measures of foot structure and function differ between planus, rectus and cavus foot types in asymptomatic individuals. Sixty-one asymptomatic healthy adults between 18 and 77 years old, that had the same foot type bilaterally (44 planus feet, 54 rectus feet, and 24 cavus feet), were recruited. Structural and functional measurements were taken using custom equipment, an emed-x plantar pressure measuring device, a GaitMat II gait pattern measurement system, and a goniometer. Generalized Estimation Equation modeling was employed to determine if each dependent variable of foot structure and function was significantly different across foot type while accounting for potential dependencies between sides. Post hoc testing was performed to assess pair wise comparisons. Several measures of foot structure (malleolar valgus index and arch height index) were significantly different between foot types. Gait pattern parameters were invariant across foot types. Peak pressure, maximum force, pressure-time-integral, force-time-integral and contact area were significantly different in several medial forefoot and arch locations between foot types. Planus feet exhibited significantly different center of pressure excursion indices compared to rectus and cavus feet. Planus, rectus and cavus feet exhibited significantly different measures of foot structure and function. Copyright © 2012 Elsevier B.V. All rights reserved.
Dynamic apical surface rings in superficial layer cells of koi Cyprinus carpio scale epidermis.

PubMed

DePasquale, J A

2016-09-01

This study examined the novel ring-shaped structures found in the apical surface of individual cells of the scale epidermis of koi Cyprinus carpio. These apical rings are highly dynamic structures with lifetimes ranging from a few to several minutes. While several ring forms were observed, the predominant ring morphology is circular or oval. Two distinct ring forms were identified and designated type I and type II. Type I rings have a well-defined outer border that encircles the surface microridges. Type II rings are smooth-surfaced, dinner-plate-like structures with membranous folds or compressed microridges in the centre. Type II rings appear less frequently than type I rings. Type I rings form spontaneously, arising from swollen or physically interrupted microridges but without initially perturbing the encircled microridges. After persisting for up to several minutes the ring closes in a centripetal movement to form a circular or irregular-shaped structure, the terminal disc. The terminal disc eventually disappears, leaving behind a submembranous vesicle-like structure, the terminal body. Type I rings can undergo multiple cycles of formation and closing. Recycling epidermal apical rings form through centrifugal expansion from the terminal disc followed by apparent contraction back to the disc structure, whereupon the cycle may repeat or cease. The findings demonstrate a novel skin surface structure in fishes and are discussed with respect to communication with the external aqueous environment. © 2016 The Fisheries Society of the British Isles.
Riboswitches: emerging themes in RNA structure and function.

PubMed

Montange, Rebecca K; Batey, Robert T

2008-01-01

Riboswitches are RNAs capable of binding cellular metabolites using a diverse array of secondary and tertiary structures to modulate gene expression. The recent determination of the three-dimensional structures of parts of six different riboswitches illuminates common features that allow riboswitches to be grouped into one of two types. Type I riboswitches, as exemplified by the purine riboswitch, are characterized by a single, localized binding pocket supported by a largely pre-established global fold. This arrangement limits ligand-induced conformational changes in the RNA to a small region. In contrast, Type II riboswitches, such as the thiamine pyrophosphate riboswitch, contain binding pockets split into at least two spatially distinct sites. As a result, binding induces both local changes to the binding pocket and global architecture. Similar organizational themes are found in other noncoding RNAs, making it possible to begin to build a hierarchical classification of RNA structure based on the spatial organization of their active sites and associated secondary structural elements.
Mangrove vegetation structure in Southeast Brazil from phased array L-band synthetic aperture radar data

NASA Astrophysics Data System (ADS)

de Souza Pereira, Francisca Rocha; Kampel, Milton; Cunha-Lignon, Marilia

2016-07-01

The potential use of phased array type L-band synthetic aperture radar (PALSAR) data for discriminating distinct physiographic mangrove types with different forest structure developments in a subtropical mangrove forest located in Cananéia on the Southern coast of São Paulo, Brazil, is investigated. The basin and fringe physiographic types and the structural development of mangrove vegetation were identified with the application of the Kruskal-Wallis statistical test to the SAR backscatter values of 10 incoherent attributes. The best results to separate basin to fringe types were obtained using copolarized HH, cross-polarized HV, and the biomass index (BMI). Mangrove structural parameters were also estimated using multiple linear regressions. BMI and canopy structure index were used as explanatory variables for canopy height, mean height, and mean diameter at breast height regression models, with significant R2=0.69, 0.73, and 0.67, respectively. The current study indicates that SAR L-band images can be used as a tool to discriminate physiographic types and to characterize mangrove forests. The results are relevant considering the crescent availability of freely distributed SAR images that can be more utilized for analysis, monitoring, and conservation of the mangrove ecosystem.
Structure of the heterotrimeric complex that regulates type III secretion needle formation

PubMed Central

Quinaud, Manuelle; Plé, Sophie; Job, Viviana; Contreras-Martel, Carlos; Simorre, Jean-Pierre; Attree, Ina; Dessen, Andréa

2007-01-01

Type III secretion systems (T3SS), found in several Gram-negative pathogens, are nanomachines involved in the transport of virulence effectors directly into the cytoplasm of target cells. T3SS are essentially composed of basal membrane-embedded ring-like structures and a hollow needle formed by a single polymerized protein. Within the bacterial cytoplasm, the T3SS needle protein requires two distinct chaperones for stabilization before its secretion, without which the entire T3SS is nonfunctional. The 2.0-Å x-ray crystal structure of the PscE-PscF55–85-PscG heterotrimeric complex from Pseudomonas aeruginosa reveals that the C terminus of the needle protein PscF is engulfed within the hydrophobic groove of the tetratricopeptide-like molecule PscG, indicating that the macromolecular scaffold necessary to stabilize the T3SS needle is totally distinct from chaperoned complexes between pilus- or flagellum-forming molecules. Disruption of specific PscG–PscF interactions leads to impairment of bacterial cytotoxicity toward macrophages, indicating that this essential heterotrimer, which possesses homologs in a wide variety of pathogens, is a unique attractive target for the development of novel antibacterials. PMID:17470796
Comparative microbial diversity analyses of modern marine thrombolitic mats by barcoded pyrosequencing.

PubMed

Mobberley, Jennifer M; Ortega, Maya C; Foster, Jamie S

2012-01-01

Thrombolites are unlaminated carbonate structures that form as a result of the metabolic interactions of complex microbial mat communities. Thrombolites have a long geological history; however, little is known regarding the microbes associated with modern structures. In this study, we use a barcoded 16S rRNA gene-pyrosequencing approach coupled with morphological analysis to assess the bacterial, cyanobacterial and archaeal diversity associated with actively forming thrombolites found in Highborne Cay, Bahamas. Analyses revealed four distinct microbial mat communities referred to as black, beige, pink and button mats on the surfaces of the thrombolites. At a coarse phylogenetic resolution, the domain bacterial sequence libraries from the four mats were similar, with Proteobacteria and Cyanobacteria being the most abundant. At the finer resolution of the rRNA gene sequences, significant differences in community structure were observed, with dramatically different cyanobacterial communities. Of the four mat types, the button mats contained the highest diversity of Cyanobacteria, and were dominated by two sequence clusters with high similarity to the genus Dichothrix, an organism associated with the deposition of carbonate. Archaeal diversity was low, but varied in all mat types, and the archaeal community was predominately composed of members of the Thaumarchaeota and Euryarchaeota. The morphological and genetic data support the hypothesis that the four mat types are distinctive thrombolitic mat communities. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.
Trait Distinctiveness and Age Specificity in Self-Referent Information Processing.

ERIC Educational Resources Information Center

Mueller, John H.; Johnson, W. Calvin

Research has indicated that certain orienting activities help integrate new experiences with pre-existing cognitive structures. The content specificity hypothesis proposes that if the self-concept is distorted so that certain information is missing, then self-referencing that type of material will be ineffective. This notion of content specificity…
Knowledge Construction and Knowledge Representation in High School Students' Design of Hypermedia Documents

ERIC Educational Resources Information Center

Chen, Pearl; McGrath, Diane

2003-01-01

This study documented the processes of knowledge construction and knowledge representation in high school students' hypermedia design projects. Analysis of knowledge construction in linking and structural building yielded distinct types and subtypes of hypermedia documents, which were characterized by four features of knowledge representation: (a)…
Exploring Teaching Concerns and Characteristics of Graduate Teaching Assistants

ERIC Educational Resources Information Center

Cho, YoonJung; Kim, Myoungsook; Svinicki, Marilla D.; Decker, Mark Lowry

2011-01-01

The purpose of the study was to explore a conceptual structure of graduate teaching assistant (GTA) teaching concerns. Results indicated that GTAs experience five distinct, inter-related types of concerns: class control, external evaluation, task, impact and role/time/communication. These "teaching concerns" were further analysed by…
Colleges and the Governance of Higher Education

ERIC Educational Resources Information Center

Parry, Gareth

2013-01-01

The governance of higher education in colleges and college sectors that offer other types of education and training is distinctive in four main respects. First, governance structures are frequently separate and different for higher education and for other segments of tertiary education. Second, the size and scope of the higher-level education…
Compositional structure of the asteroid belt.

PubMed

Gradie, J; Tedesco, E

1982-06-25

The distribution of compositional types among the asteroids is found to vary systematically with heliocentric distance. Seven distinct peaks in the relative proportion of the compositional types E, R, S, M, F, C, P, and D are found from 1.8 to 5.2 astronomical units. The inferred composition of the asteroids in each semimajor axis region is consistent with the theory that the asteroids accreted from the solar nebula at or near their present locations.
Correlation of cell surface proteins of distinct Beauveria bassiana cell types and adaption to varied environment and interaction with the host insect.

PubMed

Yang, Zhi; Jiang, Hongyan; Zhao, Xin; Lu, Zhuoyue; Luo, Zhibing; Li, Xuebing; Zhao, Jing; Zhang, Yongjun

2017-02-01

The insect fungal pathogen Beauveria bassiana produces a number of distinct cell types that include aerial conidia, blastospores and haemolymph-derived cells, termed hyphal bodies, to adapt varied environment niches and within the host insect. These cells display distinct biochemical properties and surface structures, and a highly ordered outermost brush-like structure uniquely present on hyphal bodies, but not on any in vitro cells. Here, we found that the outermost structure on the hyphal bodies mainly consisted of proteins associated to structural wall components in that most of it could be removed by dithiothreitol (DTT) or proteinase K. DTT-treatment also caused delayed germination, decreased tolerance to ultraviolet irradiation and virulence of conidia or blastospores, with decreased adherence and alternated carbohydrate epitopes, suggesting involvement in fungal development, stress responses and virulence. To characterize these cell surface molecules, proteins were released from the living cells using DTT, and identified and quantitated using label-free quantitative mass spectrometry. Thereafter, a series of bioinformatics programs were used to predict cell surface-associated proteins (CSAPs), and 96, 166 and 54 CSAPs were predicted from the identified protein pools of conidia, blastospores and hyphal bodies, respectively, which were involved in utilization of carbohydrate, nitrogen, and lipid, detoxification, pathogen-host interaction, and likely other cellular processes. Thirteen, sixty-nine and six CSAPs were exclusive in conidia, blastospores and hyphal bodies, respectively, which were verified by eGFP-tagged proteins at their N-terminus. Our data provide a crucial cue to understand mechanism of B. bassiana to adapt to varied environment and interaction with insect host. Copyright © 2016 Elsevier Inc. All rights reserved.
A monogamous pipefish has the same type of ovary as observed in monogamous seahorses.

PubMed

Sogabe, Atsushi; Matsumoto, Koji; Ohashi, Mizuki; Watanabe, Aki; Takata, Hiromi; Murakami, Yasunori; Omori, Koji; Yanagisawa, Yasunobu

2008-08-23

Syngnathid fish (pipefish and seahorses) are unique among teleost fish in that their ovary consists of a rolled sheet with germinal ridge(s) on the dorsal side running along the entire length of the sheet. A distinct difference is seen in the ovarian structure between polygamous Syngnathus pipefish and monogamous seahorses (Hippocampus spp.), the former having one germinal ridge and the latter with two ridges. This study examined the ovarian structure and the mode of egg production in a monogamous pipefish Corythoichthys haematopterus. The ovary of C. haematopterus had two germinal ridges like that observed in monogamous seahorses. There were two distinct groups of follicles in the ovary, one being a cohort of extremely small follicles and the other a cohort of follicles developing and increasing in size with the passage of time. We suggest that the ovarian structure and the mode of egg production in this pipefish are adaptations to monogamy.
In Vitro Reassembly of the Ribose ATP-binding Cassette Transporter Reveals a Distinct Set of Transport Complexes*

PubMed Central

Clifton, Matthew C.; Simon, Michael J.; Erramilli, Satchal K.; Zhang, Huide; Zaitseva, Jelena; Hermodson, Mark A.; Stauffacher, Cynthia V.

2015-01-01

Bacterial ATP-binding cassette (ABC) importers are primary active transporters that are critical for nutrient uptake. Based on structural and functional studies, ABC importers can be divided into two distinct classes, type I and type II. Type I importers follow a strict alternating access mechanism that is driven by the presence of the substrate. Type II importers accept substrates in a nucleotide-free state, with hydrolysis driving an inward facing conformation. The ribose transporter in Escherichia coli is a tripartite complex consisting of a cytoplasmic ATP-binding cassette protein, RbsA, with fused nucleotide binding domains; a transmembrane domain homodimer, RbsC2; and a periplasmic substrate binding protein, RbsB. To investigate the transport mechanism of the complex RbsABC2, we probed intersubunit interactions by varying the presence of the substrate ribose and the hydrolysis cofactors, ATP/ADP and Mg2+. We were able to purify a full complex, RbsABC2, in the presence of stable, transition state mimics (ATP, Mg2+, and VO4); a RbsAC complex in the presence of ADP and Mg2+; and a heretofore unobserved RbsBC complex in the absence of cofactors. The presence of excess ribose also destabilized complex formation between RbsB and RbsC. These observations suggest that RbsABC2 shares functional traits with both type I and type II importers, as well as possessing unique features, and employs a distinct mechanism relative to other ABC transporters. PMID:25533465

Atomic force microscopy study of the structure function relationships of the biofilm-forming bacterium Streptococcus mutans

NASA Astrophysics Data System (ADS)

Cross, Sarah E.; Kreth, Jens; Zhu, Lin; Qi, Fengxia; Pelling, Andrew E.; Shi, Wenyuan; Gimzewski, James K.

2006-02-01

Atomic force microscopy (AFM) has garnered much interest in recent years for its ability to probe the structure, function and cellular nanomechanics inherent to specific biological cells. In particular, we have used AFM to probe the important structure-function relationships of the bacterium Streptococcus mutans. S. mutans is the primary aetiological agent in human dental caries (tooth decay), and is of medical importance due to the virulence properties of these cells in biofilm initiation and formation, leading to increased tolerance to antibiotics. We have used AFM to characterize the unique surface structures of distinct mutants of S. mutans. These mutations are located in specific genes that encode surface proteins, thus using AFM we have resolved characteristic surface features for mutant strains compared to the wild type. Ultimately, our characterization of surface morphology has shown distinct differences in the local properties displayed by various S. mutans strains on the nanoscale, which is imperative for understanding the collective properties of these cells in biofilm formation.
Crystallography, chemistry and structural disorder in the new high-Tc Bi-Ca-Sr-Cu-O superconductor

NASA Technical Reports Server (NTRS)

Veblen, D. R.; Heaney, P. J.; Angel, R. J.; Finger, L. W.; Hazen, R. M.

1988-01-01

Diffraction experiments are reported which indicate that the new Bi-Ca-Sr-Cu-O layer-structure superconductor possesses a primitive orthorhombic unit cell with probable space group Pnnn. The material exhibits severe structural disorder which is primarily related to stacking within the layers. The apparent orthorhombic structure is an average resulting from orthorhombic material mixed with monoclinic domains in two twinned orientations. Two distinct types of structural disorder that are common in materials synthesized to date are also described. This disorder complicates the crystallographic analysis and suggests that X-ray and neutron diffraction methods may yield only an average structure.
A one-pot, microwave-influenced synthesis of diverse small molecules by multicomponent reaction cascades.

PubMed

Santra, Soumava; Andreana, Peter R

2007-11-22

Small molecule diversity can be achieved in a single synthetic operation from bifunctional substrates in the absence of additives and under the influence of microwaves with complete control of pathway selectivity. The preliminary Ugi four-component coupling products give rise to three structurally distinct scaffolds that are dependent on solvent effects and sterics. 2,5-Diketopiperazines (Type A), 2-azaspiro[4.5]deca-6,9-diene-3,8-diones (Type B), and thiophene-derived Diels-Alder tricyclic lactams (Type C) predominate in this reaction cascade.
Molecular architectures of benzoic acid-specific type III polyketide synthases

PubMed Central

Stewart, Charles; Woods, Kate; Macias, Greg; Allan, Andrew C.; Noel, Joseph P.

2017-01-01

Biphenyl synthase and benzophenone synthase constitute an evolutionarily distinct clade of type III polyketide synthases (PKSs) that use benzoic acid-derived substrates to produce defense metabolites in plants. The use of benzoyl-CoA as an endogenous substrate is unusual for type III PKSs. Moreover, sequence analyses indicate that the residues responsible for the functional diversification of type III PKSs are mutated in benzoic acid-specific type III PKSs. In order to gain a better understanding of structure–function relationships within the type III PKS family, the crystal structures of biphenyl synthase from Malus × domestica and benzophenone synthase from Hypericum androsaemum were compared with the structure of an archetypal type III PKS: chalcone synthase from Malus × domestica. Both biphenyl synthase and benzophenone synthase contain mutations that reshape their active-site cavities to prevent the binding of 4-coumaroyl-CoA and to favor the binding of small hydrophobic substrates. The active-site cavities of biphenyl synthase and benzophenone synthase also contain a novel pocket associated with their chain-elongation and cyclization reactions. Collectively, these results illuminate structural determinants of benzoic acid-specific type III PKSs and expand the understanding of the evolution of specialized metabolic pathways in plants. PMID:29199980
Assessing the biological contribution to microbialite growth and morphogenesis utilizing lipid biomarkers

NASA Astrophysics Data System (ADS)

Beeler, S. R.; Gomez, F. J.; Bradley, A. S.

2016-12-01

Microbialites are sedimentary structures that arise from the interaction of microbial, geochemical, and physical processes. These structures are among the oldest evidence for life on Earth, and are abundant through much of the Proterozoic before declining in the Phanerozoic. Microbialites are of great importance geobiologically as they provide a record of microbial life and its interaction with the environment throughout Earth history. Yet, our capacity to use microbialites to reconstruct biological processes on ancient Earth is complicated by our lack of understanding of the mechanisms controlling the formation of these structures. The modern microbialites of Laguna Negra in northeastern Argentina [1] offer an opportunity to examine the biological and geochemical differences among microbialites displaying distinct morphological diversity in a single setting. Three broad types of microbialites are found at this site: oncoids, stromatolites, and laminar crusts. Each of these types of microbialites are associated with visually distinct microbial mats. We have examined the structural and isotopic composition of lipid biomarkers from each of these microbialite types, and their associated mats. Sterol profiles detected from microbial mats and microbialites showed abundant C27 to C29 sterols and indicate that primary producers are dominated by algae. Decreased abundances of more labile unsaturated fatty acids relative to more recalcitrant saturated fatty acids were observed in microbialites compared to extant mats suggesting preferential loss of these compounds during diagenesis. Among the three different microbialite morphologies, no statistically discernable differences in biomarker profiles were detected. This implies that morphological changes are due to either geochemical/physical changes across the zone of microbialite formation or changes in community structure that are not observable in the present biomarker set. [1] Gomez et al. (2014) Palaios 29, 233-249
Glycosyltransferases A and B: Four Critical Amino Acids Determine Blood Type

NASA Astrophysics Data System (ADS)

Rose, Natisha L.; Palcic, Monica M.; Evans, Stephen V.

2005-12-01

Human A, B, and O blood type is determined by the presence or absence of distinct carbohydrate structures on red blood cells. Type O individuals have α-fucose(1→2)galactose disaccharides [O(H) structures] on their cell surfaces while in type A or B individuals, the O antigen is capped by the addition of an α- N -acetylgalactosamine or α-galactose residue, respectively. The addition of these monosaccharides is catalyzed by glycosyltransferase A (GTA) or glycosyltransferase B (GTB). These are homologous enzymes differing by only 4 amino acids out of 354 that change the specificity from GTA to GTB. In this review the chemistry of the blood group ABO system and the role of GTA, GTB, and the four critical amino acids in determining blood group status are discussed. See JCE Featured Molecules .
The role of structural characteristics in video-game play motivation: a Q-methodology study.

PubMed

Westwood, Dave; Griffiths, Mark D

2010-10-01

Until recently, there has been very little naturalistic study of what gaming experiences are like, and how gaming fits into people's lives. Using a recently developed structural characteristic taxonomy of video games, this study examined the psycho-structural elements of computer games that motivate gamers to play them. Using Q-Sort methodology, 40 gamers participated in an online Q-sort task. Results identified six distinct types of gamers based on the factors generated: (a) story-driven solo gamers; (b) social gamers; (c) solo limited gamers; (d) hardcore online gamers; (e) solo control/identity gamers; and (f ) casual gamers. These gaming types are discussed, and a brief evaluation of similar and unique elements of the different types of gamer is also offered. The current study shows Q-methodology to be a relevant and applicable method in the psychological research of gaming.
De Novo Chromosome Structure Prediction

NASA Astrophysics Data System (ADS)

di Pierro, Michele; Cheng, Ryan R.; Lieberman-Aiden, Erez; Wolynes, Peter G.; Onuchic, Jose'n.

Chromatin consists of DNA and hundreds of proteins that interact with the genetic material. In vivo, chromatin folds into nonrandom structures. The physical mechanism leading to these characteristic conformations, however, remains poorly understood. We recently introduced MiChroM, a model that generates chromosome conformations by using the idea that chromatin can be subdivided into types based on its biochemical interactions. Here we extend and complete our previous finding by showing that structural chromatin types can be inferred from ChIP-Seq data. Chromatin types, which are distinct from DNA sequence, are partially epigenetically controlled and change during cell differentiation, thus constituting a link between epigenetics, chromosomal organization, and cell development. We show that, for GM12878 lymphoblastoid cells we are able to predict accurate chromosome structures with the only input of genomic data. The degree of accuracy achieved by our prediction supports the viability of the proposed physical mechanism of chromatin folding and makes the computational model a powerful tool for future investigations.
Phylogenetic analysis and protein structure modelling identifies distinct Ca(2+)/Cation antiporters and conservation of gene family structure within Arabidopsis and rice species.

PubMed

Pittman, Jon K; Hirschi, Kendal D

2016-12-01

The Ca(2+)/Cation Antiporter (CaCA) superfamily is an ancient and widespread family of ion-coupled cation transporters found in nearly all kingdoms of life. In animals, K(+)-dependent and K(+)-indendent Na(+)/Ca(2+) exchangers (NCKX and NCX) are important CaCA members. Recently it was proposed that all rice and Arabidopsis CaCA proteins should be classified as NCX proteins. Here we performed phylogenetic analysis of CaCA genes and protein structure homology modelling to further characterise members of this transporter superfamily. Phylogenetic analysis of rice and Arabidopsis CaCAs in comparison with selected CaCA members from non-plant species demonstrated that these genes form clearly distinct families, with the H(+)/Cation exchanger (CAX) and cation/Ca(2+) exchanger (CCX) families dominant in higher plants but the NCKX and NCX families absent. NCX-related Mg(2+)/H(+) exchanger (MHX) and CAX-related Na(+)/Ca(2+) exchanger-like (NCL) proteins are instead present. Analysis of genomes of ten closely-related rice species and four Arabidopsis-related species found that CaCA gene family structures are highly conserved within related plants, apart from minor variation. Protein structures were modelled for OsCAX1a and OsMHX1. Despite exhibiting broad structural conservation, there are clear structural differences observed between the different CaCA types. Members of the CaCA superfamily form clearly distinct families with different phylogenetic, structural and functional characteristics, and therefore should not be simply classified as NCX proteins, which should remain as a separate gene family.
Patterns of Morphosyntactic and Functional Diversification in the Usage of Cognate Verbs in Indo-Iranian

ERIC Educational Resources Information Center

Shirtz, Shahar Baruch

2017-01-01

This is a study of processes of structural and functional diversification of the uses of three cognate verbs across the Indo-Iranian language family: "do/make", "be/become", and "give". First, this study identifies over sixty distinct construction types in which these verbs are used, including complex predicate…
A Schema Theory Account of Some Cognitive Processes in Complex Learning. Technical Report No. 81.

ERIC Educational Resources Information Center

Munro, Allen; Rigney, Joseph W.

Procedural semantics models have diminished the distinction between data structures and procedures in computer simulations of human intelligence. This development has theoretical consequences for models of cognition. One type of procedural semantics model, called schema theory, is presented, and a variety of cognitive processes are explained in…
The Primacy of Language Mixing: The Effects of a Matrix System.

ERIC Educational Resources Information Center

Field, Fredric

1999-01-01

Focuses on the differences between bilingual mixtures and creoles. In both types of language, elements and structures of two or more distinct languages are intermingled. By contrasting Nahuatl, spoken in Central Mexico, with Palenquero, a Spanish-based creole spoken near the Caribbean coast of Colombia, examines two components of language thought…
Sentence Processing: Psycholinguistic Studies Presented to Merrill Garrett.

ERIC Educational Resources Information Center

Cooper, William E., Ed.; Walker, Edward C. T., Ed.

The chapters in this volume represent a type of current psycholinguistic research that focuses both on the nature of human information processing and the coding of linguistic structure. The chapters and authors are as follows: (1) "The Wherefores and Therefores of the Competence-Performance Distinction," by V. Valian; (2) "Levels of Processing and…
On the Making and Faking of Knowledge Value in Higher Education Curricula

ERIC Educational Resources Information Center

Hordern, Jim

2016-01-01

This paper uses Bernstein's sociology of knowledge and studies of professional knowledge and expertise to identify how knowledge value is constituted in higher education curricula. It is argued that different knowledge structures and forms of disciplinary community influence how curricula are determined, and lead to distinctive types of knowledge…
Māori identity signatures: A latent profile analysis of the types of Māori identity.

PubMed

Greaves, Lara M; Houkamau, Carla; Sibley, Chris G

2015-10-01

Māori are the indigenous peoples of New Zealand. However, the term 'Māori' can refer to a wide range of people of varying ethnic compositions and cultural identity. We present a statistical model identifying 6 distinct types, or 'Māori Identity Signatures,' and estimate their proportion in the Māori population. The model is tested using a Latent Profile Analysis of a national probability sample of 686 Māori drawn from the New Zealand Attitudes and Values Study. We identify 6 distinct signatures: Traditional Essentialists (22.6%), Traditional Inclusives (16%), High Moderates (31.7%), Low Moderates (18.7%), Spiritually Orientated (4.1%), and Disassociated (6.9%). These distinct Identity Signatures predicted variation in deprivation, age, mixed-ethnic affiliation, and religion. This research presents the first formal statistical model assessing how people's identity as Māori is psychologically structured, documents the relative proportion of these different patterns of structures, and shows that these patterns reliably predict differences in core demographics. We identify a range of patterns of Māori identity far more diverse than has been previously proposed based on qualitative data, and also show that the majority of Māori fit a moderate or traditional identity pattern. The application of our model for studying Māori health and identity development is discussed. (c) 2015 APA, all rights reserved).
Diversity in recognition of glycans by F-type lectins and galectins: molecular, structural, and biophysical aspects

PubMed Central

Vasta, Gerardo R.; Ahmed, Hafiz; Bianchet, Mario A.; Fernández-Robledo, José A.; Amzel, L. Mario

2013-01-01

Although lectins are “hard-wired” in the germline, the presence of tandemly arrayed carbohydrate recognition domains (CRDs), of chimeric structures displaying distinct CRDs, of polymorphic genes resulting in multiple isoforms, and in some cases, of a considerable recognition plasticity of their carbohydrate binding sites, significantly expand the lectin ligand-recognition spectrum and lectin functional diversification. Analysis of structural/functional aspects of galectins and F-lectins—the most recently identified lectin family characterized by a unique CRD sequence motif (a distinctive structural fold) and nominal specificity for l-Fuc—has led to a greater understanding of self/nonself recognition by proteins with tandemly arrayed CRDs. For lectins with a single CRD, however, recognition of self and nonself glycans can only be rationalized in terms of protein oligomerization and ligand clustering and presentation. Spatial and temporal changes in lectin expression, secretion, and local concentrations in extracellular microenvironments, as well as structural diversity and spatial display of their carbohydrate ligands on the host or microbial cell surface, are suggestive of a dynamic interplay of their recognition and effector functions in development and immunity. PMID:22973821
Propulsion/airframe integration issues for waverider aircraft

NASA Technical Reports Server (NTRS)

Blankson, Isaiah M.; Hagseth, Paul

1993-01-01

While many propulsion concepts and technologies developed for nonwaverider-type hypersonic vehicles may apply to waveriders, some aspects of these configurations require unique technological approaches. An evaluation is made of such distinctive opportunities in the cases of engine cycle selection, inlets, nozzle designs and integration, longitudinal stability, and thermal management. Also discussed are waverider requirements for control surface effectiveness, inlet boundary layer ingestion effects, and structural/configurational optimization, giving attention to trades in volumetric/structural efficiency and vehicle L/D.
Differential expression of vesicular glutamate transporters 1 and 2 may identify distinct modes of glutamatergic transmission in the macaque visual system

PubMed Central

Balaram, Pooja; Hackett, Troy A.; Kaas, Jon H.

2013-01-01

Glutamate is the primary neurotransmitter utilized by the mammalian visual system for excitatory neurotransmission. The sequestration of glutamate into synaptic vesicles, and the subsequent transport of filled vesicles to the presynaptic terminal membrane, is regulated by a family of proteins known as vesicular glutamate transporters (VGLUTs). Two VGLUT proteins, VGLUT1 and VGLUT2, characterize distinct sets of glutamatergic projections between visual structures in rodents and prosimian primates, yet little is known about their distributions in the visual system of anthropoid primates. We have examined the mRNA and protein expression patterns of VGLUT1 and VGLUT2 in the visual system of macaque monkeys, an Old World anthropoid primate, in order to determine their relative distributions in the superior colliculus, lateral geniculate nucleus, pulvinar complex, V1 and V2. Distinct expression patterns for both VGLUT1 and VGLUT2 identified architectonic boundaries in all structures, as well as anatomical subdivisions of the superior colliculus, pulvinar complex, and V1. These results suggest that VGLUT1 and VGLUT2 clearly identify regions of glutamatergic input in visual structures, and may identify common architectonic features of visual areas and nuclei across the primate radiation. Additionally, we find that VGLUT1 and VGLUT2 characterize distinct subsets of glutamatergic projections in the macaque visual system; VGLUT2 predominates in driving or feedforward projections from lower order to higher order visual structures while VGLUT1 predominates in modulatory or feedback projections from higher order to lower order visual structures. The distribution of these two proteins suggests that VGLUT1 and VGLUT2 may identify class 1 and class 2 type glutamatergic projections within the primate visual system (Sherman and Guillery, 2006). PMID:23524295
Differential expression of vesicular glutamate transporters 1 and 2 may identify distinct modes of glutamatergic transmission in the macaque visual system.

PubMed

Balaram, Pooja; Hackett, Troy A; Kaas, Jon H

2013-05-01

Glutamate is the primary neurotransmitter utilized by the mammalian visual system for excitatory neurotransmission. The sequestration of glutamate into synaptic vesicles, and the subsequent transport of filled vesicles to the presynaptic terminal membrane, is regulated by a family of proteins known as vesicular glutamate transporters (VGLUTs). Two VGLUT proteins, VGLUT1 and VGLUT2, characterize distinct sets of glutamatergic projections between visual structures in rodents and prosimian primates, yet little is known about their distributions in the visual system of anthropoid primates. We have examined the mRNA and protein expression patterns of VGLUT1 and VGLUT2 in the visual system of macaque monkeys, an Old World anthropoid primate, in order to determine their relative distributions in the superior colliculus, lateral geniculate nucleus, pulvinar complex, V1 and V2. Distinct expression patterns for both VGLUT1 and VGLUT2 identified architectonic boundaries in all structures, as well as anatomical subdivisions of the superior colliculus, pulvinar complex, and V1. These results suggest that VGLUT1 and VGLUT2 clearly identify regions of glutamatergic input in visual structures, and may identify common architectonic features of visual areas and nuclei across the primate radiation. Additionally, we find that VGLUT1 and VGLUT2 characterize distinct subsets of glutamatergic projections in the macaque visual system; VGLUT2 predominates in driving or feedforward projections from lower order to higher order visual structures while VGLUT1 predominates in modulatory or feedback projections from higher order to lower order visual structures. The distribution of these two proteins suggests that VGLUT1 and VGLUT2 may identify class 1 and class 2 type glutamatergic projections within the primate visual system (Sherman and Guillery, 2006). Copyright © 2013 Elsevier B.V. All rights reserved.
Automated classification of mouse pup isolation syllables: from cluster analysis to an Excel-based "mouse pup syllable classification calculator".

PubMed

Grimsley, Jasmine M S; Gadziola, Marie A; Wenstrup, Jeffrey J

2012-01-01

Mouse pups vocalize at high rates when they are cold or isolated from the nest. The proportions of each syllable type produced carry information about disease state and are being used as behavioral markers for the internal state of animals. Manual classifications of these vocalizations identified 10 syllable types based on their spectro-temporal features. However, manual classification of mouse syllables is time consuming and vulnerable to experimenter bias. This study uses an automated cluster analysis to identify acoustically distinct syllable types produced by CBA/CaJ mouse pups, and then compares the results to prior manual classification methods. The cluster analysis identified two syllable types, based on their frequency bands, that have continuous frequency-time structure, and two syllable types featuring abrupt frequency transitions. Although cluster analysis computed fewer syllable types than manual classification, the clusters represented well the probability distributions of the acoustic features within syllables. These probability distributions indicate that some of the manually classified syllable types are not statistically distinct. The characteristics of the four classified clusters were used to generate a Microsoft Excel-based mouse syllable classifier that rapidly categorizes syllables, with over a 90% match, into the syllable types determined by cluster analysis.

The application of the Wigner Distribution to wave type identification in finite length beams

NASA Technical Reports Server (NTRS)

Wahl, T. J.; Bolton, J. Stuart

1994-01-01

The object of the research described in this paper was to develop a means of identifying the wave-types propagating between two points in a finite length beam. It is known that different structural wave-types possess different dispersion relations: i.e., that their group speeds and the frequency dependence of their group speeds differ. As a result of those distinct dispersion relationships, different wave-types may be associated with characteristic features when structural responses are examined in the time frequency domain. Previously, the time-frequency character of analytically generated structural responses of both single element and multi-element structures were examined by using the Wigner Distribution (WD) along with filtering techniques that were designed to detect the wave-types present in the responses. In the work to be described here, the measure time-frequency response of finite length beam is examined using the WD and filtering procedures. This paper is organized as follows. First the concept of time-frequency analysis of structural responses is explained. The WD is then introduced along with a description of the implementation of a discrete version. The time-frequency filtering techniques are then presented and explained. The results of applying the WD and the filtering techniques to the analysis of a transient response is then presented.
Stomatal cell wall composition: distinctive structural patterns associated with different phylogenetic groups.

PubMed

Shtein, Ilana; Shelef, Yaniv; Marom, Ziv; Zelinger, Einat; Schwartz, Amnon; Popper, Zoë A; Bar-On, Benny; Harpaz-Saad, Smadar

2017-04-01

Stomatal morphology and function have remained largely conserved throughout ∼400 million years of plant evolution. However, plant cell wall composition has evolved and changed. Here stomatal cell wall composition was investigated in different vascular plant groups in attempt to understand their possible effect on stomatal function. A renewed look at stomatal cell walls was attempted utilizing digitalized polar microscopy, confocal microscopy, histology and a numerical finite-elements simulation. The six species of vascular plants chosen for this study cover a broad structural, ecophysiological and evolutionary spectrum: ferns ( Asplenium nidus and Platycerium bifurcatum ) and angiosperms ( Arabidopsis thaliana and Commelina erecta ) with kidney-shaped stomata, and grasses (angiosperms, family Poaceae) with dumbbell-shaped stomata ( Sorghum bicolor and Triticum aestivum ). Three distinct patterns of cellulose crystallinity in stomatal cell walls were observed: Type I (kidney-shaped stomata, ferns), Type II (kidney-shaped stomata, angiosperms) and Type III (dumbbell-shaped stomata, grasses). The different stomatal cell wall attributes investigated (cellulose crystallinity, pectins, lignin, phenolics) exhibited taxon-specific patterns, with reciprocal substitution of structural elements in the end-walls of kidney-shaped stomata. According to a numerical bio-mechanical model, the end walls of kidney-shaped stomata develop the highest stresses during opening. The data presented demonstrate for the first time the existence of distinct spatial patterns of varying cellulose crystallinity in guard cell walls. It is also highly intriguing that in angiosperms crystalline cellulose appears to have replaced lignin that occurs in the stomatal end-walls of ferns serving a similar wall strengthening function. Such taxon-specific spatial patterns of cell wall components could imply different biomechanical functions, which in turn could be a consequence of differences in environmental selection along the course of plant evolution. © The Author 2017. Published by Oxford University Press on behalf of the Annals of Botany Company.
Temporal lobe stimulation reveals anatomic distinction between auditory naming processes.

PubMed

Hamberger, M J; Seidel, W T; Goodman, R R; Perrine, K; McKhann, G M

2003-05-13

Language errors induced by cortical stimulation can provide insight into function(s) supported by the area stimulated. The authors observed that some stimulation-induced errors during auditory description naming were characterized by tip-of-the-tongue responses or paraphasic errors, suggesting expressive difficulty, whereas others were qualitatively different, suggesting receptive difficulty. They hypothesized that these two response types reflected disruption at different stages of auditory verbal processing and that these "subprocesses" might be supported by anatomically distinct cortical areas. To explore the topographic distribution of error types in auditory verbal processing. Twenty-one patients requiring left temporal lobe surgery underwent preresection language mapping using direct cortical stimulation. Auditory naming was tested at temporal sites extending from 1 cm from the anterior tip to the parietal operculum. Errors were dichotomized as either "expressive" or "receptive." The topographic distribution of error types was explored. Sites associated with the two error types were topographically distinct from one another. Most receptive sites were located in the middle portion of the superior temporal gyrus (STG), whereas most expressive sites fell outside this region, scattered along lateral temporal and temporoparietal cortex. Results raise clinical questions regarding the inclusion of the STG in temporal lobe epilepsy surgery and suggest that more detailed cortical mapping might enable better prediction of postoperative language decline. From a theoretical perspective, results carry implications regarding the understanding of structure-function relations underlying temporal lobe mediation of auditory language processing.
Metal ions may suppress or enhance cellular differentiation in Candida albicans and Candida tropicalis biofilms.

PubMed

Harrison, Joe J; Ceri, Howard; Yerly, Jerome; Rabiei, Maryam; Hu, Yaoping; Martinuzzi, Robert; Turner, Raymond J

2007-08-01

Candida albicans and Candida tropicalis are polymorphic fungi that develop antimicrobial-resistant biofilm communities that are characterized by multiple cell morphotypes. This study investigated cell type interconversion and drug and metal resistance as well as community organization in biofilms of these microorganisms that were exposed to metal ions. To study this, Candida biofilms were grown either in microtiter plates containing gradient arrays of metal ions or in the Calgary Biofilm Device for high-throughput susceptibility testing. Biofilm formation and antifungal resistance were evaluated by viable cell counts, tetrazolium salt reduction, light microscopy, and confocal laser scanning microscopy in conjunction with three-dimensional visualization. We discovered that subinhibitory concentrations of certain metal ions (CrO(4)(2-), Co(2+), Cu(2+), Ag(+), Zn(2+), Cd(2+), Hg(2+), Pb(2+), AsO(2)(-), and SeO(3)(2-)) caused changes in biofilm structure by blocking or eliciting the transition between yeast and hyphal cell types. Four distinct biofilm community structure types were discerned from these data, which were designated "domed," "layer cake," "flat," and "mycelial." This study suggests that Candida biofilm populations may respond to metal ions to form cell-cell and solid-surface-attached assemblages with distinct patterns of cellular differentiation.
Exploring the public-private and company size differences in employees' work characteristics and burnout: data analysis of a nationwide survey in Taiwan.

PubMed

Yeh, Wan-Yu; Yeh, Ching-Ying; Chen, Chiou-Jong

2018-05-15

Distinct differences exist between public-private sector organizations with respect to the market environment and operational objectives; furthermore, among private sector businesses, organizational structures and work conditions often vary between large- and small-sized companies. Despite these obvious structural distinctions, however, sectoral differences in employees' psychosocial risks and burnout status in national level have rarely been systematically investigated. Based on 2013 national employee survey data, 15,000 full-time employees were studied. Sector types were classified into "public," "private enterprise-large (LE)," and "private enterprise-small and medium (SME);" based on the definition of SMEs by Taiwan Ministry of Economic Affairs, and the associations of sector types with self-reported burnout status (measured by the Chinese version of Copenhagen Burnout Inventory) were examined, taking into account other work characteristics and job instability indicators. Significantly longer working hours and higher perceived job insecurity were found among private sector employees than their public sector counterparts. With further consideration of company size, greater dissatisfaction of job control and career prospect were found among SME employees than the other two sector type workers. This study explores the pattern of public-private differences in work conditions and employees' stress-related problems to have policy implications for supporting mechanism for disadvantaged workers in private sectors.
Comparative histological study of the mammalian facial nucleus.

PubMed

Furutani, Rui; Sugita, Shoei

2008-04-01

We performed comparative Nissl, Klüver-Barrera and Golgi staining studies of the mammalian facial nucleus to classify the morphologically distinct subdivisions and the neuronal types in the rat, rabbit, ferret, Japanese monkey (Macaca fuscata), pig, horse, Risso's dolphin (Grampus griseus), and bottlenose dolphin (Tursiops truncatus). The medial subnucleus was observed in all examined species; however, that of the Risso's and bottlenose dolphins was a poorly-developed structure comprised of scattered neurons. The medial subnuclei of terrestrial mammals were well-developed cytoarchitectonic structures, usually a rounded column comprised of densely clustered neurons. Intermediate and lateral subnuclei were found in all studied mammals, with differences in columnar shape and neuronal types from species to species. The dorsolateral subnucleus was detected in all mammals but the Japanese monkey, whose facial neurons converged into the intermediate subnucleus. The dorsolateral subnuclei of the two dolphin species studied were expanded subdivisions comprised of densely clustered cells. The ventromedial subnuclei of the ferret, pig, and horse were richly-developed columns comprised of large multipolar neurons. Pig and horse facial nuclei contained another ventral cluster, the ventrolateral subnucleus. The facial nuclei of the Japanese monkey and the bottlenose dolphin were similar in their ventral subnuclear organization. Our findings show species-specific subnuclear organization and distribution patterns of distinct types of neurons within morphological discrete subdivisions, reflecting functional differences.
Distinct dimensions defining the Adult ADHD Self-Report Scale: Implications for assessing inattentive and hyperactive/impulsive symptoms.

PubMed

Stanton, Kasey; Forbes, Miriam K; Zimmerman, Mark

2018-06-07

There has been growing interest in studying attention-deficit/hyperactivity disorder (ADHD) in adulthood as a result of research indicating that ADHD often persists into adulthood and frequently is comorbid with other psychiatric disorders. Adult ADHD symptoms are most commonly assessed via self-report, but prior research examining the structure of self-reported adult ADHD symptoms has yielded discrepant results. Explicating the factor structure of ADHD symptom measures is essential to determine if such self-report measures assess symptom dimensions showing distinctive relations with other psychopathology and psychosocial functioning. Consequently, we examined the structure of adult ADHD symptoms in a large sample of adult outpatients (N = 1,094). Symptoms were assessed via the Adult ADHD Self-Report Scale (ASRS; Kessler et al., 2005), which has become the most widely used self-report ADHD measure. Additionally, we extended prior research by examining the relations for emergent ADHD dimensions with other psychopathology and psychosocial impairment. Results indicated that the ASRS's items define a bifactor structure with specific dimensions of inattentiveness, motor hyperactivity/impulsivity, and verbal hyperactivity/impulsivity. Our results indicate that specific ADHD factors show distinctive relations in some ways. For example, verbal hyperactivity/impulsivity showed negative relations with major depressive disorder, whereas inattentiveness showed positive relations with major depression. These results highlight the need for future research determining the extent to which making distinctions among various ADHD symptom types (i.e., distinguishing motor and verbal hyperactivity/impulsivity) is empirically warranted and clinically useful. (PsycINFO Database Record (c) 2018 APA, all rights reserved).
ACCESS 3. Approximation concepts code for efficient structural synthesis: User's guide

NASA Technical Reports Server (NTRS)

Fleury, C.; Schmit, L. A., Jr.

1980-01-01

A user's guide is presented for ACCESS-3, a research oriented program which combines dual methods and a collection of approximation concepts to achieve excellent efficiency in structural synthesis. The finite element method is used for structural analysis and dual algorithms of mathematical programming are applied in the design optimization procedure. This program retains all of the ACCESS-2 capabilities and the data preparation formats are fully compatible. Four distinct optimizer options were added: interior point penalty function method (NEWSUMT); second order primal projection method (PRIMAL2); second order Newton-type dual method (DUAL2); and first order gradient projection-type dual method (DUAL1). A pure discrete and mixed continuous-discrete design variable capability, and zero order approximation of the stress constraints are also included.
The representation of semantic knowledge in a child with Williams syndrome.

PubMed

Robinson, Sally J; Temple, Christine M

2009-05-01

This study investigated whether there are distinct types of semantic knowledge with distinct representational bases during development. The representation of semantic knowledge in a teenage child (S.T.) with Williams syndrome was explored for the categories of animals, fruit, and vegetables, manipulable objects, and nonmanipulable objects. S.T.'s lexical stores were of a normal size but the volume of "sensory feature" semantic knowledge she generated in oral descriptions was reduced. In visual recognition decisions, S.T. made more false positives to nonitems than did controls. Although overall naming of pictures was unimpaired, S.T. exhibited a category-specific anomia for nonmanipulable objects and impaired naming of visual-feature descriptions of animals. S.T.'s performance was interpreted as reflecting the impaired integration of distinctive features from perceptual input, which may impact upon nonmanipulable objects to a greater extent than the other knowledge categories. Performance was used to inform adult-based models of semantic representation, with category structure proposed to emerge due to differing degrees of dependency upon underlying knowledge types, feature correlations, and the acquisition of information from modality-specific processing modules.
An Avian Basal Ganglia-Forebrain Circuit Contributes Differentially to Syllable Versus Sequence Variability of Adult Bengalese Finch Song

PubMed Central

Hampton, Cara M.; Sakata, Jon T.; Brainard, Michael S.

2009-01-01

Behavioral variability is important for motor skill learning but continues to be present and actively regulated even in well-learned behaviors. In adult songbirds, two types of song variability can persist and are modulated by social context: variability in syllable structure and variability in syllable sequencing. The degree to which the control of both types of adult variability is shared or distinct remains unknown. The output of a basal ganglia-forebrain circuit, LMAN (the lateral magnocellular nucleus of the anterior nidopallium), has been implicated in song variability. For example, in adult zebra finches, neurons in LMAN actively control the variability of syllable structure. It is unclear, however, whether LMAN contributes to variability in adult syllable sequencing because sequence variability in adult zebra finch song is minimal. In contrast, Bengalese finches retain variability in both syllable structure and syllable sequencing into adulthood. We analyzed the effects of LMAN lesions on the variability of syllable structure and sequencing and on the social modulation of these forms of variability in adult Bengalese finches. We found that lesions of LMAN significantly reduced the variability of syllable structure but not of syllable sequencing. We also found that LMAN lesions eliminated the social modulation of the variability of syllable structure but did not detect significant effects on the modulation of sequence variability. These results show that LMAN contributes differentially to syllable versus sequence variability of adult song and suggest that these forms of variability are regulated by distinct neural pathways. PMID:19357331
Nuclear networking.

PubMed

Xie, Wei; Burke, Brian

2017-07-04

Nuclear lamins are intermediate filament proteins that represent important structural components of metazoan nuclear envelopes (NEs). By combining proteomics and superresolution microscopy, we recently reported that both A- and B-type nuclear lamins form spatially distinct filament networks at the nuclear periphery of mouse fibroblasts. In particular, A-type lamins exhibit differential association with nuclear pore complexes (NPCs). Our studies reveal that the nuclear lamina network in mammalian somatic cells is less ordered and more complex than that of amphibian oocytes, the only other system in which the lamina has been visualized at high resolution. In addition, the NPC component Tpr likely links NPCs to the A-type lamin network, an association that appears to be regulated by C-terminal modification of various A-type lamin isoforms. Many questions remain, however, concerning the structure and assembly of lamin filaments, as well as with their mode of association with other nuclear components such as peripheral chromatin.
Multivariate soil fertility relationships for predicting the environmental persistence of 2,4,6-trinitrotoluene (TNT) and 1,3,5-trinitro-1,3,5-tricyclohexane (RDX) among taxonomically distinct soils.

PubMed

Katseanes, Chelsea K; Chappell, Mark A; Hopkins, Bryan G; Durham, Brian D; Price, Cynthia L; Porter, Beth E; Miller, Lesley F

2017-12-01

After nearly a century of use in numerous munition platforms, TNT and RDX contamination has turned up largely in the environment due to ammunition manufacturing or as part of releases from low-order detonations during training activities. Although the basic knowledge governing the environmental fate of TNT and RDX are known, accurate predictions of TNT and RDX persistence in soil remain elusive, particularly given the universal heterogeneity of pedomorphic soil types. In this work, we proposed overcoming this problem by considering the environmental persistence of these munition constituents (MC) as multivariate mathematical functions over a variety of taxonomically distinct soil types, instead of a single constant or parameter of a specific absolute value. To test this idea, we conducted experiments where the disappearance kinetics of TNT and RDX were measured over a >300 h period in taxonomically distinct soils. Classical fertility-based soil measurements were log-transformed, statistically decomposed, and correlated to TNT and RDX disappearance rates (k -TNT and k -RDX ) using multivariate dimension-reduction and correlation techniques. From these efforts, we generated multivariate linear functions for k parameters across different soil types based on a statistically reduced set of their chemical and physical properties: Calculations showed that the soil properties exhibited strong covariance, with a prominent latent structure emerging as the basis for relative comparisons of the samples in reduced space. Loadings describing TNT degradation were largely driven by properties associated with alkaline/calcareous soil characteristics, while the degradation of RDX was attributed to the soil organic matter content - reflective of an important soil fertility characteristic. In spite of the differing responses to the munitions, batch data suggested that the overall nutrient dynamics were consistent for each soil type, as well as readily distinguishable from the other soil types used in this study. Thus, we hypothesized that the latent structure arising from the strong covariance of full multivariate geochemical matrix describing taxonomically distinguished "soil types" may provide the means for potentially predicting complex phenomena in soils. Published by Elsevier Ltd.
Optical properties of graphene nanoflakes: Shape matters.

PubMed

Mansilla Wettstein, Candela; Bonafé, Franco P; Oviedo, M Belén; Sánchez, Cristián G

2016-06-14

In recent years there has been significant debate on whether the edge type of graphene nanoflakes (GNFs) or graphene quantum dots (GQDs) are relevant for their electronic structure, thermal stability, and optical properties. Using computer simulations, we have proven that there is a fundamental difference in the absorption spectra between samples of the same shape, similar size but different edge type, namely, armchair or zigzag edges. These can be explained by the presence of electronic structures near the Fermi level which are localized on the edges. These features are also evident from the dependence of band gap on the GNF size, which shows three very distinct trends for different shapes and edge geometries.
Optical properties of graphene nanoflakes: Shape matters

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

Mansilla Wettstein, Candela; Bonafé, Franco P.; Sánchez, Cristián G., E-mail: cgsanchez@fcq.unc.edu.ar

In recent years there has been significant debate on whether the edge type of graphene nanoflakes (GNFs) or graphene quantum dots (GQDs) are relevant for their electronic structure, thermal stability, and optical properties. Using computer simulations, we have proven that there is a fundamental difference in the absorption spectra between samples of the same shape, similar size but different edge type, namely, armchair or zigzag edges. These can be explained by the presence of electronic structures near the Fermi level which are localized on the edges. These features are also evident from the dependence of band gap on the GNFmore » size, which shows three very distinct trends for different shapes and edge geometries.« less
Persistent hydrogen bonding in polymorphic crystal structures.

PubMed

Galek, Peter T A; Fábián, László; Allen, Frank H

2009-02-01

The significance of hydrogen bonding and its variability in polymorphic crystal structures is explored using new automated structural analysis methods. The concept of a chemically equivalent hydrogen bond is defined, which may be identified in pairs of structures, revealing those types of bonds that may persist, or not, in moving from one polymorphic form to another. Their frequency and nature are investigated in 882 polymorphic structures from the Cambridge Structural Database. A new method to compare conformations of equivalent molecules is introduced and applied to derive distinct subsets of conformational and packing polymorphs. The roles of chemical functionality and hydrogen-bond geometry in persistent interactions are systematically explored. Detailed structural comparisons reveal a large majority of persistent hydrogen bonds that are energetically crucial to structural stability.
F-region enhancements induced by solar flares

NASA Technical Reports Server (NTRS)

Donnelly, R. F.; Davies, K.; Grubb, R. N.; Fritz, R. B.

1976-01-01

ATS-6 total electron content (NT) observations during solar flares exhibit four types of response: (1) a sudden increase in NT (SITEC) for about 2 min with several maxima in growth rate, then a maximum or a distinct slowing in growth, followed by a slow smooth increase to a flat peak, and finally a slow decay in NT; (2) a SITEC that occurs during ionospheric storms, where NT decays abruptly after the first maximum; (3) slow enhancements devoid of distinct impulsive structure in growth rate; and (4) no distinct response in NT, even for relatively large soft X-ray flares. Flare-induced increases in NT are dominated by low-loss F2 ionization produced by 90-911-A emission. The impulsive flare component is relatively intense in the 90-911-A range, but is short lived and weak for flares near the edge of the visible solar disk and for certain slow flares. The impulsive flare component produces the rapid rise, the sharp maxima in growth rate, and the first maximum in SITECs. The slow flare components are strong in the 1-90-A range but relatively weak in the 90-911-A range and accumulatively contribute to the second maximum in type 1 and 3 events, except during storms when F2 loss rates are abnormally high in type 2 events.
Habitat type and Permanence determine local aquatic invertebrate community structure in the Madrean Sky Islands

Treesearch

Michael T. Bogan; Oscar Gutierrez-Ruacho; J. Andres Alvarado-Castro; David A. Lytle

2013-01-01

Aquatic environments in the Madrean Sky Islands (MSI) consist of a matrix of perennial and intermittent stream segments, seasonal ponds, and human-built cattle trough habitats that support a diverse suite of aquatic macroinvertebrates. Although environmental conditions and aquatic communities are generally distinct in lotic and lentic habitats, MSI streams are...
Organizing for Change: A Case Study of Grassroots Leadership at a Kentucky Community College

ERIC Educational Resources Information Center

Borregard, Andrea Rae

2016-01-01

Community colleges constitute a special type of higher education organization: their complex mission, dynamics, personnel structures, and values require a distinct set of understandings and skills to lead and manage them well. Most of the research on leadership in community colleges focuses on leaders in positions of power (presidents, provosts,…
Structure of a human monoclonal antibody Fab fragment against gp41 of human immunodeficiency virus type

NASA Technical Reports Server (NTRS)

He, X. M.; Ruker, F.; Casale, E.; Carter, D. C.

1992-01-01

The three-dimensional structure of a human monoclonal antibody (Fab), which binds specifically to a major epitope of the transmembrane protein gp41 of the human immunodeficiency virus type 1, has been determined by crystallographic methods to a resolution of 2.7 A. It has been previously determined that this antibody recognizes the epitope SGKLICTTAVPWNAS, belongs to the subclass IgG1 (kappa), and exhibits antibody-dependent cellular cytotoxicity. The quaternary structure of the Fab is in an extended conformation with an elbow bend angle between the constant and variable domains of 175 degrees. Structurally, four of the hypervariable loops can be classified according to previously recognized canonical structures. The third hypervariable loops of the heavy (H3) and light chain (L3) are structurally distinct. Hypervariable loop H3, residues 102H-109H, is unusually extended from the surface. The complementarity-determining region forms a hydrophobic binding pocket that is created primarily from hypervariable loops L3, H3, and H2.
Structure of a human monoclonal antibody Fab fragment against gp41 of human immunodeficiency virus type 1

NASA Technical Reports Server (NTRS)

He, Xiao M.; Rueker, Florian; Casale, Elena; Carter, Daniel C.

1992-01-01

The three-dimensional structure of a human monoclonal antibody (Fab), which binds specifically to a major epitope of the transmembrane protein gp41 of the human immunodeficiency virus type 1, has been determined by crystallographic methods to a resolution of 2.7 A. It has been previously determined that this antibody recognizes the epitope SGKLICTTAVPWNAS, belongs to the subclass IgG1 (kappa), and exhibits antibody-dependent cellular cytotoxicity. The quaternary structure of the Fab is in an extended conformation with an elbow bend angle between the constant and variable domains of 175 deg. Structurally, four of the hypervariable loops can be classified according to previously recognized canonical structures. The third hypervariable loops of the heavy (H3) and light chain (L3) are structurally distinct. Hypervariable loop H3, residues 102H-109H, is unusually extended from the surface. The complementarity-determining region forms a hydrophobic binding pocket that is created primarily from hypervariable loops L3, H3, and H2.

Three Small-Receptive-Field Ganglion Cells in the Mouse Retina Are Distinctly Tuned to Size, Speed, and Object Motion

PubMed Central

Jacoby, Jason

2017-01-01

Retinal ganglion cells (RGCs) are frequently divided into functional types by their ability to extract and relay specific features from a visual scene, such as the capacity to discern local or global motion, direction of motion, stimulus orientation, contrast or uniformity, or the presence of large or small objects. Here we introduce three previously uncharacterized, nondirection-selective ON–OFF RGC types that represent a distinct set of feature detectors in the mouse retina. The three high-definition (HD) RGCs possess small receptive-field centers and strong surround suppression. They respond selectively to objects of specific sizes, speeds, and types of motion. We present comprehensive morphological characterization of the HD RGCs and physiological recordings of their light responses, receptive-field size and structure, and synaptic mechanisms of surround suppression. We also explore the similarities and differences between the HD RGCs and a well characterized RGC with a comparably small receptive field, the local edge detector, in response to moving objects and textures. We model populations of each RGC type to study how they differ in their performance tracking a moving object. These results, besides introducing three new RGC types that together constitute a substantial fraction of mouse RGCs, provide insights into the role of different circuits in shaping RGC receptive fields and establish a foundation for continued study of the mechanisms of surround suppression and the neural basis of motion detection. SIGNIFICANCE STATEMENT The output cells of the retina, retinal ganglion cells (RGCs), are a diverse group of ∼40 distinct neuron types that are often assigned “feature detection” profiles based on the specific aspects of the visual scene to which they respond. Here we describe, for the first time, morphological and physiological characterization of three new RGC types in the mouse retina, substantially augmenting our understanding of feature selectivity. Experiments and modeling show that while these three “high-definition” RGCs share certain receptive-field properties, they also have distinct tuning to the size, speed, and type of motion on the retina, enabling them to occupy different niches in stimulus space. PMID:28100743
Electron microscopy of intermediate filaments: teaming up with atomic force and confocal laser scanning microscopy.

PubMed

Kreplak, Laurent; Richter, Karsten; Aebi, Ueli; Herrmann, Harald

2008-01-01

Intermediate filaments (IFs) were originally discovered and defined by electron microscopy in myoblasts. In the following it was demonstrated and confirmed that they constitute, in addition to microtubules and microfilaments, a third independent, general filament system in the cytoplasm of most metazoan cells. In contrast to the other two systems, IFs are present in cells in two principally distinct cytoskeletal forms: (i) extended and free-running filament arrays in the cytoplasm that are integrated into the cytoskeleton by associated proteins of the plakin type; and (ii) a membrane- and chromatin-bound thin 'lamina' of a more or less regular network of interconnected filaments made from nuclear IF proteins, the lamins, which differ in several important structural aspects from cytoplasmic IF proteins. In man, more than 65 genes code for distinct IF proteins that are expressed during embryogenesis in various routes of differentiation in a tightly controlled manner. IF proteins exhibit rather limited sequence identity implying that the different types of IFs have distinct biochemical properties. Hence, to characterize the structural properties of the various IFs, in vitro assembly regimes have been developed in combination with different visualization methods such as transmission electron microscopy of fixed and negatively stained samples as well as methods that do not use staining such as scanning transmission electron microscopy (STEM) and cryoelectron microscopy as well as atomic force microscopy. Moreover, with the generation of both IF-type specific antibodies and chimeras of fluorescent proteins and IF proteins, it has become possible to investigate the subcellular organization of IFs by correlative fluorescence and electron microscopic methods. The combination of these powerful methods should help to further develop our understanding of nuclear architecture, in particular how nuclear subcompartments are organized and in which way lamins are involved.
Structuralism, Post-Structuralism, and Neo-Liberalism: Assessing Foucault's Legacy.

ERIC Educational Resources Information Center

Olssen, Mark

2003-01-01

Traces Foucault's distinctive commitment to "post-structuralism." Argues that under the influence of Nietzsche, Foucault's approach marks a distinct break with structuralism in several crucial aspects. What results is a materialist post-structuralism that is also distinctively different from the post-structuralism of Derrida, Lyotard,…
Vegetation-Associated Impacts on Arctic Tundra Bacterial and Microeukaryotic Communities

PubMed Central

Shi, Yu; Xiang, Xingjia; Shen, Congcong; Neufeld, Josh D.; Walker, Virginia K.

2014-01-01

The Arctic is experiencing rapid vegetation changes, such as shrub and tree line expansion, due to climate warming, as well as increased wetland variability due to hydrological changes associated with permafrost thawing. These changes are of global concern because changes in vegetation may increase tundra soil biogeochemical processes that would significantly enhance atmospheric CO2 concentrations. Predicting the latter will at least partly depend on knowing the structure, functional activities, and distributions of soil microbes among the vegetation types across Arctic landscapes. Here we investigated the bacterial and microeukaryotic community structures in soils from the four principal low Arctic tundra vegetation types: wet sedge, birch hummock, tall birch, and dry heath. Sequencing of rRNA gene fragments indicated that the wet sedge and tall birch communities differed significantly from each other and from those associated with the other two dominant vegetation types. Distinct microbial communities were associated with soil pH, ammonium concentration, carbon/nitrogen (C/N) ratio, and moisture content. In soils with similar moisture contents and pHs (excluding wet sedge), bacterial, fungal, and total eukaryotic communities were correlated with the ammonium concentration, dissolved organic nitrogen (DON) content, and C/N ratio. Operational taxonomic unit (OTU) richness, Faith's phylogenetic diversity, and the Shannon species-level index (H′) were generally lower in the tall birch soil than in soil from the other vegetation types, with pH being strongly correlated with bacterial richness and Faith's phylogenetic diversity. Together, these results suggest that Arctic soil feedback responses to climate change will be vegetation specific not just because of distinctive substrates and environmental characteristics but also, potentially, because of inherent differences in microbial community structure. PMID:25362064
Vegetation-associated impacts on arctic tundra bacterial and microeukaryotic communities.

PubMed

Shi, Yu; Xiang, Xingjia; Shen, Congcong; Chu, Haiyan; Neufeld, Josh D; Walker, Virginia K; Grogan, Paul

2015-01-01

The Arctic is experiencing rapid vegetation changes, such as shrub and tree line expansion, due to climate warming, as well as increased wetland variability due to hydrological changes associated with permafrost thawing. These changes are of global concern because changes in vegetation may increase tundra soil biogeochemical processes that would significantly enhance atmospheric CO2 concentrations. Predicting the latter will at least partly depend on knowing the structure, functional activities, and distributions of soil microbes among the vegetation types across Arctic landscapes. Here we investigated the bacterial and microeukaryotic community structures in soils from the four principal low Arctic tundra vegetation types: wet sedge, birch hummock, tall birch, and dry heath. Sequencing of rRNA gene fragments indicated that the wet sedge and tall birch communities differed significantly from each other and from those associated with the other two dominant vegetation types. Distinct microbial communities were associated with soil pH, ammonium concentration, carbon/nitrogen (C/N) ratio, and moisture content. In soils with similar moisture contents and pHs (excluding wet sedge), bacterial, fungal, and total eukaryotic communities were correlated with the ammonium concentration, dissolved organic nitrogen (DON) content, and C/N ratio. Operational taxonomic unit (OTU) richness, Faith's phylogenetic diversity, and the Shannon species-level index (H') were generally lower in the tall birch soil than in soil from the other vegetation types, with pH being strongly correlated with bacterial richness and Faith's phylogenetic diversity. Together, these results suggest that Arctic soil feedback responses to climate change will be vegetation specific not just because of distinctive substrates and environmental characteristics but also, potentially, because of inherent differences in microbial community structure. Copyright © 2015, American Society for Microbiology. All Rights Reserved.
Recapitulation of Ayurveda constitution types by machine learning of phenotypic traits.

PubMed

Tiwari, Pradeep; Kutum, Rintu; Sethi, Tavpritesh; Shrivastava, Ankita; Girase, Bhushan; Aggarwal, Shilpi; Patil, Rutuja; Agarwal, Dhiraj; Gautam, Pramod; Agrawal, Anurag; Dash, Debasis; Ghosh, Saurabh; Juvekar, Sanjay; Mukerji, Mitali; Prasher, Bhavana

2017-01-01

In Ayurveda system of medicine individuals are classified into seven constitution types, "Prakriti", for assessing disease susceptibility and drug responsiveness. Prakriti evaluation involves clinical examination including questions about physiological and behavioural traits. A need was felt to develop models for accurately predicting Prakriti classes that have been shown to exhibit molecular differences. The present study was carried out on data of phenotypic attributes in 147 healthy individuals of three extreme Prakriti types, from a genetically homogeneous population of Western India. Unsupervised and supervised machine learning approaches were used to infer inherent structure of the data, and for feature selection and building classification models for Prakriti respectively. These models were validated in a North Indian population. Unsupervised clustering led to emergence of three natural clusters corresponding to three extreme Prakriti classes. The supervised modelling approaches could classify individuals, with distinct Prakriti types, in the training and validation sets. This study is the first to demonstrate that Prakriti types are distinct verifiable clusters within a multidimensional space of multiple interrelated phenotypic traits. It also provides a computational framework for predicting Prakriti classes from phenotypic attributes. This approach may be useful in precision medicine for stratification of endophenotypes in healthy and diseased populations.
Point process models for localization and interdependence of punctate cellular structures.

PubMed

Li, Ying; Majarian, Timothy D; Naik, Armaghan W; Johnson, Gregory R; Murphy, Robert F

2016-07-01

Accurate representations of cellular organization for multiple eukaryotic cell types are required for creating predictive models of dynamic cellular function. To this end, we have previously developed the CellOrganizer platform, an open source system for generative modeling of cellular components from microscopy images. CellOrganizer models capture the inherent heterogeneity in the spatial distribution, size, and quantity of different components among a cell population. Furthermore, CellOrganizer can generate quantitatively realistic synthetic images that reflect the underlying cell population. A current focus of the project is to model the complex, interdependent nature of organelle localization. We built upon previous work on developing multiple non-parametric models of organelles or structures that show punctate patterns. The previous models described the relationships between the subcellular localization of puncta and the positions of cell and nuclear membranes and microtubules. We extend these models to consider the relationship to the endoplasmic reticulum (ER), and to consider the relationship between the positions of different puncta of the same type. Our results do not suggest that the punctate patterns we examined are dependent on ER position or inter- and intra-class proximity. With these results, we built classifiers to update previous assignments of proteins to one of 11 patterns in three distinct cell lines. Our generative models demonstrate the ability to construct statistically accurate representations of puncta localization from simple cellular markers in distinct cell types, capturing the complex phenomena of cellular structure interaction with little human input. This protocol represents a novel approach to vesicular protein annotation, a field that is often neglected in high-throughput microscopy. These results suggest that spatial point process models provide useful insight with respect to the spatial dependence between cellular structures. © 2016 International Society for Advancement of Cytometry. © 2016 International Society for Advancement of Cytometry.
New science in plain sight: Citizen scientists lead to the discovery of optical structure in the upper atmosphere.

PubMed

MacDonald, Elizabeth A; Donovan, Eric; Nishimura, Yukitoshi; Case, Nathan A; Gillies, D Megan; Gallardo-Lacourt, Bea; Archer, William E; Spanswick, Emma L; Bourassa, Notanee; Connors, Martin; Heavner, Matthew; Jackel, Brian; Kosar, Burcu; Knudsen, David J; Ratzlaff, Chris; Schofield, Ian

2018-03-01

A glowing ribbon of purple light running east-west in the night sky has recently been observed by citizen scientists. This narrow, subauroral, visible structure, distinct from the traditional auroral oval, was largely undocumented in the scientific literature and little was known about its formation. Amateur photo sequences showed colors distinctly different from common types of aurora and occasionally indicated magnetic field-aligned substructures. Observations from the Swarm satellite as it crossed the arc have revealed an unusual level of electron temperature enhancement and density depletion, along with a strong westward ion flow, indicating that a pronounced subauroral ion drift (SAID) is associated with this structure. These early results suggest the arc is an optical manifestation of SAID, presenting new opportunities for investigation of the dynamic SAID signatures from the ground. On the basis of the measured ion properties and original citizen science name, we propose to identify this arc as a Strong Thermal Emission Velocity Enhancement (STEVE).
Highlights on distinctive structural and functional properties of HTLV Tax proteins

PubMed Central

Romanelli, Maria Grazia; Diani, Erica; Bergamo, Elisa; Casoli, Claudio; Ciminale, Vincenzo; Bex, Françoise; Bertazzoni, Umberto

2013-01-01

Human T cell leukemia viruses (HTLVs) are complex human retroviruses of the Deltaretrovirus genus. Four types have been identified thus far, with HTLV-1 and HTLV-2 much more prevalent than HTLV-3 or HTLV-4. HTLV-1 and HTLV-2 possess strictly related genomic structures, but differ significantly in pathogenicity, as HTLV-1 is the causative agent of adult T cell leukemia and of HTLV-associated myelopathy/tropical spastic paraparesis, whereas HTLV-2 is not associated with neoplasia. HTLVs code for a protein named Tax that is responsible for enhancing viral expression and drives cell transformation. Much effort has been invested to dissect the impact of Tax on signal transduction pathways and to identify functional differences between the HTLV Tax proteins that may explain the distinct oncogenic potential of HTLV-1 and HTLV-2. This review summarizes our current knowledge of Tax-1 and Tax-2 with emphasis on their structure, role in activation of the NF-κB (nuclear factor kappa-B) pathway, and interactions with host factors. PMID:24058363
New science in plain sight: Citizen scientists lead to the discovery of optical structure in the upper atmosphere

PubMed Central

MacDonald, Elizabeth A.; Donovan, Eric; Nishimura, Yukitoshi; Case, Nathan A.; Gillies, D. Megan; Gallardo-Lacourt, Bea; Archer, William E.; Spanswick, Emma L.; Bourassa, Notanee; Connors, Martin; Heavner, Matthew; Jackel, Brian; Kosar, Burcu; Knudsen, David J.; Ratzlaff, Chris; Schofield, Ian

2018-01-01

A glowing ribbon of purple light running east-west in the night sky has recently been observed by citizen scientists. This narrow, subauroral, visible structure, distinct from the traditional auroral oval, was largely undocumented in the scientific literature and little was known about its formation. Amateur photo sequences showed colors distinctly different from common types of aurora and occasionally indicated magnetic field–aligned substructures. Observations from the Swarm satellite as it crossed the arc have revealed an unusual level of electron temperature enhancement and density depletion, along with a strong westward ion flow, indicating that a pronounced subauroral ion drift (SAID) is associated with this structure. These early results suggest the arc is an optical manifestation of SAID, presenting new opportunities for investigation of the dynamic SAID signatures from the ground. On the basis of the measured ion properties and original citizen science name, we propose to identify this arc as a Strong Thermal Emission Velocity Enhancement (STEVE). PMID:29546244
27 CFR 4.62 - Mandatory statements.

Code of Federal Regulations, 2010 CFR

2010-04-01

..., type, and distinctive designation. The advertisement shall contain a conspicuous statement of the class, type, or distinctive designation to which the product belongs, corresponding with the statement of class, type, or distinctive designation which is required to appear on the label of the product. (c...
Lysozymes in the animal kingdom.

PubMed

Callewaert, Lien; Michiels, Chris W

2010-03-01

Lysozymes (EC 3.2.1.17) are hydrolytic enzymes, characterized by their ability to cleave the beta-(1,4)-glycosidic bond between N-acetylmuramic acid and N-acetylglucosamine in peptidoglycan, the major bacterial cell wall polymer. In the animal kingdom, three major distinct lysozyme types have been identified--the c-type (chicken or conventional type), the g-type (goose-type) and the i-type (invertebrate type) lysozyme. Examination of the phylogenetic distribution of these lysozymes reveals that c-type lysozymes are predominantly present in the phylum of the Chordata and in different classes of the Arthropoda. Moreover, g-type lysozymes (or at least their corresponding genes) are found in members of the Chordata, as well as in some bivalve mollusks belonging to the invertebrates. In general, the latter animals are known to produce i-type lysozymes. Although the homology in primary structure for representatives of these three lysozyme types is limited, their three-dimensional structures show striking similarities. Nevertheless, some variation exists in their catalytic mechanisms and the genomic organization of their genes. Regarding their biological role, the widely recognized function of lysozymes is their contribution to antibacterial defence but, additionally, some lysozymes (belonging to different types) are known to function as digestive enzymes.
X-ray diffraction and spectroscopy study of nano-Eu 2O 3 structural transformation under high pressure

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

Yu, Zhenhai; Wang, Qinglin; Ma, Yanzhang

Nanoscale materials exhibit properties that are quite distinct from those of bulk materials because of their size restricted nature. Here, we investigated the high-pressure structural stability of cubic (C-type) nano-Eu2O3 using in situ synchrotron X-ray diffraction (XRD), Raman and luminescence spectroscopy, and impedance spectra techniques. Our high-pressure XRD experimental results revealed a pressure-induced structural phase transition in nano-Eu2O3 from the C-type phase (space group: Ia-3) to a hexagonal phase (A-type, space group: P-3m1). Our reported transition pressure (9.3 GPa) in nano-Eu2O3 is higher than that of the corresponding bulk-Eu2O3 (5.0 GPa), which is contrary to the preceding reported experimental result.more » After pressure release, the A-type phase of Eu2O3 transforms into a new monoclinic phase (B-type, space group: C2/m). Compared with bulk-Eu2O3, C-type and A-type nano-Eu2O3 exhibits a larger bulk modulus. Our Raman and luminescence findings and XRD data provide consistent evidence of a pressure-induced structural phase transition in nano-Eu2O3. To our knowledge, we have performed the first high-pressure impedance spectra investigation on nano-Eu2O3 to examine the effect of the structural phase transition on its transport properties. We propose that the resistance inflection exhibited at ~12 GPa results from the phase boundary between the C-type and A-type phases. Besides, we summarized and discussed the structural evolution process by the phase diagram of lanthanide sesquioxides (Ln2O3) under high pressure.« less
Structural and Developmental Disparity in the Tentacles of the Moon Jellyfish Aurelia sp.1

PubMed Central

Gold, David A.; Nakanishi, Nagayasu; Hensley, Nicholai M.; Cozzolino, Kira; Tabatabaee, Mariam; Martin, Michelle; Hartenstein, Volker; Jacobs, David K.

2015-01-01

Tentacles armed with stinging cells (cnidocytes) are a defining trait of the cnidarians, a phylum that includes sea anemones, corals, jellyfish, and hydras. While cnidarian tentacles are generally characterized as structures evolved for feeding and defense, significant variation exists between the tentacles of different species, and within the same species across different life stages and/or body regions. Such diversity suggests cryptic distinctions exist in tentacle function. In this paper, we use confocal and transmission electron microscopy to contrast the structure and development of tentacles in the moon jellyfish, Aurelia species 1. We show that polyp oral tentacles and medusa marginal tentacles display markedly different cellular and muscular architecture, as well as distinct patterns of cellular proliferation during growth. Many structural differences between these tentacle types may reflect biomechanical solutions to different feeding strategies, although further work would be required for a precise mechanistic understanding. However, differences in cell proliferation dynamics suggests that the two tentacle forms lack a conserved mechanism of development, challenging the textbook-notion that cnidarian tentacles can be homologized into a conserved bauplan. PMID:26241309
Structural and Developmental Disparity in the Tentacles of the Moon Jellyfish Aurelia sp.1.

PubMed

Gold, David A; Nakanishi, Nagayasu; Hensley, Nicholai M; Cozzolino, Kira; Tabatabaee, Mariam; Martin, Michelle; Hartenstein, Volker; Jacobs, David K

2015-01-01

Tentacles armed with stinging cells (cnidocytes) are a defining trait of the cnidarians, a phylum that includes sea anemones, corals, jellyfish, and hydras. While cnidarian tentacles are generally characterized as structures evolved for feeding and defense, significant variation exists between the tentacles of different species, and within the same species across different life stages and/or body regions. Such diversity suggests cryptic distinctions exist in tentacle function. In this paper, we use confocal and transmission electron microscopy to contrast the structure and development of tentacles in the moon jellyfish, Aurelia species 1. We show that polyp oral tentacles and medusa marginal tentacles display markedly different cellular and muscular architecture, as well as distinct patterns of cellular proliferation during growth. Many structural differences between these tentacle types may reflect biomechanical solutions to different feeding strategies, although further work would be required for a precise mechanistic understanding. However, differences in cell proliferation dynamics suggests that the two tentacle forms lack a conserved mechanism of development, challenging the textbook-notion that cnidarian tentacles can be homologized into a conserved bauplan.
Manipulating type-I and type-II Dirac polaritons in cavity-embedded honeycomb metasurfaces.

PubMed

Mann, Charlie-Ray; Sturges, Thomas J; Weick, Guillaume; Barnes, William L; Mariani, Eros

2018-06-06

Pseudorelativistic Dirac quasiparticles have emerged in a plethora of artificial graphene systems that mimic the underlying honeycomb symmetry of graphene. However, it is notoriously difficult to manipulate their properties without modifying the lattice structure. Here we theoretically investigate polaritons supported by honeycomb metasurfaces and, despite the trivial nature of the resonant elements, we unveil rich Dirac physics stemming from a non-trivial winding in the light-matter interaction. The metasurfaces simultaneously exhibit two distinct species of massless Dirac polaritons, namely type-I and type-II. By modifying only the photonic environment via an enclosing cavity, one can manipulate the location of the type-II Dirac points, leading to qualitatively different polariton phases. This enables one to alter the fundamental properties of the emergent Dirac polaritons while preserving the lattice structure-a unique scenario which has no analog in real or artificial graphene systems. Exploiting the photonic environment will thus give rise to unexplored Dirac physics at the subwavelength scale.
Cognitive foundations of organizational learning: re-introducing the distinction between declarative and non-declarative knowledge

PubMed Central

Kump, Barbara; Moskaliuk, Johannes; Cress, Ulrike; Kimmerle, Joachim

2015-01-01

Contemporary research into socio-cognitive foundations of organizational learning tends to disregard the distinction between declarative and non-declarative knowledge. By reviewing the literature from organizational learning research and cognitive psychology we explain that this distinction is crucial. We describe the foundations of organizational learning by referring to models that consider the interplay between individual and collective knowledge-related processes in organizations. We highlight the existence of a research gap resulting from the finding that these approaches have widely neglected the existence of different types of knowledge. We then elaborate on characteristics of declarative and non-declarative knowledge in general, consider organizations as structures of distributed cognition, and discuss the relationship between organizational knowledge and practice. Subsequently, we examine the role of declarative and non-declarative knowledge in the context of organizational learning. Here, we analyze (1) the cognitive and social mechanisms underlying the development of declarative and non-declarative knowledge within structures of distributed cognition; and (2) the relationship between alterations in declarative and non-declarative types of knowledge on the one hand and changes in organizational practice on the other. Concluding, we discuss implications of our analysis for organizational learning research. We explain how our integrative perspective may offer starting points for a refined understanding of the sub-processes involved in organizational learning and unlearning and may support a better understanding of practical problems related to organizational learning and change. PMID:26483739
Distinctive features of the microbiota associated with different forms of apical periodontitis

PubMed Central

Siqueira, José F.; Rôças, Isabela N.

2009-01-01

Microorganisms infecting the dental root canal system play an unequivocal role as causative agents of apical periodontitis. Although fungi, archaea, and viruses have been found in association with some forms of apical periodontitis, bacteria are the main microbial etiologic agents of this disease. Bacteria colonizing the root canal are usually organized in communities similar to biofilm structures. Culture and molecular biology technologies have demonstrated that the endodontic bacterial communities vary in species richness and abundance depending on the different types of infection and different forms of apical periodontitis. This review paper highlights the distinctive features of the endodontic microbiota associated with diverse clinical conditions. PMID:21523208
Diversity in the structure of electrocommunication signals within a genus of electric fish, Apteronotus.

PubMed

Dunlap, K D; Larkins-Ford, J

2003-02-01

Some gymnotiform electric fish modulate their electric organ discharge for intraspecific communication. In Apteronotus leptorhynchus, chirps are usually rapid (10-30 ms) modulations that are activated through non- N-methyl- d-aspartate (non-NMDA) glutamate receptors in the hindbrain pacemaker nucleus. Males produce longer chirp types than females and chirp at higher rates. In Apteronotus albifrons, chirp rate is sexually monomorphic, but chirp structure (change in frequency and amplitude during a chirp) was unknown. To better understand the neural regulation and evolution of chirping behavior, we compared chirp structure in these two species under identical stimulus regimes. A. albifrons, like A. leptorhynchus, produced distinct types of chirps that varied, in part, by frequency excursion. However, unlike in A. leptorhynchus, chirp types in A. albifrons varied little in duration, and chirps were all longer (70-200 ms) than those of A. leptorhynchus. Chirp type production was not sexually dimorphic in A. albifrons, but within two chirp types males produced longer chirps than females. We suggest that species differences in chirp duration might be attributable to differences in the relative proportions of fast-acting (non-NMDA) and slow-acting (NMDA) glutamate receptors in the pacemaker. Additionally, we map species difference onto a phylogeny and hypothesize an evolutionary sequence for the diversification of chirp structure.
Interactions of localized wave structures and dynamics in the defocusing coupled nonlinear Schrödinger equations.

PubMed

Zhang, Guoqiang; Yan, Zhenya; Wen, Xiao-Yong; Chen, Yong

2017-04-01

We investigate the defocusing coupled nonlinear Schrödinger equations from a 3×3 Lax pair. The Darboux transformations with the nonzero plane-wave solutions are presented to derive the newly localized wave solutions including dark-dark and bright-dark solitons, breather-breather solutions, and different types of new vector rogue wave solutions, as well as interactions between distinct types of localized wave solutions. Moreover, we analyze these solutions by means of parameters modulation. Finally, the perturbed wave propagations of some obtained solutions are explored by means of systematic simulations, which demonstrates that nearly stable and strongly unstable solutions. Our research results could constitute a significant contribution to explore the distinct nonlinear waves (e.g., dark solitons, breather solutions, and rogue wave solutions) dynamics of the coupled system in related fields such as nonlinear optics, plasma physics, oceanography, and Bose-Einstein condensates.

Job loss, human capital job feature, and work condition job feature as distinct job insecurity constructs.

PubMed

Blau, Gary; Tatum, Donna Surges; McCoy, Keith; Dobria, Lidia; Ward-Cook, Kory

2004-01-01

The projected growth of new technologies, increasing use of automation, and continued consolidation of health-related services suggest that continued study of job insecurity is needed for health care professionals. Using a sample of 178 medical technologists over a 5-year period, this study's findings extend earlier work by Blau and Sharp (2000) and suggest that job loss insecurity, human capital job feature insecurity, and work condition job feature insecurity are related but distinct types of job insecurity. A seven-item measure of job loss insecurity, a four-item measure of human capital job feature insecurity, and a four-item measure of work condition job feature insecurity were analyzed. Confirmatory factor analysis using a more heterogeneous sample of 447 working adults supported this three-factor structure. Using correlation and path analysis, different significant relationships of antecedent variables and subsequent organizational withdrawal cognitions to these three types of job insecurity were found.
Biogenetically inspired synthesis and skeletal diversification of indole alkaloids.

PubMed

Mizoguchi, Haruki; Oikawa, Hideaki; Oguri, Hiroki

2014-01-01

To access architecturally complex natural products, chemists usually devise a customized synthetic strategy for constructing a single target skeleton. In contrast, biosynthetic assembly lines often employ divergent intramolecular cyclizations of a polyunsaturated common intermediate to produce diverse arrays of scaffolds. With the aim of integrating such biogenetic strategies, we show the development of an artificial divergent assembly line generating unprecedented numbers of scaffold variations of terpenoid indole alkaloids. This approach not only allows practical access to multipotent intermediates, but also enables systematic diversification of skeletal, stereochemical and functional group properties without structural simplification of naturally occurring alkaloids. Three distinct modes of [4+2] cyclizations and two types of redox-mediated annulations provided divergent access to five skeletally distinct scaffolds involving iboga-, aspidosperma-, andranginine- and ngouniensine-type skeletons and a non-natural variant within six to nine steps from tryptamine. The efficiency of our approach was demonstrated by successful total syntheses of (±)-vincadifformine, (±)-andranginine and (-)-catharanthine.
Immersion in altered experience: An investigation of the relationship between absorption and psychopathology

PubMed Central

Rosen, Cherise; Jones, Nev; Chase, Kayla A.; Melbourne, Jennifer K.; Grossman, Linda S.; Sharma, Rajiv P.

2017-01-01

Understanding alterations in perceptual experiences as a component of the basic symptom structure of psychosis may improve early detection and the identification of subtle shifts that can precede symptom exacerbation. We explored the phenomenological construct of absorption and psychotic experiences in both clinical (bipolar psychosis and schizophrenia spectrum) and non-clinical participants. Participants with psychosis endorsed significantly higher absorption compared to the non-clinical group. Absorption was positively correlated with all types of hallucinations and multiple types of delusions. The analysis yielded two distinct cluster groups that demarcated a distinction along the continuum of self-disturbance: on characterized by attenuated ego boundaries and the other stable ego boundaries. The study suggests that absorption is a potentially important but under-researched component of psychosis that overlaps with, but is not identical to the more heavily theorized constructs of aberrant salience and hyperreflexivity. PMID:28219788
A new oxytelluride: Perovskite and CsCl intergrowth in Ba 3Yb 2O 5Te

DOE PAGES

Whalen, J. B.; Besara, T.; Vasquez, R.; ...

2013-04-27

The new oxytelluride Ba 3Yb 2O 5Te was obtained from an alkaline earth flux. Ba3Yb2O5Te crystallizes in the tetragonal space group P4/ mmm (#123), with a=4.3615(3) Å and c=11.7596(11) angstrom, Z=1. The structure combines two distinct building blocks, a Ba 2Yb 2O 5 perovskite-like double layer with square bipyramidal coordination of the ytterbium ions, and a CsCl-type BaTe layer. Short range magnetic order is apparent at below 5 K, with the magnetic behavior above this temperature dominated by crystal field effects. The structure may be considered as an analog to the Ruddlesden-Popper phases, where the NaCl-type layer has been replacedmore » by the CsCl-type layer. Finally, the two-dimensional magnetic behavior is expected based on the highly anisotropic nature of the structure.« less
Followers are not enough: a multifaceted approach to community detection in online social networks.

PubMed

Darmon, David; Omodei, Elisa; Garland, Joshua

2015-01-01

In online social media networks, individuals often have hundreds or even thousands of connections, which link these users not only to friends, associates, and colleagues, but also to news outlets, celebrities, and organizations. In these complex social networks, a 'community' as studied in the social network literature, can have very different meaning depending on the property of the network under study. Taking into account the multifaceted nature of these networks, we claim that community detection in online social networks should also be multifaceted in order to capture all of the different and valuable viewpoints of 'community.' In this paper we focus on three types of communities beyond follower-based structural communities: activity-based, topic-based, and interaction-based. We analyze a Twitter dataset using three different weightings of the structural network meant to highlight these three community types, and then infer the communities associated with these weightings. We show that interesting insights can be obtained about the complex community structure present in social networks by studying when and how these four community types give rise to similar as well as completely distinct community structure.
Crystal structure of the cytoplasmic phosphatase and tensin homolog (PTEN)-like region of Ciona intestinalis voltage-sensing phosphatase provides insight into substrate specificity and redox regulation of the phosphoinositide phosphatase activity.

PubMed

Matsuda, Makoto; Takeshita, Kohei; Kurokawa, Tatsuki; Sakata, Souhei; Suzuki, Mamoru; Yamashita, Eiki; Okamura, Yasushi; Nakagawa, Atsushi

2011-07-01

Ciona intestinalis voltage-sensing phosphatase (Ci-VSP) has a transmembrane voltage sensor domain and a cytoplasmic region sharing similarity to the phosphatase and tensin homolog (PTEN). It dephosphorylates phosphatidylinositol 4,5-bisphosphate and phosphatidylinositol 3,4,5-trisphosphate upon membrane depolarization. The cytoplasmic region is composed of a phosphatase domain and a putative membrane interaction domain, C2. Here we determined the crystal structures of the Ci-VSP cytoplasmic region in three distinct constructs, wild-type (248-576), wild-type (236-576), and G365A mutant (248-576). The crystal structure of WT-236 and G365A-248 had the disulfide bond between the catalytic residue Cys-363 and the adjacent residue Cys-310. On the other hand, the disulfide bond was not present in the crystal structure of WT-248. These suggest the possibility that Ci-VSP is regulated by reactive oxygen species as found in PTEN. These structures also revealed that the conformation of the TI loop in the active site of the Ci-VSP cytoplasmic region was distinct from the corresponding region of PTEN; Ci-VSP has glutamic acid (Glu-411) in the TI loop, orienting toward the center of active site pocket. Mutation of Glu-411 led to acquirement of increased activity toward phosphatidylinositol 3,5-bisphosphate, suggesting that this site is required for determining substrate specificity. Our results provide the basic information of the enzymatic mechanism of Ci-VSP.
Natural Microbial Assemblages Reflect Distinct Organismal and Functional Partitioning

NASA Astrophysics Data System (ADS)

Wilmes, P.; Andersson, A.; Kalnejais, L. H.; Verberkmoes, N. C.; Lefsrud, M. G.; Wexler, M.; Singer, S. W.; Shah, M.; Bond, P. L.; Thelen, M. P.; Hettich, R. L.; Banfield, J. F.

2007-12-01

The ability to link microbial community structure to function has long been a primary focus of environmental microbiology. With the advent of community genomic and proteomic techniques, along with advances in microscopic imaging techniques, it is now possible to gain insights into the organismal and functional makeup of microbial communities. Biofilms growing within highly acidic solutions inside the Richmond Mine (Iron Mountain, Redding, California) exhibit distinct macro- and microscopic morphologies. They are composed of microorganisms belonging to the three domains of life, including archaea, bacteria and eukarya. The proportion of each organismal type depends on sampling location and developmental stage. For example, mature biofilms floating on top of acid mine drainage (AMD) pools exhibit layers consisting of a densely packed bottom layer of the chemoautolithotroph Leptospirillum group II, a less dense top layer composed mainly of archaea, and fungal filaments spanning across the entire biofilm. The expression of cytochrome 579 (the most highly abundant protein in the biofilm, believed to be central to iron oxidation and encoded by Leptospirillum group II) is localized at the interface of the biofilm with the AMD solution, highlighting that biofilm architecture is reflected at the functional gene expression level. Distinct functional partitioning is also apparent in a biological wastewater treatment system that selects for distinct polyphosphate accumulating organisms. Community genomic data from " Candidatus Accumulibacter phosphatis" dominated activated sludge has enabled high mass-accuracy shotgun proteomics for identification of key metabolic pathways. Comprehensive genome-wide alignment of orthologous proteins suggests distinct partitioning of protein variants involved in both core-metabolism and specific metabolic pathways among the dominant population and closely related species. In addition, strain- resolved proteogenomic analysis of the AMD biofilms also highlights the importance of strain heterogeneity for the maintenance of community structure and function. These findings explain the importance of genetic diversity in facilitating the stable performance of complex microbial processes. Furthermore, although very different in terms of habitat, both microbial communities exhibit distinct functional compartmentalization and demonstrate its role in sustaining microbial community structure.
MC carbide structures in M(lc2)ar-M247. M.S. Thesis - Final Report

NASA Technical Reports Server (NTRS)

Wawro, S. W.

1982-01-01

The morphologies and distribution of the MC carbides in Mar-M247 ingot stock and castings were investigated using metallographic, X-ray diffraction and energy-dispersive X-ray analysis techniques. The MC carbides were found to form script structures during solidification. The script structures were composed of three distinct parts. The central cores and elongated arms of the MC carbide script structures had compositions (Ti, Cr, Hf, Ta, W)C and lattice parameters of 4.39 A. The elongated script arms terminated in enlarged, angular "heads". The heads had compositions (Ti, Hf, Ta, W)C and lattice parameters of approximately 4.50 A. The heads had a higher Hf content than the cores and arms. The size of the script structures, as well as the relative amount of head-type to core and arm-type MC carbide, was found to be determined by solidification conditions. No carryover of the MC carbides from the ingot stock to the remelted and cast material was observed.
Characterization and Structural Analysis of a Novel exo-Type Enzyme Acting on β-1,2-Glucooligosaccharides from Parabacteroides distasonis.

PubMed

Shimizu, Hisaka; Nakajima, Masahiro; Miyanaga, Akimasa; Takahashi, Yuta; Tanaka, Nobukiyo; Kobayashi, Kaito; Sugimoto, Naohisa; Nakai, Hiroyuki; Taguchi, Hayao

2018-05-25

β-1,2-Glucan is a polysaccharide produced mainly by some Gram-negative bacteria as a symbiosis and infectious factor. We recently identified endo-β-1,2-glucanase from Chitinophaga pinensis ( CpSGL) as an enzyme comprising a new family. Here, we report the characteristics and crystal structure of a CpSGL homologue from Parabacteroides distasonis, an intestinal bacterium (BDI_3064 protein), which exhibits distinctive properties of known β-1,2-glucan-degrading enzymes. BDI_3064 hydrolyzed linear β-1,2-glucan and β-1,2-glucooligosaccharides with degrees of polymerization (DPs) of ≥4 to produce sophorose specifically but did not hydrolyze cyclic β-1,2-glucan. This result indicates that BDI_3064 is a new exo-type enzyme. BDI_3064 also produced sophorose from β-1,2-glucooligosaccharide analogues that have a modified reducing end, indicating that BDI_3064 acts on its substrates from the nonreducing end. The crystal structure showed that BDI_3064 possesses additional N-terminal domains 1 and 2, unlike CpSGL. Superimposition of BDI_3064 and CpSGL complexed with ligands showed that R93 in domain 1 overlapped subsite -3 in CpSGL. Docking analysis involving a β-1,2-glucooligosaccharide with DP4 showed that R93 completely blocks the nonreducing end of the docked β-1,2-glucooligosaccharide. This indicates that BDI_3064 employs a distinct mechanism of recognition at the nonreducing end of substrates to act as an exo-type enzyme. Thus, we propose 2-β-d-glucooligosaccharide sophorohydrolase (nonreducing end) as a systematic name for BDI_3064.
Staphylococcus aureus β-Toxin Mutants Are Defective in Biofilm Ligase and Sphingomyelinase Activity, and Causation of Infective Endocarditis and Sepsis.

PubMed

Herrera, Alfa; Vu, Bao G; Stach, Christopher S; Merriman, Joseph A; Horswill, Alexander R; Salgado-Pabón, Wilmara; Schlievert, Patrick M

2016-05-03

β-Toxin is an important virulence factor of Staphylococcus aureus, contributing to colonization and development of disease [Salgado-Pabon, W., et al. (2014) J. Infect. Dis. 210, 784-792; Huseby, M. J., et al. (2010) Proc. Natl. Acad. Sci. U.S.A. 107, 14407-14412; Katayama, Y., et al. (2013) J. Bacteriol. 195, 1194-1203]. This cytotoxin has two distinct mechanisms of action: sphingomyelinase activity and DNA biofilm ligase activity. However, the distinct mechanism that is most important for its role in infective endocarditis is unknown. We characterized the active site of β-toxin DNA biofilm ligase activity by examining deficiencies in site-directed mutants through in vitro DNA precipitation and biofilm formation assays. Possible conformational changes in mutant structure compared to that of wild-type toxin were assessed preliminarily by trypsin digestion analysis, retention of sphingomyelinase activity, and predicted structures based on the native toxin structure. We addressed the contribution of each mechanism of action to producing infective endocarditis and sepsis in vivo in a rabbit model. The H289N β-toxin mutant, lacking sphingomyelinase activity, exhibited lower sepsis lethality and infective endocarditis vegetation formation compared to those of the wild-type toxin. β-Toxin mutants with disrupted biofilm ligase activity did not exhibit decreased sepsis lethality but were deficient in infective endocarditis vegetation formation compared to the wild-type protein. Our study begins to characterize the DNA biofilm ligase active site of β-toxin and suggests β-toxin functions importantly in infective endocarditis through both of its mechanisms of action.
Book Lovers, Technophiles, Pragmatists, and Printers: The Social and Demographic Structure of User Attitudes toward E-Books

ERIC Educational Resources Information Center

Revelle, Andy; Messner, Kevin; Shrimplin, Aaron; Hurst, Susan

2012-01-01

Q-methodology was used to identify clusters of opinions about e-books at Miami University. The research identified four distinct opinion types among those investigated: Book Lovers, Technophiles, Pragmatists, and Printers. The initial Q-methodology study results were then used as a basis for a large-n survey of undergraduates, graduate students,…
The Concept of Openness behind c- and x-MOOCs (Massive Open Online Courses)

ERIC Educational Resources Information Center

Rodriguez, Osvaldo

2013-01-01

The last five years have witnessed a hype about MOOCs (Massive Open Online Courses) presaging a revolution in higher education. Although all MOOCs have in common their scale and free access, they have already bifurcated in two very distinct types of courses when compared in terms of their underpinning theory, format and structure, known as c-MOOCs…
Structural, electronic and magnetic properties of chevron-type graphene, BN and BC{sub 2}N nanoribbons

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

Guerra, T.; Azevedo, S.; Kaschny, J.R.

2017-04-15

Graphene nanoribbons are predicted to be essential components in future nanoelectronics. The size, edge type, arrangement of atoms and width of nanoribbons drastically change their properties. Boronnitrogencarbon nanoribbons properties are not fully understood so far. In the present contribution it was investigated the structural, electronic and magnetic properties of chevron-type carbon, boron nitride and BC{sub 2}N nanoribbons, using first-principles calculations. The results indicate that the structural stability is closely related to the discrepancies in the bond lengths, which can induce structural deformations and stress. Such nanoribbons present a wide range of electronic behaviors, depending on their composition and particularities ofmore » the atomic arrangement. A net magnetic moment is found for structures that present carbon atoms at the nanoribbon borders. Nevertheless, the calculated magnetic moment depends on the peculiarities of the symmetric arrangement of atoms and imbalance of carbon atoms between different sublattices. It was found that all structures which have a significant energy gap do not present magnetic moment, and vice-versa. Such result indicates the strong correlation between the electronic and magnetic properties of the chevron-type nanoribbons. - Highlights: • Small discrepancies between distinct bond lengths can influence the formation energy of the BC{sub 2}N nanoribbons. • The electronic behavior of the BC{sub 2}N chevron-type nanoribbons depends on the atomic arrangement and structural symmetries. • There is a strong correlation between the electronic and magnetic properties for the BC{sub 2}N structures.« less
Effects of the amino acid sequence on thermal conduction through β-sheet crystals of natural silk protein.

PubMed

Zhang, Lin; Bai, Zhitong; Ban, Heng; Liu, Ling

2015-11-21

Recent experiments have discovered very different thermal conductivities between the spider silk and the silkworm silk. Decoding the molecular mechanisms underpinning the distinct thermal properties may guide the rational design of synthetic silk materials and other biomaterials for multifunctionality and tunable properties. However, such an understanding is lacking, mainly due to the complex structure and phonon physics associated with the silk materials. Here, using non-equilibrium molecular dynamics, we demonstrate that the amino acid sequence plays a key role in the thermal conduction process through β-sheets, essential building blocks of natural silks and a variety of other biomaterials. Three representative β-sheet types, i.e. poly-A, poly-(GA), and poly-G, are shown to have distinct structural features and phonon dynamics leading to different thermal conductivities. A fundamental understanding of the sequence effects may stimulate the design and engineering of polymers and biopolymers for desired thermal properties.
Structural reducibility of multilayer networks

NASA Astrophysics Data System (ADS)

de Domenico, Manlio; Nicosia, Vincenzo; Arenas, Alexandre; Latora, Vito

2015-04-01

Many complex systems can be represented as networks consisting of distinct types of interactions, which can be categorized as links belonging to different layers. For example, a good description of the full protein-protein interactome requires, for some organisms, up to seven distinct network layers, accounting for different genetic and physical interactions, each containing thousands of protein-protein relationships. A fundamental open question is then how many layers are indeed necessary to accurately represent the structure of a multilayered complex system. Here we introduce a method based on quantum theory to reduce the number of layers to a minimum while maximizing the distinguishability between the multilayer network and the corresponding aggregated graph. We validate our approach on synthetic benchmarks and we show that the number of informative layers in some real multilayer networks of protein-genetic interactions, social, economical and transportation systems can be reduced by up to 75%.
Multivariate functions for predicting the sorption of 2,4,6-trinitrotoluene (TNT) and 1,3,5-trinitro-1,3,5-tricyclohexane (RDX) among taxonomically distinct soils.

PubMed

Katseanes, Chelsea K; Chappell, Mark A; Hopkins, Bryan G; Durham, Brian D; Price, Cynthia L; Porter, Beth E; Miller, Lesley F

2016-11-01

After nearly a century of use in numerous munition platforms, TNT and RDX contamination has turned up largely in the environment due to ammunition manufacturing or as part of releases from low-order detonations during training activities. Although the basic knowledge governing the environmental fate of TNT and RDX are known, accurate predictions of TNT and RDX persistence in soil remain elusive, particularly given the universal heterogeneity of pedomorphic soil types. In this work, we proposed a new solution for modeling the sorption and persistence of these munition constituents as multivariate mathematical functions correlating soil attribute data over a variety of taxonomically distinct soil types to contaminant behavior, instead of a single constant or parameter of a specific absolute value. To test this idea, we conducted experiments measuring the sorption of TNT and RDX on taxonomically different soil types that were extensively physical and chemically characterized. Statistical decomposition of the log-transformed, and auto-scaled soil characterization data using the dimension-reduction technique PCA (principal component analysis) revealed a strong latent structure based in the multiple pairwise correlations among the soil properties. TNT and RDX sorption partitioning coefficients (KD-TNT and KD-RDX) were regressed against this latent structure using partial least squares regression (PLSR), generating a 3-factor, multivariate linear functions. Here, PLSR models predicted KD-TNT and KD-RDX values based on attributes contributing to endogenous alkaline/calcareous and soil fertility criteria, respectively, exhibited among the different soil types: We hypothesized that the latent structure arising from the strong covariance of full multivariate geochemical matrix describing taxonomically distinguished soil types may provide the means for potentially predicting complex phenomena in soils. The development of predictive multivariate models tuned to a local soil's taxonomic designation would have direct benefit to military range managers seeking to anticipate the environmental risks of training activities on impact sites. Published by Elsevier Ltd.
Meteor stream activity. 2: Meteor outbursts

NASA Technical Reports Server (NTRS)

Jenniskens, P.

1995-01-01

In the past two centuries, alert amateur and professional meteor astronomers have documented 35 outbursts of 17 individual meteor streams well enough to allow the construction of a homogeneous set of activity curves. These curves add to similar profiles of the annual streams in a previous paper (Paper 1). This paper attempts to define the type and range of phenomena that classify as meteor outbursts from which the following is concluded: Outbursts are associated with the return of the comet to perihelion (near-comet type outbursts), but occur also when the parent comet is far from perihelion and far from the Earth (far-comet type). All outbursts of a given type only, depending on encounter geometry. The activity curves, expressed in terms of Zenith Hourly Rates (ZHR), have a shape that is generally well described by: ZHR = ZHR(sub max) 10(sup(-B (the absolute value of lambda (sub dot in a circle) - lambda (sup max) (sub dot in a circle))). The steepness of the slopes varies from an exponent of B = 7 to B = 220 per degree of solar longitude, with a typical value of B = 30. In addition, most near-comet type outbursts have a broader component underlying the main peak with B approximately 1 - 7.The duration Delta t is approximately 1/B of the main peak is almost independent of location near the comet, while the background component varies considerably in duration and relative intensity from one return to another. The two components in the activity curve are due to two distinct structures in the dust distribution near the parent comet, where the main component can be due to a sheet of dust that emanates from the IRAS dust trail. This brings the total number of distinct structures in meteor streams to four, including the two structures from the annual stream activity in Paper 1.
Atomic Structure of Type VI Contractile Sheath from Pseudomonas aeruginosa.

PubMed

Salih, Osman; He, Shaoda; Planamente, Sara; Stach, Lasse; MacDonald, James T; Manoli, Eleni; Scheres, Sjors H W; Filloux, Alain; Freemont, Paul S

2018-02-06

Pseudomonas aeruginosa has three type VI secretion systems (T6SSs), H1-, H2-, and H3-T6SS, each belonging to a distinct group. The two T6SS components, TssB/VipA and TssC/VipB, assemble to form tubules that conserve structural/functional homology with tail sheaths of contractile bacteriophages and pyocins. Here, we used cryoelectron microscopy to solve the structure of the H1-T6SS P. aeruginosa TssB1C1 sheath at 3.3 Å resolution. Our structure allowed us to resolve some features of the T6SS sheath that were not resolved in the Vibrio cholerae VipAB and Francisella tularensis IglAB structures. Comparison with sheath structures from other contractile machines, including T4 phage and R-type pyocins, provides a better understanding of how these systems have conserved similar functions/mechanisms despite evolution. We used the P. aeruginosa R2 pyocin as a structural template to build an atomic model of the TssB1C1 sheath in its extended conformation, allowing us to propose a coiled-spring-like mechanism for T6SS sheath contraction. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.
The shells of BMC-type microcompartment organelles in bacteria.

PubMed

Yeates, Todd O; Jorda, Julien; Bobik, Thomas A

2013-01-01

Bacterial microcompartments are large proteinaceous structures that act as metabolic organelles in many bacterial cells. A shell or capsid, which is composed of a few thousand protein subunits, surrounds a series of sequentially acting enzymes and controls the diffusion of substrates and products into and out of the lumen. The carboxysome and the propanediol utilization microcompartment represent two well-studied systems among seven or more distinct types that can be delineated presently. Recent structural studies have highlighted a number of sophisticated mechanisms that underlie the function of bacterial microcompartment shell proteins. This review updates our understanding of bacterial microcompartment shells, how they are assembled, and how they carry out their functions in molecular transport and enzyme organization. Copyright © 2013 S. Karger AG, Basel.
Crystal structure of tetrawickmanite, Mn2+Sn4+(OH)6

PubMed Central

Lafuente, Barbara; Yang, Hexiong; Downs, Robert T.

2015-01-01

The crystal structure of tetrawickmanite, ideally Mn2+Sn4+(OH)6 [manganese(II) tin(IV) hexahydroxide], has been determined based on single-crystal X-ray diffraction data collected from a natural sample from Långban, Sweden. Tetrawickmanite belongs to the octahedral-framework group of hydroxide-perovskite minerals, described by the general formula BB’(OH)6 with a perovskite derivative structure. The structure differs from that of an ABO3 perovskite in that the A site is empty while each O atom is bonded to an H atom. The perovskite B-type cations split into ordered B and B′ sites, which are occupied by Mn2+ and Sn4+, respectively. Tetrawickmanite exhibits tetragonal symmetry and is topologically similar to its cubic polymorph, wickmanite. The tetrawickmanite structure is characterized by a framework of alternating corner-linked [Mn2+(OH)6] and [Sn4+(OH)6] octahedra, both with point-group symmetry -1. Four of the five distinct H atoms in the structure are statistically disordered. The vacant A site is in a cavity in the centre of a distorted cube formed by eight octahedra at the corners. However, the hydrogen-atom positions and their hydrogen bonds are not equivalent in every cavity, resulting in two distinct environments. One of the cavities contains a ring of four hydrogen bonds, similar to that found in wickmanite, while the other cavity is more distorted and forms crankshaft-type chains of hydrogen bonds, as previously proposed for tetragonal stottite, Fe2+Ge4+(OH)6. PMID:25878828

Bacteria use type IV pili to walk upright and detach from surfaces.

PubMed

Gibiansky, Maxsim L; Conrad, Jacinta C; Jin, Fan; Gordon, Vernita D; Motto, Dominick A; Mathewson, Margie A; Stopka, Wiktor G; Zelasko, Daria C; Shrout, Joshua D; Wong, Gerard C L

2010-10-08

Bacterial biofilms are structured multicellular communities involved in a broad range of infections. Knowing how free-swimming bacteria adapt their motility mechanisms near surfaces is crucial for understanding the transition between planktonic and biofilm phenotypes. By translating microscopy movies into searchable databases of bacterial behavior, we identified fundamental type IV pili-driven mechanisms for Pseudomonas aeruginosa surface motility involved in distinct foraging strategies. Bacteria stood upright and "walked" with trajectories optimized for two-dimensional surface exploration. Vertical orientation facilitated surface detachment and could influence biofilm morphology.
Structure change of β-hairpin induced by turn optimization: an enhanced sampling molecular dynamics simulation study.

PubMed

Shao, Qiang; Yang, Lijiang; Gao, Yi Qin

2011-12-21

Our previous study showed that for the tested polypeptides which have similar β-hairpin structures but different sequences, their folding free energy pathways are dominantly determined by the turn conformational propensity. In this study, we study how the turn conformational propensity affects the structure of hairpins. The folding of two mutants of GB1p peptide (GB1m2 and GB1m3), which have the optimized turn sequence ((6)DDATK(11)T → (6)NPATG(11)K) with native structures unsolved, were simulated using integrated tempering sampling molecular dynamics simulations and the predicted stable structures were compared to wild-type GB1p. It was observed that the turn optimization of GB1p generates a more favored 5-residue type I(') turn in addition to the 6-residue type I turn in wild-type GB1p. As a result two distinctly different hairpin structures are formed corresponding to the "misfolded" (M) and the "folded" (F) states. M state is a one-residue-shifted asymmetric β-hairpin structure whereas F state has the similar symmetric hairpin structure as wild-type GB1p. The formation of the favored type I(') turn has a small free energy barrier and leads to the shifted β-hairpin structure, following the modified "zipping" model. The presence of disfavored type I turn structure makes the folding of a β-hairpin consistent with the "hydrophobic-core-centric" model. On the other hand, the folding simulations on other two GB1p mutants (GB1r1 and GBr2), which have the position of the hydrophobic core cluster further away from the turn compared to wild-type GB1p, showed that moving the hydrophobic core cluster away from the turn region destabilizes but does not change the hairpin structure. Therefore, the present study showed that the turn conformational propensity is a key factor in affecting not only the folding pathways but also the stable structure of β-hairpins, and the turn conformational change induced by the turn optimization leads to significant changes of β-hairpin structure.
Polymer ligand–induced autonomous sorting and reversible phase separation in binary particle blends

DOE PAGES

Schmitt, Michael; Zhang, Jianan; Lee, Jaejun; ...

2016-12-23

The tethering of ligands to nanoparticles has emerged as an important strategy to control interactions and organization in particle assembly structures. Here, we demonstrate that ligand interactions in mixtures of polymer-tethered nanoparticles (which are modified with distinct types of polymer chains) can impart upper or lower critical solution temperature (UCST/LCST)–type phase behavior on binary particle mixtures in analogy to the phase behavior of the corresponding linear polymer blends. Therefore, cooling (or heating) of polymer-tethered particle blends with appropriate architecture to temperatures below (or above) the UCST (or LCST) results in the organization of the individual particle constituents into monotype microdomainmore » structures. The shape (bicontinuous or island-type) and lengthscale of particle microdomains can be tuned by variation of the composition and thermal process conditions. Thermal cycling of LCST particle brush blends through the critical temperature enables the reversible growth and dissolution of monoparticle domain structures. The ability to autonomously and reversibly organize multicomponent particle mixtures into monotype microdomain structures could enable transformative advances in the high-throughput fabrication of solid films with tailored and mutable structures and properties that play an important role in a range of nanoparticle-based material technologies.« less
Polymer ligand–induced autonomous sorting and reversible phase separation in binary particle blends

PubMed Central

Schmitt, Michael; Zhang, Jianan; Lee, Jaejun; Lee, Bongjoon; Ning, Xin; Zhang, Ren; Karim, Alamgir; Davis, Robert F.; Matyjaszewski, Krzysztof; Bockstaller, Michael R.

2016-01-01

The tethering of ligands to nanoparticles has emerged as an important strategy to control interactions and organization in particle assembly structures. We demonstrate that ligand interactions in mixtures of polymer-tethered nanoparticles (which are modified with distinct types of polymer chains) can impart upper or lower critical solution temperature (UCST/LCST)–type phase behavior on binary particle mixtures in analogy to the phase behavior of the corresponding linear polymer blends. Therefore, cooling (or heating) of polymer-tethered particle blends with appropriate architecture to temperatures below (or above) the UCST (or LCST) results in the organization of the individual particle constituents into monotype microdomain structures. The shape (bicontinuous or island-type) and lengthscale of particle microdomains can be tuned by variation of the composition and thermal process conditions. Thermal cycling of LCST particle brush blends through the critical temperature enables the reversible growth and dissolution of monoparticle domain structures. The ability to autonomously and reversibly organize multicomponent particle mixtures into monotype microdomain structures could enable transformative advances in the high-throughput fabrication of solid films with tailored and mutable structures and properties that play an important role in a range of nanoparticle-based material technologies. PMID:28028538
Structure of human POFUT2: insights into thrombospondin type 1 repeat fold and O-fucosylation

PubMed Central

Chen, Chun-I; Keusch, Jeremy J; Klein, Dominique; Hess, Daniel; Hofsteenge, Jan; Gut, Heinz

2012-01-01

Protein O-fucosylation is a post-translational modification found on serine/threonine residues of thrombospondin type 1 repeats (TSR). The fucose transfer is catalysed by the enzyme protein O-fucosyltransferase 2 (POFUT2) and >40 human proteins contain the TSR consensus sequence for POFUT2-dependent fucosylation. To better understand O-fucosylation on TSR, we carried out a structural and functional analysis of human POFUT2 and its TSR substrate. Crystal structures of POFUT2 reveal a variation of the classical GT-B fold and identify sugar donor and TSR acceptor binding sites. Structural findings are correlated with steady-state kinetic measurements of wild-type and mutant POFUT2 and TSR and give insight into the catalytic mechanism and substrate specificity. By using an artificial mini-TSR substrate, we show that specificity is not primarily encoded in the TSR protein sequence but rather in the unusual 3D structure of a small part of the TSR. Our findings uncover that recognition of distinct conserved 3D fold motifs can be used as a mechanism to achieve substrate specificity by enzymes modifying completely folded proteins of very wide sequence diversity and biological function. PMID:22588082
Crystallization and preliminary X-ray diffraction analysis of the two distinct types of zebrafish β2-microglobulin

PubMed Central

Chen, Zhaosan; Zhang, Nianzhi; Lu, Shuangshuang; Tariq, Mansoor; Wang, Junya; Xia, Chun

2015-01-01

β2-Microglobulin (β2m) noncovalently associates with the heavy chain of major histocompatibility complex class I (MHC I) molecules, which bind foreign antigen peptides to control the cytotoxic T lymphocyte (CTL) immune response. In contrast to mammals, there are distinct types of β2ms derived from two loci in a number of teleost species. In order to clarify the structures of the β2ms, the zebrafish (Danio rerio) β2ms Dare-β2m-I and Dare-β2m-II were expressed in Escherichia coli, purified and crystallized, and diffraction data were collected to 1.6 and 1.9 Å resolution, respectively. Both crystals belonged to space group P212121. The unit-cell parameters were determined to be a = 38.2, b = 50.4, c = 50.9 Å for Dare-β2m-I and a = 38.9, b = 52.7, c = 65.8 Å for Dare-β2m-II. Each asymmetric unit was constituted of one molecule, with Matthews coefficients of 2.22 and 3.01 Å3 Da−1 and solvent contents of 45 and 59% for Dare-β2m-I and Dare-β2m-II, respectively. These two β2m structures will provide relevant information for further studies of the structures of the MHC I complex. PMID:26057815
Mineral Ecology: Surface Specific Colonization and Geochemical Drivers of Biofilm Accumulation, Composition, and Phylogeny

PubMed Central

Jones, Aaron A.; Bennett, Philip C.

2017-01-01

This study tests the hypothesis that surface composition influences microbial community structure and growth of biofilms. We used laboratory biofilm reactors (inoculated with a diverse subsurface community) to explore the phylogenetic and taxonomic variability in microbial communities as a function of surface type (carbonate, silicate, aluminosilicate), media pH, and carbon and phosphate availability. Using high-throughput pyrosequencing, we found that surface type significantly controlled ~70–90% of the variance in phylogenetic diversity regardless of environmental pressures. Consistent patterns also emerged in the taxonomy of specific guilds (sulfur-oxidizers/reducers, Gram-positives, acidophiles) due to variations in media chemistry. Media phosphate availability was a key property associated with variation in phylogeny and taxonomy of whole reactors and was negatively correlated with biofilm accumulation and α-diversity (species richness and evenness). However, mineral-bound phosphate limitations were correlated with less biofilm. Carbon added to the media was correlated with a significant increase in biofilm accumulation and overall α-diversity. Additionally, planktonic communities were phylogenetically distant from those in biofilms. All treatments harbored structurally (taxonomically and phylogenetically) distinct microbial communities. Selective advantages within each treatment encouraged growth and revealed the presence of hundreds of additional operational taxonomix units (OTU), representing distinct consortiums of microorganisms. Ultimately, these results provide evidence that mineral/rock composition significantly influences microbial community structure, diversity, membership, phylogenetic variability, and biofilm growth in subsurface communities. PMID:28400754
Bacterial phylogeny structures soil resistomes across habitats

PubMed Central

Forsberg, Kevin J.; Patel, Sanket; Gibson, Molly K.; Lauber, Christian L.; Knight, Rob; Fierer, Noah; Dantas, Gautam

2014-01-01

Summary Ancient and diverse antibiotic resistance genes (ARGs) have previously been identified from soil1–3, including genes identical to those in human pathogens4. Despite the apparent overlap between soil and clinical resistomes4–6, factors influencing ARG composition in soil and their movement between genomes and habitats remain largely unknown3. General metagenome functions often correlate with the underlying structure of bacterial communities7–12. However, ARGs are hypothesized to be highly mobile4,5,13, prompting speculation that resistomes may not correlate with phylogenetic signatures or ecological divisions13,14. To investigate these relationships, we performed functional metagenomic selections for resistance to 18 antibiotics from 18 agricultural and grassland soils. The 2895 ARGs we discovered were predominantly novel, and represent all major resistance mechanisms15. We demonstrate that distinct soil types harbor distinct resistomes, and that nitrogen fertilizer amendments strongly influenced soil ARG content. Resistome composition also correlated with microbial phylogenetic and taxonomic structure, both across and within soil types. Consistent with this strong correlation, mobility elements syntenic with ARGs were rare in soil compared to sequenced pathogens, suggesting that ARGs in the soil may not transfer between bacteria as readily as is observed in the clinic. Together, our results indicate that bacterial community composition is the primary determinant of soil ARG content, challenging previous hypotheses that horizontal gene transfer effectively decouples resistomes from phylogeny13,14. PMID:24847883
Structure of a PE-PPE-EspG complex from Mycobacterium tuberculosis reveals molecular specificity of ESX protein secretion

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

Ekiert, Damian C.; Cox, Jeffery S.

Nearly 10% of the coding capacity of the Mycobacterium tuberculosis genome is devoted to two highly expanded and enigmatic protein families called PE and PPE, some of which are important virulence/immunogenicity factors and are secreted during infection via a unique alternative secretory system termed "type VII." How PE-PPE proteins function during infection and how they are translocated to the bacterial surface through the five distinct type VII secretion systems [ESAT-6 secretion system (ESX)] of M. tuberculosis is poorly understood. Here in this paper, we report the crystal structure of a PE-PPE heterodimer bound to ESX secretion-associated protein G (EspG), whichmore » adopts a novel fold. This PE-PPE-EspG complex, along with structures of two additional EspGs, suggests that EspG acts as an adaptor that recognizes specific PE-PPE protein complexes via extensive interactions with PPE domains, and delivers them to ESX machinery for secretion. Surprisingly, secretion of most PE-PPE proteins in M. tuberculosis is likely mediated by EspG from the ESX-5 system, underscoring the importance of ESX-5 in mycobacterial pathogenesis. Furthermore, our results indicate that PE-PPE domains function as cis-acting targeting sequences that are read out by EspGs, revealing the molecular specificity for secretion through distinct ESX pathways.« less
Structure of a PE-PPE-EspG complex from Mycobacterium tuberculosis reveals molecular specificity of ESX protein secretion

DOE PAGES

Ekiert, Damian C.; Cox, Jeffery S.

2014-10-01

Nearly 10% of the coding capacity of the Mycobacterium tuberculosis genome is devoted to two highly expanded and enigmatic protein families called PE and PPE, some of which are important virulence/immunogenicity factors and are secreted during infection via a unique alternative secretory system termed "type VII." How PE-PPE proteins function during infection and how they are translocated to the bacterial surface through the five distinct type VII secretion systems [ESAT-6 secretion system (ESX)] of M. tuberculosis is poorly understood. Here in this paper, we report the crystal structure of a PE-PPE heterodimer bound to ESX secretion-associated protein G (EspG), whichmore » adopts a novel fold. This PE-PPE-EspG complex, along with structures of two additional EspGs, suggests that EspG acts as an adaptor that recognizes specific PE-PPE protein complexes via extensive interactions with PPE domains, and delivers them to ESX machinery for secretion. Surprisingly, secretion of most PE-PPE proteins in M. tuberculosis is likely mediated by EspG from the ESX-5 system, underscoring the importance of ESX-5 in mycobacterial pathogenesis. Furthermore, our results indicate that PE-PPE domains function as cis-acting targeting sequences that are read out by EspGs, revealing the molecular specificity for secretion through distinct ESX pathways.« less
Bacterial phylogeny structures soil resistomes across habitats

NASA Astrophysics Data System (ADS)

Forsberg, Kevin J.; Patel, Sanket; Gibson, Molly K.; Lauber, Christian L.; Knight, Rob; Fierer, Noah; Dantas, Gautam

2014-05-01

Ancient and diverse antibiotic resistance genes (ARGs) have previously been identified from soil, including genes identical to those in human pathogens. Despite the apparent overlap between soil and clinical resistomes, factors influencing ARG composition in soil and their movement between genomes and habitats remain largely unknown. General metagenome functions often correlate with the underlying structure of bacterial communities. However, ARGs are proposed to be highly mobile, prompting speculation that resistomes may not correlate with phylogenetic signatures or ecological divisions. To investigate these relationships, we performed functional metagenomic selections for resistance to 18 antibiotics from 18 agricultural and grassland soils. The 2,895 ARGs we discovered were mostly new, and represent all major resistance mechanisms. We demonstrate that distinct soil types harbour distinct resistomes, and that the addition of nitrogen fertilizer strongly influenced soil ARG content. Resistome composition also correlated with microbial phylogenetic and taxonomic structure, both across and within soil types. Consistent with this strong correlation, mobility elements (genes responsible for horizontal gene transfer between bacteria such as transposases and integrases) syntenic with ARGs were rare in soil by comparison with sequenced pathogens, suggesting that ARGs may not transfer between soil bacteria as readily as is observed between human pathogens. Together, our results indicate that bacterial community composition is the primary determinant of soil ARG content, challenging previous hypotheses that horizontal gene transfer effectively decouples resistomes from phylogeny.
Herringbone bursts associated with type II solar radio emission

NASA Technical Reports Server (NTRS)

Cairns, I. H.; Robinson, R. D.

1987-01-01

Detailed observations of the herringbone (HB) fine structure on type II solar radio bursts are presented. Data from the Culgoora radiospectrograph, radiometer and radioheliograph are analyzed. The characteristic spectral profiles, frequency drift rates and exciter velocities, fluxes, source sizes, brightness temperatures, and polarizations of individual HB bursts are determined. Correlations between individual bursts within the characteristic groups of bursts and the properties of the associated type II bursts are examined. These data are compatible with HB bursts being radiation at multiples of the plasma frequency generated by electron streams accelerated by the type II shock. HB bursts are physically distinct phenomena from type II and type III bursts, differing significantly in emission processes and/or source conditions; this conclusion indicates that many of the presently available theoretical ideas for HB bursts are incorrect.
Soft CP violation and the global matter-antimatter symmetry of the universe

NASA Technical Reports Server (NTRS)

Senjanovic, G.; Stecker, F. W.

1980-01-01

Scenarios for baryon production are considered within the context of SU(5) and SO(10) grand unified theories where CP violation arises spontaneously. The spontaneous CP symmetry breaking then results in a matter-antimatter domain structure in the universe. Two possible, distinct types of theories of soft CP violation are defined. In the first type the CP nonconservation originates only from the breaking of SU(2) sub L X U(1) symmetry, and in the second type, even at the unification temperature scale, CP violation can emerge as a result of symmetry breaking by the vacuum expectation values of the superheavy Higgs sector scalars.
A computational study of the topology of vortex breakdown

NASA Technical Reports Server (NTRS)

Spall, Robert E.; Gatski, Thomas B.

1991-01-01

A fully three-dimensional numerical simulation of vortex breakdown using the unsteady, incompressible Navier-Stokes equations has been performed. Solutions to four distinct types of breakdown are identified and compared with experimental results. The computed solutions include weak helical, double helix, spiral, and bubble-type breakdowns. The topological structure of the various breakdowns as well as their interrelationship are studied. The data reveal that the asymmetric modes of breakdown may be subject to additional breakdowns as the vortex core evolves in the streamwise direction. The solutions also show that the freestream axial velocity distribution has a significant effect on the position and type of vortex breakdown.
Endogenous New World primate type C viruses isolated from owl monkey (Aotus trivirgatus) kidney cell line.

PubMed Central

Todaro, G J; Sherr, C J; Sen, A; King, N; Daniel, M D; Fleckenstein, B

1978-01-01

A type C virus (OMC-1) detected in a culture of owl monkey kidney cells resembled typical type C viruses morphologically, but was slightly larger than previously characterized mammalian type C viruses. OMC-1 can be transmitted to bat lung cells and cat embryo fibroblasts. The virions band at a density of 1.16 g/ml in isopycnic sucrose density gradients and contain reverse transcriptase and a 60-65S RNA genome composed of approximately 32S subunits. The reverse transcriptase is immunologically and biochemically distinct from the polymerases of othe retroviruses. Radioimmunoassays directed to the interspecies antigenic determinants of the major structure proteins of other type C viruses do not detect a related antigen in OMC-1. Nucleic acid hybridization experiments using labeled viral genomic RNA or proviral cDNA transcripts to normal cellular DNA of different species show that OMC-1 is an endogenous virus with multiple virogene copies (20-50 per haploid genome) present in normal owl monkey cells and is distinct from previously isolated type C and D viruses. Sequences related to the OMC-1 genome can be detected in other New World monkeys. Thus, similar to the Old World primates (e.g., baboons as a prototype), the New World monkeys contain endogenous type C viral genes that appear to have been transmitted in the primate germ line. Images PMID:76312
Grosnaja ABCs: Magnesium isotope compositions

NASA Technical Reports Server (NTRS)

Goswami, J. N.; Srinivasan, G.; Ulyanov, A. A.

1993-01-01

Three CAI's from the Grosnaja CV3 chondrite were analyzed for their magnesium isotopic compositions by the ion microprobe. The selected CAI's represent three distinct types: GR4(compact Type A), GR7(Type B) and GR2(Type C). Petrographic studies indicate that all three Grosnaja inclusions were subjected to secondary alterations. The Type A CAI GR4 is primarily composed of melilite with spinel and pyroxene occurring as minor phases. The rim of the inclusion does not exhibit distinct layered structure and secondary alteration products (garnet, Fe-rich olivine and Na-rich plagioclase) are present in some localized areas near the rim region. The average major element compositions of different mineral phases in GR4 are given. Preliminary REE data suggest a depletion of HREE relative to LREE by about a factor of 3 without any clear indication of interelement fractionation. The CAI GR7 has textural and minerological characteristics similar to Type B inclusions. The REE data show a pattern that is similar to Group 6 with enrichment in Eu and Yb. In addition, a depletion of HREE compared to LREE is also evident in this object. Melilite composition shows a broad range of akermanite content (Ak(sub 15-55)). Detailed petrographic study is in progress. GR2 is a anorthite-rich Type C inclusion with large plagioclase laths intergrown with Ti-rich pyroxene. The average plagioclase composition is close to pure anorthite (An99).
Asymmetries in the individual distinctiveness and maternal recognition of infant contact calls and distress screams in baboons

PubMed Central

Rendall, Drew; Notman, Hugh; Owren, Michael J.

2009-01-01

A key component of nonhuman primate vocal communication is the production and recognition of clear cues to social identity that function in the management of these species’ individualistic social relationships. However, it remains unclear how ubiquitous such identity cues are across call types and age-sex classes and what the underlying vocal production mechanisms responsible might be. This study focused on two structurally distinct call types produced by infant baboons in contexts that place a similar functional premium on communicating clear cues to caller identity: (1) contact calls produced when physically separated from, and attempting to relocate, mothers and (2) distress screams produced when aggressively attacked by other group members. Acoustic analyses and field experiments were conducted to examine individual differentiation in single vocalizations of each type and to test mothers’ ability to recognize infant calls. Both call types showed statistically significant individual differentiation, but the magnitude of the differentiation was substantially higher in contact calls. Mothers readily discriminated own-offspring contact calls from those of familiar but unrelated infants, but did not do so when it came to distress screams. Several possible explanations for these asymmetries in call differentiation and recognition are considered. PMID:19275336
Structural determinants for antagonist pharmacology that distinguish the rho1 GABAC receptor from GABAA receptors.

PubMed

Zhang, Jianliang; Xue, Fenqin; Chang, Yongchang

2008-10-01

GABA receptor (GABAR) types C (GABACR) and A (GABAAR) are both GABA-gated chloride channels that are distinguished by their distinct competitive antagonist properties. The structural mechanism underlying these distinct properties is not well understood. In this study, using previously identified binding residues as a guide, we made individual or combined mutations of nine binding residues in the rho1 GABACR subunit to their counterparts in the alpha1beta2gamma2 GABAAR or reverse mutations in alpha1 or beta2 subunits. The mutants were expressed in Xenopus laevis oocytes and tested for sensitivities of GABA-induced currents to the GABAA and GABAC receptor antagonists. The results revealed that bicuculline insensitivity of the rho1 GABACR was mainly determined by Tyr106, Phe138 and Phe240 residues. Gabazine insensitivity of the rho1 GABACR was highly dependent on Tyr102, Tyr106, and Phe138. The sensitivity of the rho1 GABACR to 3-aminopropyl-phosphonic acid and its analog 3-aminopropyl-(methyl)phosphinic acid mainly depended on residues Tyr102, Val140, FYS240-242, and Phe138. Thus, the residues Tyr102, Tyr106, Phe138, and Phe240 in the rho1 GABACR are major determinants for its antagonist properties distinct from those in the GABAAR. In addition, Val140 in the GABACR contributes to 3-APA binding. In conclusion, we have identified the key structural elements underlying distinct antagonist properties for the GABACR. The mechanistic insights were further extended and discussed in the context of antagonists docking to the homology models of GABAA or GABAC receptors.
Statistical manifestation of quantum correlations via disequilibrium

NASA Astrophysics Data System (ADS)

Pennini, F.; Plastino, A.

2017-12-01

The statistical notion of disequilibrium (D) was introduced by López-Ruiz, Mancini, and Calbet (LMC) (1995) [1] more than 20 years ago. D measures the amount of ;correlational structure; of a system. We wish to use D to analyze one of the simplest types of quantum correlations, those present in gaseous systems due to symmetry considerations. To this end we extend the LMC formalism to the grand canonical environment and show that D displays distinctive behaviors for simple gases, that allow for interesting insights into their structural properties.
Distinct roles of a tyrosine-associated hydrogen-bond network in fine-tuning the structure and function of heme proteins: two cases designed for myoglobin.

PubMed

Liao, Fei; Yuan, Hong; Du, Ke-Jie; You, Yong; Gao, Shu-Qin; Wen, Ge-Bo; Lin, Ying-Wu; Tan, Xiangshi

2016-10-20

A hydrogen-bond (H-bond) network, specifically a Tyr-associated H-bond network, plays key roles in regulating the structure and function of proteins, as exemplified by abundant heme proteins in nature. To explore an approach for fine-tuning the structure and function of artificial heme proteins, we herein used myoglobin (Mb) as a model protein and introduced a Tyr residue in the secondary sphere of the heme active site at two different positions (107 and 138). We performed X-ray crystallography, UV-Vis spectroscopy, stopped-flow kinetics, and electron paramagnetic resonance (EPR) studies for the two single mutants, I107Y Mb and F138Y Mb, and compared to that of wild-type Mb under the same conditions. The results showed that both Tyr107 and Tyr138 form a distinct H-bond network involving water molecules and neighboring residues, which fine-tunes ligand binding to the heme iron and enhances the protein stability, respectively. Moreover, the Tyr107-associated H-bond network was shown to fine-tune both H2O2 binding and activation. With two cases demonstrated for Mb, this study suggests that the Tyr-associated H-bond network has distinct roles in regulating the protein structure, properties and functions, depending on its location in the protein scaffold. Therefore, it is possible to design a Tyr-associated H-bond network in general to create other artificial heme proteins with improved properties and functions.

Knowledge of the human body: a distinct semantic domain.

PubMed

Coslett, H Branch; Saffran, Eleanor M; Schwoebel, John

2002-08-13

Patients with selective deficits in the naming and comprehension of animals, plants, and artifacts have been reported. These descriptions of specific semantic category deficits have contributed substantially to the understanding of the architecture of semantic representations. This study sought to further understanding of the organization of the semantic system by demonstrating that another semantic category, knowledge of the human body, may be selectively preserved. The performance of a patient with semantic dementia was compared with the performance of healthy controls on a variety of tasks assessing distinct types of body representations, including the body schema, body image, and body structural description. Despite substantial deficits on tasks involving language and knowledge of the world generally, the patient performed normally on all tests of body knowledge except body part naming; even in this naming task, however, her performance with body parts was significantly better than on artifacts. The demonstration that body knowledge may be preserved despite substantial semantic deficits involving other types of semantic information argues that body knowledge is a distinct and dissociable semantic category. These data are interpreted as support for a model of semantics that proposes that knowledge is distributed across different cortical regions reflecting the manner in which the information was acquired.
Mechanical adaptability of the Bouligand-type structure in natural dermal armour.

PubMed

Zimmermann, Elizabeth A; Gludovatz, Bernd; Schaible, Eric; Dave, Neil K N; Yang, Wen; Meyers, Marc A; Ritchie, Robert O

2013-01-01

Arapaima gigas, a fresh water fish found in the Amazon Basin, resist predation by piranhas through the strength and toughness of their scales, which act as natural dermal armour. Arapaima scales consist of a hard, mineralized outer shell surrounding a more ductile core. This core region is composed of aligned mineralized collagen fibrils arranged in distinct lamellae. Here we show how the Bouligand-type (twisted plywood) arrangement of collagen fibril lamellae has a key role in developing their unique protective properties, by using in situ synchrotron small-angle X-ray scattering during mechanical tensile tests to observe deformation mechanisms in the fibrils. Specifically, the Bouligand-type structure allows the lamellae to reorient in response to the loading environment; remarkably, most lamellae reorient towards the tensile axis and deform in tension through stretching/sliding mechanisms, whereas other lamellae sympathetically rotate away from the tensile axis and compress, thereby enhancing the scale's ductility and toughness to prevent fracture.
An Evaluation of WRF Microphysics Schemes for Simulating the Warm-Type Heavy Rain over the Korean Peninsula

NASA Astrophysics Data System (ADS)

Song, Hwan-Jin; Sohn, Byung-Ju

2018-05-01

The Korean peninsula is the region of distinctly showing the heavy rain associated with relatively low storm height and small ice water content in the upper part of cloud system (i.e., so-called warm-type heavy rainfall). The satellite observations for the warm-type rain over Korea led to a conjecture that the cloud microphysics parameterization suitable for the continental deep convection may not work well for the warm-type heavy rainfall over the Korean peninsula. Therefore, there is a growing need to examine the performance of cloud microphysics schemes for simulating the warm-type heavy rain structures over the Korean peninsula. This study aims to evaluate the capabilities of eight microphysics schemes in the Weather Research and Forecasting (WRF) model how warm-type heavy rain structures can be simulated, in reference to the Tropical Rainfall Measuring Mission (TRMM) Precipitation Radar (PR) reflectivity measurements. The results indicate that the WRF Double Moment 6-class (WDM6) scheme simulated best the vertical structure of warm-type heavy rain by virtue of a reasonable collision-coalescence process between liquid droplets and the smallest amount of snow. Nonetheless the WDM6 scheme appears to have limitations that need to be improved upon for a realistic reflectivity structure, in terms of the reflectivity slope below the melting layer, discontinuity in reflectivity profiles around the melting layer, and overestimation of upper-level reflectivity due to high graupel content.
Control of hierarchical polymer mechanics with bioinspired metal-coordination dynamics

PubMed Central

Grindy, Scott C.; Learsch, Robert; Mozhdehi, Davoud; Cheng, Jing; Barrett, Devin G.; Guan, Zhibin; Messersmith, Phillip B.; Holten-Andersen, Niels

2015-01-01

In conventional polymer materials, mechanical performance is traditionally engineered via material structure, using motifs such as polymer molecular weight, polymer branching, or copolymer-block design1. Here, by means of a model system of 4-arm poly(ethylene glycol) hydrogels crosslinked with multiple, kinetically distinct dynamic metal-ligand coordinate complexes, we show that polymer materials with decoupled spatial structure and mechanical performance can be designed. By tuning the relative concentration of two types of metal-ligand crosslinks, we demonstrate control over the material’s mechanical hierarchy of energy-dissipating modes under dynamic mechanical loading, and therefore the ability to engineer a priori the viscoelastic properties of these materials by controlling the types of crosslinks rather than by modifying the polymer itself. This strategy to decouple material mechanics from structure may inform the design of soft materials for use in complex mechanical environments. PMID:26322715
Structural features of biomass in a hybrid MBBR reactor.

PubMed

Xiao, G Y; Ganczarczyk, J

2006-03-01

The structural features of biomass present in the hybrid MBBR (Moving Bed Biofilm Reactor) aeration tank were studied in two subsequent periods, which differed in hydraulic and substrate loads. The physical characteristics of attached-growth biomass, such as, biofilm thickness, density, porosity, inner and surface fractal dimensions, and those of suspended-growth biomass, such as, floc size distribution, density, porosity, inner and surface fractal dimensions, were investigated in each study period and then compared. The results indicated that biofilm always had a higher density, geometric porosity, and a larger boundary fractal dimension than flocs. Both types of biomass were found to exhibit at least two distinct Sierpinski fractal dimensions, indicating two major different pore space populations. With the increasing wastewater flow, both types of biomass were found to shift their structural properties to larger values, except porosity and surface roughness, which decreased. Floc density and biomass Sierpinski fractals were not affected much by the system loadings.
Combining ligand-induced quantum-confined stark effect with type II heterojunction bilayer structure in CdTe and CdSe nanocrystal-based solar cells.

PubMed

Yaacobi-Gross, Nir; Garphunkin, Natalia; Solomeshch, Olga; Vaneski, Aleksandar; Susha, Andrei S; Rogach, Andrey L; Tessler, Nir

2012-04-24

We show that it is possible to combine several charge generation strategies in a single device structure, the performance of which benefits from all methods used. Exploiting the inherent type II heterojunction between layered structures of CdSe and CdTe colloidal quantum dots, we systematically study different ways of combining such nanocrystals of different size and surface chemistry and with different linking agents in a bilayer solar cell configuration. We demonstrate the beneficial use of two distinctly different sizes of NCs not only to improve the solar spectrum matching but also to reduce exciton binding energy, allowing their efficient dissociation at the interface. We further make use of the ligand-induced quantum-confined Stark effect in order to enhance charge generation and, hence, overall efficiency of nanocrystal-based solar cells.
First principles study of crystal Si-doped Ge2Sb2Te5

NASA Astrophysics Data System (ADS)

Yan, Beibei; Yang, Fei; Chen, Tian; Wang, Minglei; Chang, Hong; Ke, Daoming; Dai, Yuehua

2017-02-01

Ge2Sb2Te5 (GST) and Si-doped GST with hexagonal structure were investigated by means of First-principles calcucations. We performed many kinds of doping types and studied the electronic properties of Si-doped GST with various Si concentrations. The theoretical calculations show that the lowest formation energy appeared when Si atoms substitute the Sb atoms (SiSb). With the increasing of Si concentrations from 10% to 30%, the impurity states arise around the Fermi level and the band gap of the SiSb structure broadens. Meanwhile, the doping supercell has the most favorable structure when the doping concentration keeps in 20%. The Si-doped GST exhibits p-type metallic characteristics more distinctly owing to the Fermi level moves toward the valence band. The Te p, d-orbitals electrons have greater impact on electronic properties than that of Te s-orbitals.
Room temperature electroluminescence from the n-ZnO/p-GaN heterojunction device grown by MOCVD

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

Yang, T.P.; Zhu, H.C.; Bian, J.M.

2008-12-01

The heterojunction light-emitting diode with n-ZnO/p-GaN structure was grown on (0 0 0 1) sapphire substrate by metalorganic chemical vapor deposition (MOCVD) technique. The heterojunction structure was consisted of an Mg-doped p-type GaN layer with a hole concentration of {approx}10{sup 17} cm{sup -3} and a unintentionally doped n-type ZnO layer with an electron concentration of {approx}10{sup 18} cm{sup -3}. A distinct blue-violet electroluminescence with a dominant emission peak centered at {approx}415 nm was observed at room temperature from the heterojunction structure under forward bias conditions. The origins of the electroluminescence (EL) emissions are discussed in comparison with the photoluminescence spectra,more » and it was supposed to be attributed to a radiative recombination in both n-ZnO and p-GaN sides.« less
Preparation of positional renal slices for study of cell-specific toxicity.

PubMed

Ruegg, C E; Gandolfi, A J; Nagle, R B; Krumdieck, C L; Brendel, K

1987-04-01

To reduce structural complexity, rabbit kidneys were sliced perpendicular to their cortical-papillary axis to isolate four distinct cell groupings. This positional orientation allows identification of each renal cell type based on its location within the slice. A mechanical slicer was used to make several precision-cut slices rapidly from an oriented cylindrical core of renal tissue, with minimal tissue trauma. Slices were then submerged under a gently circulating oxygenated media in a fritted glass support system that maintains viability (intracellular K+/DNA ratio) and structural integrity (histology) for at least 30 h. A high dose of mercuric chloride (10(-3) M) was used to demonstrate the structural and biochemical changes of intoxicated slices. This method provides a controlled subchronic in vitro system for the study of the individual cell types involved in cell-specific renal toxicities and may also be a useful tool for addressing other pharmacological and physiological research questions.
A polyoxometalate-encapsulating cationic metal-organic framework as a heterogeneous catalyst for desulfurization.

PubMed

Hao, Xiu-Li; Ma, Yuan-Yuan; Zang, Hong-Ying; Wang, Yong-Hui; Li, Yang-Guang; Wang, En-Bo

2015-02-23

A new cationic triazole-based metal-organic framework encapsulating Keggin-type polyoxometalates, with the molecular formula [Co(BBPTZ)3][HPMo12O40]⋅24 H2O [compound 1; BBPTZ = 4,4'-bis(1,2,4-triazol-1-ylmethyl)biphenyl] is hydrothermally synthesized and characterized by elemental analysis, IR spectroscopy, thermogravimetric analysis, powder X-ray diffraction, and single-crystal X-ray diffraction. The structure of compound 1 contains a non-interpenetrated 3D CdSO4 (cds)-type framework with two types of channels that are interconnected with each other; straight channels that are occupied by the Keggin-type POM anions, and wavelike channels that contain lattice water molecules. The catalytic activity of compound 1 in the oxidative desulfurization reaction indicates that it is not only an effective and size-selective heterogeneous catalyst, but it also exhibits distinct structural stability in the catalytic reaction system. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Regulation of chromatin structure in the cardiovascular system.

PubMed

Rosa-Garrido, Manuel; Karbassi, Elaheh; Monte, Emma; Vondriska, Thomas M

2013-01-01

It has been appreciated for some time that cardiovascular disease involves large-scale transcriptional changes in various cell types. What has become increasingly clear only in the past few years, however, is the role of chromatin remodeling in cardiovascular phenotypes in normal physiology, as well as in development and disease. This review summarizes the state of the chromatin field in terms of distinct mechanisms to regulate chromatin structure in vivo, identifying when these modes of regulation have been demonstrated in cardiovascular tissues. We describe areas in which a better understanding of chromatin structure is leading to new insights into the fundamental biology of cardiovascular disease.
Compositional changes of soil organic matter with cropping time were more profound in subsoils and distinct between Phaeozem and Chernozem in Northeast China

USDA-ARS?s Scientific Manuscript database

Soil organic matter (SOM) contributes to soil processes and is found both in shallow and deep soil layers. Its activity can be affected by its chemical composition, yet knowledge is incomplete of how land use alters the structural composition of SOM throughout the profiles of different soil types. T...
Differentiation and Characterization of Excitatory and Inhibitory Synapses by Cryo-electron Tomography and Correlative Microscopy

PubMed Central

Sun, Rong; Zhang, Bin; Qi, Lei; Shivakoti, Sakar; Tian, Chong-Li; Lau, Pak-Ming

2018-01-01

As key functional units in neural circuits, different types of neuronal synapses play distinct roles in brain information processing, learning, and memory. Synaptic abnormalities are believed to underlie various neurological and psychiatric disorders. Here, by combining cryo-electron tomography and cryo-correlative light and electron microscopy, we distinguished intact excitatory and inhibitory synapses of cultured hippocampal neurons, and visualized the in situ 3D organization of synaptic organelles and macromolecules in their native state. Quantitative analyses of >100 synaptic tomograms reveal that excitatory synapses contain a mesh-like postsynaptic density (PSD) with thickness ranging from 20 to 50 nm. In contrast, the PSD in inhibitory synapses assumes a thin sheet-like structure ∼12 nm from the postsynaptic membrane. On the presynaptic side, spherical synaptic vesicles (SVs) of 25–60 nm diameter and discus-shaped ellipsoidal SVs of various sizes coexist in both synaptic types, with more ellipsoidal ones in inhibitory synapses. High-resolution tomograms obtained using a Volta phase plate and electron filtering and counting reveal glutamate receptor-like and GABAA receptor-like structures that interact with putative scaffolding and adhesion molecules, reflecting details of receptor anchoring and PSD organization. These results provide an updated view of the ultrastructure of excitatory and inhibitory synapses, and demonstrate the potential of our approach to gain insight into the organizational principles of cellular architecture underlying distinct synaptic functions. SIGNIFICANCE STATEMENT To understand functional properties of neuronal synapses, it is desirable to analyze their structure at molecular resolution. We have developed an integrative approach combining cryo-electron tomography and correlative fluorescence microscopy to visualize 3D ultrastructural features of intact excitatory and inhibitory synapses in their native state. Our approach shows that inhibitory synapses contain uniform thin sheet-like postsynaptic densities (PSDs), while excitatory synapses contain previously known mesh-like PSDs. We discovered “discus-shaped” ellipsoidal synaptic vesicles, and their distributions along with regular spherical vesicles in synaptic types are characterized. High-resolution tomograms further allowed identification of putative neurotransmitter receptors and their heterogeneous interaction with synaptic scaffolding proteins. The specificity and resolution of our approach enables precise in situ analysis of ultrastructural organization underlying distinct synaptic functions. PMID:29311144
Subtypes of the Type II Pit Pattern Reflect Distinct Molecular Subclasses in the Serrated Neoplastic Pathway.

PubMed

Aoki, Hironori; Yamamoto, Eiichiro; Yamano, Hiro-O; Sugai, Tamotsu; Kimura, Tomoaki; Tanaka, Yoshihito; Matsushita, Hiro-O; Yoshikawa, Kenjiro; Takagi, Ryo; Harada, Eiji; Nakaoka, Michiko; Yoshida, Yuko; Harada, Taku; Sudo, Gota; Eizuka, Makoto; Yorozu, Akira; Kitajima, Hiroshi; Niinuma, Takeshi; Kai, Masahiro; Nojima, Masanori; Suzuki, Hiromu; Nakase, Hiroshi

2018-03-15

Colorectal serrated lesions (SLs) are important premalignant lesions whose clinical and biological features are not fully understood. We aimed to establish accurate colonoscopic diagnosis and treatment of SLs through evaluation of associations among the morphological, pathological, and molecular characteristics of SLs. A total of 388 premalignant and 18 malignant colorectal lesions were studied. Using magnifying colonoscopy, microsurface structures were assessed based on Kudo's pit pattern classification system, and the Type II pit pattern was subcategorized into classical Type II, Type II-Open (Type II-O) and Type II-Long (Type II-L). BRAF/KRAS mutations and DNA methylation of CpG island methylator phenotype (CIMP) markers (MINT1, - 2, - 12, - 31, p16, and MLH1) were analyzed through pyrosequencing. Type II-O was tightly associated with sessile serrated adenoma/polyps (SSA/Ps) with BRAF mutation and CIMP-high. Most lesions with simple Type II or Type II-L were hyperplastic polyps, while mixtures of Type II or Type II-L plus more advanced pit patterns (III/IV) were characteristic of traditional serrated adenomas (TSAs). Type II-positive TSAs frequently exhibited BRAF mutation and CIMP-low, while Type II-L-positive TSAs were tightly associated with KRAS mutation and CIMP-low. Analysis of lesions containing both premalignant and cancerous components suggested Type II-L-positive TSAs may develop into KRAS-mutated/CIMP-low/microsatellite stable cancers, while Type II-O-positive SSA/Ps develop into BRAF-mutated/CIMP-high/microsatellite unstable cancers. These results suggest that Type II subtypes reflect distinct molecular subclasses in the serrated neoplasia pathway and that they could be useful hallmarks for identifying SLs at high risk of developing into CRC.
Distinction of Fly Artifacts from Human Blood using Immunodetection.

PubMed

Rivers, David B; Acca, Gillian; Fink, Marc; Brogan, Rebecca; Chen, Dorothy; Schoeffield, Andrew

2018-02-21

Insect stains produced by necrophagous flies are indistinguishable morphologically from human bloodstains. At present, no diagnostic tests exist to overcome this deficiency. As the first step toward developing a chemical test to recognize fly artifacts, polyclonal antisera were generated in rats against three distinct antigenic sequences of fly cathepsin D-like proteinase, an enzyme that is structurally distinct in cyclorrhaphous Diptera from other animals. The resulting rat antisera bound to artifacts produced by Protophormia terraenovae and synthetic peptides used to generate the polyclonal antisera, but not with any type of mammalian blood tested in immunoassays. Among the three antisera, anti-md3 serum displayed the highest reactivity for fly stains, demonstrated cross-reactivity for all synthetic peptides representing antigenic sequences of the mature fly enzyme, and bound artifacts originating from the fly digestive tract. Further work is needed to determine whether the antisera are suitable for non-laboratory conditions. © 2018 American Academy of Forensic Sciences.
The LIM and POU homeobox genes ttx-3 and unc-86 act as terminal selectors in distinct cholinergic and serotonergic neuron types.

PubMed

Zhang, Feifan; Bhattacharya, Abhishek; Nelson, Jessica C; Abe, Namiko; Gordon, Patricia; Lloret-Fernandez, Carla; Maicas, Miren; Flames, Nuria; Mann, Richard S; Colón-Ramos, Daniel A; Hobert, Oliver

2014-01-01

Transcription factors that drive neuron type-specific terminal differentiation programs in the developing nervous system are often expressed in several distinct neuronal cell types, but to what extent they have similar or distinct activities in individual neuronal cell types is generally not well explored. We investigate this problem using, as a starting point, the C. elegans LIM homeodomain transcription factor ttx-3, which acts as a terminal selector to drive the terminal differentiation program of the cholinergic AIY interneuron class. Using a panel of different terminal differentiation markers, including neurotransmitter synthesizing enzymes, neurotransmitter receptors and neuropeptides, we show that ttx-3 also controls the terminal differentiation program of two additional, distinct neuron types, namely the cholinergic AIA interneurons and the serotonergic NSM neurons. We show that the type of differentiation program that is controlled by ttx-3 in different neuron types is specified by a distinct set of collaborating transcription factors. One of the collaborating transcription factors is the POU homeobox gene unc-86, which collaborates with ttx-3 to determine the identity of the serotonergic NSM neurons. unc-86 in turn operates independently of ttx-3 in the anterior ganglion where it collaborates with the ARID-type transcription factor cfi-1 to determine the cholinergic identity of the IL2 sensory and URA motor neurons. In conclusion, transcription factors operate as terminal selectors in distinct combinations in different neuron types, defining neuron type-specific identity features.
Band-gap analysis of a novel lattice with a hierarchical periodicity using the spectral element method

NASA Astrophysics Data System (ADS)

Wu, Zhijing; Li, Fengming; Zhang, Chuanzeng

2018-05-01

Inspired by the hierarchical structures of butterfly wing surfaces, a new kind of lattice structures with a two-order hierarchical periodicity is proposed and designed, and the band-gap properties are investigated by the spectral element method (SEM). The equations of motion of the whole structure are established considering the macro and micro periodicities of the system. The efficiency of the SEM is exploited in the modeling process and validated by comparing the results with that of the finite element method (FEM). Based on the highly accurate results in the frequency domain, the dynamic behaviors of the proposed two-order hierarchical structures are analyzed. An original and interesting finding is the existence of the distinct macro and micro stop-bands in the given frequency domain. The mechanisms for these two types of band-gaps are also explored. Finally, the relations between the hierarchical periodicities and the different types of the stop-bands are investigated by analyzing the parametrical influences.
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.
White Matter Connectivity of the Thalamus Delineates the Functional Architecture of Competing Thalamocortical Systems

PubMed Central

O'Muircheartaigh, Jonathan; Keller, Simon S.; Barker, Gareth J.; Richardson, Mark P.

2015-01-01

There is an increasing awareness of the involvement of thalamic connectivity on higher level cortical functioning in the human brain. This is reflected by the influence of thalamic stimulation on cortical activity and behavior as well as apparently cortical lesion syndromes occurring as a function of small thalamic insults. Here, we attempt to noninvasively test the correspondence of structural and functional connectivity of the human thalamus using diffusion-weighted and resting-state functional MRI. Using a large sample of 102 adults, we apply tensor independent component analysis to diffusion MRI tractography data to blindly parcellate bilateral thalamus according to diffusion tractography-defined structural connectivity. Using resting-state functional MRI collected in the same subjects, we show that the resulting structurally defined thalamic regions map to spatially distinct, and anatomically predictable, whole-brain functional networks in the same subjects. Although there was significant variability in the functional connectivity patterns, the resulting 51 structural and functional patterns could broadly be reduced to a subset of 7 similar core network types. These networks were distinct from typical cortical resting-state networks. Importantly, these networks were distributed across the brain and, in a subset, map extremely well to known thalamocortico-basal-ganglial loops. PMID:25899706
Structural and electronic properties of the alkali metal incommensurate phases

NASA Astrophysics Data System (ADS)

Woolman, Gavin; Naden Robinson, Victor; Marqués, Miriam; Loa, Ingo; Ackland, Graeme J.; Hermann, Andreas

2018-05-01

Under pressure, the alkali elements sodium, potassium, and rubidium adopt nonperiodic structures based on two incommensurate interpenetrating lattices. While all elements form the same "host" lattice, their "guest" lattices are all distinct. The physical mechanism that stabilizes these phases is not known, and detailed calculations are challenging due to the incommensurability of the lattices. Using a series of commensurate approximant structures, we tackle this issue using density functional theory calculations. In Na and K, the calculations prove accurate enough to reproduce not only the stability of the host-guest phases, but also the complicated pressure dependence of the host-guest ratio and the two guest-lattice transitions. We find Rb-IV to be metastable at all pressures, and suggest it is a high-temperature phase. The electronic structure of these materials is unique: they exhibit two distinct, coexisting types of electride behavior, with both fully localized pseudoanions and electrons localized in 1D wells in the host lattice, leading to low conductivity. While all phases feature pseudogaps in the electronic density of states, the perturbative free-electron picture applies to Na, but not to K and Rb, due to significant d -orbital population in the latter.

Neurodegenerative disease mutations in TREM2 reveal a functional surface and distinct loss-of-function mechanisms

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

Kober, Daniel L.; Alexander-Brett, Jennifer M.; Karch, Celeste M.

Genetic variations in the myeloid immune receptor TREM2 are linked to several neurodegenerative diseases. To determine how TREM2 variants contribute to these diseases, we performed structural and functional studies of wild-type and variant proteins. Our 3.1 Å TREM2 crystal structure revealed that mutations found in Nasu-Hakola disease are buried whereas Alzheimer’s disease risk variants are found on the surface, suggesting that these mutations have distinct effects on TREM2 function. Biophysical and cellular methods indicate that Nasu-Hakola mutations impact protein stability and decrease folded TREM2 surface expression, whereas Alzheimer’s risk variants impact binding to a TREM2 ligand. Additionally, the Alzheimer’s riskmore » variants appear to epitope map a functional surface on TREM2 that is unique within the larger TREM family. These findings provide a guide to structural and functional differences among genetic variants of TREM2, indicating that therapies targeting the TREM2 pathway should be tailored to these genetic and functional differences with patient-specific medicine approaches for neurodegenerative disorders.« less
Characterization and differentiation of rock varnish types from different environments by microanalytical techniques

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

Macholdt, D. S.; Jochum, K. P.; Pöhlker, C.

We investigated rock varnishes collected from several locations and environments worldwide by a wide range of microanalytical techniques. These techniques were selected to address the challenges posed by the chemical and structural complexity within the micrometer- to nanometer-sized structures in these geological materials. Femtosecond laser ablation-inductively coupled plasma-mass spectrometry (fs LA-ICP-MS), scanning transmission X-ray microscopy-near edge X-ray adsorption fine structure spectroscopy (STXM-NEXAFS) in combination with scanning electron microscopy (SEM) of focused ion beam (FIB) ultra-thin (100–200 nm) sections, conventional and polarization microscopy, as well as electron paramagnetic resonance (EPR) measurements were used to obtain information about these rock varnishes. Rockmore » varnishes from different environments, which cannot readily be distinguished based on their macroscopic appearance, differ significantly in their constituent elemental mass fractions, e.g., of Mn, Fe, Ni, Co, Ba, and Pb, and their rare earth element (REE) patterns. Structural characteristics such as the particle sizes of embedded dust grains, internal structures such as layers of Mn-, Fe-, and Ca -rich material, and structures such as cavities varied between varnishes from different environments and regions in the world. The EPR spectra were consistent with aged biogenic Mn oxides in all samples, but showed subtle differences between samples of different origin. Our observations allow us to separate rock varnishes into different types, with differences that might be indicators of distinct geneses. Five different types of rock varnish could be distinguished, Type I–V, of which only Type I might be used as potential paleoclimate archive. Each varnish type has specific characteristics in terms of their elemental composition, element distribution, and structures. The combination of element ratios (Mn/Ba, Al/Ni, Mn/REY, Mn/Ce, Mn/Pb, La N /Yb N , and Ce/Ce*), total REE contents, and structures can be used to separate the different types of rock varnish from each other.« less
Insights into plant cell wall structure, architecture, and integrity using glycome profiling of native and AFEXTM-pre-treated biomass

PubMed Central

Pattathil, Sivakumar; Hahn, Michael G.; Dale, Bruce E.; Chundawat, Shishir P. S.

2015-01-01

Cell walls, which constitute the bulk of plant biomass, vary considerably in their structure, composition, and architecture. Studies on plant cell walls can be conducted on both native and pre-treated plant biomass samples, allowing an enhanced understanding of these structural and compositional variations. Here glycome profiling was employed to determine the relative abundance of matrix polysaccharides in several phylogenetically distinct native and pre-treated plant biomasses. Eight distinct biomass types belonging to four different subgroups (i.e. monocot grasses, woody dicots, herbaceous dicots, and softwoods) were subjected to various regimes of AFEX™ (ammonia fiber expansion) pre-treatment [AFEX is a trademark of MBI, Lansing (http://www.mbi.org]. This approach allowed detailed analysis of close to 200 cell wall glycan epitopes and their relative extractability using a high-throughput platform. In general, irrespective of the phylogenetic origin, AFEX™ pre-treatment appeared to cause loosening and improved accessibility of various xylan epitope subclasses in most plant biomass materials studied. For most biomass types analysed, such loosening was also evident for other major non-cellulosic components including subclasses of pectin and xyloglucan epitopes. The studies also demonstrate that AFEX™ pre-treatment significantly reduced cell wall recalcitrance among diverse phylogenies (except softwoods) by inducing structural modifications to polysaccharides that were not detectable by conventional gross composition analyses. It was found that monitoring changes in cell wall glycan compositions and their relative extractability for untreated and pre-treated plant biomass can provide an improved understanding of variations in structure and composition of plant cell walls and delineate the role(s) of matrix polysaccharides in cell wall recalcitrance. PMID:25911738
Insights into plant cell wall structure, architecture, and integrity using glycome profiling of native and AFEX TM -pre-treated biomass

DOE PAGES

Pattathil, Sivakumar; Hahn, Michael G.; Dale, Bruce E.; ...

2015-04-23

We report that cell walls, which constitute the bulk of plant biomass, vary considerably in their structure, composition, and architecture. Studies on plant cell walls can be conducted on both native and pre-treated plant biomass samples, allowing an enhanced understanding of these structural and compositional variations. Here glycome profiling was employed to determine the relative abundance of matrix polysaccharides in several phylogenetically distinct native and pre-treated plant biomasses. Eight distinct biomass types belonging to four different subgroups (i.e. monocot grasses, woody dicots, herbaceous dicots, and softwoods) were subjected to various regimes of AFEX™ (ammonia fiber expansion) pre-treatment [AFEX is amore » trademark of MBI, Lansing (http://www.mbi.org]. This approach allowed detailed analysis of close to 200 cell wall glycan epitopes and their relative extractability using a high-throughput platform. In general, irrespective of the phylogenetic origin, AFEX™ pre-treatment appeared to cause loosening and improved accessibility of various xylan epitope subclasses in most plant biomass materials studied. For most biomass types analysed, such loosening was also evident for other major non-cellulosic components including subclasses of pectin and xyloglucan epitopes. The studies also demonstrate that AFEX™ pre-treatment significantly reduced cell wall recalcitrance among diverse phylogenies (except softwoods) by inducing structural modifications to polysaccharides that were not detectable by conventional gross composition analyses. Lastly, we found that monitoring changes in cell wall glycan compositions and their relative extractability for untreated and pre-treated plant biomass can provide an improved understanding of variations in structure and composition of plant cell walls and delineate the role(s) of matrix polysaccharides in cell wall recalcitrance.« less
Epidemic spreading on dual-structure networks with mobile agents

NASA Astrophysics Data System (ADS)

Yao, Yiyang; Zhou, Yinzuo

2017-02-01

The rapid development of modern society continually transforms the social structure which leads to an increasingly distinct dual structure of higher population density in urban areas and lower density in rural areas. Such structure may induce distinctive spreading behavior of epidemics which does not happen in a single type structure. In this paper, we study the epidemic spreading of mobile agents on dual structure networks based on SIRS model. First, beyond the well known epidemic threshold for generic epidemic model that when the infection rate is below the threshold a pertinent infectious disease will die out, we find the other epidemic threshold which appears when the infection rate of a disease is relatively high. This feature of two thresholds for the SIRS model may lead to the elimination of infectious disease when social network has either high population density or low population density. Interestingly, however, we find that when a high density area is connected to a low density may cause persistent spreading of the infectious disease, even though the same disease will die out when it spreads in each single area. This phenomenon indicates the critical role of the connection between the two areas which could radically change the behavior of spreading dynamics. Our findings, therefore, provide new understanding of epidemiology pertinent to the characteristic modern social structure and have potential to develop controlling strategies accordingly.
Intracellular Localization and Cellular Factors Interaction of HTLV-1 and HTLV-2 Tax Proteins: Similarities and Functional Differences

PubMed Central

Bertazzoni, Umberto; Turci, Marco; Avesani, Francesca; Di Gennaro, Gianfranco; Bidoia, Carlo; Romanelli, Maria Grazia

2011-01-01

Human T-lymphotropic viruses type 1 (HTLV-1) and type 2 (HTLV-2) present very similar genomic structures but HTLV-1 is more pathogenic than HTLV-2. Is this difference due to their transactivating Tax proteins, Tax-1 and Tax-2, which are responsible for viral and cellular gene activation? Do Tax-1 and Tax-2 differ in their cellular localization and in their interaction pattern with cellular factors? In this review, we summarize Tax-1 and Tax-2 structural and phenotypic properties, their interaction with factors involved in signal transduction and their localization-related behavior within the cell. Special attention will be given to the distinctions between Tax-1 and Tax-2 that likely play an important role in their transactivation activity. PMID:21994745
Differentiation of the intracellular structure of slow- versus fast-twitch muscle fibers through evaluation of the dielectric properties of tissue

PubMed Central

Sanchez, B; Li, J; Bragos, R; Rutkove, S B

2014-01-01

Slow-twitch (type 1) skeletal muscle fibers have markedly greater mitochondrial content than fast-twitch (type 2) fibers. Accordingly, we sought to determine whether the dielectric properties of these two fiber types differed, consistent with their distinct intracellular morphologies. The longitudinal and transverse dielectric spectrum of the ex vivo rat soleus (a predominantly type 1 muscle) and the superficial layers of rat gastrocnemius (predominantly type 2) (n = 15) were measured in the 1 kHz–10 MHz frequency range and modeled to a resistivity Cole–Cole function. Major differences were especially apparent in the dielectric spectrum in the 1 to 10 MHz range. Specifically, the gastrocnemius demonstrated a well-defined, higher center frequency than the soleus muscle, whereas the soleus muscle showed a greater difference in the modeled zero and infinite resistivities than the gastrocnemius. These findings are consistent with the fact that soleus tissue has larger and more numerous mitochondria than gastrocnemius. Evaluation of tissue at high frequency could provide a novel approach for assessing intracellular structure in health and disease. PMID:24743385
Differentiation of the intracellular structure of slow- versus fast-twitch muscle fibers through evaluation of the dielectric properties of tissue

NASA Astrophysics Data System (ADS)

Sanchez, B.; Li, J.; Bragos, R.; Rutkove, S. B.

2014-05-01

Slow-twitch (type 1) skeletal muscle fibers have markedly greater mitochondrial content than fast-twitch (type 2) fibers. Accordingly, we sought to determine whether the dielectric properties of these two fiber types differed, consistent with their distinct intracellular morphologies. The longitudinal and transverse dielectric spectrum of the ex vivo rat soleus (a predominantly type 1 muscle) and the superficial layers of rat gastrocnemius (predominantly type 2) (n = 15) were measured in the 1 kHz-10 MHz frequency range and modeled to a resistivity Cole-Cole function. Major differences were especially apparent in the dielectric spectrum in the 1 to 10 MHz range. Specifically, the gastrocnemius demonstrated a well-defined, higher center frequency than the soleus muscle, whereas the soleus muscle showed a greater difference in the modeled zero and infinite resistivities than the gastrocnemius. These findings are consistent with the fact that soleus tissue has larger and more numerous mitochondria than gastrocnemius. Evaluation of tissue at high frequency could provide a novel approach for assessing intracellular structure in health and disease.
Followers Are Not Enough: A Multifaceted Approach to Community Detection in Online Social Networks

PubMed Central

2015-01-01

In online social media networks, individuals often have hundreds or even thousands of connections, which link these users not only to friends, associates, and colleagues, but also to news outlets, celebrities, and organizations. In these complex social networks, a ‘community’ as studied in the social network literature, can have very different meaning depending on the property of the network under study. Taking into account the multifaceted nature of these networks, we claim that community detection in online social networks should also be multifaceted in order to capture all of the different and valuable viewpoints of ‘community.’ In this paper we focus on three types of communities beyond follower-based structural communities: activity-based, topic-based, and interaction-based. We analyze a Twitter dataset using three different weightings of the structural network meant to highlight these three community types, and then infer the communities associated with these weightings. We show that interesting insights can be obtained about the complex community structure present in social networks by studying when and how these four community types give rise to similar as well as completely distinct community structure. PMID:26267868
Solid-state synthesis in the system Na 0.8Nb yW 1-yO 3 with 0⩽ y⩽0.4: A new phase, Na 0.5NbO 2.75, with perovskite-type structure

NASA Astrophysics Data System (ADS)

Debnath, Tapas; Rüscher, Claus H.; Gesing, Thorsten M.; Koepke, Jürgen; Hussain, Altaf

2008-04-01

Series of compounds in the system Na xNb yW 1-yO 3 were prepared according to the appropriate molar ratio of Na 2WO 4, WO 3, WO 2 and Nb 2O 5 with x=0.80 and 0.0⩽ y⩽0.4 at 600 °C in evacuated silica glass tubes. These compounds were investigated by X-ray powder diffraction, optical microscopy, microprobe analysis, Raman and optical microspectroscopy. A y-dependent separation into three distinct coloured crystallites with cubic perovskite-type structures is observed: (i) red-orange crystallites with composition Na xWO 3 with slightly decreasing x (i.e. 0.8-0.72) with increasing nominal y, (ii) bluish solid solution of composition Na xNb yW 1-yO 3 and (iii) white crystallites of a new phase having defect perovskite-type structure with composition Na 0.5NbO 2.75.
Damage/fault diagnosis in an operating wind turbine under uncertainty via a vibration response Gaussian mixture random coefficient model based framework

NASA Astrophysics Data System (ADS)

Avendaño-Valencia, Luis David; Fassois, Spilios D.

2017-07-01

The study focuses on vibration response based health monitoring for an operating wind turbine, which features time-dependent dynamics under environmental and operational uncertainty. A Gaussian Mixture Model Random Coefficient (GMM-RC) model based Structural Health Monitoring framework postulated in a companion paper is adopted and assessed. The assessment is based on vibration response signals obtained from a simulated offshore 5 MW wind turbine. The non-stationarity in the vibration signals originates from the continually evolving, due to blade rotation, inertial properties, as well as the wind characteristics, while uncertainty is introduced by random variations of the wind speed within the range of 10-20 m/s. Monte Carlo simulations are performed using six distinct structural states, including the healthy state and five types of damage/fault in the tower, the blades, and the transmission, with each one of them characterized by four distinct levels. Random vibration response modeling and damage diagnosis are illustrated, along with pertinent comparisons with state-of-the-art diagnosis methods. The results demonstrate consistently good performance of the GMM-RC model based framework, offering significant performance improvements over state-of-the-art methods. Most damage types and levels are shown to be properly diagnosed using a single vibration sensor.
Design of nano- and microfiber combined scaffolds by electrospinning of collagen onto starch-based fiber meshes: a man-made equivalent of natural extracellular matrix.

PubMed

Tuzlakoglu, Kadriye; Santos, Marina I; Neves, Nuno; Reis, Rui L

2011-02-01

Mimicking the structural organization and biologic function of natural extracellular matrix has been one of the main goals of tissue engineering. Nevertheless, the majority of scaffolding materials for bone regeneration highlights biochemical functionality in detriment of mechanical properties. In this work we present a rather innovative construct that combines in the same structure electrospun type I collagen nanofibers with starch-based microfibers. These combined structures were obtained by a two-step methodology and structurally consist in a type I collagen nano-network incorporated on a macro starch-based support. The morphology of the developed structures was assessed by several microscopy techniques and the collagenous nature of the nano-network was confirmed by immunohistochemistry. In addition, and especially regarding the requirements of large bone defects, we also successfully introduced the concept of layer by layer, as a way to produce thicker structures. In an attempt to recreate bone microenvironment, the design and biochemical composition of the combined structures also envisioned bone-forming cells and endothelial cells (ECs). The inclusion of a type I collagen nano-network induced a stretched morphology and improved the metabolic activity of osteoblasts. Regarding ECs, the presence of type I collagen on the combined structures provided adhesive support and obviated the need of precoating with fibronectin. It was also importantly observed that ECs on the nano-network organized into circular structures, a three-dimensional arrangement distinct from that observed for osteoblasts and resembling the microcappillary-like organizations formed during angiogenesis. By providing simultaneously physical and chemical cues for cells, the herein-proposed combined structures hold a great potential in bone regeneration as a man-made equivalent of extracellular matrix.
Highly Discriminatory Variable-Number Tandem-Repeat Markers for Genotyping of Trichophyton interdigitale Strains

PubMed Central

Drira, Ines; Hadrich, Ines; Neji, Sourour; Mahfouth, Nedia; Trabelsi, Houaida; Sellami, Hayet; Makni, Fattouma

2014-01-01

Trichophyton interdigitale is the second most frequent cause of superficial fungal infections of various parts of the human body. Studying the population structure and genotype differentiation of T. interdigitale strains may lead to significant improvements in clinical practice. The present study aimed to develop and select suitable variable-number tandem-repeat (VNTR) markers for 92 clinical strains of T. interdigitale. On the basis of an analysis of four VNTR markers, four to eight distinct alleles were detected for each marker. The marker with the highest discriminatory power had eight alleles and a D value of 0.802. The combination of all four markers yielded a D value of 0.969 with 29 distinct multilocus genotypes. VNTR typing revealed the genetic diversity of the strains, identifying three populations according to their colonization sites. A correlation between phenotypic characteristics and multilocus genotypes was observed. Seven patients harbored T. interdigitale strains with different genotypes. Typing of clinical T. interdigitale samples by VNTR markers displayed excellent discriminatory power and 100% reproducibility. PMID:24989614
Disentangling functions of online aggression: The Cyber-Aggression Typology Questionnaire (CATQ).

PubMed

Runions, Kevin C; Bak, Michal; Shaw, Thérèse

2017-01-01

Aggression in online contexts has received much attention over the last decade, yet there is a need for measures identifying the proximal psychological drivers of cyber-aggressive behavior. The purpose of this study was to present data on the newly developed Cyber-Aggression Typology Questionnaire (CATQ) designed to distinguish between four distinct types of cyber-aggression on dimensions of motivational valence and self-control. A sample 314 undergraduate students participated in the study. The results confirmed the predicted four-factor structure providing evidence for distinct and independent impulsive-aversive, controlled-aversive, impulsive-appetitive, and controlled-appetitive cyber-aggression types. Further analyses with the Berlin Cyberbullying Questionnaire, Reactive Proactive Aggression Questionnaire, and the Behavior Inhibition and Activation Systems Scale provide support for convergent and divergent validity. Understanding the motivations facilitating cyber-aggressive behavior could aid researchers in the development of new prevention and intervention strategies that focus on individual differences in maladaptive proximal drivers of aggression. Aggr. Behav. 43:74-84, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.
Extracellular signals that define distinct and coexisting cell fates in Bacillus subtilis.

PubMed

López, Daniel; Kolter, Roberto

2010-03-01

The soil-dwelling bacterium Bacillus subtilis differentiates into distinct subpopulations of specialized cells that coexist within highly structured communities. The coordination and interplay between these cell types requires extensive extracellular communication driven mostly by sensing self-generated secreted signals. These extracellular signals activate a set of sensor kinases, which respond by phosphorylating three major regulatory proteins, Spo0A, DegU and ComA. Each phosphorylated regulator triggers a specific differentiation program while at the same time repressing other differentiation programs. This allows a cell to differentiate in response to a specific cue, even in the presence of other, possibly conflicting, signals. The sensor kinases involved respond to an eclectic group of extracellular signals, such as quorum-sensing molecules, natural products, temperature, pH or scarcity of nutrients. This article reviews the cascades of cell differentiation pathways that are triggered by sensing extracellular signals. We also present a tentative developmental model in which the diverse cell types sequentially differentiate to achieve the proper development of the bacterial community.
Galaxy interactions and strength of nuclear activity

NASA Technical Reports Server (NTRS)

Simkin, S. M.

1990-01-01

Analysis of data in the literature for differential velocities and projected separations of nearby Seyfert galaxies with possible companions shows a clear difference in projected separations between type 1's and type 2's. This kinematic difference between the two activity classes reinforces other independent evidence that their different nuclear characteristics are related to a non-nuclear physical distinction between the two classes. The differential velocities and projected separations of the galaxy pairs in this sample yield mean galaxy masses, sizes, and mass to light ratios which are consistent with those found by the statistical methods of Karachentsev. Although the galaxy sample discussed here is too small and too poorly defined to provide robust support for these conclusions, the results strongly suggest that nuclear activity in Seyfert galaxies is associated with gravitational perturbations from companion galaxies, and that there are physical distinctions between the host companions of Seyfert 1 and Seyfert 2 nuclei which may depend both on the environment and the structure of the host galaxy itself.
Contribution of species-specific chemical signatures to soil organic matter in Kohala, HI.

NASA Astrophysics Data System (ADS)

Stewart, C. E.; Amatangelo, K.; Neff, J. C.

2008-12-01

Soil organic matter (SOM) inherits much of its chemical structure from the dominant vegetation, including phenolic (lignin-derived), aromatic, and aliphatic (cutin and wax-derived) compounds. The Hawaiian fern species Dicranopteris decomposes more slowly than the angiosperm, Cheirodendron due to high concentrations of recalcitrant C compounds. These aliphatic fern leaf waxes are well-preserved and may comprise a large portion of the recalcitrant organic matter in these soils. Our objective was to determine the chemical signature of fern and angiosperm vegetation types and trace the preservation or loss of those compounds into the soil. We collected live tissue, litter, roots, and soil (<53 μm) from five dominant vegetation types including two angiosperms Cheirodendron and Metrosideros, two basal ferns Dicranopteris and Cibotium and a polypod fern Diplazium in Kohala, HI. We characterized them via TMAH-pyrolysis-gas chromatography-mass spectrometry. We found distinct chemical differences between angiosperm and fern vegetation; angiosperm contained more G- and S-derived lignin structures and the fern species contained greater relative abundances of P-derived lignin and tannin-derivatives. There was a general decrease of lignin-derived phenolic compounds from live to litter to soils and an increase in more recalcitrant, aromatic and aliphatic C. Recalcitrant fern-derived cutin and leaf waxes (alkene and alkanes structures) were evident in the soils, but clear species differences were not observed. Although ferns contain distinct lipid and wax-derived compounds, soils developed under fern do not appear to accumulate these compounds in SOM.
Functional Specialization of Cellulose Synthase Isoforms in a Moss Shows Parallels with Seed Plants1[OPEN

PubMed Central

Li, Xingxing; Huang, Shixin; Van de Meene, Allison M.L.; Tran, Mai L.; Killeavy, Erin; Mercure, Danielle; Burton, Rachel A.

2017-01-01

The secondary cell walls of tracheary elements and fibers are rich in cellulose microfibrils that are helically oriented and laterally aggregated. Support cells within the leaf midribs of mosses deposit cellulose-rich secondary cell walls, but their biosynthesis and microfibril organization have not been examined. Although the Cellulose Synthase (CESA) gene families of mosses and seed plants diversified independently, CESA knockout analysis in the moss Physcomitrella patens revealed parallels with Arabidopsis (Arabidopsis thaliana) in CESA functional specialization, with roles for both subfunctionalization and neofunctionalization. The similarities include regulatory uncoupling of the CESAs that synthesize primary and secondary cell walls, a requirement for two or more functionally distinct CESA isoforms for secondary cell wall synthesis, interchangeability of some primary and secondary CESAs, and some CESA redundancy. The cellulose-deficient midribs of ppcesa3/8 knockouts provided negative controls for the structural characterization of stereid secondary cell walls in wild type P. patens. Sum frequency generation spectra collected from midribs were consistent with cellulose microfibril aggregation, and polarization microscopy revealed helical microfibril orientation only in wild type leaves. Thus, stereid secondary walls are structurally distinct from primary cell walls, and they share structural characteristics with the secondary walls of tracheary elements and fibers. We propose a mechanism for the convergent evolution of secondary walls in which the deposition of aggregated and helically oriented microfibrils is coupled to rapid and highly localized cellulose synthesis enabled by regulatory uncoupling from primary wall synthesis. PMID:28768816
Microfocus diffraction from different regions of a protein crystal: structural variations and unit-cell polymorphism

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

Thompson, Michael C.; Cascio, Duilio; Yeates, Todd O.

Real macromolecular crystals can be non-ideal in a myriad of ways. This often creates challenges for structure determination, while also offering opportunities for greater insight into the crystalline state and the dynamic behavior of macromolecules. To evaluate whether different parts of a single crystal of a dynamic protein, EutL, might be informative about crystal and protein polymorphism, a microfocus X-ray synchrotron beam was used to collect a series of 18 separate data sets from non-overlapping regions of the same crystal specimen. A principal component analysis (PCA) approach was employed to compare the structure factors and unit cells across the datamore » sets, and it was found that the 18 data sets separated into two distinct groups, with largeRvalues (in the 40% range) and significant unit-cell variations between the members of the two groups. This categorization mapped the different data-set types to distinct regions of the crystal specimen. Atomic models of EutL were then refined against two different data sets obtained by separately merging data from the two distinct groups. A comparison of the two resulting models revealed minor but discernable differences in certain segments of the protein structure, and regions of higher deviation were found to correlate with regions where larger dynamic motions were predicted to occur by normal-mode molecular-dynamics simulations. The findings emphasize that large spatially dependent variations may be present across individual macromolecular crystals. This information can be uncovered by simultaneous analysis of multiple partial data sets and can be exploited to reveal new insights about protein dynamics, while also improving the accuracy of the structure-factor data ultimately obtained in X-ray diffraction experiments.« less
Motivational Pathways to Unique Types of Alcohol Consequences

PubMed Central

Merrill, Jennifer E.; Read, Jennifer P.

2010-01-01

Individuals consume alcohol for a variety of reasons (motives), and these reasons may be differentially associated with the types of drinking outcomes that result. The present study examined whether specific affect-relevant motivations for alcohol use (i.e., coping, enhancement) are associated with distinct types of consequences, and whether such associations occur directly, or only as a function of increased alcohol use. It was hypothesized that enhancement motives would be associated with distinct problem types only through alcohol use, whereas coping motives would be linked directly to hypothesized problem types. Regularly drinking undergraduates (N= 192, 93 female) completed self-report measures of drinking motives and alcohol involvement. Using structural equation modeling, we tested direct associations between Coping motives and indirect associations between Enhancement motives and eight unique alcohol problem domains: Risky Behaviors, Blackout Drinking, Physiological Dependence, Academic/Occupational problems, Poor Self-care, Diminished Self-perception, Social/Interpersonal problems, and Impaired Control. We observed direct effects of Coping motives on three unique problem domains (Academic/Occupational problems, Risky Behaviors, and Poor Self-care). Both Coping and Enhancement motives were indirectly associated (through Use) with several problem types. Unhypothesized associations between Conformity motives and unique consequence types also were observed. Findings suggest specificity in the consequences experienced by individuals who drink to cope with negative affect versus to enhance positive affect, and may have intervention implications. Findings depict the coping motivated student as one who is struggling across multiple domains, regardless of levels of drinking. Such students may need to be prioritized for interventions. PMID:20822194

Kingella kingae expresses four structurally distinct polysaccharide capsules that differ in their correlation with invasive disease

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

Starr, Kimberly F.; Porsch, Eric A.; Seed, Patrick C.

Kingella kingae is an encapsulated gram-negative organism that is a common cause of osteoarticular infections in young children. In earlier work, we identified a glycosyltransferase gene called csaA that is necessary for synthesis of the [3)-β-GalpNAc-(1→5)-β-Kdop-(2→] polysaccharide capsule (type a) in K. kingae strain 269–492. In the current study, we analyzed a large collection of invasive and carrier isolates from Israel and found that csaA was present in only 47% of the isolates. Further examination of this collection using primers based on the sequence that flanks csaA revealed three additional gene clusters (designated the csb, csc, and csd loci), allmore » encoding predicted glycosyltransferases. The csb locus contains the csbA, csbB, and csbC genes and is associated with a capsule that is a polymer of [6)-α-GlcpNAc-(1→5)-β-(8-OAc)Kdop-(2→] (type b). The csc locus contains the cscA, cscB, and cscC genes and is associated with a capsule that is a polymer of [3)-β-Ribf-(1→2)-β-Ribf-(1→2)-β-Ribf-(1→4)-β-Kdop-(2→] (type c). The csd locus contains the csdA, csdB, and csdC genes and is associated with a capsule that is a polymer of [P-(O→3)[β-Galp-(1→4)]-β-GlcpNAc-(1→3)-α-GlcpNAc-1-] (type d). Introduction of the csa, csb, csc, and csd loci into strain KK01Δcsa, a strain 269–492 derivative that lacks the native csaA gene, was sufficient to produce the type a capsule, type b capsule, type c capsule, and type d capsule, respectively, indicating that these loci are solely responsible for determining capsule type in K. kingae. Further analysis demonstrated that 96% of the invasive isolates express either the type a or type b capsule and that a disproportionate percentage of carrier isolates express the type c or type d capsule. Lastly, these results establish that there are at least four structurally distinct K. kingae capsule types and suggest that capsule type plays an important role in promoting K. kingae invasive disease« less
Kingella kingae expresses four structurally distinct polysaccharide capsules that differ in their correlation with invasive disease

DOE PAGES

Starr, Kimberly F.; Porsch, Eric A.; Seed, Patrick C.; ...

2016-10-19

Kingella kingae is an encapsulated gram-negative organism that is a common cause of osteoarticular infections in young children. In earlier work, we identified a glycosyltransferase gene called csaA that is necessary for synthesis of the [3)-β-GalpNAc-(1→5)-β-Kdop-(2→] polysaccharide capsule (type a) in K. kingae strain 269–492. In the current study, we analyzed a large collection of invasive and carrier isolates from Israel and found that csaA was present in only 47% of the isolates. Further examination of this collection using primers based on the sequence that flanks csaA revealed three additional gene clusters (designated the csb, csc, and csd loci), allmore » encoding predicted glycosyltransferases. The csb locus contains the csbA, csbB, and csbC genes and is associated with a capsule that is a polymer of [6)-α-GlcpNAc-(1→5)-β-(8-OAc)Kdop-(2→] (type b). The csc locus contains the cscA, cscB, and cscC genes and is associated with a capsule that is a polymer of [3)-β-Ribf-(1→2)-β-Ribf-(1→2)-β-Ribf-(1→4)-β-Kdop-(2→] (type c). The csd locus contains the csdA, csdB, and csdC genes and is associated with a capsule that is a polymer of [P-(O→3)[β-Galp-(1→4)]-β-GlcpNAc-(1→3)-α-GlcpNAc-1-] (type d). Introduction of the csa, csb, csc, and csd loci into strain KK01Δcsa, a strain 269–492 derivative that lacks the native csaA gene, was sufficient to produce the type a capsule, type b capsule, type c capsule, and type d capsule, respectively, indicating that these loci are solely responsible for determining capsule type in K. kingae. Further analysis demonstrated that 96% of the invasive isolates express either the type a or type b capsule and that a disproportionate percentage of carrier isolates express the type c or type d capsule. Lastly, these results establish that there are at least four structurally distinct K. kingae capsule types and suggest that capsule type plays an important role in promoting K. kingae invasive disease« less
Combining Ion Mobility and Cryogenic Spectroscopy for Structural and Analytical Studies of Biomolecular Ions.

PubMed

Kamrath, Michael Z; Rizzo, Thomas R

2018-05-10

Ion mobility spectrometry (IMS) has become a valuable tool in biophysical and bioanalytical chemistry because of its ability to separate and characterize the structure of gas-phase biomolecular ions on the basis of their collisional cross section (CCS). Its importance has grown with the realization that in many cases, biomolecular ions retain important structural characteristics when produced in the gas phase by electrospray ionization (ESI). While a CCS can help distinguish between structures of radically different types, one cannot expect a single number to differentiate similar conformations of a complex molecule. Molecular spectroscopy has also played an increasingly important role for structural characterization of biomolecular ions. Spectroscopic measurements, particularly when performed at cryogenic temperatures, can be extremely sensitive to small changes in a molecule's conformation and provide tight constraints for calculations of biomolecular structures. However, spectra of complex molecules can be heavily congested due to the presence of multiple stable conformations, each of which can have a distinct spectrum. This congestion can inhibit spectral analysis and complicate the extraction of structural information. Even when a single conformation is present, the conformational search process needed to match a measured spectrum with a computed structure can be overwhelming for peptides of more than a few amino acids, for example. We have recently combined ion mobility spectrometry and cryogenic ion spectroscopy (CIS) to characterize the structures of gas-phase biomolecular ions. In this Account, we illustrate how the coupling of IMS and CIS is by nature synergistic. On the one hand, IMS can be used as a conformational filter to reduce spectral congestion that arises from heterogeneous samples, facilitating structural analysis. On the other hand, highly resolved, cryogenic spectra can serve as a selective detector for IMS that can increase the effective resolution and hence the maximum number of distinct species that can be detected. Taken together, spectra and CCS measurements on the same system facilitates structural analysis and strengthens the conclusions that can be drawn from each type of data. After describing different approaches to combining these two techniques in such a way as to simplify the data obtained from each one separately, we present two examples that illustrate the type of insight gained from using spectra and CCS data together for characterizing gas-phase biomolecular ions. In one example, the CCS is used as a constraint for quantum chemical structure calculations of kinetically trapped species, where a lowest-energy criterion is not applicable. In a second example, we use both the CCS and a cryogenic infrared spectrum as a means to distinguish isomeric glycans.
Chaotic structure of oil prices

NASA Astrophysics Data System (ADS)

Bildirici, Melike; Sonustun, Fulya Ozaksoy

2018-01-01

The fluctuations in oil prices are very complicated and therefore, it is unable to predict its effects on economies. For modelling complex system of oil prices, linear economic models are not sufficient and efficient tools. Thus, in recent years, economists attached great attention to non-linear structure of oil prices. For analyzing this relationship, GARCH types of models were used in some papers. Distinctively from the other papers, in this study, we aimed to analyze chaotic pattern of oil prices. Thus, it was used the Lyapunov Exponents and Hennon Map to determine chaotic behavior of oil prices for the selected time period.
Global Displacement of Canine Parvovirus by a Host-Adapted Variant: Structural Comparison between Pandemic Viruses with Distinct Host Ranges

PubMed Central

Organtini, Lindsey J.; Allison, Andrew B.; Lukk, Tiit; Parrish, Colin R.

2014-01-01

Canine parvovirus type 2 (CPV-2) emerged in 1978 and spread worldwide within 2 years. Subsequently, CPV-2 was completely replaced by the variant CPV-2a, which is characterized by four specific capsid (VP2) mutations. The X-ray crystal structure of the CPV-2a capsid shows that each mutation confers small local changes. The loss of a hydrogen bond and introduction of a glycine residue likely introduce flexibility to sites that control interactions with the host receptor, antibodies, and sialic acids. PMID:25410876
The rodent ultrasound production mechanism.

PubMed

Roberts, L H

1975-03-01

Rodents produce two types of sounds, audible and ultrasonic, that differ markedly in physical structure. Studies of sound production in light gases show that whereas the audible cries appear to be produced, as in the case of most other mammals, by vibrating structures in the larynx, the ultrasonic cries are produced by a different mechanism, probably a whistle. 'Bird-call' whistles are shown to have all the properties of rodent ultrasonic cries and to mimic them in almost every detail. Thus it is concluded that rodents have two distinct sound production mechanisms, one for audible cries and one for ultrasonic cries.
Structural Genomics of Protein Phosphatases

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

Almo,S.; Bonanno, J.; Sauder, J.

The New York SGX Research Center for Structural Genomics (NYSGXRC) of the NIGMS Protein Structure Initiative (PSI) has applied its high-throughput X-ray crystallographic structure determination platform to systematic studies of all human protein phosphatases and protein phosphatases from biomedically-relevant pathogens. To date, the NYSGXRC has determined structures of 21 distinct protein phosphatases: 14 from human, 2 from mouse, 2 from the pathogen Toxoplasma gondii, 1 from Trypanosoma brucei, the parasite responsible for African sleeping sickness, and 2 from the principal mosquito vector of malaria in Africa, Anopheles gambiae. These structures provide insights into both normal and pathophysiologic processes, including transcriptionalmore » regulation, regulation of major signaling pathways, neural development, and type 1 diabetes. In conjunction with the contributions of other international structural genomics consortia, these efforts promise to provide an unprecedented database and materials repository for structure-guided experimental and computational discovery of inhibitors for all classes of protein phosphatases.« less
Solution structure of CXCL5--a novel chemokine and adipokine implicated in inflammation and obesity.

PubMed

Sepuru, Krishna Mohan; Poluri, Krishna Mohan; Rajarathnam, Krishna

2014-01-01

The chemokine CXCL5 is selectively expressed in highly specialized cells such as epithelial type II cells in the lung and white adipose tissue macrophages in muscle, where it mediates diverse functions from combating microbial infections by regulating neutrophil trafficking to promoting obesity by inhibiting insulin signaling. Currently very little is known regarding the structural basis of how CXCL5 mediates its novel functions. Towards this missing knowledge, we have solved the solution structure of the CXCL5 dimer by NMR spectroscopy. CXCL5 is a member of a subset of seven CXCR2-activating chemokines (CAC) that are characterized by the highly conserved ELR motif in the N-terminal tail. The structure shows that CXCL5 adopts the typical chemokine fold, but also reveals several distinct differences in the 30 s loop and N-terminal residues; not surprisingly, crosstalk between N-terminal and 30 s loop residues have been implicated as a major determinant of receptor activity. CAC function also involves binding to highly sulfated glycosaminoglycans (GAG), and the CXCL5 structure reveals a distinct distribution of positively charged residues, suggesting that differences in GAG interactions also influence function. The availability of the structure should now facilitate the design of experiments to better understand the molecular basis of various CXCL5 functions, and also serve as a template for the design of inhibitors for use in a clinical setting.
A multi-cloak bifunctional device

NASA Astrophysics Data System (ADS)

Raza, Muhammad; Liu, Yichao; Ma, Yungui

2015-01-01

Invisibility cloak has attracted the attention of electromagnetic researchers due to its magical properties and marvelous potential applications in the field of applied physics and engineering. Recently, a multiphysics cloaking has put the new spirit into this field. In this paper, we introduce a device, composed of three shells and each shell works as an invisibility cloak for a specific physical phenomenon. Following this technique, a number of cloaks with different implementation approaches can be proposed for distinct physical phenomena in a single structure. Here, we restrict ourselves for the case of two physical behaviors: thermal and electrical conductivities. This type of multi-cloaking structure can be best used in mechanically designed structures to better control heating and electrical effects.
Heteroleptic Copper(I)-Based Complexes for Photocatalysis: Combinatorial Assembly, Discovery, and Optimization.

PubMed

Minozzi, Clémentine; Caron, Antoine; Grenier-Petel, Jean-Christophe; Santandrea, Jeffrey; Collins, Shawn K

2018-05-04

A library of 50 copper-based complexes derived from bisphosphines and diamines was prepared and evaluated in three mechanistically distinct photocatalytic reactions. In all cases, a copper-based catalyst was identified to afford high yields, where new heteroleptic complexes derived from the bisphosphine BINAP displayed high efficiency across all reaction types. Importantly, the evaluation of the library of copper complexes revealed that even when photophysical data is available, it is not always possible to predict which catalyst structure will be efficient or inefficient in a given process, emphasizing the advantages for catalyst structures with high modularity and structural variability. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
Structure of myostatin·follistatin-like 3: N-terminal domains of follistatin-type molecules exhibit alternate modes of binding.

PubMed

Cash, Jennifer N; Angerman, Elizabeth B; Kattamuri, Chandramohan; Nolan, Kristof; Zhao, Huaying; Sidis, Yisrael; Keutmann, Henry T; Thompson, Thomas B

2012-01-06

TGF-β family ligands are involved in a variety of critical physiological processes. For instance, the TGF-β ligand myostatin is a staunch negative regulator of muscle growth and a therapeutic target for muscle-wasting disorders. Therefore, it is important to understand the molecular mechanisms of TGF-β family regulation. One form of regulation is through inhibition by extracellular antagonists such as the follistatin (Fst)-type proteins. Myostatin is tightly controlled by Fst-like 3 (Fstl3), which is the only Fst-type molecule that has been identified in the serum bound to myostatin. Here, we present the crystal structure of myostatin in complex with Fstl3. The structure reveals that the N-terminal domain (ND) of Fstl3 interacts uniquely with myostatin as compared with activin A, because it utilizes different surfaces on the ligand. This results in conformational differences in the ND of Fstl3 that alter its position in the type I receptor-binding site of the ligand. We also show that single point mutations in the ND of Fstl3 are detrimental to ligand binding, whereas corresponding mutations in Fst have little effect. Overall, we have shown that the NDs of Fst-type molecules exhibit distinctive modes of ligand binding, which may affect overall affinity of ligand·Fst-type protein complexes.
An Evolutionary Perspective on Yeast Mating-Type Switching

PubMed Central

Hanson, Sara J.; Wolfe, Kenneth H.

2017-01-01

Cell differentiation in yeast species is controlled by a reversible, programmed DNA-rearrangement process called mating-type switching. Switching is achieved by two functionally similar but structurally distinct processes in the budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. In both species, haploid cells possess one active and two silent copies of the mating-type locus (a three-cassette structure), the active locus is cleaved, and synthesis-dependent strand annealing is used to replace it with a copy of a silent locus encoding the opposite mating-type information. Each species has its own set of components responsible for regulating these processes. In this review, we summarize knowledge about the function and evolution of mating-type switching components in these species, including mechanisms of heterochromatin formation, MAT locus cleavage, donor bias, lineage tracking, and environmental regulation of switching. We compare switching in these well-studied species to others such as Kluyveromyces lactis and the methylotrophic yeasts Ogataea polymorpha and Komagataella phaffii. We focus on some key questions: Which cells switch mating type? What molecular apparatus is required for switching? Where did it come from? And what is the evolutionary purpose of switching? PMID:28476860
Assembly of the Type II Secretion System such as Found in Vibrio cholerae Depends on the Novel Pilotin AspS

PubMed Central

Dunstan, Rhys A.; Heinz, Eva; Wijeyewickrema, Lakshmi C.; Pike, Robert N.; Purcell, Anthony W.; Evans, Timothy J.; Praszkier, Judyta; Robins-Browne, Roy M.; Strugnell, Richard A.; Korotkov, Konstantin V.; Lithgow, Trevor

2013-01-01

The Type II Secretion System (T2SS) is a molecular machine that drives the secretion of fully-folded protein substrates across the bacterial outer membrane. A key element in the machinery is the secretin: an integral, multimeric outer membrane protein that forms the secretion pore. We show that three distinct forms of T2SSs can be distinguished based on the sequence characteristics of their secretin pores. Detailed comparative analysis of two of these, the Klebsiella-type and Vibrio-type, showed them to be further distinguished by the pilotin that mediates their transport and assembly into the outer membrane. We have determined the crystal structure of the novel pilotin AspS from Vibrio cholerae, demonstrating convergent evolution wherein AspS is functionally equivalent and yet structurally unrelated to the pilotins found in Klebsiella and other bacteria. AspS binds to a specific targeting sequence in the Vibrio-type secretins, enhances the kinetics of secretin assembly, and homologs of AspS are found in all species of Vibrio as well those few strains of Escherichia and Shigella that have acquired a Vibrio-type T2SS. PMID:23326233
Heritability of Nociception IV: Neuropathic pain assays are genetically distinct across methods of peripheral nerve injury

PubMed Central

Young, Erin E.; Costigan, Michael; Herbert, Teri A.; Lariviere, William R.

2013-01-01

Prior genetic correlation analysis of 22 heritable behavioral measures of nociception and hypersensitivity in the mouse identified five genetically distinct pain types. In the present study, we reanalyzed that dataset and included the results of an additional nine assays of nociception and hypersensitivity to: 1) replicate the previously identified five pain types; 2) test whether any of the newly added pain assays represent novel genetically distinct pain types; 3) test the level of genetic relatedness among nine commonly employed neuropathic pain assays. Multivariate analysis of pairwise correlations between assays shows that the newly added zymosan-induced heat hypersensitivity assay does not conform to the two previously identified groups of heat hypersensitivity assays and cyclophosphamide-induced cystitis, the first organ-specific visceral pain model examined, is genetically distinct from other inflammatory assays. The four included mechanical hypersensitivity assays are genetically distinct, and do not comprise a single pain type as previously reported. Among the nine neuropathic pain assays including autotomy, chemotherapy, nerve ligation and spared nerve injury assays, at least four genetically distinct types of neuropathic sensory abnormalities were identified, corresponding to differences in nerve injury method. In addition, two itch assays and Comt genotype were compared to the expanded set of nociception and hypersensitivity assays. Comt genotype was strongly related only to spontaneous inflammatory nociception assays. These results indicate the priority for continued investigation of genetic mechanisms in several assays newly identified to represent genetically distinct pain types. PMID:24071598
Conservation of Dynamics Associated with Biological Function in an Enzyme Superfamily.

PubMed

Narayanan, Chitra; Bernard, David N; Bafna, Khushboo; Gagné, Donald; Chennubhotla, Chakra S; Doucet, Nicolas; Agarwal, Pratul K

2018-03-06

Enzyme superfamily members that share common chemical and/or biological functions also share common features. While the role of structure is well characterized, the link between enzyme function and dynamics is not well understood. We present a systematic characterization of intrinsic dynamics of over 20 members of the pancreatic-type RNase superfamily, which share a common structural fold. This study is motivated by the fact that the range of chemical activity as well as molecular motions of RNase homologs spans over 10 5 folds. Dynamics was characterized using a combination of nuclear magnetic resonance experiments and computer simulations. Phylogenetic clustering led to the grouping of sequences into functionally distinct subfamilies. Detailed characterization of the diverse RNases showed conserved dynamical traits for enzymes within subfamilies. These results suggest that selective pressure for the conservation of dynamical behavior, among other factors, may be linked to the distinct chemical and biological functions in an enzyme superfamily. Copyright © 2018 Elsevier Ltd. All rights reserved.
Nanomechanical properties of distinct fibrillar polymorphs of the protein α-synuclein.

PubMed

Makky, Ali; Bousset, Luc; Polesel-Maris, Jérôme; Melki, Ronald

2016-11-30

Alpha-synuclein (α-Syn) is a small presynaptic protein of 140 amino acids. Its pathologic intracellular aggregation within the central nervous system yields protein fibrillar inclusions named Lewy bodies that are the hallmarks of Parkinson's disease (PD). In solution, pure α-Syn adopts an intrinsically disordered structure and assembles into fibrils that exhibit considerable morphological heterogeneity depending on their assembly conditions. We recently established tightly controlled experimental conditions allowing the assembly of α-Syn into highly homogeneous and pure polymorphs. The latter exhibited differences in their shape, their structure but also in their functional properties. We have conducted an AFM study at high resolution and performed a statistical analysis of fibrillar α-Syn shape and thermal fluctuations to calculate the persistence length to further assess the nanomechanical properties of α-Syn polymorphs. Herein, we demonstrated quantitatively that distinct polymorphs made of the same protein (wild-type α-Syn) show significant differences in their morphology (height, width and periodicity) and physical properties (persistence length, bending rigidity and axial Young's modulus).
Nanomechanical properties of distinct fibrillar polymorphs of the protein α-synuclein

NASA Astrophysics Data System (ADS)

Makky, Ali; Bousset, Luc; Polesel-Maris, Jérôme; Melki, Ronald

2016-11-01

Alpha-synuclein (α-Syn) is a small presynaptic protein of 140 amino acids. Its pathologic intracellular aggregation within the central nervous system yields protein fibrillar inclusions named Lewy bodies that are the hallmarks of Parkinson’s disease (PD). In solution, pure α-Syn adopts an intrinsically disordered structure and assembles into fibrils that exhibit considerable morphological heterogeneity depending on their assembly conditions. We recently established tightly controlled experimental conditions allowing the assembly of α-Syn into highly homogeneous and pure polymorphs. The latter exhibited differences in their shape, their structure but also in their functional properties. We have conducted an AFM study at high resolution and performed a statistical analysis of fibrillar α-Syn shape and thermal fluctuations to calculate the persistence length to further assess the nanomechanical properties of α-Syn polymorphs. Herein, we demonstrated quantitatively that distinct polymorphs made of the same protein (wild-type α-Syn) show significant differences in their morphology (height, width and periodicity) and physical properties (persistence length, bending rigidity and axial Young’s modulus).
Meta-analyses of structural regional cerebral effects in type 1 and type 2 diabetes.

PubMed

Moulton, Calum D; Costafreda, Sergi G; Horton, Paul; Ismail, Khalida; Fu, Cynthia H Y

2015-12-01

Diabetes is associated with macrovascular and microvascular complications and is a major risk factor for neurological and psychiatric disorders, such as dementia and depression. Type 1 diabetes (T1DM) and type 2 diabetes (T2DM) have distinct etiologies and pathophysiological effects while sharing a common endpoint of persistent hyperglycemia. Neuroimaging studies in T1DM have revealed reductions in numerous regions, including the parahippocampal and occipital regions, while in T2DM there have been numerous reports of hippocampal atrophy. This meta-analysis aimed to identify consistent regional abnormalities in cerebral structures in T1DM and T2DM respectively, and also to examine the impact of potential confounds, including age, depression and vascular risk factors. Neuroimaging studies of both voxel-based morphometry (VBM) data and volumetric data were included. Ten T1DM studies (n = 613 patients) and 23 T2DM studies (n = 1364 patients) fulfilled inclusion criteria. The T1DM meta-analysis revealed reduced bilateral thalamus grey matter density in adults. The T2DM meta-analysis revealed reduced global brain volume and regional atrophy in the hippocampi, basal ganglia, and orbitofrontal and occipital lobes. Moreover, hippocampal atrophy in T2DM was not modified by hypertension, although there were more marked reductions in younger patients relative to healthy controls. In conclusion, T1DM and T2DM demonstrated distinct cerebral effects with generalised and specific target areas of grey matter reduction. Thalamic atrophy in T1DM may be a substrate of associated cognitive deficits. In T2DM, global cerebral atrophy may reflect atherosclerotic factors, while hippocampal atrophy was an independent effect providing a potential common neuropathological etiology for the comorbidity of T2DM with dementia and depression.
Selective depletion of uropathogenic E. coli from the gut by a FimH antagonist

PubMed Central

Spaulding, Caitlin N.; Klein, Roger D.; Ruer, Ségolène; Kau, Andrew L.; Schreiber, Henry L.; Cusumano, Zachary T.; Dodson, Karen W.; Pinkner, Jerome S.; Fremont, Daved H.; Janetka, James W.; Remaut, Han; Gordon, Jeffrey I.; Hultgren, Scott J.

2017-01-01

Summary Urinary tract infections (UTI) caused by uropathogenic E. coli (UPEC) affect 150 million people annually1,2. Despite effective antibiotic therapy, 30–50% of patients experience recurrent UTI (rUTI)1. Additionally, the growing prevelance of UPEC resistant to last-line antibiotic treatments, and more recently carbapenems and colistin, make UTIs a prime example of the antibiotic-resistance crisis and emphasize the need for new approaches to treat and prevent bacterial infections3–5. UPEC strains establish reservoirs in the gut from which they are shed in the feces, can colonize the peri-urethral area or vagina and subsequently ascend through the urethra to the urinary tract, where they cause UTI6. UPEC isolates encode up to 16 distinct chaperone-usher pathway (CUP) pili and each pilus type likely enables colonization of a habitat in the host or environment7. For example, the type 1 pilus adhesin, FimH, binds mannose on the bladder surface, mediating bladder colonization. However, little is known regarding the mechanisms underlying UPEC persistence in the gut5. Using a mouse model, we found that F17-like and type 1 pili promote intestinal colonization and show distinct binding to epithelial cells distributed along colonic crypts. Phylogenomic and structural analyses reveal that F17-like pili are closely related to pilus types carried by intestinal pathogens, but are restricted to extra-intestinal pathogenic E. coli. Moreover, we show that targeting FimH with a high-affinity inhibitor, mannoside M4284, reduces intestinal colonization of genetically diverse UPEC isolates, while simultaneously treating UTI, without significantly disrupting the the structural configuration of the gut microbiota. By selectively depleting the intestinal UPEC reservoir, mannosides could significantly reduce the rate of UTI and rUTI. PMID:28614296
Genetic address book for retinal cell types.

PubMed

Siegert, Sandra; Scherf, Brigitte Gross; Del Punta, Karina; Didkovsky, Nick; Heintz, Nathaniel; Roska, Botond

2009-09-01

The mammalian brain is assembled from thousands of neuronal cell types that are organized in distinct circuits to perform behaviorally relevant computations. Transgenic mouse lines with selectively marked cell types would facilitate our ability to dissect functional components of complex circuits. We carried out a screen for cell type-specific green fluorescent protein expression in the retina using BAC transgenic mice from the GENSAT project. Among others, we identified mouse lines in which the inhibitory cell types of the night vision and directional selective circuit were selectively labeled. We quantified the stratification patterns to predict potential synaptic connectivity between marked cells of different lines and found that some of the lines enabled targeted recordings and imaging of cell types from developing or mature retinal circuits. Our results suggest the potential use of a stratification-based screening approach for characterizing neuronal circuitry in other layered brain structures, such as the neocortex.

Differences between the bacterial community structures of first- and multi-year Arctic sea ice in the Lincoln Sea.

NASA Astrophysics Data System (ADS)

Hatam, I.; Beckers, J. F.; Haas, C.; Lanoil, B. D.

2014-12-01

The Arctic sea ice composition is shifting from predominantly thick perennial ice (multiyear ice -MYI) to thinner, seasonal ice (first year ice -FYI). The effects of the shift on the Arctic ecosystem and macro-organisms of the Arctic Ocean have been the focus of many studies and have also been extensively debated in the public domain. The effect of this shift on the microbial constituents of the Arctic sea ice has been grossly understudied, although it is a vast habitat for a microbial community that plays a key role in the biogeochemical cycles and energy flux of the Arctic Ocean. MYI and FYI differ in many chemical and physical attributes (e.g. bulk salinity, brine volume, thickness and age), therefore comparing and contrasting the structure and composition of microbial communities from both ice types will be crucial to our understanding of the challenges that the Arctic Ocean ecosystem faces as MYI cover continues to decline. Here, we contend that due to the differences in abiotic conditions, differences in bacterial community structure will be greater between samples from different ice types than within samples from the same ice type. We also argue that since FYI is younger, its community structure will be closer to that of the surface sea water (SW). To test this hypotheses, we extracted DNA and used high throughput sequencing to sequence V1-V3 regions of the bacterial 16s rRNA gene from 10 sea ice samples (5 for each ice type) and 4 surface sea water (SW) collected off the shore of Northern Ellesmere Island, NU, CAN, during the month of May from 2010-2012. Our results showed that observed richness was higher in FYI than MYI. FYI and MYI shared 26% and 36% of their observed richness respectively. While FYI shared 23% of its observed richness with SW, MYI only shared 17%. Both ice types showed similar levels of endemism (61% of the observed richness). This high level of endemism results in the grouping of microbial communities from MYI, FYI, and SW to three distinct groups when looking at membership (jclass dissimilarity index, tested by AMOVA). However, when looking at composition (θYC dissimilarity index) while communities from MYI and SW samples still clustered as two distinct groups, communities from FYI samples show no significant clustering (tested by AMOVA).
Fine structure and optical properties of biological polarizers in crustaceans and cephalopods

NASA Astrophysics Data System (ADS)

Chiou, Tsyr-Huei; Caldwell, Roy L.; Hanlon, Roger T.; Cronin, Thomas W.

2008-04-01

The lighting of the underwater environment is constantly changing due to attenuation by water, scattering by suspended particles, as well as the refraction and reflection caused by the surface waves. These factors pose a great challenge for marine animals which communicate through visual signals, especially those based on color. To escape this problem, certain cephalopod mollusks and stomatopod crustaceans utilize the polarization properties of light. While the mechanisms behind the polarization vision of these two animal groups are similar, several distinctive types of polarizers (i.e. the structure producing the signal) have been found in these animals. To gain a better knowledge of how these polarizers function, we studied the relationships between fine structures and optical properties of four types of polarizers found in cephalopods and stomatopods. Although all the polarizers share a somewhat similar spectral range, around 450- 550 nm, the reflectance properties of the signals and the mechanisms used to produce them have dramatic differences. In cephalopods, stack-plates polarizers produce the polarization patterns found on the arms and around their eyes. In stomatopods, we have found one type of beam-splitting polarizer based on photonic structures and two absorptive polarizer types based on dichroic molecules. These stomatopod polarizers may be found on various appendages, and on the cuticle covering dorsal or lateral sides of the animal. Since the efficiencies of all these polarizer types are somewhat sensitive to the change of illumination and viewing angle, how these animals compensate with different behaviors or fine structural features of the polarizer also varies.
Circuit variability interacts with excitatory-inhibitory diversity of interneurons to regulate network encoding capacity.

PubMed

Tsai, Kuo-Ting; Hu, Chin-Kun; Li, Kuan-Wei; Hwang, Wen-Liang; Chou, Ya-Hui

2018-05-23

Local interneurons (LNs) in the Drosophila olfactory system exhibit neuronal diversity and variability, yet it is still unknown how these features impact information encoding capacity and reliability in a complex LN network. We employed two strategies to construct a diverse excitatory-inhibitory neural network beginning with a ring network structure and then introduced distinct types of inhibitory interneurons and circuit variability to the simulated network. The continuity of activity within the node ensemble (oscillation pattern) was used as a readout to describe the temporal dynamics of network activity. We found that inhibitory interneurons enhance the encoding capacity by protecting the network from extremely short activation periods when the network wiring complexity is very high. In addition, distinct types of interneurons have differential effects on encoding capacity and reliability. Circuit variability may enhance the encoding reliability, with or without compromising encoding capacity. Therefore, we have described how circuit variability of interneurons may interact with excitatory-inhibitory diversity to enhance the encoding capacity and distinguishability of neural networks. In this work, we evaluate the effects of different types and degrees of connection diversity on a ring model, which may simulate interneuron networks in the Drosophila olfactory system or other biological systems.
Surgical Management of Compound Odontoma Associated with Unerupted Tooth

PubMed Central

Marini, Roberta; Pacifici, Luciano

2015-01-01

Odontomas represent the most common type of odontogenic benign jaws tumors among patients younger than 20 years of age. These tumors are composed of enamel, dentine, cementum, and pulp tissue. According to the World Health Organization classification, two distinct types of odontomas are acknowledged: complex and compound odontoma. In complex odontomas, all dental tissues are formed, but appeared without an organized structure. In compound odontomas, all dental tissues are arranged in numerous tooth-like structures known as denticles. Compound odontomas are often associated with impacted adjacent permanent teeth and their surgical removal represents the best therapeutic option. A case of a 20-year-old male patient with a compound odontoma-associated of impacted maxillary canine is presented. A minimally invasive surgical technique is adopted to remove the least amount of bone tissue as far as possible. PMID:26199762
Nanostructure and molecular mechanics of spider dragline silk protein assemblies

PubMed Central

Keten, Sinan; Buehler, Markus J.

2010-01-01

Spider silk is a self-assembling biopolymer that outperforms most known materials in terms of its mechanical performance, despite its underlying weak chemical bonding based on H-bonds. While experimental studies have shown that the molecular structure of silk proteins has a direct influence on the stiffness, toughness and failure strength of silk, no molecular-level analysis of the nanostructure and associated mechanical properties of silk assemblies have been reported. Here, we report atomic-level structures of MaSp1 and MaSp2 proteins from the Nephila clavipes spider dragline silk sequence, obtained using replica exchange molecular dynamics, and subject these structures to mechanical loading for a detailed nanomechanical analysis. The structural analysis reveals that poly-alanine regions in silk predominantly form distinct and orderly beta-sheet crystal domains, while disorderly regions are formed by glycine-rich repeats that consist of 31-helix type structures and beta-turns. Our structural predictions are validated against experimental data based on dihedral angle pair calculations presented in Ramachandran plots, alpha-carbon atomic distances, as well as secondary structure content. Mechanical shearing simulations on selected structures illustrate that the nanoscale behaviour of silk protein assemblies is controlled by the distinctly different secondary structure content and hydrogen bonding in the crystalline and semi-amorphous regions. Both structural and mechanical characterization results show excellent agreement with available experimental evidence. Our findings set the stage for extensive atomistic investigations of silk, which may contribute towards an improved understanding of the source of the strength and toughness of this biological superfibre. PMID:20519206
Nanostructure and molecular mechanics of spider dragline silk protein assemblies.

PubMed

Keten, Sinan; Buehler, Markus J

2010-12-06

Spider silk is a self-assembling biopolymer that outperforms most known materials in terms of its mechanical performance, despite its underlying weak chemical bonding based on H-bonds. While experimental studies have shown that the molecular structure of silk proteins has a direct influence on the stiffness, toughness and failure strength of silk, no molecular-level analysis of the nanostructure and associated mechanical properties of silk assemblies have been reported. Here, we report atomic-level structures of MaSp1 and MaSp2 proteins from the Nephila clavipes spider dragline silk sequence, obtained using replica exchange molecular dynamics, and subject these structures to mechanical loading for a detailed nanomechanical analysis. The structural analysis reveals that poly-alanine regions in silk predominantly form distinct and orderly beta-sheet crystal domains, while disorderly regions are formed by glycine-rich repeats that consist of 3₁-helix type structures and beta-turns. Our structural predictions are validated against experimental data based on dihedral angle pair calculations presented in Ramachandran plots, alpha-carbon atomic distances, as well as secondary structure content. Mechanical shearing simulations on selected structures illustrate that the nanoscale behaviour of silk protein assemblies is controlled by the distinctly different secondary structure content and hydrogen bonding in the crystalline and semi-amorphous regions. Both structural and mechanical characterization results show excellent agreement with available experimental evidence. Our findings set the stage for extensive atomistic investigations of silk, which may contribute towards an improved understanding of the source of the strength and toughness of this biological superfibre.
An evaluation of WRF microphysics schemes for simulating the warm-type heavy rain over the Korean peninsula

NASA Astrophysics Data System (ADS)

Song, Hwan-Jin; Sohn, Byung-Ju

2018-01-01

The Korean peninsula is the region of distinctly showing the heavy rain associated with relatively low storm height and small ice water content in the upper part of cloud system (i.e., so-called warm-type heavy rainfall). The satellite observations for the warmtype rain over Korea led to a conjecture that the cloud microphysics parameterization suitable for the continental deep convection may not work well for the warm-type heavy rainfall over the Korean peninsula. Therefore, there is a growing need to examine the performance of cloud microphysics schemes for simulating the warm-type heavy rain structures over the Korean peninsula. This study aims to evaluate the capabilities of eight microphysics schemes in the Weather Research and Forecasting (WRF) model how warmtype heavy rain structures can be simulated, in reference to the Tropical Rainfall Measuring Mission (TRMM) Precipitation Radar (PR) reflectivity measurements. The results indicate that the WRF Double Moment 6-class (WDM6) scheme simulated best the vertical structure of warm-type heavy rain by virtue of a reasonable collisioncoalescence process between liquid droplets and the smallest amount of snow. Nonetheless the WDM6 scheme appears to have limitations that need to be improved upon for a realistic reflectivity structure, in terms of the reflectivity slope below the melting layer, discontinuity in reflectivity profiles around the melting layer, and overestimation of upper-level reflectivity due to high graupel content.
Propulsion Systems Panel deliberations

NASA Technical Reports Server (NTRS)

Bianca, Carmelo J.; Miner, Robert; Johnston, Lawrence M.; Bruce, R.; Dennies, Daniel P.; Dickenson, W.; Dreshfield, Robert; Karakulko, Walt; Mcgaw, Mike; Munafo, Paul M.

1993-01-01

The Propulsion Systems Panel was established because of the specialized nature of many of the materials and structures technology issues related to propulsion systems. This panel was co-chaired by Carmelo Bianca, MSFC, and Bob Miner, LeRC. Because of the diverse range of missions anticipated for the Space Transportation program, three distinct propulsion system types were identified in the workshop planning process: liquid propulsion systems, solid propulsion systems and nuclear electric/nuclear thermal propulsion systems.
Propulsion Systems Panel deliberations

NASA Astrophysics Data System (ADS)

Bianca, Carmelo J.; Miner, Robert; Johnston, Lawrence M.; Bruce, R.; Dennies, Daniel P.; Dickenson, W.; Dreshfield, Robert; Karakulko, Walt; McGaw, Mike; Munafo, Paul M.

1993-02-01

The Propulsion Systems Panel was established because of the specialized nature of many of the materials and structures technology issues related to propulsion systems. This panel was co-chaired by Carmelo Bianca, MSFC, and Bob Miner, LeRC. Because of the diverse range of missions anticipated for the Space Transportation program, three distinct propulsion system types were identified in the workshop planning process: liquid propulsion systems, solid propulsion systems and nuclear electric/nuclear thermal propulsion systems.
Characterization of cell surface and extracellular matrix remodeling of Azospirillum brasilense chemotaxis-like 1 signal transduction pathway mutants by atomic force microscopy.

PubMed

Edwards, Amanda Nicole; Siuti, Piro; Bible, Amber N; Alexandre, Gladys; Retterer, Scott T; Doktycz, Mitchel J; Morrell-Falvey, Jennifer L

2011-01-01

To compete in complex microbial communities, bacteria must sense environmental changes and adjust cellular functions for optimal growth. Chemotaxis-like signal transduction pathways are implicated in the regulation of multiple behaviors in response to changes in the environment, including motility patterns, exopolysaccharide production, and cell-to-cell interactions. In Azospirillum brasilense, cell surface properties, including exopolysaccharide production, are thought to play a direct role in promoting flocculation. Recently, the Che1 chemotaxis-like pathway from A. brasilense was shown to modulate flocculation, suggesting an associated modulation of cell surface properties. Using atomic force microscopy, distinct changes in the surface morphology of flocculating A. brasilense Che1 mutant strains were detected. Whereas the wild-type strain produces a smooth mucosal extracellular matrix after 24 h, the flocculating Che1 mutant strains produce distinctive extracellular fibril structures. Further analyses using flocculation inhibition, lectin-binding assays, and comparison of lipopolysaccharides profiles suggest that the extracellular matrix differs between the cheA1 and the cheY1 mutants, despite an apparent similarity in the macroscopic floc structures. Collectively, these data indicate that disruption of the Che1 pathway is correlated with distinctive changes in the extracellular matrix, which likely result from changes in surface polysaccharides structure and/or composition. FEMS Microbiology Letters © 2010 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. No claim to original US government works.
Bacterial microbiomes of individual ectomycorrhizal Pinus sylvestris roots are shaped by soil horizon and differentially sensitive to nitrogen addition.

PubMed

Marupakula, Srisailam; Mahmood, Shahid; Jernberg, Johanna; Nallanchakravarthula, Srivathsa; Fahad, Zaenab A; Finlay, Roger D

2017-11-01

Plant roots select non-random communities of fungi and bacteria from the surrounding soil that have effects on their health and growth, but we know little about the factors influencing their composition. We profiled bacterial microbiomes associated with individual ectomycorrhizal Pinus sylvestris roots colonized by different fungi and analyzed differences in microbiome structure related to soils from distinct podzol horizons and effects of short-term additions of N, a growth-limiting nutrient commonly applied as a fertilizer, but known to influence patterns of carbon allocation to roots. Ectomycorrhizal roots growing in soil from different horizons harboured distinct bacterial communities. The fungi colonizing individual roots had a strong effect on the associated bacterial communities. Even closely related species within the same ectomycorrhizal genus had distinct bacterial microbiomes in unfertilized soil, but fertilization removed this specificity. Effects of N were rapid and context dependent, being influenced by both soil type and the particular ectomycorrhizal fungi involved. Fungal community composition changed in soil from all horizons, but bacteria only responded strongly to N in soil from the B horizon where community structure was different and bacterial diversity was significantly reduced, possibly reflecting changed carbon allocation patterns. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.
Extensive genetic diversity, unique population structure and evidence of genetic exchange in the sexually transmitted parasite Trichomonas vaginalis.

PubMed

Conrad, Melissa D; Gorman, Andrew W; Schillinger, Julia A; Fiori, Pier Luigi; Arroyo, Rossana; Malla, Nancy; Dubey, Mohan Lal; Gonzalez, Jorge; Blank, Susan; Secor, William E; Carlton, Jane M

2012-01-01

Trichomonas vaginalis is the causative agent of human trichomoniasis, the most common non-viral sexually transmitted infection world-wide. Despite its prevalence, little is known about the genetic diversity and population structure of this haploid parasite due to the lack of appropriate tools. The development of a panel of microsatellite makers and SNPs from mining the parasite's genome sequence has paved the way to a global analysis of the genetic structure of the pathogen and association with clinical phenotypes. Here we utilize a panel of T. vaginalis-specific genetic markers to genotype 235 isolates from Mexico, Chile, India, Australia, Papua New Guinea, Italy, Africa and the United States, including 19 clinical isolates recently collected from 270 women attending New York City sexually transmitted disease clinics. Using population genetic analysis, we show that T. vaginalis is a genetically diverse parasite with a unique population structure consisting of two types present in equal proportions world-wide. Parasites belonging to the two types (type 1 and type 2) differ significantly in the rate at which they harbor the T. vaginalis virus, a dsRNA virus implicated in parasite pathogenesis, and in their sensitivity to the widely-used drug, metronidazole. We also uncover evidence of genetic exchange, indicating a sexual life-cycle of the parasite despite an absence of morphologically-distinct sexual stages. Our study represents the first robust and comprehensive evaluation of global T. vaginalis genetic diversity and population structure. Our identification of a unique two-type structure, and the clinically relevant phenotypes associated with them, provides a new dimension for understanding T. vaginalis pathogenesis. In addition, our demonstration of the possibility of genetic exchange in the parasite has important implications for genetic research and control of the disease.
Mechanical adaptability of the Bouligand-type structure in natural dermal armour

NASA Astrophysics Data System (ADS)

Zimmermann, Elizabeth A.; Gludovatz, Bernd; Schaible, Eric; Dave, Neil K. N.; Yang, Wen; Meyers, Marc A.; Ritchie, Robert O.

2013-10-01

Arapaima gigas, a fresh water fish found in the Amazon Basin, resist predation by piranhas through the strength and toughness of their scales, which act as natural dermal armour. Arapaima scales consist of a hard, mineralized outer shell surrounding a more ductile core. This core region is composed of aligned mineralized collagen fibrils arranged in distinct lamellae. Here we show how the Bouligand-type (twisted plywood) arrangement of collagen fibril lamellae has a key role in developing their unique protective properties, by using in situ synchrotron small-angle X-ray scattering during mechanical tensile tests to observe deformation mechanisms in the fibrils. Specifically, the Bouligand-type structure allows the lamellae to reorient in response to the loading environment; remarkably, most lamellae reorient towards the tensile axis and deform in tension through stretching/sliding mechanisms, whereas other lamellae sympathetically rotate away from the tensile axis and compress, thereby enhancing the scale’s ductility and toughness to prevent fracture.
Cell fate control in the developing central nervous system

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

Guérout, Nicolas; Li, Xiaofei; Barnabé-Heider, Fanie, E-mail: Fanie.Barnabe-Heider@ki.se

The principal neural cell types forming the mature central nervous system (CNS) are now understood to be diverse. This cellular subtype diversity originates to a large extent from the specification of the earlier proliferating progenitor populations during development. Here, we review the processes governing the differentiation of a common neuroepithelial cell progenitor pool into mature neurons, astrocytes, oligodendrocytes, ependymal cells and adult stem cells. We focus on studies performed in mice and involving two distinct CNS structures: the spinal cord and the cerebral cortex. Understanding the origin, specification and developmental regulators of neural cells will ultimately impact comprehension and treatmentsmore » of neurological disorders and diseases. - Highlights: • Similar mechanisms regulate cell fate in different CNS cell types and structures. • Cell fate regulators operate in a spatial–temporal manner. • Different neural cell types rely on the generation of a diversity of progenitor cells. • Cell fate decision is dictated by the integration of intrinsic and extrinsic signals.« less
Unique Conformation in a Natural Interruption Sequence of Type XIX Collagen Revealed by Its High-Resolution Crystal Structure.

PubMed

Xu, Tingting; Zhou, Cong-Zhao; Xiao, Jianxi; Liu, Jinsong

2018-02-20

Naturally occurring interruptions in nonfibrillar collagen play key roles in molecular flexibility, collagen degradation, and ligand binding. The structural feature of the interruption sequences and the molecular basis for their functions have not been well studied. Here, we focused on a G5G type natural interruption sequence G-POALO-G from human type XIX collagen, a homotrimer collagen, as this sequence possesses distinct properties compared with those of a pathological similar Gly mutation sequence in collagen mimic peptides. We determined the crystal structures of the host-guest peptide (GPO) 3 -GPOALO-(GPO) 4 to 1.03 Å resolution in two crystal forms. In these structures, the interruption zone brings localized disruptions to the triple helix and introduces a light 6-8° bend with the same directional preference to the whole molecule, which may correspond structurally to the first physiological kink site in type XIX collagen. Furthermore, at the G5G interruption site, the presence of Ala and Leu residues, both with free N-H groups, allows the formation of more direct and water-mediated interchain hydrogen bonds than in the related Gly → Ala structure. These could partly explain the difference in thermal stability between the different interruptions. In addition, our structures provide a detailed view of the dynamic property of such an interrupted zone with respect to hydrogen bonding topology, torsion angles, and helical parameters. Our results, for the first time, also identified the binding of zinc to the end of the triple helix. These findings will shed light on how the interruption sequence influences the conformation of the collagen molecule and provide a structural basis for further functional studies.
Architectural Design Drives the Biogeography of Indoor Bacterial Communities

PubMed Central

O’Connor, Timothy K.; Mhuireach, Gwynne; Northcutt, Dale; Kline, Jeff; Moriyama, Maxwell; Brown, G. Z.; Bohannan, Brendan J. M.; Green, Jessica L.

2014-01-01

Background Architectural design has the potential to influence the microbiology of the built environment, with implications for human health and well-being, but the impact of design on the microbial biogeography of buildings remains poorly understood. In this study we combined microbiological data with information on the function, form, and organization of spaces from a classroom and office building to understand how design choices influence the biogeography of the built environment microbiome. Results Sequencing of the bacterial 16S gene from dust samples revealed that indoor bacterial communities were extremely diverse, containing more than 32,750 OTUs (operational taxonomic units, 97% sequence similarity cutoff), but most communities were dominated by Proteobacteria, Firmicutes, and Deinococci. Architectural design characteristics related to space type, building arrangement, human use and movement, and ventilation source had a large influence on the structure of bacterial communities. Restrooms contained bacterial communities that were highly distinct from all other rooms, and spaces with high human occupant diversity and a high degree of connectedness to other spaces via ventilation or human movement contained a distinct set of bacterial taxa when compared to spaces with low occupant diversity and low connectedness. Within offices, the source of ventilation air had the greatest effect on bacterial community structure. Conclusions Our study indicates that humans have a guiding impact on the microbial biodiversity in buildings, both indirectly through the effects of architectural design on microbial community structure, and more directly through the effects of human occupancy and use patterns on the microbes found in different spaces and space types. The impact of design decisions in structuring the indoor microbiome offers the possibility to use ecological knowledge to shape our buildings in a way that will select for an indoor microbiome that promotes our health and well-being. PMID:24489843
Discriminative Stimulus Effects of Psychostimulants and Hallucinogens in S(+)-3,4-Methylenedioxymethamphetamine (MDMA) and R(−)-MDMA Trained Mice

PubMed Central

Murnane, K. S.; Murai, N.; Howell, L. L.

2009-01-01

3,4-Methylenedioxymethamphetamine (MDMA) is a substituted phenethylamine more commonly known as the drug of abuse “ecstasy.” The acute and persistent neurochemical effects of MDMA in the mice are distinct from those in other species. MDMA shares biological effects with both amphetamine-type stimulants and mescaline-type hallucinogens, which may be attributable to distinct effects of its two enantiomers, both of which are active in vivo. In this regard, among the substituted phenethylamines, R(−)-enantiomers tend to have hallucinogen-like effects, whereas S(+)-enantiomers tend to have stimulant-like effects. In the present study, mice were trained to discriminate S(+)- or R(−)-MDMA from vehicle. Drug substitution tests were then undertaken with the structurally similar phenethylamine dopamine/norepinephrine releaser S(+)-amphetamine, the structurally dissimilar tropane nonselective monoamine reuptake inhibitor cocaine, the structurally similar phenethylamine 5-hydroxytryptamine (5-HT)2A agonist 2,5-dimethoxy-4-(n)-propylthiophenethylamine (2C-T-7), and the structurally dissimilar mixed action tryptamine 5-HT2A agonist/monoamine reuptake inhibitor N,N-dipropyltryptamine (DPT). S(+)-amphetamine fully substituted in the S(+)-MDMA-treated animals but did not substitute for the R(−)-MDMA cue. 2C-T-7 fully substituted in the R(−)-MDMA-trained animals but did not substitute for the S(+)-MDMA cue. Cocaine and DPT substituted for both training drugs, but whereas cocaine was more potent in S(+)-MDMA-trained mice, DPT was more potent in R(−)-MDMA-trained mice. These data suggest that qualitative differences in the discriminative stimulus effects of each stereoisomer of MDMA exist in mice and further our understanding of the complex nature of the interoceptive effects of MDMA. PMID:19684254
Accurate detection of hierarchical communities in complex networks based on nonlinear dynamical evolution

NASA Astrophysics Data System (ADS)

Zhuo, Zhao; Cai, Shi-Min; Tang, Ming; Lai, Ying-Cheng

2018-04-01

One of the most challenging problems in network science is to accurately detect communities at distinct hierarchical scales. Most existing methods are based on structural analysis and manipulation, which are NP-hard. We articulate an alternative, dynamical evolution-based approach to the problem. The basic principle is to computationally implement a nonlinear dynamical process on all nodes in the network with a general coupling scheme, creating a networked dynamical system. Under a proper system setting and with an adjustable control parameter, the community structure of the network would "come out" or emerge naturally from the dynamical evolution of the system. As the control parameter is systematically varied, the community hierarchies at different scales can be revealed. As a concrete example of this general principle, we exploit clustered synchronization as a dynamical mechanism through which the hierarchical community structure can be uncovered. In particular, for quite arbitrary choices of the nonlinear nodal dynamics and coupling scheme, decreasing the coupling parameter from the global synchronization regime, in which the dynamical states of all nodes are perfectly synchronized, can lead to a weaker type of synchronization organized as clusters. We demonstrate the existence of optimal choices of the coupling parameter for which the synchronization clusters encode accurate information about the hierarchical community structure of the network. We test and validate our method using a standard class of benchmark modular networks with two distinct hierarchies of communities and a number of empirical networks arising from the real world. Our method is computationally extremely efficient, eliminating completely the NP-hard difficulty associated with previous methods. The basic principle of exploiting dynamical evolution to uncover hidden community organizations at different scales represents a "game-change" type of approach to addressing the problem of community detection in complex networks.
Similar bowtie structures and distinct largest strong components are identified in the transcriptional regulatory networks of Arabidopsis thaliana during photomorphogenesis and heat shock.

PubMed

Luo, Shitao; Zhang, Fengming; Ruan, Yingfei; Li, Jie; Zhang, Zheng; Sun, Yan; Deng, Shixiong; Peng, Rui

2018-06-01

Photomorphogenesis and heat shock are critical biological processes of plants. A recent research constructed the transcriptional regulatory networks (TRNs) of Arabidopsis thaliana during these processes using DNase-seq. In this study, by strong decomposition, we revealed that each of these TRNs can be represented as a similar bowtie structure with only one non-trivial and distinct strong component. We further identified distinct patterns of variation of a few light-related genes in these bowtie structures during photomorphogenesis. These results suggest that bowtie structure may be a common property of TRNs of plants, and distinct variation patterns of genes in bowtie structures of TRNs during biological processes may reflect distinct functions. Overall, our study provides an insight into the molecular mechanisms underlying photomorphogenesis and heat shock, and emphasizes the necessity to investigate the strong connectivity structures while studying TRNs. Copyright © 2018 Elsevier B.V. All rights reserved.
Low Cost Structures, but How Much are we Paying for Them?

NASA Astrophysics Data System (ADS)

Gomez Molinero, Vincent

2014-06-01

Based on more than 37 years developing spacecraft structures - both for launchers starting with Ariane-1 up to the most modern ones and for satellites of any type - a critical review of the current trends, aiming specially to low cost solutions, will be presented.Airbus Defence and Space (CASA Espacio previously) has been developing structures for launchers and satellites during more than 4 decades. All types of spacecraft structures - primary and secondary ones, high stability ones and special critical cases like antenna reflectors, high stiffness structures and load carrying ones - have been developed using different types of materials and structural constructions. Although our main expertise is concentrated on composite structures, we have also developed many types of metallic ones, when the best solution was that one, not necessarily only based on pure technical reasons.From that perspective and experience, this paper tries to review the current trend of imposing the low cost as the main requirement for the development of satellites and launchers and its intrinsic characteristic of being a non- ending process: the spacecraft structures are never sufficiently cheaper.The main ways used today to justify low cost spacecraft structures will be reviewed trying to understand their rationale and some prejudices always present when the trade-off studies are performed. Some of the reviewed cost-killing factors will be (non-exhaustive list) Material type (i.e.: metallic vs composite). Low cost materials in general. Manufacturing process (i.e.: autoclave curing vs out-of-autoclave one). Automation in manufacturing. Automation in assembly. Automation in inspection and verification. Lean manufacturing techniques. Standardization. Some insight about how to solve this problem without losing our distinctive nature (we are developing high performance systems many of them unique prototypes and thought to work in environments not perfectly known and highly unknown in some cases) will be provided from the author's point of view.

Ectomycorrhizal fungal diversity and community structure associated with cork oak in different landscapes.

PubMed

Reis, Francisca; Valdiviesso, Teresa; Varela, Carolina; Tavares, Rui M; Baptista, Paula; Lino-Neto, Teresa

2018-05-01

Cork oak (Quercus suber L.) forests play an important ecological and economic role. Ectomycorrhizal fungi (ECMF) are key components for the sustainability and functioning of these ecosystems. The community structure and composition of ECMF associated with Q. suber in different landscapes of distinct Mediterranean bioclimate regions have not previously been compared. In this work, soil samples from cork oak forests residing in different bioclimates (arid, semi-arid, sub-humid, and humid) were collected and surveyed for ectomycorrhizal (ECM) root tips. A global analysis performed on 3565 ECM root tips revealed that the ECMF community is highly enriched in Russula, Tomentella, and Cenoccocum, which correspond to the ECMF genera that mainly contribute to community differences. The ECMF communities from the rainiest and the driest cork oak forests were distinct, with soils from the rainiest climates being more heterogeneous than those from the driest climates. The analyses of several abiotic factors on the ECMF communities revealed that bioclimate, precipitation, soil texture, and forest management strongly influenced ECMF structure. Shifts in ECMF with different hyphal exploration types were also detected among forests, with precipitation, forest system, and soil texture being the main drivers controlling their composition. Understanding the effects of environmental factors on the structuring of ECM communities could be the first step for promoting the sustainability of this threatened ecosystem.
Spatial diversity of bacterioplankton communities in surface water of northern South China Sea.

PubMed

Li, Jialin; Li, Nan; Li, Fuchao; Zou, Tao; Yu, Shuxian; Wang, Yinchu; Qin, Song; Wang, Guangyi

2014-01-01

The South China Sea is one of the largest marginal seas, with relatively frequent passage of eddies and featuring distinct spatial variation in the western tropical Pacific Ocean. Here, we report a phylogenetic study of bacterial community structures in surface seawater of the northern South China Sea (nSCS). Samples collected from 31 sites across large environmental gradients were used to construct clone libraries and yielded 2,443 sequences grouped into 170 OTUs. Phylogenetic analysis revealed 23 bacterial classes with major components α-, β- and γ-Proteobacteria, as well as Cyanobacteria. At class and genus taxon levels, community structure of coastal waters was distinctively different from that of deep-sea waters and displayed a higher diversity index. Redundancy analyses revealed that bacterial community structures displayed a significant correlation with the water depth of individual sampling sites. Members of α-Proteobacteria were the principal component contributing to the differences of the clone libraries. Furthermore, the bacterial communities exhibited heterogeneity within zones of upwelling and anticyclonic eddies. Our results suggested that surface bacterial communities in nSCS had two-level patterns of spatial distribution structured by ecological types (coastal VS. oceanic zones) and mesoscale physical processes, and also provided evidence for bacterial phylogenetic phyla shaped by ecological preferences.
MgCu metallic glass

NASA Astrophysics Data System (ADS)

Durandurdu, Murat

2018-03-01

We generate an amorphous MgCu model using the rapid solidification of the melt through a first-principles molecular dynamics approach within a generalised gradient approximation and reveal, for the first time, its structural features and mechanical properties in details. The liquid and glassy MgCu are found to acquire slightly distinct local structures. Yet in both forms of MgCu, most Cu atoms have a tendency to form the ideal and defective icosahedrons while Mg atoms are arranged in complex configurations. The mean coordination number of Cu and Mg at 300 K is 11.31 and 13.73, respectively. The short-range order of MgCu glass is projected to be different than the known crystalline MgCu and Mg2Cu phases. The mechanical properties of MgCu glass and the CsCl-type MgCu crystal are computed and compared. On the basis of the enthalpy analyses, a possible pressure-induced crystallisation of the MgCu glass into a CsCl-type structure is proposed to occur at around 11 GPa.
An insight into the active site of a type I DNA topoisomerase from the kinetoplastid protozoan Leishmania donovani

PubMed Central

Das, Aditi; Mandal, Chhabinath; Dasgupta, Arindam; Sengupta, Tanushri; Majumder, Hemanta K.

2002-01-01

DNA topoisomerases are ubiquitous enzymes that govern the topological interconversions of DNA thereby playing a key role in many aspects of nucleic acid metabolism. Recently determined crystal structures of topoisomerase fragments, representing nearly all the known subclasses, have been solved. The type IB enzymes are structurally distinct from other known topoisomerases but are similar to a class of enzymes referred to as tyrosine recombinases. A putative topoisomerase I open reading frame from the kinetoplastid Leishmania donovani was reported which shared a substantial degree of homology with type IB topoisomerases but having a variable C-terminus. Here we present a molecular model of the above parasite gene product, using the human topoisomerase I crystal structure in complex with a 22 bp oligonucleotide as a template. Our studies indicate that the overall structure of the parasite protein is similar to the human enzyme; however, major differences occur in the C-terminal loop, which harbors a serine in place of the usual catalytic tyrosine. Most other structural themes common to type IB topoisomerases, including secondary structural folds, hinged clamps that open and close to bind DNA, nucleophilic attack on the scissile DNA strand and formation of a ternary complex with the topoisomerase I inhibitor camptothecin could be visualized in our homology model. The validity of serine acting as the nucleophile in the case of the parasite protein model was corroborated with our biochemical mapping of the active site with topoisomerase I enzyme purified from L.donovani promastigotes. PMID:11809893
Expression of the Diabetes-Associated Gene TCF7L2 in Adult Mouse Brain

PubMed Central

LEE, SYANN; LEE, CHARLOTTE E.; ELIAS, CAROL F.; ELMQUIST, JOEL K.

2014-01-01

Polymorphisms of the gene TCF7L2 (transcription factor 7-like 2) are strongly associated with the development and progression of type 2 diabetes. TCF7L2 is important in the development of peripheral organs such as adipocytes, pancreas, and the intestine. However, very little is known about its expression elsewhere. In this study we used in situ hybridization histochemistry to show that TCF7L2 has a unique expression pattern in the mouse brain. TCF7L2 is expressed in two distinct populations. First, it is highly ex pressed in thalamic and tectal structures. Additionally, TCF7L2 mRNA is expressed at moderate to low levels in specific cells of the hypothalamus, preoptic nucleus, and circumventricular organs. Collectively, these patterns of expression suggest that TCF7L2 has distinct functions within the brain, with a general role in the development and maintenance of thalamic and midbrain neurons, and then a distinct role in autonomic homeostasis. PMID:19845015
Tauroursodeoxycholic acid prevents E22Q Alzheimer’s Aβ toxicity in human cerebral endothelial cells

PubMed Central

Viana, R. J. S.; Nunes, A. F.; Castro, R. E.; Ramalho, R. M.; Meyerson, J.; Fossati, S.; Ghiso, J.; Rostagno, A.

2009-01-01

The vasculotropic E22Q mutant of the amyloid-β (Aβ) peptide is associated with hereditary cerebral hemorrhage with amyloidosis Dutch type. The cellular mechanism(s) of toxicity and nature of the AβE22Q toxic assemblies are not completely understood. Comparative assessment of structural parameters and cell death mechanisms elicited in primary human cerebral endothelial cells by AβE22Q and wild-type Aβ revealed that only AβE22Q triggered the Bax mitochondrial pathway of apoptosis. AβE22Q neither matched the fast oligomerization kinetics of Aβ42 nor reached its predominant β-sheet structure, achieving a modest degree of oligomerization with a secondary structure that remained a mixture of β and random conformations. The endogenous molecule tauroursodeoxycholic acid (TUDCA) was a strong modulator of AβE22Q-triggered apoptosis but did not significantly change the secondary structures and fibrillogenic propensities of Aβ peptides. These data dissociate the pro-apoptotic properties of Aβ peptides from their distinct mechanisms of aggregation/fibrillization in vitro, providing new perspectives for modulation of amyloid toxicity. PMID:19189048
Duality, phase structures, and dilemmas in symmetric quantum games

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

Ichikawa, Tsubasa; Tsutsui, Izumi

Symmetric quantum games for 2-player, 2-qubit strategies are analyzed in detail by using a scheme in which all pure states in the 2-qubit Hilbert space are utilized for strategies. We consider two different types of symmetric games exemplified by the familiar games, the Battle of the Sexes (BoS) and the Prisoners' Dilemma (PD). These two types of symmetric games are shown to be related by a duality map, which ensures that they share common phase structures with respect to the equilibria of the strategies. We find eight distinct phase structures possible for the symmetric games, which are determined by themore » classical payoff matrices from which the quantum games are defined. We also discuss the possibility of resolving the dilemmas in the classical BoS, PD, and the Stag Hunt (SH) game based on the phase structures obtained in the quantum games. It is observed that quantization cannot resolve the dilemma fully for the BoS, while it generically can for the PD and SH if appropriate correlations for the strategies of the players are provided.« less
Community structural characteristics and the adoption of fluoridation.

PubMed Central

Smith, R A

1981-01-01

A study of community structural characteristics associated with fluoridation outcomes was conducted in 47 communities. A three-part outcome distinction was utilized: communities never having publicly considered the fluoridation issue, those rejecting it, and those accepting it. The independent variables reflect the complexity of the community social and economic structure, social integration, and the centralization of authority. Results of mean comparisons show statistically significant differences between the three outcome types on the independent variables. A series of discriminant analyses provides furtheor evidence of how the independent variables are associated with each outcome type. Non-considering communities are shown to be low in complexity, and high in social integration and the centralization of governmental authority. Rejecters are shown to be high in complexity, but low in social integration and centralized authority. Adopters are relatively high on all three sets of variables. Theretical reasoning is provided to support the hypothesis and why these results are expected. The utility of these results and structural explanations in general are discussed, especially for public/environmental health planning and political activities. PMID:7258427
Raman spectroscopic studies of defect structures and phase transition in hyper-stoichiometric UO(2+x).

PubMed

He, Heming; Shoesmith, David

2010-07-28

A method to determine the defect structures in hyper-stoichiometric UO(2+x) using a combination of XRD and Raman spectroscopy has been developed. A sequence of phase transitions, from cubic to tetragonal symmetry, occurs with increasing degree of non-stoichiometry. This sequence proceeds from a cubic phase through an intermediate t''-type tetragonal (axial ratio c/a = 1) phase to a final t-type tetragonal (c/a not = 1) phase. Four distinct structural defect regions can be identified in the stoichiometry range, UO(2) to U(3)O(7): (i) a random point defect structure (x (in UO(2+x)) < or = 0.05); (ii) a non-stoichiometry region (0.05 < or = x < or = 0.15) over which point defects are gradually eliminated and replaced by the Willis 2:2:2 cluster; (iii) a mixture of Willis and cuboctahedral clusters (0.15 < or = x < or = 0.23); (iv) the cuboctahedral cluster (x > or = 0.23). The geometry and steric arrangement of these defects is primarily determined by the concentration of the excess-oxygen interstitials.
Noninvasive two-photon imaging reveals retinyl ester storage structures in the eye

PubMed Central

Imanishi, Yoshikazu; Batten, Matthew L.; Piston, David W.; Baehr, Wolfgang; Palczewski, Krzysztof

2004-01-01

Visual sensation in vertebrates is triggered when light strikes retinal photoreceptor cells causing photoisomerization of the rhodopsin chromophore 11-cis-retinal to all-trans-retinal. The regeneration of preillumination conditions of the photoreceptor cells requires formation of 11-cis-retinal in the adjacent retinal pigment epithelium (RPE). Using the intrinsic fluorescence of all-trans-retinyl esters, noninvasive two-photon microscopy revealed previously uncharacterized structures (6.9 ± 1.1 μm in length and 0.8 ± 0.2 μm in diameter) distinct from other cellular organelles, termed the retinyl ester storage particles (RESTs), or retinosomes. These structures form autonomous all-trans-retinyl ester-rich intracellular compartments distinct from other organelles and colocalize with adipose differentiation-related protein. As demonstrated by in vivo experiments using wild-type mice, the RESTs participate in 11-cis-retinal formation. RESTs accumulate in Rpe65 −/− mice incapable of carrying out the enzymatic isomerization, and correspondingly, are absent in the eyes of Lrat −/− mice deficient in retinyl ester synthesis. These results indicate that RESTs located close to the RPE plasma membrane are essential components in 11-cis-retinal production. PMID:14745001
Structural Effects of Two Camelid Nanobodies Directed to Distinct C-Terminal Epitopes on α-Synuclein.

PubMed

El-Turk, Farah; Newby, Francisco N; De Genst, Erwin; Guilliams, Tim; Sprules, Tara; Mittermaier, Anthony; Dobson, Christopher M; Vendruscolo, Michele

2016-06-07

α-Synuclein is an intrinsically disordered protein whose aggregation is associated with Parkinson's disease and other related neurodegenerative disorders. Recently, two single-domain camelid antibodies (nanobodies) were shown to bind α-synuclein with high affinity. Herein, we investigated how these two nanobodies (NbSyn2 and NbSyn87), which are directed to two distinct epitopes within the C-terminal domain of α-synuclein, affect the conformational properties of this protein. Our results suggest that nanobody NbSyn2, which binds to the five C-terminal residues of α-synuclein (residues 136-140), does not disrupt the transient long-range interactions that generate a degree of compaction within the native structural ensemble of α-synuclein. In contrast, the data that we report indicate that NbSyn87, which targets a central region within the C-terminal domain (residues 118-128), has more substantial effects on the fluctuating secondary and tertiary structure of the protein. These results are consistent with the different effects that the two nanobodies have on the aggregation behavior of α-synuclein in vitro. Our findings thus provide new insights into the type of effects that nanobodies can have on the conformational ensemble of α-synuclein.
Nitrate and periplasmic nitrate reductases

PubMed Central

Sparacino-Watkins, Courtney; Stolz, John F.; Basu, Partha

2014-01-01

The nitrate anion is a simple, abundant and relatively stable species, yet plays a significant role in global cycling of nitrogen, global climate change, and human health. Although it has been known for quite some time that nitrate is an important species environmentally, recent studies have identified potential medical applications. In this respect the nitrate anion remains an enigmatic species that promises to offer exciting science in years to come. Many bacteria readily reduce nitrate to nitrite via nitrate reductases. Classified into three distinct types – periplasmic nitrate reductase (Nap), respiratory nitrate reductase (Nar) and assimilatory nitrate reductase (Nas), they are defined by their cellular location, operon organization and active site structure. Of these, Nap proteins are the focus of this review. Despite similarities in the catalytic and spectroscopic properties Nap from different Proteobacteria are phylogenetically distinct. This review has two major sections: in the first section, nitrate in the nitrogen cycle and human health, taxonomy of nitrate reductases, assimilatory and dissimilatory nitrate reduction, cellular locations of nitrate reductases, structural and redox chemistry are discussed. The second section focuses on the features of periplasmic nitrate reductase where the catalytic subunit of the Nap and its kinetic properties, auxiliary Nap proteins, operon structure and phylogenetic relationships are discussed. PMID:24141308
Cellulose synthase complexes act in a concerted fashion to synthesize highly aggregated cellulose in secondary cell walls of plants

PubMed Central

Li, Shundai; Bashline, Logan; Zheng, Yunzhen; Xin, Xiaoran; Huang, Shixin; Kong, Zhaosheng; Kim, Seong H.; Cosgrove, Daniel J.; Gu, Ying

2016-01-01

Cellulose, often touted as the most abundant biopolymer on Earth, is a critical component of the plant cell wall and is synthesized by plasma membrane-spanning cellulose synthase (CESA) enzymes, which in plants are organized into rosette-like CESA complexes (CSCs). Plants construct two types of cell walls, primary cell walls (PCWs) and secondary cell walls (SCWs), which differ in composition, structure, and purpose. Cellulose in PCWs and SCWs is chemically identical but has different physical characteristics. During PCW synthesis, multiple dispersed CSCs move along a shared linear track in opposing directions while synthesizing cellulose microfibrils with low aggregation. In contrast, during SCW synthesis, we observed swaths of densely arranged CSCs that moved in the same direction along tracks while synthesizing cellulose microfibrils that became highly aggregated. Our data support a model in which distinct spatiotemporal features of active CSCs during PCW and SCW synthesis contribute to the formation of cellulose with distinct structure and organization in PCWs and SCWs of Arabidopsis thaliana. This study provides a foundation for understanding differences in the formation, structure, and organization of cellulose in PCWs and SCWs. PMID:27647923
Cellulose synthase complexes act in a concerted fashion to synthesize highly aggregated cellulose in secondary cell walls of plants.

PubMed

Li, Shundai; Bashline, Logan; Zheng, Yunzhen; Xin, Xiaoran; Huang, Shixin; Kong, Zhaosheng; Kim, Seong H; Cosgrove, Daniel J; Gu, Ying

2016-10-04

Cellulose, often touted as the most abundant biopolymer on Earth, is a critical component of the plant cell wall and is synthesized by plasma membrane-spanning cellulose synthase (CESA) enzymes, which in plants are organized into rosette-like CESA complexes (CSCs). Plants construct two types of cell walls, primary cell walls (PCWs) and secondary cell walls (SCWs), which differ in composition, structure, and purpose. Cellulose in PCWs and SCWs is chemically identical but has different physical characteristics. During PCW synthesis, multiple dispersed CSCs move along a shared linear track in opposing directions while synthesizing cellulose microfibrils with low aggregation. In contrast, during SCW synthesis, we observed swaths of densely arranged CSCs that moved in the same direction along tracks while synthesizing cellulose microfibrils that became highly aggregated. Our data support a model in which distinct spatiotemporal features of active CSCs during PCW and SCW synthesis contribute to the formation of cellulose with distinct structure and organization in PCWs and SCWs of Arabidopsis thaliana This study provides a foundation for understanding differences in the formation, structure, and organization of cellulose in PCWs and SCWs.
System and technique for retrieving depth information about a surface by projecting a composite image of modulated light patterns

NASA Technical Reports Server (NTRS)

Hassebrook, Laurence G. (Inventor); Lau, Daniel L. (Inventor); Guan, Chun (Inventor)

2010-01-01

A technique, associated system and program code, for retrieving depth information about at least one surface of an object, such as an anatomical feature. Core features include: projecting a composite image comprising a plurality of modulated structured light patterns, at the anatomical feature; capturing an image reflected from the surface; and recovering pattern information from the reflected image, for each of the modulated structured light patterns. Pattern information is preferably recovered for each modulated structured light pattern used to create the composite, by performing a demodulation of the reflected image. Reconstruction of the surface can be accomplished by using depth information from the recovered patterns to produce a depth map/mapping thereof. Each signal waveform used for the modulation of a respective structured light pattern, is distinct from each of the other signal waveforms used for the modulation of other structured light patterns of a composite image; these signal waveforms may be selected from suitable types in any combination of distinct signal waveforms, provided the waveforms used are uncorrelated with respect to each other. The depth map/mapping to be utilized in a host of applications, for example: displaying a 3-D view of the object; virtual reality user-interaction interface with a computerized device; face--or other animal feature or inanimate object--recognition and comparison techniques for security or identification purposes; and 3-D video teleconferencing/telecollaboration.
System and technique for retrieving depth information about a surface by projecting a composite image of modulated light patterns

NASA Technical Reports Server (NTRS)

Guan, Chun (Inventor); Hassebrook, Laurence G. (Inventor); Lau, Daniel L. (Inventor)

2008-01-01

A technique, associated system and program code, for retrieving depth information about at least one surface of an object. Core features include: projecting a composite image comprising a plurality of modulated structured light patterns, at the object; capturing an image reflected from the surface; and recovering pattern information from the reflected image, for each of the modulated structured light patterns. Pattern information is preferably recovered for each modulated structured light pattern used to create the composite, by performing a demodulation of the reflected image. Reconstruction of the surface can be accomplished by using depth information from the recovered patterns to produce a depth map/mapping thereof. Each signal waveform used for the modulation of a respective structured light pattern, is distinct from each of the other signal waveforms used for the modulation of other structured light patterns of a composite image; these signal waveforms may be selected from suitable types in any combination of distinct signal waveforms, provided the waveforms used are uncorrelated with respect to each other. The depth map/mapping to be utilized in a host of applications, for example: displaying a 3-D view of the object; virtual reality user-interaction interface with a computerized device; face--or other animal feature or inanimate object--recognition and comparison techniques for security or identification purposes; and 3-D video teleconferencing/telecollaboration.
Differentiation and Characterization of Excitatory and Inhibitory Synapses by Cryo-electron Tomography and Correlative Microscopy.

PubMed

Tao, Chang-Lu; Liu, Yun-Tao; Sun, Rong; Zhang, Bin; Qi, Lei; Shivakoti, Sakar; Tian, Chong-Li; Zhang, Peijun; Lau, Pak-Ming; Zhou, Z Hong; Bi, Guo-Qiang

2018-02-07

As key functional units in neural circuits, different types of neuronal synapses play distinct roles in brain information processing, learning, and memory. Synaptic abnormalities are believed to underlie various neurological and psychiatric disorders. Here, by combining cryo-electron tomography and cryo-correlative light and electron microscopy, we distinguished intact excitatory and inhibitory synapses of cultured hippocampal neurons, and visualized the in situ 3D organization of synaptic organelles and macromolecules in their native state. Quantitative analyses of >100 synaptic tomograms reveal that excitatory synapses contain a mesh-like postsynaptic density (PSD) with thickness ranging from 20 to 50 nm. In contrast, the PSD in inhibitory synapses assumes a thin sheet-like structure ∼12 nm from the postsynaptic membrane. On the presynaptic side, spherical synaptic vesicles (SVs) of 25-60 nm diameter and discus-shaped ellipsoidal SVs of various sizes coexist in both synaptic types, with more ellipsoidal ones in inhibitory synapses. High-resolution tomograms obtained using a Volta phase plate and electron filtering and counting reveal glutamate receptor-like and GABA A receptor-like structures that interact with putative scaffolding and adhesion molecules, reflecting details of receptor anchoring and PSD organization. These results provide an updated view of the ultrastructure of excitatory and inhibitory synapses, and demonstrate the potential of our approach to gain insight into the organizational principles of cellular architecture underlying distinct synaptic functions. SIGNIFICANCE STATEMENT To understand functional properties of neuronal synapses, it is desirable to analyze their structure at molecular resolution. We have developed an integrative approach combining cryo-electron tomography and correlative fluorescence microscopy to visualize 3D ultrastructural features of intact excitatory and inhibitory synapses in their native state. Our approach shows that inhibitory synapses contain uniform thin sheet-like postsynaptic densities (PSDs), while excitatory synapses contain previously known mesh-like PSDs. We discovered "discus-shaped" ellipsoidal synaptic vesicles, and their distributions along with regular spherical vesicles in synaptic types are characterized. High-resolution tomograms further allowed identification of putative neurotransmitter receptors and their heterogeneous interaction with synaptic scaffolding proteins. The specificity and resolution of our approach enables precise in situ analysis of ultrastructural organization underlying distinct synaptic functions. Copyright © 2018 Tao, Liu et al.
Diagnosis of extent of early gastric cancer using flexible spectral imaging color enhancement

PubMed Central

Osawa, Hiroyuki; Yamamoto, Hironori; Miura, Yoshimasa; Yoshizawa, Mitsuyo; Sunada, Keijiro; Satoh, Kiichi; Sugano, Kentaro

2012-01-01

The demarcation line between the cancerous lesion and the surrounding area could be easily recognized with flexible spectral imaging color enhancement (FICE) system compared with conventional white light images. The characteristic finding of depressed-type early gastric cancer (EGC) in most cases was revealed as reddish lesions distinct from the surrounding yellowish non-cancerous area without magnification. Conventional endoscopic images provide little information regarding depressed lesions located in the tangential line, but FICE produces higher color contrast of such cancers. Histological findings in depressed area with reddish color changes show a high density of glandular structure and an apparently irregular microvessel in intervening parts between crypts, resulting in the higher color contrast of FICE image between cancer and surrounding area. Some depressed cancers are shown as whitish lesion by conventional endoscopy. FICE also can produce higher color contrast between whitish cancerous lesions and surrounding atrophic mucosa. For nearly flat cancer, FICE can produce an irregular structural pattern of cancer distinct from that of the surrounding mucosa, leading to a clear demarcation. Most elevated-type EGCs are detected easily as yellowish lesions with clearly contrasting demarcation. In some cases, a partially reddish change is accompanied on the tumor surface similar to depressed type cancer. In addition, the FICE system is quite useful for the detection of minute gastric cancer, even without magnification. These new contrasting images with the FICE system may have the potential to increase the rate of detection of gastric cancers and screen for them more effectively as well as to determine the extent of EGC. PMID:22912909
PRISM 3: expanded prediction of natural product chemical structures from microbial genomes

PubMed Central

Skinnider, Michael A.; Merwin, Nishanth J.; Johnston, Chad W.

2017-01-01

Abstract Microbial natural products represent a rich resource of pharmaceutically and industrially important compounds. Genome sequencing has revealed that the majority of natural products remain undiscovered, and computational methods to connect biosynthetic gene clusters to their corresponding natural products therefore have the potential to revitalize natural product discovery. Previously, we described PRediction Informatics for Secondary Metabolomes (PRISM), a combinatorial approach to chemical structure prediction for genetically encoded nonribosomal peptides and type I and II polyketides. Here, we present a ground-up rewrite of the PRISM structure prediction algorithm to derive prediction of natural products arising from non-modular biosynthetic paradigms. Within this new version, PRISM 3, natural product scaffolds are modeled as chemical graphs, permitting structure prediction for aminocoumarins, antimetabolites, bisindoles and phosphonate natural products, and building upon the addition of ribosomally synthesized and post-translationally modified peptides. Further, with the addition of cluster detection for 11 new cluster types, PRISM 3 expands to detect 22 distinct natural product cluster types. Other major modifications to PRISM include improved sequence input and ORF detection, user-friendliness and output. Distribution of PRISM 3 over a 300-core server grid improves the speed and capacity of the web application. PRISM 3 is available at http://magarveylab.ca/prism/. PMID:28460067
Structure of the Yersinia pestis type III secretion chaperone SycH in complex with a stable fragment of YscM2

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

Phan, Jason; Tropea, Joseph E.; Waugh, David S.

2010-11-16

Pathogenic Yersinia species use a type III secretion system to inject cytotoxic effector proteins directly into the cytosol of mammalian cells, where they neutralize the innate immune response by interfering with the signal-transduction pathways that control phagocytosis and inflammation. To be exported efficiently, some effectors must transiently associate with cognate cytoplasmic secretion chaperones. SycH is the chaperone for YopH, a potent eukaryotic-like protein tyrosine phosphatase that is essential for virulence. SycH also binds two negative regulators of type III secretion, YscM1 and YscM2, both of which share significant sequence homology with the chaperone-binding domain of YopH. Here, the structure ofmore » a complex between SycH and a stable fragment of YscM2 that was designed on the basis of limited proteolysis experiments is presented. The overall fold of SycH is very similar to the structures of other homodimeric secretion chaperones that have been determined to date. YscM2 wraps around SycH in an extended fashion, with some secondary but no tertiary structure, assuming a conformation distinct from the globular fold that it is predicted to adopt in the absence of SycH.« less

Halogen bonds in some dihalogenated phenols: applications to crystal engineering.

PubMed

Mukherjee, Arijit; Desiraju, Gautam R

2014-01-01

3,4-Dichlorophenol (1) crystallizes in the tetragonal space group I41/a with a short axis of 3.7926 (9) Å. The structure is unique in that both type I and type II Cl⋯Cl interactions are present, these contact types being distinguished by the angle ranges of the respective C-Cl⋯Cl angles. The present study shows that these two types of contacts are utterly different. The crystal structures of 4-bromo-3-chlorophenol (2) and 3-bromo-4-chlorophenol (3) have been determined. The crystal structure of (2) is isomorphous to that of (1) with the Br atom in the 4-position participating in a type II interaction. However, the monoclinic P21/c packing of compound (3) is different; while the structure still has O-H⋯O hydrogen bonds, the tetramer O-H⋯O synthon seen in (1) and (2) is not seen. Rather than a type I Br⋯Br interaction which would have been mandated if (3) were isomorphous to (1) and (2), Br forms a Br⋯O contact wherein its electrophilic character is clearly evident. Crystal structures of the related compounds 4-chloro-3-iodophenol (4) and 3,5-dibromophenol (5) were also determined. A computational survey of the structural landscape was undertaken for (1), (2) and (3), using a crystal structure prediction protocol in space groups P21/c and I41/a with the COMPASS26 force field. While both tetragonal and monoclinic structures are energetically reasonable for all compounds, the fact that (3) takes the latter structure indicates that Br prefers type II over type I contacts. In order to differentiate further between type I and type II halogen contacts, which being chemically distinct are expected to have different distance fall-off properties, a variable-temperature crystallography study was performed on compounds (1), (2) and (4). Length variations with temperature are greater for type II contacts compared with type I. The type II Br⋯Br interaction in (2) is stronger than the corresponding type II Cl⋯Cl interaction in (1), leading to elastic bending of the former upon application of mechanical stress, which contrasts with the plastic deformation of (1). The observation of elastic deformation in (2) is noteworthy; in that it finds an explanation based on the strengths of the respective halogen bonds, it could also be taken as a good starting model for future property design. Cl/Br isostructurality is studied with the Cambridge Structural Database and it is indicated that this isostructurality is based on shape and size similarity of Cl and Br, rather than arising from any chemical resemblance.
Indications for Three Independent Domestication Events for the Tea Plant (Camellia sinensis (L.) O. Kuntze) and New Insights into the Origin of Tea Germplasm in China and India Revealed by Nuclear Microsatellites

PubMed Central

Meegahakumbura, M. K.; Wambulwa, M. C.; Thapa, K. K.; Li, M. M.; Möller, M.; Xu, J. C.; Yang, J. B.; Liu, B. Y.; Ranjitkar, S.; Liu, J.; Li, D. Z.; Gao, L. M.

2016-01-01

Background Tea is the world’s most popular non-alcoholic beverage. China and India are known to be the largest tea producing countries and recognized as the centers for the domestication of the tea plant (Camellia sinensis (L.) O. Kuntze). However, molecular studies on the origin, domestication and relationships of the main teas, China type, Assam type and Cambod type are lacking. Methodology/Principal Findings Twenty-three nuclear microsatellite markers were used to investigate the genetic diversity, relatedness, and domestication history of cultivated tea in both China and India. Based on a total of 392 samples, high levels of genetic diversity were observed for all tea types in both countries. The cultivars clustered into three distinct genetic groups (i.e. China tea, Chinese Assam tea and Indian Assam tea) based on STRUCTURE, PCoA and UPGMA analyses with significant pairwise genetic differentiation, corresponding well with their geographical distribution. A high proportion (30%) of the studied tea samples were shown to possess genetic admixtures of different tea types suggesting a hybrid origin for these samples, including the Cambod type. Conclusions We demonstrate that Chinese Assam tea is a distinct genetic lineage from Indian Assam tea, and that China tea sampled from India was likely introduced from China directly. Our results further indicate that China type tea, Chinese Assam type tea and Indian Assam type tea are likely the result of three independent domestication events from three separate regions across China and India. Our findings have important implications for the conservation of genetic stocks, as well as future breeding programs. PMID:27218820
Convergent functional architecture of the superior parietal lobule unraveled with multimodal neuroimaging approaches.

PubMed

Wang, Jiaojian; Yang, Yong; Fan, Lingzhong; Xu, Jinping; Li, Changhai; Liu, Yong; Fox, Peter T; Eickhoff, Simon B; Yu, Chunshui; Jiang, Tianzi

2015-01-01

The superior parietal lobule (SPL) plays a pivotal role in many cognitive, perceptive, and motor-related processes. This implies that a mosaic of distinct functional and structural subregions may exist in this area. Recent studies have demonstrated that the ongoing spontaneous fluctuations in the brain at rest are highly structured and, like coactivation patterns, reflect the integration of cortical locations into long-distance networks. This suggests that the internal differentiation of a complex brain region may be revealed by interaction patterns that are reflected in different neuroimaging modalities. On the basis of this perspective, we aimed to identify a convergent functional organization of the SPL using multimodal neuroimaging approaches. The SPL was first parcellated based on its structural connections as well as on its resting-state connectivity and coactivation patterns. Then, post hoc functional characterizations and connectivity analyses were performed for each subregion. The three types of connectivity-based parcellations consistently identified five subregions in the SPL of each hemisphere. The two anterior subregions were found to be primarily involved in action processes and in visually guided visuomotor functions, whereas the three posterior subregions were primarily associated with visual perception, spatial cognition, reasoning, working memory, and attention. This parcellation scheme for the SPL was further supported by revealing distinct connectivity patterns for each subregion in all the used modalities. These results thus indicate a convergent functional architecture of the SPL that can be revealed based on different types of connectivity and is reflected by different functions and interactions. © 2014 Wiley Periodicals, Inc.
Membranous glomerulopathy with spherules: an uncommon variant with obscure pathogenesis.

PubMed

Kowalewska, Jolanta; Smith, Kelly D; Hudkins, Kelly L; Chang, Anthony; Fogo, Agnes B; Houghton, Donald; Leslie, Deena; Aitchison, John; Nicosia, Roberto F; Alpers, Charles E

2006-06-01

Occasional case reports of membranous glomerulopathy described unique subepithelial accumulations of an unusual type of immune deposit composed of spherular structures. The identity of such structures as nuclear pores has been suggested, but not established. We identified a cohort of patients (n = 14, including 1 patient with disease recurrence in an allograft) who presented with nephrotic syndrome and had renal biopsy specimens with light and immunofluorescence microscopic findings characteristic of membranous glomerulopathy. These patients were distinguished by ultrastructural studies that showed glomerular capillary wall accumulations of subepithelial immune deposits composed of uniform spherular structures, while lacking the typical granular electron-dense deposits seen in membranous glomerulopathy. The molecular identity of these spherular structures as nuclear pores was tested by using immunofluorescence microscopy and immunohistochemistry with mouse monoclonal antinuclear pore antibodies (Covance, Princeton, NJ) and anti-Nuclear Pore-O-Linked Glycoprotein (Affinity BioReagents Inc, Golden, CO) antibodies. Measurement of spherular structures by using high-magnification electron microscopy showed an average diameter of 84.5 nm, which correlated well with accepted diameters of nuclear pores (80 to 120 nm). Immunofluorescence microscopy and immunoperoxidase staining with both antibodies showed characteristic beaded staining of nuclear membranes of multiple cell types within normal control kidney, but no staining of immune-type deposits within glomerular basement membranes. These cases form a rare, but distinctive, morphological subclass of membranous glomerulopathy. The antigenic specificity of immune deposits in these cases remains elusive.
Collagen in Human Tissues: Structure, Function, and Biomedical Implications from a Tissue Engineering Perspective

NASA Astrophysics Data System (ADS)

Balasubramanian, Preethi; Prabhakaran, Molamma P.; Sireesha, Merum; Ramakrishna, Seeram

The extracellular matrix is a complex biological structure encoded with various proteins, among which the collagen family is the most significant and abundant of all, contributing 30-35% of the whole-body protein. "Collagen" is a generic term for proteins that forms a triple-helical structure with three polypeptide chains, and around 29 types of collagen have been identified up to now. Although most of the members of the collagen family form such supramolecular structures, extensive diversity exists between each type of collagen. The diversity is not only based on the molecular assembly and supramolecular structures of collagen types but is also observed within its tissue distribution, function, and pathology. Collagens possess complex hierarchical structures and are present in various forms such as collagen fibrils (1.5-3.5 nm wide), collagen fibers (50-70 nm wide), and collagen bundles (150-250 nm wide), with distinct properties characteristic of each tissue providing elasticity to skin, softness of the cartilage, stiffness of the bone and tendon, transparency of the cornea, opaqueness of the sclera, etc. There exists an exclusive relation between the structural features of collagen in human tissues (such as the collagen composition, collagen fibril length and diameter, collagen distribution, and collagen fiber orientation) and its tissue-specific mechanical properties. In bone, a transverse collagen fiber orientation prevails in regions of higher compressive stress whereas longitudinally oriented collagen fibers correlate to higher tensile stress. The immense versatility of collagen compels a thorough understanding of the collagen types and this review discusses the major types of collagen found in different human tissues, highlighting their tissue-specific uniqueness based on their structure and mechanical function. The changes in collagen during a specific tissue damage or injury are discussed further, focusing on the many tissue engineering applications for which collagen scaffolds are currently being applied.
Crystal structure of langbeinite-related Rb0.743K0.845Co0.293Ti1.707(PO4)3.

PubMed

Strutynska, Nataliia Yu; Bondarenko, Marina A; Ogorodnyk, Ivan V; Baumer, Vyacheslav N; Slobodyanik, Nikolay S

2015-03-01

Potassium rubidium cobalt(II)/titanium(IV) tris-(orthophosphate), Rb0.743K0.845Co0.293Ti1.707(PO4)3, has been obtained using a high-temperature crystallization method. The obtained compound has a langbeinite-type structure. The three-dimensional framework is built up from mixed-occupied (Co/Ti(IV))O6 octa-hedra (point group symmetry .3.) and PO4 tetra-hedra. The K(+) and Rb(+) cations are statistically distributed over two distinct sites (both with site symmetry .3.) in the large cavities of the framework. They are surrounded by 12 O atoms.
The TiPS/TINS lecture: the molecular biology of mammalian glutamate receptor channels.

PubMed

Seeburg, P H

1993-08-01

In native brain membranes the principal excitatory neurotransmitter L-glutamate activates cation-conducting channels with distinct biophysical and pharmacological properties. Molecular cloning has revealed the existence of 16 channel subunits that can assemble in homomeric or heteromeric configurations in vitro to form receptor channels with disparate functional properties. This review describes the different channel types obtained by recombinant means and the genetic mechanisms controlling the expression of functionally important channel structures.
The TINS/TiPS Lecture. The molecular biology of mammalian glutamate receptor channels.

PubMed

Seeburg, P H

1993-09-01

In native brain membranes the principal excitatory neurotransmitter L-glutamate activates cation-conducting channels with distinct biophysical and pharmacological properties. Molecular cloning has revealed the existence of 16 channel subunits that can assemble in homomeric or heteromeric configurations in vitro to form receptor channels with disparate functional properties. This review describes the different channel types obtained by recombinant means and the genetic mechanisms controlling the expression of functionally important channel structures.
Three-Dimensional Gene Map of Cancer Cell Types: Structural Entropy Minimisation Principle for Defining Tumour Subtypes

PubMed Central

Li, Angsheng; Yin, Xianchen; Pan, Yicheng

2016-01-01

In this study, we propose a method for constructing cell sample networks from gene expression profiles, and a structural entropy minimisation principle for detecting natural structure of networks and for identifying cancer cell subtypes. Our method establishes a three-dimensional gene map of cancer cell types and subtypes. The identified subtypes are defined by a unique gene expression pattern, and a three-dimensional gene map is established by defining the unique gene expression pattern for each identified subtype for cancers, including acute leukaemia, lymphoma, multi-tissue, lung cancer and healthy tissue. Our three-dimensional gene map demonstrates that a true tumour type may be divided into subtypes, each defined by a unique gene expression pattern. Clinical data analyses demonstrate that most cell samples of an identified subtype share similar survival times, survival indicators and International Prognostic Index (IPI) scores and indicate that distinct subtypes identified by our algorithms exhibit different overall survival times, survival ratios and IPI scores. Our three-dimensional gene map establishes a high-definition, one-to-one map between the biologically and medically meaningful tumour subtypes and the gene expression patterns, and identifies remarkable cells that form singleton submodules. PMID:26842724
Genome Re-Sequencing of Semi-Wild Soybean Reveals a Complex Soja Population Structure and Deep Introgression

PubMed Central

Wu, Sanling; Wang, Ying-Ying; Ye, Chu-Yu; Bai, Xuefei; Li, Zefeng; Yan, Chenghai; Wang, Weidi; Wang, Ziqiang; Shu, Qingyao; Xie, Jiahua; Lee, Suk-Ha; Fan, Longjiang

2014-01-01

Semi-wild soybean is a unique type of soybean that retains both wild and domesticated characteristics, which provides an important intermediate type for understanding the evolution of the subgenus Soja population in the Glycine genus. In this study, a semi-wild soybean line (Maliaodou) and a wild line (Lanxi 1) collected from the lower Yangtze regions were deeply sequenced while nine other semi-wild lines were sequenced to a 3-fold genome coverage. Sequence analysis revealed that (1) no independent phylogenetic branch covering all 10 semi-wild lines was observed in the Soja phylogenetic tree; (2) besides two distinct subpopulations of wild and cultivated soybean in the Soja population structure, all semi-wild lines were mixed with some wild lines into a subpopulation rather than an independent one or an intermediate transition type of soybean domestication; (3) high heterozygous rates (0.19–0.49) were observed in several semi-wild lines; and (4) over 100 putative selective regions were identified by selective sweep analysis, including those related to the development of seed size. Our results suggested a hybridization origin for the semi-wild soybean, which makes a complex Soja population structure. PMID:25265539
A SYSTEMATIC REVIEW OF PLACENTAL PATHOLOGY IN MATERNAL DIABETES MELLITUS

PubMed Central

Huynh, J.; Dawson, D.; Roberts, D.; Bentley-Lewis, R.

2014-01-01

During a pregnancy complicated by diabetes, the human placenta undergoes a number of functional and structural pathologic changes, such as increased placental weight and increased incidence of placental lesions including villous maturational defects and fibrinoid necrosis. The pathologic findings reported have differed among studies, potentially reflecting differences in type of diabetes, study methodology, or glycemic control of study participants. Alternatively, these discrepancies may represent different biologic adaptations to distinct metabolic diseases. In order to clarify these distinctions, we conducted a comprehensive review of English language citations in Pubmed and Embase using the keywords “diabetes”, “placenta”, AND “pathology”. Abstracts were reviewed for relevance then full-text articles were reviewed in order to extract a comprehensive summary of current pathological findings associated with pregestational and gestational diabetes mellitus, as well as an understanding of the impact of glycemic control on placental pathology. Placental abnormalities most consistently associated with maternal diabetes are an increased incidence of villous immaturity, increased measures of angiogenesis, and increased placental weight. The literature suggests that, despite similarities in placental abnormalities, differences in placental pathology may reflect differences in pathophysiology among different types of diabetes. Consequently, standardization of terminology used to define placental lesions is warranted. Moreover, further research is needed to investigate the impact of pathophysiology, glycemic control and clinical factors, such as infant sex, weight and race, on placental structure and function. PMID:25524060
Empirically derived subtypes of serious emotional disturbance in a large adolescent sample.

PubMed

Peiper, Nicholas; Clayton, Richard; Wilson, Richard; Illback, Robert; O'Brien, Elizabeth; Kerber, Richard; Baumgartner, Richard; Hornung, Carlton

2015-06-01

The heterogeneity of serious emotional disturbance has been thoroughly documented among adolescents with nationally representative data derived from structured interviews, although use of these interviews may not be feasible within the context of brief and self-administered school surveys. This study seeks to identify distinct subtypes of serious emotional disturbance in a large school-based sample. A total of 108,736 students fully completed the K6 scale that was included on the 2012 Kentucky Incentives for Prevention Survey. Latent class analysis was used to derive subtypes of serious emotional disturbance among students receiving a positive screen (n = 15,147). To determine significant predictors of class membership, adjusted rate ratios and 95 % confidence intervals were calculated using multinomial logistic regression. A four-class model was the most parsimonious, with four distinct subtypes emerging that varied by both symptom type and severity: comorbid moderate severity, comorbid high severity, anxious moderate severity, and depressed high severity. Age, gender, race/ethnicity, family structure, substance use, antisocial behavior, role impairments, and peer victimization were significant predictors of class membership, although the magnitude of these effects was stronger for the two high severity groups. Our results suggest heterogeneity of serious emotional disturbance by both symptom type and severity. Prevention programs may benefit by shifting focus from specific disorders to the core features of serious emotional disturbance, including psychological distress, high comorbidity, and role impairments.
Two novel AGXT mutations identified in primary hyperoxaluria type-1 and distinct morphological and structural difference in kidney stones

PubMed Central

Wang, Cui; Lu, Jingru; Lang, Yanhua; Liu, Ting; Wang, Xiaoling; Zhao, Xiangzhong; Shao, Leping

2016-01-01

Primary hyperoxaluria type 1 (PH1) is a rare genetic disease characterized by excessive oxalate accumulation in plasma and urine, resulting in various phenotypes because of allelic and clinical heterogeneity. This study aimed to detect disease-associated genetic mutations in three PH1 patients in a Chinese family. All AGXT exons and 3 common polymorphisms which might synergistically interact with mutations, including P11L, I340 M and IVSI+74 bp were analyzed by direct sequencing in all family members. It demonstrated that in each of three patients, a previously reported nonsense mutation p.R333* was in cis with a novel missense mutation p.M49L in the minor allele characterized by the polymorphism of 74-bp duplication in intron 1, while the other novel missense mutation p.N72I was in trans with both p.R333* and P.M49L in the major allele. Kidney stones from two sibling patients were also observed though stereomicroscopic examination and scanning electron microscopy. Distinct morphological and inner-structure differences in calculi were noticed, suggesting clinical heterozygosity of PH1 to a certain extent. In brief, two novel missense mutations were identified probably in association with PH1, a finding which should provide an accurate tool for prenatal diagnosis, genetic counseling and screening for potential presymptomatic individuals. PMID:27644547
Two novel AGXT mutations identified in primary hyperoxaluria type-1 and distinct morphological and structural difference in kidney stones.

PubMed

Wang, Cui; Lu, Jingru; Lang, Yanhua; Liu, Ting; Wang, Xiaoling; Zhao, Xiangzhong; Shao, Leping

2016-09-20

Primary hyperoxaluria type 1 (PH1) is a rare genetic disease characterized by excessive oxalate accumulation in plasma and urine, resulting in various phenotypes because of allelic and clinical heterogeneity. This study aimed to detect disease-associated genetic mutations in three PH1 patients in a Chinese family. All AGXT exons and 3 common polymorphisms which might synergistically interact with mutations, including P11L, I340 M and IVSI+74 bp were analyzed by direct sequencing in all family members. It demonstrated that in each of three patients, a previously reported nonsense mutation p.R333(*) was in cis with a novel missense mutation p.M49L in the minor allele characterized by the polymorphism of 74-bp duplication in intron 1, while the other novel missense mutation p.N72I was in trans with both p.R333(*) and P.M49L in the major allele. Kidney stones from two sibling patients were also observed though stereomicroscopic examination and scanning electron microscopy. Distinct morphological and inner-structure differences in calculi were noticed, suggesting clinical heterozygosity of PH1 to a certain extent. In brief, two novel missense mutations were identified probably in association with PH1, a finding which should provide an accurate tool for prenatal diagnosis, genetic counseling and screening for potential presymptomatic individuals.
Insights into channel dysfunction from modelling and molecular dynamics simulations.

PubMed

Musgaard, Maria; Paramo, Teresa; Domicevica, Laura; Andersen, Ole Juul; Biggin, Philip C

2018-04-01

Developments in structural biology mean that the number of different ion channel structures has increased significantly in recent years. Structures of ion channels enable us to rationalize how mutations may lead to channelopathies. However, determining the structures of ion channels is still not trivial, especially as they necessarily exist in many distinct functional states. Therefore, the use of computational modelling can provide complementary information that can refine working hypotheses of both wild type and mutant ion channels. The simplest but still powerful tool is homology modelling. Many structures are available now that can provide suitable templates for many different types of ion channels, allowing a full three-dimensional interpretation of mutational effects. These structural models, and indeed the structures themselves obtained by X-ray crystallography, and more recently cryo-electron microscopy, can be subjected to molecular dynamics simulations, either as a tool to help explore the conformational dynamics in detail or simply as a means to refine the models further. Here we review how these approaches have been used to improve our understanding of how diseases might be linked to specific mutations in ion channel proteins. This article is part of the Special Issue entitled 'Channelopathies.' Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.
Inside the Mechanics of Network Development: How Competition and Strategy Reorganize European Air Traffic

NASA Technical Reports Server (NTRS)

Huber, Hans

2006-01-01

Air transport forms complex networks that can be measured in order to understand its structural characteristics and functional properties. Recent models for network growth (i.e., preferential attachment, etc.) remain stochastic and do not seek to understand other network-specific mechanisms that may account for their development in a more microscopic way. Air traffic is made up of many constituent airlines that are either privately or publicly owned and that operate their own networks. They follow more or less similar business policies each. The way these airline networks organize among themselves into distinct traffic distributions reveals complex interaction among them, which in turn can be aggregated into larger (macro-) traffic distributions. Our approach allows for a more deterministic methodology that will assess the impact of airline strategies on the distinct distributions for air traffic, particularly inside Europe. One key question this paper is seeking to answer is whether there are distinct patterns of preferential attachment for given classes of airline networks to distinct types of European airports. Conclusions about the advancing degree of concentration in this industry and the airline operators that accelerate this process can be drawn.
Social network ties beyond nonredundancy: an experimental investigation of the effect of knowledge content and tie strength on creativity.

PubMed

Perry-Smith, Jill E

2014-09-01

Social network research emphasizes the access to nonredundant knowledge content that network ties provide. I suggest that some content is more beneficial than others and that tie strength may affect creativity for reasons other than the associated structure. That is, tie strength may affect how individuals process nonredundant knowledge. I investigate 2 types of knowledge content--information (i.e., facts or data) and frames (i.e., interpretations or impressions)--and explore whether tie strength influences their effect on creativity. Drawing on creativity theory, I employ an experimental design to provide greater theoretical clarity and to isolate causality. According to the results from 2 studies, distinct frames received from contacts facilitate creativity, but the effect of distinct information is more complex. When individuals receive distinct information from strong ties, it constrains creativity compared to distinct frames. Content from weak ties appears to facilitate creativity across all scenarios. The results of mediated moderation analysis indicate the effect of framing versus information for strong ties is driven by decision-making time, as an indicator of cognitive expansion. PsycINFO Database Record (c) 2014 APA, all rights reserved.
The Curious Case of Orthographic Distinctiveness: Disruption of Categorical Processing

ERIC Educational Resources Information Center

McDaniel, Mark A.; Cahill, Michael J.; Bugg, Julie M.

2016-01-01

How does orthographic distinctiveness affect recall of structured (categorized) word lists? On one theory, enhanced item-specific information (e.g., more distinct encoding) in concert with robust relational information (e.g., categorical information) optimally supports free recall. This predicts that for categorically structured lists,…
Structure-guided statistical textural distinctiveness for salient region detection in natural images.

PubMed

Scharfenberger, Christian; Wong, Alexander; Clausi, David A

2015-01-01

We propose a simple yet effective structure-guided statistical textural distinctiveness approach to salient region detection. Our method uses a multilayer approach to analyze the structural and textural characteristics of natural images as important features for salient region detection from a scale point of view. To represent the structural characteristics, we abstract the image using structured image elements and extract rotational-invariant neighborhood-based textural representations to characterize each element by an individual texture pattern. We then learn a set of representative texture atoms for sparse texture modeling and construct a statistical textural distinctiveness matrix to determine the distinctiveness between all representative texture atom pairs in each layer. Finally, we determine saliency maps for each layer based on the occurrence probability of the texture atoms and their respective statistical textural distinctiveness and fuse them to compute a final saliency map. Experimental results using four public data sets and a variety of performance evaluation metrics show that our approach provides promising results when compared with existing salient region detection approaches.
A critical approach to the definition of Darwinian units of selection.

PubMed

Rinkevich, B

2000-12-01

What are the biological units of selection? In fact, the notion of "unit of selection" (UOS) is blurred by ambiguity and controversy. To further evaluate the biological entities that are the objects of natural selection, three novel conceptual criteria (holism, minimalism, functionalism) are critically applied; they reveal, in addition to the self-evident case of the "individual," at least six distinct types of UOSs. These UOSs do not always have a defined structural organization; they can be parts of a living organism, a cohesive group of conspecifics, a multiunit entity, a totipotent cell, a DNA fragment, or a whole organism. UOS types diversify by amalgamation or parcelation processes of apparent entities. Therefore, previous attempts to characterize the UOSs solely on some morphological levels (gene, individual, group) without applying stringent criteria have failed to cope with the structural variations of natural phenomena and have led to the ambiguity of terms used.

Integrating sequence and structural biology with DAS

PubMed Central

Prlić, Andreas; Down, Thomas A; Kulesha, Eugene; Finn, Robert D; Kähäri, Andreas; Hubbard, Tim JP

2007-01-01

Background The Distributed Annotation System (DAS) is a network protocol for exchanging biological data. It is frequently used to share annotations of genomes and protein sequence. Results Here we present several extensions to the current DAS 1.5 protocol. These provide new commands to share alignments, three dimensional molecular structure data, add the possibility for registration and discovery of DAS servers, and provide a convention how to provide different types of data plots. We present examples of web sites and applications that use the new extensions. We operate a public registry of DAS sources, which now includes entries for more than 250 distinct sources. Conclusion Our DAS extensions are essential for the management of the growing number of services and exchange of diverse biological data sets. In addition the extensions allow new types of applications to be developed and scientific questions to be addressed. The registry of DAS sources is available at PMID:17850653
Fish mouths as engineering structures for vortical cross-step filtration

NASA Astrophysics Data System (ADS)

Sanderson, S. Laurie; Roberts, Erin; Lineburg, Jillian; Brooks, Hannah

2016-03-01

Suspension-feeding fishes such as goldfish and whale sharks retain prey without clogging their oral filters, whereas clogging is a major expense in industrial crossflow filtration of beer, dairy foods and biotechnology products. Fishes' abilities to retain particles that are smaller than the pore size of the gill-raker filter, including extraction of particles despite large holes in the filter, also remain unexplained. Here we show that unexplored combinations of engineering structures (backward-facing steps forming d-type ribs on the porous surface of a cone) cause fluid dynamic phenomena distinct from current biological and industrial filter operations. This vortical cross-step filtration model prevents clogging and explains the transport of tiny concentrated particles to the oesophagus using a hydrodynamic tongue. Mass transfer caused by vortices along d-type ribs in crossflow is applicable to filter-feeding duck beak lamellae and whale baleen plates, as well as the fluid mechanics of ventilation at fish gill filaments.
Secondary structure and phylogeny of Staphylococcus and Micrococcus 5S rRNAs.

PubMed Central

Dekio, S; Yamasaki, R; Jidoi, J; Hori, H; Osawa, S

1984-01-01

Nucleotide sequences of 5S rRNAs from four bacteria, Staphylococcus aureus Smith (diffuse), Staphylococcus epidermidis ATCC 14990, Micrococcus luteus ATCC 9341 and Micrococcus luteus ATCC 4698, were determined. The secondary structural models of S. aureus and S. epidermidis sequences showed characteristics of the gram-positive bacterial 5S rRNA (116-N type [H. Hori and S. Osawa, Proc. Natl. Acad. Sci. U.S.A. 76:381-385, 1979]). Those of M. luteus ATCC 9341 and M. luteus ATCC 4698 together with that of Streptomyces griseus (A. Simoncsits, Nucleic Acids Res. 8:4111-4124, 1980) showed intermediary characteristics between the gram-positive and gram-negative (120-N type [H. Hori and S. Osawa, 1979]) 5S rRNAs. This and previous studies revealed that there exist at least three major groups of eubacteria having distinct 5S rRNA and belonging to different stems in the 5S rRNA phylogenic tree. PMID:6735981
The Tuscarora Au-Ag district: Eocene volcanic-hosted epithermal deposits in the Carlin gold region, Nevada

USGS Publications Warehouse

Castor, S.B.; Boden, D.R.; Henry, C.D.; Cline, J.S.; Hofstra, A.H.; McIntosh, W.C.; Tosdal, R.M.; Wooden, J.P.

2003-01-01

The Tuscarora mining district contains the oldest and the only productive Eocene epithermal deposits in Nevada. The district is a particularly clear example of association of low-sulfidation deposits with igneous activity and structure, and it is unusual in that it consists of two adjoining but physically and chemically distinct types of low-sulfidation deposits. Moreover, Tuscarora deposits are of interest because they formed contemporaneously with nearby, giant Carlin-type gold deposits. The Tuscarora deposits formed within the 39.9 to 39.3 Ma Tuscarora volcanic field, along and just outside the southeastern margin of the caldera-like Mount Blitzen volcanic center. Both deposit types formed at 39.3 Ma, contemporaneous with the only major intrusive activity in the volcanic field. No deposits are known to have formed during any of the intense volcanic phases of the field. Intrusions were the apparent heat source, and structures related to the Mount Blitzen center were conduits for hydrothermal circulation. The ore-forming fluids interacted dominantly with Eocene igneous rocks. The two deposit types occur in a northern silver-rich zone that is characterized by relatively high Ag/Au ratios (110-150), narrow alteration zones, and quartz and carbonate veins developed mostly in intrusive dacite, and in a southern gold-rich zone that is typified by relatively low Ag/Au ratios (4-14), more widespread alteration, and quartz-fissure and stockwork veins commonly developed in tuffaceous sedimentary rocks. The deposit types have similar fluid inclusion and Pb and S isotope characteristics but different geochemical signatures. Quartz veins from both zones have similar thermal and paragenetic histories and contain fluid inclusions that indicate that fluids cooled from between 260?? and 230??C to less than 200??C. Fluid boiling may have contributed to precious-metal deposition. Veins in both zones have relatively high As and Sb and low Bi, Te, and W. The silver zone has high Ca, Pb, Mn, Zn, Cd, Tl, and Se. The gold zone has high Hg and Mo. A few samples from an area of overlap between the two zones share chemical characteristics of both deposit types. The deposit types could represent a single zoned or evolving system in which hydrothermal fluids rose along structures within the silver zone, preferentially deposited Ag and base metals, and then spread into the gold zone. Alternatively, the deposit types could represent two distinct but temporally indistinguishable hydrothermal cells that only narrowly overlapped spatially. As noted in previous studies, the hydrothermal fluids that generated the Tuscarora and other epithermal deposits could have evolved from Carlin-type fluids by boiling and mixing with meteoric water. If so, the Tuscarora deposit may represent epithermal conditions above Carlin-type deposits, and Carlin-type deposits may lie beneath the district.
Effective numbers in the partitioning of biological diversity.

PubMed

Gregorius, Hans-Rolf

2016-11-21

Admissible measures of diversity allow specification of the number of types (species, alleles, etc.) that are "effectively" involved in producing the diversity (the "diversity effective number", also referred to as "true diversity") of a community or population. In metacommunities, effective numbers additionally serve in partitioning the total diversity (symbolized by γ) into one component summarizing the diversity within communities (symbolized by α) and an independent component summarizing the differences between communities (symbolized by β). There is growing consensus that the β-component should be treated in terms of an effective number of "distinct" communities in the metacommunity. Yet, the notion of distinctness is shown in the present paper to remain conceptually ambiguous at least with respect to the diversity within the "distinct" communities. To overcome this ambiguity and to provide the means for designing further desirable effective numbers, a new approach is taken that involves a generalized concept of effective number. The approach relies on first specifying the distributional characteristics of partitioning diversity among communities (among which are differentiation, where the same types tend to occur in the same communities, and apportionment, where different types tend to occur in different communities), then developing the indices which measure these characteristics, and finally inferring the effective numbers from these indices. (1) The β-component reflects apportionment characteristics of metacommunity structure and is quantified by the "apportionment effective number" of communities (number of effectively monomorphic communities). Since differentiation between communities arises only as a side effect of apportionment, the common interpretation of the β-component in terms of differentiation is unwarranted. (2) Multiplicative as well as additive methods of partitioning the total type diversity (γ) involve apportionment effective numbers of communities that are based on different apportionment indices. (3) "Differentiation effective numbers" of communities exist but do not conform with the classical concept of partitioning total type diversity into components within and between communities. (4) Differentiation characteristics are measured as effective numbers of distinct types (rather than communities) from the dual perspective, in which the roles of type and community membership are exchanged. This is relevant e.g. in studies of endemism and competitive exclusion. (5) For Shannon-Wiener diversity, all of the differentiation and apportionment effective numbers are equal, with the exception of those representing additive partitioning. (6) Under either perspective, that is dual or non-dual, measures of compositional differentiation (as originally suggested for the assessment of β-diversity) do not figure in the partitioning of total diversity into components, since they do not build on the intrinsic concept of diversity. Copyright © 2016 Elsevier Ltd. All rights reserved.
A Low Cost Structurally Optimized Design for Diverse Filter Types

PubMed Central

Kazmi, Majida; Aziz, Arshad; Akhtar, Pervez; Ikram, Nassar

2016-01-01

A wide range of image processing applications deploys two dimensional (2D)-filters for performing diversified tasks such as image enhancement, edge detection, noise suppression, multi scale decomposition and compression etc. All of these tasks require multiple type of 2D-filters simultaneously to acquire the desired results. The resource hungry conventional approach is not a viable option for implementing these computationally intensive 2D-filters especially in a resource constraint environment. Thus it calls for optimized solutions. Mostly the optimization of these filters are based on exploiting structural properties. A common shortcoming of all previously reported optimized approaches is their restricted applicability only for a specific filter type. These narrow scoped solutions completely disregard the versatility attribute of advanced image processing applications and in turn offset their effectiveness while implementing a complete application. This paper presents an efficient framework which exploits the structural properties of 2D-filters for effectually reducing its computational cost along with an added advantage of versatility for supporting diverse filter types. A composite symmetric filter structure is introduced which exploits the identities of quadrant and circular T-symmetries in two distinct filter regions simultaneously. These T-symmetries effectually reduce the number of filter coefficients and consequently its multipliers count. The proposed framework at the same time empowers this composite filter structure with additional capabilities of realizing all of its Ψ-symmetry based subtypes and also its special asymmetric filters case. The two-fold optimized framework thus reduces filter computational cost up to 75% as compared to the conventional approach as well as its versatility attribute not only supports diverse filter types but also offers further cost reduction via resource sharing for sequential implementation of diversified image processing applications especially in a constraint environment. PMID:27832133
TYPE 3 NEOVASCULARIZATION IMAGED WITH CROSS-SECTIONAL AND EN FACE OPTICAL COHERENCE TOMOGRAPHY ANGIOGRAPHY.

PubMed

Tan, Anna C S; Dansingani, Kunal K; Yannuzzi, Lawrence A; Sarraf, David; Freund, K Bailey

2017-02-01

To study the cross-sectional and en face optical coherence tomography angiography (OCTA) findings in Type 3 neovascularization (NV). Optical coherence tomography angiography imaging of 27 eyes of 23 patients with Type 3 NV was analyzed with 9 eyes having consecutive follow-up OCTA studies. Type 3 NV appeared as a linear high-flow structure on cross-sectional OCTA corresponding to a high-flow tuft of vessels seen on en face OCTA. Cross-sectional OCTA seemed to enable the distinction between vascular and nonvascular intraretinal hyperreflective foci. Two patterns of flow were observed; Pattern 1 (11%): a flow signal confined to the neurosensory retina and Pattern 2 (74%): a flow signal extending through the retinal pigment epithelium. No definitive retinal-choroidal anastomosis was observed; however, projection artifacts confounded the interpretation of deeper structures. An increase in the intensity of the high-flow tuft was seen during the progression or recurrence of Type 3 NV. Intravitreal anti-vascular endothelial growth factor therapy caused a reduction in the intensity of the high-flow tuft which was not sustained. Compared with conventional imaging, OCTA may improve detection and delineation of vascular changes occurring in Type 3 NV. Cross-sectional and en face OCTA may prove useful in studying the pathogenesis and guiding the management of these lesions.
Reliability and validity of the adolescent health profile-types.

PubMed

Riley, A W; Forrest, C B; Starfield, B; Green, B; Kang, M; Ensminger, M

1998-08-01

The purpose of this study was to demonstrate the preliminary reliability and validity of a set 13 profiles of adolescent health that describe distinct patterns of health and health service requirements on four domains of health. Reliability and validity were tested in four ethnically diverse population samples of urban and rural youths aged 11 to 17-years-old in public schools (N = 4,066). The reliability of the classification procedure and construct validity were examined in terms of the predicted and actual distributions of age, gender, race, socioeconomic status, and family type. School achievement, medical conditions, and the proportion of youths with a psychiatric disorder also were examined as tests of construct validity. The classification method was shown to produce consistent results across the four populations in terms of proportions of youths assigned with specific sociodemographic characteristics. Variations in health described by specific profiles showed expected relations to sociodemographic characteristics, family structure, school achievement, medical disorders, and psychiatric disorders. This taxonomy of health profile-types appears to effectively describe a set of patterns that characterize adolescent health. The profile-types provide a unique and practical method for identifying subgroups having distinct needs for health services, with potential utility for health policy and planning. Such integrative reporting methods are critical for more effective utilization of health status instruments in health resource planning and policy development.
Nematode-associated microbial taxa do not correlate with host phylogeny, geographic region or feeding morphology in marine sediment habitats.

PubMed

Schuelke, Taruna; Pereira, Tiago José; Hardy, Sarah M; Bik, Holly M

2018-04-01

Studies of host-associated microbes are critical for advancing our understanding of ecology and evolution across diverse taxa and ecosystems. Nematode worms are ubiquitous across most habitats on earth, yet little is known about host-associated microbial assemblages within the phylum. Free-living nematodes are globally abundant and diverse in marine sediments, with species exhibiting distinct buccal cavity (mouth) morphologies that are thought to play an important role in feeding ecology and life history strategies. Here, we investigated patterns in marine nematode microbiomes, by characterizing host-associated microbial taxa in 281 worms isolated from a range of habitat types (deep-sea, shallow water, methane seeps, Lophelia coral mounds, kelp holdfasts) across three distinct geographic regions (Arctic, Southern California and Gulf of Mexico). Microbiome profiles were generated from single worms spanning 33 distinct morphological genera, using a two-gene metabarcoding approach to amplify the V4 region of the 16S ribosomal RNA (rRNA) gene targeting bacteria/archaea and the V1-V2 region of the 18S rRNA gene targeting microbial eukaryotes. Contrary to our expectations, nematode microbiome profiles demonstrated no distinct patterns either globally (across depths and ocean basins) or locally (within site); prokaryotic and eukaryotic microbial assemblages did not correlate with nematode feeding morphology, host phylogeny or morphological identity, ocean region or marine habitat type. However, fine-scale analysis of nematode microbiomes revealed a variety of novel ecological interactions, including putative parasites and symbionts, and potential associations with bacterial/archaeal taxa involved in nitrogen and methane cycling. Our results suggest that in marine habitats, free-living nematodes may utilize diverse and generalist foraging strategies that are not correlated with host genotype or feeding morphology. Furthermore, some abiotic factors such as geographic region and habitat type do not appear to play an obvious role in structuring host-microbe associations or feeding preferences. © 2018 John Wiley & Sons Ltd.
Band-offset-induced lateral shift of valley electrons in ferromagnetic MoS2/WS2 planar heterojunctions

NASA Astrophysics Data System (ADS)

Ghadiri, Hassan; Saffarzadeh, Alireza

2018-03-01

Low-energy coherent transport and a Goos-Hänchen (GH) lateral shift of valley electrons in planar heterojunctions composed of normal MoS2 and ferromagnetic WS2 monolayers are theoretically investigated. Two types of heterojunctions in the forms of WS2/MoS2/WS2 (type-A) and MoS2/WS2/MoS2 (type-B) with incident electrons in the MoS2 region are considered in which the lateral shift of electrons is induced by band alignments of the two constituent semiconductors. It is shown that the type-A heterojunction can act as an electron waveguide due to electron confinement between the two WS2/MoS2 interfaces which cause the incident electrons with an appropriate incidence angle to propagate along the interfaces. In this case, the spin- and valley-dependent GH shifts of totally reflected electrons from the interface lead to separated electrons with distinct spin-valley indexes after traveling a sufficiently long distance. In the type-B heterojunction, however, transmission resonances occur for incident electron beams passing through the structure, and large spin- and valley-dependent lateral shift values in propagating states can be achieved. Consequently, the transmitted electrons are spatially well-separated into electrons with distinct spin-valley indexes. Our findings reveal that the planar heterojunctions of transition metal dichalcogenides can be utilized as spin-valley beam filters and/or splitters without external gating.
β-Catenin activity in the dermal papilla of the hair follicle regulates pigment-type switching

PubMed Central

Enshell-Seijffers, David; Lindon, Catherine; Wu, Eleanor; Taketo, Makoto M.; Morgan, Bruce A.

2010-01-01

The switch between black and yellow pigment is mediated by the interaction between Melanocortin receptor 1 (Mc1r) and its antagonist Agouti, but the genetic and developmental mechanisms that modify this interaction to obtain different coat color in distinct environments are poorly understood. Here, the role of Wnt/β-catenin signaling in the regulation of pigment-type switching was studied. Loss and gain of function of β-catenin in the dermal papilla (DP) of the hair follicle results in yellow and black animals, respectively. β-Catenin activity in the DP suppresses Agouti expression and activates Corin, a negative regulator of Agouti activity. In addition, β-catenin activity in the DP regulates melanocyte activity by a mechanism that is independent of both Agouti and Corin. The coordinate and inverse regulation of Agouti and Corin renders pelage pigmentation sensitive to changes in β-catenin activity in the DP that do not alter pelage structure. As a result, the signals that specify two biologically distinct quantitative traits are partially uncoupled despite their common regulation by the β-catenin pathway in the same cells. PMID:21098273
Identification of binding domains in the herpes simplex virus type 1 small capsid protein pUL35 (VP26).

PubMed

Apcarian, Arin; Cunningham, Anthony L; Diefenbach, Russell J

2010-11-01

In this study, fragments of the small capsid protein pUL35 (VP26) from herpes simplex virus type 1 (HSV-1) were generated to identify binding domains for a number of known ligands. Analysis of the binding of dynein light chain subunits, DYNLT1 and DYNLT3, as well the HSV-1 structural proteins pUL19 (VP5) and pUL37 was then undertaken using the LexA yeast two-hybrid assay. The N-terminal half of pUL35, in particular residues 30-43, was identified as a common region for the binding of DYNLT1 and DYNLT3. Additional distinct regions in the C terminus of pUL35 also contribute to the binding of DYNLT1 and DYNLT3. In contrast, only the C-terminal half of pUL35 was found to mediate the binding of pUL19 and pUL37 through distinct regions. The relevance of this information to the role of pUL35 in viral transport and assembly is discussed.
Sample size determination for GEE analyses of stepped wedge cluster randomized trials.

PubMed

Li, Fan; Turner, Elizabeth L; Preisser, John S

2018-06-19

In stepped wedge cluster randomized trials, intact clusters of individuals switch from control to intervention from a randomly assigned period onwards. Such trials are becoming increasingly popular in health services research. When a closed cohort is recruited from each cluster for longitudinal follow-up, proper sample size calculation should account for three distinct types of intraclass correlations: the within-period, the inter-period, and the within-individual correlations. Setting the latter two correlation parameters to be equal accommodates cross-sectional designs. We propose sample size procedures for continuous and binary responses within the framework of generalized estimating equations that employ a block exchangeable within-cluster correlation structure defined from the distinct correlation types. For continuous responses, we show that the intraclass correlations affect power only through two eigenvalues of the correlation matrix. We demonstrate that analytical power agrees well with simulated power for as few as eight clusters, when data are analyzed using bias-corrected estimating equations for the correlation parameters concurrently with a bias-corrected sandwich variance estimator. © 2018, The International Biometric Society.
Transancestral fine-mapping of four type 2 diabetes susceptibility loci highlights potential causal regulatory mechanisms

PubMed Central

Horikoshi, Momoko; Pasquali, Lorenzo; Wiltshire, Steven; Huyghe, Jeroen R.; Mahajan, Anubha; Asimit, Jennifer L.; Ferreira, Teresa; Locke, Adam E.; Robertson, Neil R.; Wang, Xu; Sim, Xueling; Fujita, Hayato; Hara, Kazuo; Young, Robin; Zhang, Weihua; Choi, Sungkyoung; Chen, Han; Kaur, Ismeet; Takeuchi, Fumihiko; Fontanillas, Pierre; Thuillier, Dorothée; Yengo, Loic; Below, Jennifer E.; Tam, Claudia H.T.; Wu, Ying; Abecasis, Gonçalo; Altshuler, David; Bell, Graeme I.; Blangero, John; Burtt, Noél P.; Duggirala, Ravindranath; Florez, Jose C.; Hanis, Craig L.; Seielstad, Mark; Atzmon, Gil; Chan, Juliana C.N.; Ma, Ronald C.W.; Froguel, Philippe; Wilson, James G.; Bharadwaj, Dwaipayan; Dupuis, Josee; Meigs, James B.; Cho, Yoon Shin; Park, Taesung; Kooner, Jaspal S.; Chambers, John C.; Saleheen, Danish; Kadowaki, Takashi; Tai, E. Shyong; Mohlke, Karen L.; Cox, Nancy J.; Ferrer, Jorge; Zeggini, Eleftheria; Kato, Norihiro; Teo, Yik Ying; Boehnke, Michael; McCarthy, Mark I.; Morris, Andrew P.

2016-01-01

To gain insight into potential regulatory mechanisms through which the effects of variants at four established type 2 diabetes (T2D) susceptibility loci (CDKAL1, CDKN2A-B, IGF2BP2 and KCNQ1) are mediated, we undertook transancestral fine-mapping in 22 086 cases and 42 539 controls of East Asian, European, South Asian, African American and Mexican American descent. Through high-density imputation and conditional analyses, we identified seven distinct association signals at these four loci, each with allelic effects on T2D susceptibility that were homogenous across ancestry groups. By leveraging differences in the structure of linkage disequilibrium between diverse populations, and increased sample size, we localised the variants most likely to drive each distinct association signal. We demonstrated that integration of these genetic fine-mapping data with genomic annotation can highlight potential causal regulatory elements in T2D-relevant tissues. These analyses provide insight into the mechanisms through which T2D association signals are mediated, and suggest future routes to understanding the biology of specific disease susceptibility loci. PMID:26911676
3D-printing and mechanics of bio-inspired articulated and multi-material structures.

PubMed

Porter, Michael M; Ravikumar, Nakul; Barthelat, Francois; Martini, Roberto

2017-09-01

3D-printing technologies allow researchers to build simplified physical models of complex biological systems to more easily investigate their mechanics. In recent years, a number of 3D-printed structures inspired by the dermal armors of various fishes have been developed to study their multiple mechanical functionalities, including flexible protection, improved hydrodynamics, body support, or tail prehensility. Natural fish armors are generally classified according to their shape, material and structural properties as elasmoid scales, ganoid scales, placoid scales, carapace scutes, or bony plates. Each type of dermal armor forms distinct articulation patterns that facilitate different functional advantages. In this paper, we highlight recent studies that developed 3D-printed structures not only to inform the design and application of some articulated and multi-material structures, but also to explain the mechanics of the natural biological systems they mimic. Copyright © 2017 Elsevier Ltd. All rights reserved.
Topological Classification of Crystalline Insulators through Band Structure Combinatorics

NASA Astrophysics Data System (ADS)

Kruthoff, Jorrit; de Boer, Jan; van Wezel, Jasper; Kane, Charles L.; Slager, Robert-Jan

2017-10-01

We present a method for efficiently enumerating all allowed, topologically distinct, electronic band structures within a given crystal structure in all physically relevant dimensions. The algorithm applies to crystals without time-reversal, particle-hole, chiral, or any other anticommuting or anti-unitary symmetries. The results presented match the mathematical structure underlying the topological classification of these crystals in terms of K -theory and therefore elucidate this abstract mathematical framework from a simple combinatorial perspective. Using a straightforward counting procedure, we classify all allowed topological phases of spinless particles in crystals in class A . Employing this classification, we study transitions between topological phases within class A that are driven by band inversions at high-symmetry points in the first Brillouin zone. This enables us to list all possible types of phase transitions within a given crystal structure and to identify whether or not they give rise to intermediate Weyl semimetallic phases.
Structure of a quasi-parallel, quasi-laminar bow shock

NASA Technical Reports Server (NTRS)

Greenstadt, E. W.; Russell, C. T.; Formisano, V.; Hedgecock, P. C.; Scarf, F. L.; Neugebauer, M.; Holzer, R. E.

1976-01-01

A thick, quasi-parallel bow shock structure was observed with field and particle detectors of both HEOS 1 and OGO 5. The typical magnetic pulsation structure was at least 1 to 2 earth radii thick radially and was accompanied by irregular but distinct plasma distributions characteristic of neither the solar wind nor the magnetosheath. Waves constituting the large pulsations were polarized principally in the plane of the nominal shock, therefore also in the plane perpendicular to the average interplanetary field. A separate interpulsation regime detected between bursts of large amplitude oscillations was similar to the upstream wave region magnetically, but was characterized by disturbed plasma flux and enhanced noise around the ion plasma frequency. The shock structure appeared to be largely of an oblique, whistler type, probably complicated by counterstreaming high energy protons. Evidence for firehose instability-based structure was weak at best and probably negative.
Helical Antifreeze Proteins Have Independently Evolved in Fishes on Four Occasions

PubMed Central

Graham, Laurie A.; Hobbs, Rod S.; Fletcher, Garth L.; Davies, Peter L.

2013-01-01

Alanine-rich α-helical (type I) antifreeze proteins (AFPs) are produced by a variety of fish species from three different orders to protect against freezing in icy seawater. Interspersed amongst and within these orders are fishes making AFPs that are completely different in both sequence and structure. The origin of this variety of types I, II, III and antifreeze glycoproteins (AFGPs) has been attributed to adaptation following sea-level glaciations that occurred after the divergence of most of the extant families of fish. The presence of similar types of AFPs in distantly related fishes has been ascribed to lateral gene transfer in the case of the structurally complex globular type II lectin-like AFPs and to convergent evolution for the AFGPs, which consist of a well-conserved tripeptide repeat. In this paper, we examine the genesis of the type I AFPs, which are intermediate in complexity. These predominantly α-helical peptides share many features, such as putative capping structures, Ala-richness and amphipathic character. We have added to the type I repertoire by cloning additional sequences from sculpin and have found that the similarities between the type I AFPs of the four distinct groups of fishes are not borne out at the nucleotide level. Both the non-coding sequences and the codon usage patterns are strikingly different. We propose that these AFPs arose via convergence from different progenitor helices with a weak affinity for ice and that their similarity is dictated by the propensity of specific amino acids to form helices and to align water on one side of the helix into an ice-like pattern. PMID:24324684
The ÖX˜ absorption of vinoxy radical revisited: Normal and Herzberg-Teller bands observed via cavity ringdown spectroscopy

NASA Astrophysics Data System (ADS)

Thomas, Phillip S.; Chhantyal-Pun, Rabi; Kline, Neal D.; Miller, Terry A.

2010-03-01

The ÖX˜ electronic absorption spectrum of vinoxy radical has been investigated using room temperature cavity ringdown spectroscopy. Analysis of the observed bands on the basis of computed vibrational frequencies and rotational envelopes reveals that two distinct types of features are present with comparable intensities. The first type corresponds to "normal" allowed electronic transitions to the origin and symmetric vibrations in the Ã state. The second type is interpreted in terms of excitations to asymmetric Ã state vibrations, which are only vibronically allowed by Herzberg-Teller coupling to the B˜ state. Results of electronic structure calculations indicate that the magnitude of the Herzberg-Teller coupling is appropriate to produce vibronically induced transitions with intensities comparable to those of the normal bands.
Dynamic Structure of a Molecular Liquid S0.5Cl0.5: Ab initio Molecular-Dynamics Simulations

NASA Astrophysics Data System (ADS)

Ohmura, Satoshi; Shimakura, Hironori; Kawakita, Yukinobu; Shimojo, Fuyuki; Yao, Makoto

2013-07-01

The static and dynamic structures of a molecular liquid S0.5Cl0.5 consisting of Cl--S--S--Cl (S2Cl2) type molecules are studied by means of ab initio molecular dynamics simulations. Both the calculated static and dynamic structure factors are in good agreement with experimental results. The dynamic structures are discussed based on van-Hove distinct correlation functions, molecular translational mean-square displacements (TMSD) and rotational mean-square displacements (RMSD). In the TMSD and RMSD, there are ballistic and diffusive regimes in the sub-picosecond and picosecond time regions, respectively. These time scales are consistent with the decay time observed experimentally. The interaction between molecules in the liquid is also discussed in comparison with that in another liquid chalcogen--halogen system Se0.5Cl0.5.

Soil Type Has a Stronger Role than Dipterocarp Host Species in Shaping the Ectomycorrhizal Fungal Community in a Bornean Lowland Tropical Rain Forest

PubMed Central

Essene, Adam L.; Shek, Katherine L.; Lewis, J. D.; Peay, Kabir G.; McGuire, Krista L.

2017-01-01

The role that mycorrhizal fungal associations play in the assembly of long-lived tree communities is poorly understood, especially in tropical forests, which have the highest tree diversity of any ecosystem. The lowland tropical rain forests of Southeast Asia are characterized by high levels of species richness within the family Dipterocarpaceae, the entirety of which has been shown to form obligate ectomycorrhizal (ECM) fungal associations. Differences in ECM assembly between co-occurring species of dipterocarp have been suggested, but never tested in adult trees, as a mechanism for maintaining the coexistence of closely related tree species in this family. Testing this hypothesis has proven difficult because the assembly of both dipterocarps and their ECM associates co-varies with the same edaphic variables. In this study, we used high-throughput DNA sequencing of soils and Sanger sequencing of root tips to evaluate how ECM fungi were structured within and across a clay–sand soil nutrient ecotone in a mixed-dipterocarp rain forest in Malaysian Borneo. We compared assembly patterns of ECM fungi in bulk soil to ECM root tips collected from three ecologically distinct species of dipterocarp. This design allowed us to test whether ECM fungi are more strongly structured by soil type or host specificity. As with previous studies of ECM fungi on this plot, we observed that clay vs. sand soil type strongly structured both the bulk soil and root tip ECM fungal communities. However, we also observed significantly different ECM communities associated with two of the three dipterocarp species evaluated on this plot. These results suggest that ECM fungal assembly on these species is shaped by a combination of biotic and abiotic factors, and that the soil edaphic niche occupied by different dipterocarp species may be mediated by distinct ECM fungal assemblages. PMID:29163567
Molecular Diversity of Cyanobacteria Inhabiting Coniform Structures and Surrounding Mat in a Yellowstone Hot Spring

NASA Astrophysics Data System (ADS)

Lau, Evan; Nash, Cody Z.; Vogler, Detlev R.; Cullings, K. W.

2005-02-01

Lithified coniform structures are common within cyanobacterial mats in Yellowstone National Park hot springs. It is unknown whether these structures and the mats from which they develop are inhabited by the same cyanobacterial populations. Denaturing gradient gel electrophoresis and sequencing and phylogenetic analysis of 16S rDNA was used to determine whether (1) three different morphological types of lithified coniform structures are inhabited by different cyanobacterial species, (2) these species are partitioned along a vertical gradient of these structures, and (3) lithified and non-lithified sections of mat are inhabited by different cyanobacterial species. Our results, based on multiple samplings, indicate that the cyanobacterial community compositions in the three lithified morphological types were identical and lacked any vertical differentiation. However, lithified and non-lithified portions of the same mat were inhabited by distinct and different populations of cyanobacteria. Cyanobacteria inhabiting lithified structures included at least one undefined Oscillatorialean taxon, which may represent the dominant cyanobacteria genus in lithified coniform stromatolites, Phormidium, three Synechococcus-like species, and two unknown cyanobacterial taxa. In contrast, the surrounding mats contained four closely related Synechococcus-like species. Our results indicate that the distribution of lithified coniform stromatolites may be dependent on the presence of one or more microorganisms, which are phylogenetically different from those inhabiting surrounding non-lithified mats.
Nanomechanical properties of distinct fibrillar polymorphs of the protein α-synuclein

PubMed Central

Makky, Ali; Bousset, Luc; Polesel-Maris, Jérôme; Melki, Ronald

2016-01-01

Alpha-synuclein (α-Syn) is a small presynaptic protein of 140 amino acids. Its pathologic intracellular aggregation within the central nervous system yields protein fibrillar inclusions named Lewy bodies that are the hallmarks of Parkinson’s disease (PD). In solution, pure α-Syn adopts an intrinsically disordered structure and assembles into fibrils that exhibit considerable morphological heterogeneity depending on their assembly conditions. We recently established tightly controlled experimental conditions allowing the assembly of α-Syn into highly homogeneous and pure polymorphs. The latter exhibited differences in their shape, their structure but also in their functional properties. We have conducted an AFM study at high resolution and performed a statistical analysis of fibrillar α-Syn shape and thermal fluctuations to calculate the persistence length to further assess the nanomechanical properties of α-Syn polymorphs. Herein, we demonstrated quantitatively that distinct polymorphs made of the same protein (wild-type α-Syn) show significant differences in their morphology (height, width and periodicity) and physical properties (persistence length, bending rigidity and axial Young’s modulus). PMID:27901068
Bacterial protease uses distinct thermodynamic signatures for substrate recognition.

PubMed

Bezerra, Gustavo Arruda; Ohara-Nemoto, Yuko; Cornaciu, Irina; Fedosyuk, Sofiya; Hoffmann, Guillaume; Round, Adam; Márquez, José A; Nemoto, Takayuki K; Djinović-Carugo, Kristina

2017-06-06

Porphyromonas gingivalis and Porphyromonas endodontalis are important bacteria related to periodontitis, the most common chronic inflammatory disease in humans worldwide. Its comorbidity with systemic diseases, such as type 2 diabetes, oral cancers and cardiovascular diseases, continues to generate considerable interest. Surprisingly, these two microorganisms do not ferment carbohydrates; rather they use proteinaceous substrates as carbon and energy sources. However, the underlying biochemical mechanisms of their energy metabolism remain unknown. Here, we show that dipeptidyl peptidase 11 (DPP11), a central metabolic enzyme in these bacteria, undergoes a conformational change upon peptide binding to distinguish substrates from end products. It binds substrates through an entropy-driven process and end products in an enthalpy-driven fashion. We show that increase in protein conformational entropy is the main-driving force for substrate binding via the unfolding of specific regions of the enzyme ("entropy reservoirs"). The relationship between our structural and thermodynamics data yields a distinct model for protein-protein interactions where protein conformational entropy modulates the binding free-energy. Further, our findings provide a framework for the structure-based design of specific DPP11 inhibitors.
A novel partitioning method for block-structured adaptive meshes

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

Fu, Lin, E-mail: lin.fu@tum.de; Litvinov, Sergej, E-mail: sergej.litvinov@aer.mw.tum.de; Hu, Xiangyu Y., E-mail: xiangyu.hu@tum.de

We propose a novel partitioning method for block-structured adaptive meshes utilizing the meshless Lagrangian particle concept. With the observation that an optimum partitioning has high analogy to the relaxation of a multi-phase fluid to steady state, physically motivated model equations are developed to characterize the background mesh topology and are solved by multi-phase smoothed-particle hydrodynamics. In contrast to well established partitioning approaches, all optimization objectives are implicitly incorporated and achieved during the particle relaxation to stationary state. Distinct partitioning sub-domains are represented by colored particles and separated by a sharp interface with a surface tension model. In order to obtainmore » the particle relaxation, special viscous and skin friction models, coupled with a tailored time integration algorithm are proposed. Numerical experiments show that the present method has several important properties: generation of approximately equal-sized partitions without dependence on the mesh-element type, optimized interface communication between distinct partitioning sub-domains, continuous domain decomposition which is physically localized and implicitly incremental. Therefore it is particularly suitable for load-balancing of high-performance CFD simulations.« less
Importance of MAP Kinases during Protoperithecial Morphogenesis in Neurospora crassa

PubMed Central

Jeffree, Chris E.; Oborny, Radek; Boonyarungsrit, Patid; Read, Nick D.

2012-01-01

In order to produce multicellular structures filamentous fungi combine various morphogenetic programs that are fundamentally different from those used by plants and animals. The perithecium, the female sexual fruitbody of Neurospora crassa, differentiates from the vegetative mycelium in distinct morphological stages, and represents one of the more complex multicellular structures produced by fungi. In this study we defined the stages of protoperithecial morphogenesis in the N. crassa wild type in greater detail than has previously been described; compared protoperithecial morphogenesis in gene-deletion mutants of all nine mitogen-activated protein (MAP) kinases conserved in N. crassa; confirmed that all three MAP kinase cascades are required for sexual development; and showed that the three different cascades each have distinctly different functions during this process. However, only MAP kinases equivalent to the budding yeast pheromone response and cell wall integrity pathways, but not the osmoregulatory pathway, were essential for vegetative cell fusion. Evidence was obtained for MAP kinase signaling cascades performing roles in extracellular matrix deposition, hyphal adhesion, and envelopment during the construction of fertilizable protoperithecia. PMID:22900028
Two distinct domains contribute to the substrate acyl chain length selectivity of plant acyl-ACP thioesterase.

PubMed

Jing, Fuyuan; Zhao, Le; Yandeau-Nelson, Marna D; Nikolau, Basil J

2018-02-28

The substrate specificity of acyl-ACP thioesterase (TE) plays an essential role in controlling the fatty acid profile produced by type II fatty acid synthases. Here we identify two groups of residues that synergistically determine different substrate specificities of two acyl-ACP TEs from Cuphea viscosissima (CvFatB1 and CvFatB2). One group (V194, V217, N223, R226, R227, and I268 in CvFatB2) is critical in determining the structure and depth of a hydrophobic cavity in the N-terminal hotdog domain that binds the substrate's acyl moiety. The other group (255-RKLSKI-260 and 285-RKLPKL-289 in CvFatB2) defines positively charged surface patches that may facilitate binding of the ACP moiety. Mutagenesis of residues within these two groups results in distinct synthetic acyl-ACP TEs that efficiently hydrolyze substrates with even shorter chains (C4- to C8-ACPs). These insights into structural determinants of acyl-ACP TE substrate specificity are useful in modifying this enzyme for tailored fatty acid production in engineered organisms.
A novel partitioning method for block-structured adaptive meshes

NASA Astrophysics Data System (ADS)

Fu, Lin; Litvinov, Sergej; Hu, Xiangyu Y.; Adams, Nikolaus A.

2017-07-01

We propose a novel partitioning method for block-structured adaptive meshes utilizing the meshless Lagrangian particle concept. With the observation that an optimum partitioning has high analogy to the relaxation of a multi-phase fluid to steady state, physically motivated model equations are developed to characterize the background mesh topology and are solved by multi-phase smoothed-particle hydrodynamics. In contrast to well established partitioning approaches, all optimization objectives are implicitly incorporated and achieved during the particle relaxation to stationary state. Distinct partitioning sub-domains are represented by colored particles and separated by a sharp interface with a surface tension model. In order to obtain the particle relaxation, special viscous and skin friction models, coupled with a tailored time integration algorithm are proposed. Numerical experiments show that the present method has several important properties: generation of approximately equal-sized partitions without dependence on the mesh-element type, optimized interface communication between distinct partitioning sub-domains, continuous domain decomposition which is physically localized and implicitly incremental. Therefore it is particularly suitable for load-balancing of high-performance CFD simulations.
The Structural Basis for Matrix Metalloproteinase 1 Catalyzed Collagenolysis

PubMed Central

Bertini, Ivano; Fragai, Marco; Luchinat, Claudio; Melikian, Maxime; Toccafondi, Mirco; Lauer, Janelle L.; Fields, Gregg B.

2012-01-01

The proteolysis of collagen triple-helical structure (collagenolysis) is a poorly understood yet critical physiological process. Presently, matrix metalloproteinase 1 (MMP-1) and collagen triple-helical peptide models have been utilized to characterize the events and calculate the energetics of collagenolysis via NMR spectroscopic analysis of 12 enzyme-substrate complexes. The triple-helix is bound initially by the MMP-1 hemopexin-like (HPX) domain via a four amino acid stretch (analogous to type I collagen residues 782–785). The triple-helix is then presented to the MMP-1 catalytic (CAT) domain in a distinct orientation. The HPX and CAT domains are rotated with respect to one another compared with the X-ray “closed” conformation of MMP-1. Back-rotation of the CAT and HPX domains to the X-ray closed conformation releases one chain out of the triple-helix, and this chain is properly positioned in the CAT domain active site for subsequent hydrolysis. The aforementioned steps provide a detailed, experimentally-derived, and energetically favorable collagenolytic mechanism, as well as significant insight into the roles of distinct domains in extracellular protease function. PMID:22239621
Lanthanide coordination polymers: Synthesis, diverse structure and luminescence properties

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

Song, Xue-Qin, E-mail: songxq@mail.lzjtu.cn; Lei, Yao-Kun; Wang, Xiao-Run

2014-10-15

The new semirigid exo-bidentate ligand incorporating furfurysalicylamide terminal groups, namely, 1,4-bis([(2′-furfurylaminoformyl)phenoxyl]methyl)-2,5-bismethylbenzene (L) was synthesized and used as building blocks for constructing lanthanide coordination polymers with luminescent properties. The series of lanthanide nitrate complexes have been characterized by elemental analysis, IR spectroscopy, and X-ray diffraction analysis. The semirigid ligand L, as a bridging ligand, reacts with lanthanide nitrates forming three distinct structure types: chiral noninterpenetrated two-dimensional (2D) honeycomblike (6,3) (hcb, Schläfli symbol 6{sup 3}, vertex symbol 6 6 6) topological network as type I, 1D zigzag chain as type II and 1D trapezoid ladder-like chain as type III. The structural diversitiesmore » indicate that lanthanide contraction effect played significant roles in the structural self-assembled process. The luminescent properties of Eu{sup III}, Tb{sup III} and Dy{sup III} complexes are discussed in detail. Due to the good match between the lowest triplet state of the ligand and the resonant energy level of the lanthanide ion, the lanthanide ions in Eu{sup III}, Tb{sup III} and Dy{sup III} complexes can be efficiently sensitized by the ligand. - Graphical abstract: We present herein six lanthanide coordination polymers of a new semirigid exo-bidentate ligand which not only display diverse structures but also possess strong luminescence properties. - Highlights: • We present lanthanide coordination polymers of a new semirigid exo-bidentate ligand. • The lanthanide coordination polymers exhibit diverse structures. • The luminescent properties of Tb{sup III}, Eu{sup III} and Dy{sup III} complexes are discussed in detail.« less
The structure of Serratia marcescens Lip, a membrane-bound component of the type VI secretion system

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

Rao, Vincenzo A.; Shepherd, Sharon M.; English, Grant

2011-12-01

The high-resolution crystal structure of S. marcescens Lip reveals a new member of the transthyretin family of proteins. Lip, a core component of the type VI secretion apparatus, is localized to the outer membrane and is positioned to interact with other proteins forming this complex system. Lip is a membrane-bound lipoprotein and a core component of the type VI secretion system found in Gram-negative bacteria. The structure of a Lip construct (residues 29–176) from Serratia marcescens (SmLip) has been determined at 1.92 Å resolution. Experimental phases were derived using a single-wavelength anomalous dispersion approach on a sample cocrystallized with iodide.more » The membrane localization of the native protein was confirmed. The structure is that of the globular domain lacking only the lipoprotein signal peptide and the lipidated N-terminus of the mature protein. The protein fold is dominated by an eight-stranded β-sandwich and identifies SmLip as a new member of the transthyretin family of proteins. Transthyretin and the only other member of the family fold, 5-hydroxyisourate hydrolase, form homotetramers important for their function. The asymmetric unit of SmLip is a tetramer with 222 symmetry, but the assembly is distinct from that previously noted for the transthyretin protein family. However, structural comparisons and bacterial two-hybrid data suggest that the SmLip tetramer is not relevant to its role as a core component of the type VI secretion system, but rather reflects a propensity for SmLip to participate in protein–protein interactions. A relatively low level of sequence conservation amongst Lip homologues is noted and is restricted to parts of the structure that might be involved in interactions with physiological partners.« less
The Rise of Complexity: Do the Pavilion Lake Microbialites Suggest a Way to Build a Macroorganism?

NASA Astrophysics Data System (ADS)

Schulze-Makuch, D.; Laval, B.; Lim, D. S.; Irwin, L. N.

2005-12-01

The distinctive assemblage of freshwater calcite microbialites discovered at Pavilion Lake, BC, has been associated with organisms such as Epiphyton and Girvanella, fossils from just before the Cambrian explosion about 550 million years ago (Laval et al., 2000). The presence of the microbialite structures in a dimictic mid-latitude lake and their establishment after the last ice age about 10,000 years ago is puzzling. Their distinctive morphologies include cone-shaped seepage structures 2 m or more in height with hollow internal conduits that open at the top of the cones, and dense artichoke-like structures with calcite "leaves" greater than 1 m in height. These structures are astounding as they imply functional properties. In principle, this is not unlike the interaction of individual cells in a macroorganism, in which many different types of specialized cells interact with each other to the benefit of the whole organism (e.g. interaction of blood, integument, and organ cells within animals). Certainly, the complex interaction of these microbial cells is not equivalent to the collaboration of cells within an individual multicellular organism, where each cell has the same genetic information but differential gene expression provides well-defined cellular specializations. However, the microbialites raise the question of how much complexity and structure can be achieved by a high degree of communication within a multitude of microbial cells. Our findings indicate a complex and interacting microbial consortium associated with the structures at Pavilion Lake, and revealed biomarkers for proteobacteria, sulphur reducing bacteria, and firmicutes (possibly photosynthetic heliobacteria), among others. Types of genetic exchange among these microbial cells may include lateral gene transfer via conjugation, transformation, and transduction, or other mechanisms. This finding may have significant implications for the evolution of life on Earth and possible life on other planets. References: Laval, B., Cady, S.L., Pollack, J.C., McKay, C.P., Bird, J.S., Grotzinger, J.P., Ford, D.C., and Bohm, H.R. (2000) Modern freshwater microbialite analogues for ancient dendritic reef structures. Nature 407, 626-629.
Tales from the tomb: the microbial ecology of exposed rock surfaces.

PubMed

Brewer, Tess E; Fierer, Noah

2018-03-01

Although a broad diversity of eukaryotic and bacterial taxa reside on rock surfaces where they can influence the weathering of rocks and minerals, these communities and their contributions to mineral weathering remain poorly resolved. To build a more comprehensive understanding of the diversity, ecology and potential functional attributes of microbial communities living on rock, we sampled 149 tombstones across three continents and analysed their bacterial and eukaryotic communities via marker gene and shotgun metagenomic sequencing. We found that geographic location and climate were important factors structuring the composition of these communities. Moreover, the tombstone-associated microbial communities varied as a function of rock type, with granite and limestone tombstones from the same cemeteries harbouring taxonomically distinct microbial communities. The granite and limestone-associated communities also had distinct functional attributes, with granite-associated bacteria having more genes linked to acid tolerance and chemotaxis, while bacteria on limestone were more likely to be lichen associated and have genes involved in photosynthesis and radiation resistance. Together these results indicate that rock-dwelling microbes exhibit adaptations to survive the stresses of the rock surface, differ based on location, climate and rock type, and seem pre-disposed to different ecological strategies (symbiotic versus free-living lifestyles) depending on the rock type. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.
Discovery of 4-Methyl-N-(4-((4-methylpiperazin-1-yl)methyl)-3-(trifluoromethyl)phenyl)-3-((1-nicotinoylpiperidin-4-yl)oxy)benzamide (CHMFL-ABL/KIT-155) as a Novel Highly Potent Type II ABL/KIT Dual Kinase Inhibitor with a Distinct Hinge Binding.

PubMed

Wang, Qiang; Liu, Feiyang; Wang, Beilei; Zou, Fengming; Qi, Ziping; Chen, Cheng; Yu, Kailin; Hu, Chen; Qi, Shuang; Wang, Wenchao; Hu, Zhenquan; Liu, Juan; Wang, Wei; Wang, Li; Liang, Qianmao; Zhang, Shanchun; Ren, Tao; Liu, Qingsong; Liu, Jing

2017-01-12

The discovery of a novel potent type II ABL/c-KIT dual kinase inhibitor compound 34 (CHMFL-ABL/KIT-155), which utilized a hydrogen bond formed by NH on the kinase backbone and carbonyl oxygen of 34 as a unique hinge binding, is described. 34 potently inhibited purified ABL (IC 50 : 46 nM) and c-KIT kinase (IC 50 : 75 nM) in the biochemical assays and displayed high selectivity (S Score (1) = 0.03) at the concentration of 1 μM among 468 kinases/mutants in KINOMEscan assay. It exhibited strong antiproliferative activities against BCR-ABL/c-KIT driven CML/GISTs cancer cell lines through blockage of the BCR-ABL/c-KIT mediated signaling pathways, arresting cell cycle progression and induction of apoptosis. 34 possessed a good oral PK property and effectively suppressed the tumor progression in the K562 (CML) and GIST-T1 (GISTs) cells mediated xenograft mouse model. The distinct hinge-binding mode of 34 provided a novel pharmacophore for expanding the chemical structure diversity for the type II kinase inhibitors discovery.
Local unitary invariants for N-qubit pure states

NASA Astrophysics Data System (ADS)

Sharma, S. Shelly; Sharma, N. K.

2010-11-01

The concept of negativity font, a basic unit of multipartite entanglement, is introduced. Transformation properties of determinants of negativity fonts under local unitary (LU) transformations are exploited to obtain relevant N-qubit polynomial invariants and construct entanglement monotones from first principles. It is shown that entanglement monotones that detect the entanglement of specific parts of the composite system may be constructed to distinguish between states with distinct types of entanglement. The structural difference between entanglement monotones for an odd and even number of qubits is brought out.
Zoonotic Babesia microti in the northeastern U.S.: Evidence for the expansion of a specific parasite lineage

PubMed Central

Molloy, Philip; Weeks, Karen

2018-01-01

The recent range expansion of human babesiosis in the northeastern United States, once found only in restricted coastal sites, is not well understood. This study sought to utilize a large number of samples to examine the population structure of the parasites on a fine scale to provide insights into the mode of emergence across the region. 228 B. microti samples collected in endemic northeastern U.S. sites were genotyped using published Variable number tandem repeat (VNTR) markers. The genetic diversity and population structure were analysed on a geographic scale using Phyloviz and TESS, programs that utilize two different methods to identify population membership without predefined population data. Three distinct populations were detected in northeastern US, each dominated by a single ancestral type. In contrast to the limited range of the Nantucket and Cape Cod populations, the mainland population dominated from New Jersey eastward to Boston. Ancestral populations of B. microti were sufficiently isolated to differentiate into distinct populations. Despite this, a single population was detected across a large geographic area of the northeast that historically had at least 3 distinct foci of transmission, central New Jersey, Long Island and southeastern Connecticut. We conclude that a single B. microti genotype has expanded across the northeastern U.S. The biological attributes associated with this parasite genotype that have contributed to such a selective sweep remain to be identified. PMID:29565993
Characterizing the distinct structural changes associated with self-reported knee injury among individuals with incident knee osteoarthritis: Data from the osteoarthritis initiative.

PubMed

Davis, Julie E; Harkey, Matthew S; Ward, Robert J; Mackay, James W; Lu, Bing; Price, Lori Lyn; Eaton, Charles B; Barbe, Mary F; Lo, Grace H; McAlindon, Timothy E; Driban, Jeffrey B

2018-04-01

We aimed to characterize the agreement between distinct structural changes on magnetic resonance (MR) imaging and self-reported injury in the 12 months leading to incident common or accelerated knee osteoarthritis (KOA). We conducted a descriptive study using data from baseline and the first 4 annual visits of the Osteoarthritis Initiative. Knees had no radiographic KOA at baseline (Kellgren-Lawrence [KL]<2). We classified two groups: (1) accelerated KOA: a knee developed advanced-stage KOA (KL = 3 or 4) within 48 months and (2) common KOA: a knee increased in radiographic severity (excluding those with accelerated KOA). Adults were 1:1 matched based on sex. The index visit was when a person met the accelerated or common KOA criteria. We limited our sample to people with MR images and self-reported injury data at index visit and year prior. Among 226 people, we found fair agreement between self-reported injuries and distinct structural changes (kappa = 0.24 to 0.31). Most distinct structural changes were medial meniscal pathology. No distinct structural changes (e.g., root or radial tears) appeared to differ between adults who reported or did not report an injury; except, all subchondral fractures occurred in adults who developed accelerated KOA and reported an injury. While there is fair agreement between self-reported knee injuries and distinct structural changes, there is some discordance. Self-reported injury may represent a different construct from distinct structural changes that occur after joint trauma. Clin. Anat. 31:330-334, 2018. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.
Insight into the functional organization of nuclear lamins in health and disease.

PubMed

Tatli, Meltem; Medalia, Ohad

2018-05-22

Lamins are the main component of the nuclear lamina, a protein meshwork at the inner nuclear membrane which primarily provide mechanical stability to the nucleus. Lamins, type V intermediate filament proteins, are also involved in many nuclear activities. Structural analysis of nuclei revealed that lamins form 3.5nm thick filaments often interact with nuclear pore complexes. Mutations in the LMNA gene, encoding A-type lamins, have been associated with at least 15 distinct diseases collectively termed laminopathies, including muscle, metabolic and neurological disorders, and premature aging syndrome. It is unclear how laminopathic mutations lead to such a wide array of diseases, essentially affecting almost all tissues. Copyright © 2018 Elsevier Ltd. All rights reserved.
[Clinical and molecular study in a child with X-linked hypohidrotic ectodermal dysplasia].

PubMed

Callea, Michele; Yavuz, Izzet; Clarich, Gabriella; Cammarata-Scalisi, Francisco

2015-12-01

Ectodermal dysplasia encompasses more than 200 clinically distinct entities, which affect at least two structures derived from the ectoderm, including the skin, hair, nails, teeth, sweat glands, and sebaceous glands. X-linked hypohidrotic ectodermal dysplasia is the most common type and is caused by mutation of the EDA gene that encodes Ectodysplasin-A. It occurs in less than 1 in 100 000 individuals and is clinically characterized by hypodontia, hypohidrosis, hypotrichosis, and eye dis orders. We present a child evaluated in a multidisciplinary manner with clinical and molecular diagnosis of X-linked hypohidrotic ectodermal dysplasia with type missense mutation c.1133C> T; p.T378M in EDA gene.
Epithelial Patterning, Morphogenesis, and Evolution: Drosophila Eggshell as a Model.

PubMed

Osterfield, Miriam; Berg, Celeste A; Shvartsman, Stanislav Y

2017-05-22

Understanding the mechanisms driving tissue and organ formation requires knowledge across scales. How do signaling pathways specify distinct tissue types? How does the patterning system control morphogenesis? How do these processes evolve? The Drosophila egg chamber, where EGF and BMP signaling intersect to specify unique cell types that construct epithelial tubes for specialized eggshell structures, has provided a tractable system to ask these questions. Work there has elucidated connections between scales of development, including across evolutionary scales, and fostered the development of quantitative modeling tools. These tools and general principles can be applied to the understanding of other developmental processes across organisms. Copyright © 2017 Elsevier Inc. All rights reserved.

Molecular Basis of Cardiac Delayed Rectifier Potassium Channel Function and Pharmacology.

PubMed

Wu, Wei; Sanguinetti, Michael C

2016-06-01

Human cardiomyocytes express 3 distinct types of delayed rectifier potassium channels. Human ether-a-go-go-related gene (hERG) channels conduct the rapidly activating current IKr; KCNQ1/KCNE1 channels conduct the slowly activating current IKs; and Kv1.5 channels conduct an ultrarapid activating current IKur. Here the authors provide a general overview of the mechanistic and structural basis of ion selectivity, gating, and pharmacology of the 3 types of cardiac delayed rectifier potassium ion channels. Most blockers bind to S6 residues that line the central cavity of the channel, whereas activators interact with the channel at 4 symmetric binding sites outside the cavity. Copyright © 2016 Elsevier Inc. All rights reserved.
Differential timing of granule cell production during cerebellum development underlies generation of the foliation pattern.

PubMed

Legué, Emilie; Gottshall, Jackie L; Jaumouillé, Edouard; Roselló-Díez, Alberto; Shi, Wei; Barraza, Luis Humberto; Washington, Senna; Grant, Rachel L; Joyner, Alexandra L

2016-09-08

The mouse cerebellum (Cb) has a remarkably complex foliated three-dimensional (3D) structure, but a stereotypical cytoarchitecture and local circuitry. Little is known of the cellular behaviors and genes that function during development to determine the foliation pattern. In the anteroposterior axis the mammalian cerebellum is divided by lobules with distinct sizes, and the foliation pattern differs along the mediolateral axis defining a medial vermis and two lateral hemispheres. In the vermis, lobules are further grouped into four anteroposterior zones (anterior, central, posterior and nodular zones) based on genetic criteria, and each has distinct lobules. Since each cerebellar afferent group projects to particular lobules and zones, it is critical to understand how the 3D structure of the Cb is acquired. During cerebellar development, the production of granule cells (gcs), the most numerous cell type in the brain, is required for foliation. We hypothesized that the timing of gc accumulation is different in the four vermal zones during development and contributes to the distinct lobule morphologies. In order to test this idea, we used genetic inducible fate mapping to quantify accumulation of gcs in each lobule during the first two postnatal weeks in mice. The timing of gc production was found to be particular to each lobule, and delayed in the central zone lobules relative to the other zones. Quantification of gc proliferation and differentiation at three time-points in lobules representing different zones, revealed the delay involves a later onset of maximum differentiation and prolonged proliferation of gc progenitors in the central zone. Similar experiments in Engrailed mutants (En1 (-/+) ;En2 (-/-) ), which have a smaller Cb and altered foliation pattern preferentially outside the central zone, showed that gc production, proliferation and differentiation are altered such that the differences between zones are attenuated compared to wild-type mice. Our results reveal that gc production is differentially regulated in each zone of the cerebellar vermis, and our mutant analysis indicates that the dynamics of gc production plays a role in determining the 3D structure of the Cb.
Compact groups in theory and practice - IV. The connection to large-scale structure

NASA Astrophysics Data System (ADS)

Mendel, J. Trevor; Ellison, Sara L.; Simard, Luc; Patton, David R.; McConnachie, Alan W.

2011-12-01

We investigate the properties of photometrically selected compact groups (CGs) in the Sloan Digital Sky Survey. In this paper, the fourth in a series, we focus on understanding the characteristics of our observed CG sample with particular attention paid to quantifying and removing contamination from projected foreground or background galaxies. Based on a simple comparison of pairwise redshift likelihoods, we find that approximately half of CGs in the parent sample contain one or more projected (interloping) members; our final clean sample contains 4566 galaxies in 1086 CGs. We show that half of the remaining CGs are associated with rich groups (or clusters), i.e. they are embedded sub-structure. The other half have spatial distributions and number-density profiles consistent with the interpretation that they are either independently distributed structures within the field (i.e. they are isolated) or associated with relatively poor structures. Comparisons of late-type and red-sequence fractions in radial annuli show that galaxies around apparently isolated CGs resemble the field population by 300 to 500 kpc from the group centre. In contrast, the galaxy population surrounding embedded CGs appears to remain distinct from the field out beyond 1 to 2 Mpc, consistent with results for rich groups. We take this as additional evidence that the observed distinction between CGs, i.e. isolated versus embedded, is a separation between different host environments.
Epidermolysis Bullosa Acquitsita

PubMed Central

Gupta, Rishu; Woodley, David T.; Chen, Mei

2011-01-01

EBA is a rare, acquired, chronic subepidermal bullous disease of the skin and mucosa characterized by autoantibodies to type VII collagen structures, a major component of anchoring fibrils, that attach the epidermis onto the dermis. EBA patients have tissue-bound as well as circulating anti-type VII collagen autoantibodies that attack type VII collagen and result in a reduction or perturbation of normally functioning anchoring fibrils. Patients with EBA have skin fragility, blisters, erosions, scars, milia, and nail loss: all features reminiscent of genetic dystrophic epidermolysis bullosa. These anti-type VII collagen antibodies are “pathogenic” because when injected into mice, the mice develop an EBA-like blistering disease. In addition to the classical mechanobullous presentation, EBA also has several other distinct clinical syndromes similar to bullous pemphigoid, Brunsting-Perry pemphigoid, or cicatricial pemphigoid. Although treatment for EBA is often unsatisfactory, some therapeutic success has been achieved with colchicine, dapsone, plasmaphoresis, photopheresis, infliximab, and intravenous immunoglobulin. PMID:22137228
Trivial and topological Fermi arcs in the type-II Weyl semimetal candidate MoTe2

NASA Astrophysics Data System (ADS)

Tamai, Anna; Wu, Quansheng; Cucchi, Irene; Bruno, Flavio; Barreteau, Celine; Giannini, Enrico; Soluyanov, Alexey; Baumberger, Felix

Weyl semimetals are commonly identified by detecting their characteristic open surface state Fermi arcs in angle-resolved photoemission (ARPES) experiments. However, in type-II Weyl semimetals the Fermi arcs generally disappear in the bulk carrier pockets before reaching the Weyl points where they terminate - making it harder to unambiguously identify this new electronic state. Using laser-based ARPES, we have resolved multiple distinct Fermi arcs on the inequivalent top and bottom (001) surfaces of the candidate type-II Weyl semimetal MoTe2. By comparing our ARPES data with systematic electronic structure calculations simulating different Weyl point arrangements, we show that some of these arcs are false positives as they can be explained without Weyl points, while others are only reproduced in scenarios with at least eight Weyl points. Our results thus suggest that MoTe2 is the first experimental realisation of a type-II Weyl semimetal.
Enamel microarchitecture of a tribosphenic molar.

PubMed

Spoutil, Frantisek; Vlcek, Vojtĕch; Horácek, Ivan

2010-10-01

The tribosphenic molar is a dental apomorphy of mammals and the molar type from which all derived types originated. Its enamel coat is expected to be ancestral: a thin, evenly distributed layer of radial prismatic enamel. In the bat Myotis myotis, we reinvestigated the 3D architecture of the dental enamel using serial sectioning combined with scanning electron microscopy analyses, biometrics of enamel prisms and crystallites, and X-ray diffraction. We found distinct heterotopies in enamel thickness (thick enamel on the convex sides of the crests, thin on the concave ones), angularity of enamel prisms, and in distribution of particular enamel types (prismatic, interprismatic, aprismatic) and demonstrated structural relations of these heterotopies to the cusp and crest organization of the tribosphenic molar. X-ray diffraction demonstrated that the crystallites composing the enamel are actually the aggregates of much smaller primary crystallites. The differences among particular enamel types in degree of crystallite aggregation and the variation in structural microstrain of the primary crystallites (depending upon the duration and the mechanical context of mineralization) represent factors not fully understood as yet that may contribute to the complexity of enamel microarchitecture in a significant way. © 2010 Wiley-Liss, Inc.
Ropizine concurrently enhances and inhibits ( sup 3 H) dextromethorpan binding to different structures of the guinea pig brain: Autoradiographic evidence for multiple binding sites

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

Canoll, P.D.; Smith, P.R.; and Musacchio, J.M.

1990-01-01

Ropizine produces a simultaneous enhancement and inhibition of ({sup 3}H) dextromethorphan (DM) high-affinity binding to different areas of the guinea pig brain. These results imply that there are two distinct types of high-affinity ({sup 3}H)DM binding sites, which are present in variable proportions in different brain structures. The ropizine-enhances ({sup 3}H)DM binding type was preferentially inhibited by (+)-pentazocine. This is consistent with the presumption that the (+)-pentazocine-sensitive site is identical with the common site for DM and 3-(-3-Hydroxphenyl)-N-(1-propyl)piperidine ((+)-3-PPP). The second binding type, which is inhibited by ropizine and is not so sensitive to (+){minus} pentazocine, has not been fullymore » characterized. This study demonstrates that the biphasic effects to ropizine are due, at least in part, to the effects of ropizine on two different types of ({sup 3}H)DM binding sites. However, this study does not rule out that the common DM/(+)-3-PPP site also might be inhibited by higher concentrations of ropizine.« less
Rupture testing for the quality control of electrodeposited copper interconnections in high-speed, high-density circuits

NASA Technical Reports Server (NTRS)

Zakraysek, Louis

1987-01-01

Printed Wiring Multilayer Board (PWMLB) structures for high speed, high density circuits are prone to failure due to the microcracking of electrolytic copper interconnections. The failure can occur in the foil that makes up the inner layer traces or in the plated through holes (PTH) deposit that forms the layer to layer interconnections. It is shown that there are some distinctive differences in the quality of Type E copper and that these differences can be detected before its use in a PWMLB. It is suggested that the strength of some Type E copper can be very low when the material is hot and that it is the use of this poor quality material in a PWMLB that results in PTH and inner layer microcracking. Since the PWMLB failure in question are induced by a thermal stress, and since the poorer grades of Type E materials used in these structures are susceptible to premature failure under thermal stress, the use of elevated temperature rupture and creep rupture testing is proposed as a means for screening copper foil, or its PTH equivalent, in order to eliminate the problem of Type E copper microcracking in advanced PWMLBs.
Molecular epidemiology of methicillin-resistant Staphylococcus aureus isolated in serial cultures from the respiratory tract of children with cystic fibrosis.

PubMed

Al-Zubeidi, Duha; Hogan, Patrick G; Boyle, Mary; Burnham, Carey-Ann D; Fritz, Stephanie A

2014-06-01

Little is known about strain relatedness of methicillin-resistant Staphyloccocus aureus (MRSA) isolated at serial time points from the respiratory tract of patients with cystic fibrosis (CF). The objectives are to interrogate the genetic diversity of MRSA recovered in serial cultures from children with CF and to correlate strain relatedness with clinical characteristics. We performed a retrospective analysis of children with CF from whom MRSA was isolated from serial respiratory cultures from 2005 to 2011. Within individual patients, relatedness of isolated strains was determined by repetitive-sequence polymerase chain reaction, and the staphylococcal cassette chromosome mec type of each isolate was characterized. Medical records corresponding to the MRSA cultures were reviewed. We identified 54 CF patients with serial MRSA cultures (145 distinct cultures). Over time, 45 (83%) patients maintained the same strain type and 9 (17%) possessed at least 2 distinct strain types. A total of 91 pairs of isolates were analyzed for strain relatedness. Of these, 81 (89%) were identical and 10 (11%) were distinct strain types. About 117 (83%) isolates were staphylococcal cassette chromosome mec type II, 24 (17%) were staphylococcal cassette chromosome mec type IV and 4 were other types not resolvable with our assay. Clinical factors, including time interval and prescription of antibiotics effective against MRSA between positive cultures, did not correlate with acquisition of a distinct MRSA strain by individual patients. Our data suggest that sustained presence of MRSA in CF patients is most commonly attributable to identical strain types. Acquisition of distinct MRSA strains in the airway is infrequent.
UbSRD: The Ubiquitin Structural Relational Database.

PubMed

Harrison, Joseph S; Jacobs, Tim M; Houlihan, Kevin; Van Doorslaer, Koenraad; Kuhlman, Brian

2016-02-22

The structurally defined ubiquitin-like homology fold (UBL) can engage in several unique protein-protein interactions and many of these complexes have been characterized with high-resolution techniques. Using Rosetta's structural classification tools, we have created the Ubiquitin Structural Relational Database (UbSRD), an SQL database of features for all 509 UBL-containing structures in the PDB, allowing users to browse these structures by protein-protein interaction and providing a platform for quantitative analysis of structural features. We used UbSRD to define the recognition features of ubiquitin (UBQ) and SUMO observed in the PDB and the orientation of the UBQ tail while interacting with certain types of proteins. While some of the interaction surfaces on UBQ and SUMO overlap, each molecule has distinct features that aid in molecular discrimination. Additionally, we find that the UBQ tail is malleable and can adopt a variety of conformations upon binding. UbSRD is accessible as an online resource at rosettadesign.med.unc.edu/ubsrd. Copyright © 2015 Elsevier Ltd. All rights reserved.
The Cultural Evolution of Structured Languages in an Open-Ended, Continuous World.

PubMed

Carr, Jon W; Smith, Kenny; Cornish, Hannah; Kirby, Simon

2017-05-01

Language maps signals onto meanings through the use of two distinct types of structure. First, the space of meanings is discretized into categories that are shared by all users of the language. Second, the signals employed by the language are compositional: The meaning of the whole is a function of its parts and the way in which those parts are combined. In three iterated learning experiments using a vast, continuous, open-ended meaning space, we explore the conditions under which both structured categories and structured signals emerge ex nihilo. While previous experiments have been limited to either categorical structure in meanings or compositional structure in signals, these experiments demonstrate that when the meaning space lacks clear preexisting boundaries, more subtle morphological structure that lacks straightforward compositionality-as found in natural languages-may evolve as a solution to joint pressures from learning and communication. Copyright © 2016 The Authors. Cognitive Science published by Wiley Periodicals, Inc. on behalf of Cognitive Science Society.
Structural and electronic properties of double-walled boron nitride nanocones

NASA Astrophysics Data System (ADS)

Brito, E.; Silva, T. S.; Guerra, T.; Leite, L.; Azevedo, S.; Freitas, A.; Kaschny, J. R.

2018-01-01

First principles calculations were applied to study the structural and electronic properties of different configurations of double-walled boron nitride nanocones with a disclination angle of 60°. The analysis includes different rotation angles, distance between apexes, as well as distinct types of antiphase boundaries. The calculations indicate that the non-rotated configuration of double-walled nanocone with a defective line composed by C and N atoms, forming C-N bonds, is the most stable configuration. It was found that the yam angle, apexes distance and defective line composition present significant influence on the electronic properties of such structures. Moreover, analyzing the spin charge density, for the electronic states near the Fermi level, it was also found that the configuration with a defective line containing C atoms presents a net magnetic moment.
Amorphous Metal Polysulfides: Electrode Materials with Unique Insertion/Extraction Reactions.

PubMed

Sakuda, Atsushi; Ohara, Koji; Fukuda, Katsutoshi; Nakanishi, Koji; Kawaguchi, Tomoya; Arai, Hajime; Uchimoto, Yoshiharu; Ohta, Toshiaki; Matsubara, Eiichiro; Ogumi, Zempachi; Okumura, Toyoki; Kobayashi, Hironori; Kageyama, Hiroyuki; Shikano, Masahiro; Sakaebe, Hikari; Takeuchi, Tomonari

2017-07-05

A unique charge/discharge mechanism of amorphous TiS 4 is reported. Amorphous transition metal polysulfide electrodes exhibit anomalous charge/discharge performance and should have a unique charge/discharge mechanism: neither the typical intercalation/deintercalation mechanism nor the conversion-type one, but a mixture of the two. Analyzing the mechanism of such electrodes has been a challenge because fewer tools are available to examine the "amorphous" structure. It is revealed that the electrode undergoes two distinct structural changes: (i) the deformation and formation of S-S disulfide bonds and (ii) changes in the coordination number of titanium. These structural changes proceed continuously and concertedly for Li insertion/extraction. The results of this study provide a novel and unique model of amorphous electrode materials with significantly larger capacities.
Headache associated with sexual activity: demography, clinical features, and comorbidity.

PubMed

Frese, A; Eikermann, A; Frese, K; Schwaag, S; Husstedt, I-W; Evers, S

2003-09-23

S: To provide data on the demography, clinical features, and comorbidity of headache associated with sexual activity (HSA). Between 1996 and 2001, 51 patients with the diagnosis of HSA were questioned using a structured interview. The mean age at onset was 39.2 (+/-11.1) years. There was a clear male preponderance (2.9:1). The age at onset had two peaks, with a first peak between the 20th and 24th (n = 13) years of life and a second peak between the 35th and 44th (n = 20) years of life. Eleven patients had HSA type 1 (dull subtype), which gradually increased with increasing sexual excitement. The remaining (n = 40) had HSA type 2 (explosive subtype). The pain was predominantly bilateral (67%), and diffuse or occipital (76%). The quality was nearly equally distributed among dull, throbbing, and stabbing. HSA was not dependent on specific sexual habits and most often occurred during sexual activity with the usual partner (94%) and during masturbation (35%). There was a high comorbidity with migraine (25%), benign exertional headache (29%), and tension-type headache (45%). HSA types 1 and 2 did not significantly differ in demography, clinical features, or comorbidity, except for a higher probability of stopping the attack by breaking off sexual activity in HSA type 1. There were no cases with HSA type 3 (postural subtype). Mean age at onset, a male preponderance, a predominantly bilateral and occipital pain, and a high comorbidity with other primary headaches are in concordance with case reports in the literature. The authors found two peaks for the age at onset, however. There was no clinical evidence proving subtypes 1 and 2 to be distinct disorders. HSA types 1 and 2 may be different manifestations of the same disease rather than distinct entities.
Upregulation of distinct collagen transcripts in post-surgery scar tissue: a study of conjunctival fibrosis.

PubMed

Seet, Li-Fong; Toh, Li Zhen; Chu, Stephanie W L; Finger, Sharon N; Chua, Jocelyn L L; Wong, Tina T

2017-06-01

Excessive accumulation of collagen is often used to assess the development of fibrosis. This study aims to identify collagen genes that define fibrosis in the conjunctiva following glaucoma filtration surgery (GFS). Using the mouse model of GFS, we have identified collagen transcripts that were upregulated in the fibrotic phase of wound healing via RNA-seq. The collagen transcripts that were increased the most were encoded by Col8a1 , Col11a1 and Col8a2 Further analysis of the Col8a1 , Col11a1 and Col8a2 transcripts revealed their increase by 67-, 54- and 18-fold, respectively, in the fibrotic phase, compared with 12-fold for Col1a1 , the most commonly evaluated collagen gene for fibrosis. However, only type I collagen was significantly upregulated at the protein level in the fibrotic phase. Type VIII and type I collagens colocalized in fibrous structures and in ACTA2-positive pericytes, and appeared to compensate for each other in expression levels. Type XI collagen showed low colocalization with both type VIII and type I collagens but can be found in association with macrophages. Furthermore, we show that both mouse and human conjunctival fibroblasts expressed elevated levels of the most highly expressed collagen genes in response to TGFβ2 treatment. Importantly, conjunctival tissues from individuals whose GF surgeries have failed due to scarring showed 3.60- and 2.78-fold increases in type VIII and I collagen transcripts, respectively, compared with those from individuals with no prior surgeries. These data demonstrate that distinct collagen transcripts are expressed at high levels in the conjunctiva after surgery and their unique expression profiles may imply differential influences on the fibrotic outcome. © 2017. Published by The Company of Biologists Ltd.
Muscular anatomy of an entoproct creeping-type larva reveals extraordinary high complexity and potential shared characters with mollusks.

PubMed

Merkel, Julia; Lieb, Bernhard; Wanninger, Andreas

2015-07-03

Entoprocta (Kamptozoa) is an enigmatic, acoelomate, tentacle-bearing phylum with indirect development, either via a swimming- or a creeping-type larva and still debated phylogenetic position within Lophotrochozoa. Recent morphological and neuro-anatomical studies on the creeping-type larva support a close relationship of Entoprocta and Mollusca, with a number of shared apomorphies including a tetraneurous nervous system and a complex serotonin-expressing apical organ. However, many morphological traits of entoproct larvae, in particular of the putative basal creeping-type larva, remain elusive. Applying fluorescent markers and 3D modeling, we found that this larval type has the most complex musculature hitherto described for any lophotrochozoan larva. The muscle systems identified include numerous novel and most likely creeping-type larva-specific structures such as frontal organ retractors, several other muscle fibers originating from the frontal organ, and longitudinal prototroch muscles. Interestingly, we found distinct muscle sets that are also present in several mollusks. These include paired sets of dorso-ventral muscles that intercross ventrally above the foot sole and a paired enrolling muscle that is distinct from the musculature of the body wall. Our data add further morphological support for an entoproct-mollusk relationship (Tetraneuralia) and strongly argue for the presence of an enrolling musculature as well as seriality (but not segmentation) in the last common tetraneuralian ancestor. The evolutionary driving forces that have led to the emergence of the extraordinarily complex muscular architecture in this short-lived, non-feeding entoproct larval type remain unknown, as are the processes that give rise to the highly different and much simpler muscular bodyplan of the adult entoproct during metamorphosis.
Microbiome Profiles in Periodontitis in Relation to Host and Disease Characteristics

PubMed Central

Hong, Bo-Young; Furtado Araujo, Michel V.; Strausbaugh, Linda D.; Terzi, Evimaria; Ioannidou, Effie; Diaz, Patricia I.

2015-01-01

Periodontitis is an inflammatory condition that affects the supporting tissues surrounding teeth. The occurrence of periodontitis is associated with shifts in the structure of the communities that inhabit the gingival sulcus. Although great inter-subject variability in the subgingival microbiome has been observed in subjects with periodontitis, it is unclear whether distinct community types exist and if differences in microbial signatures correlate with host characteristics or with the variable clinical presentations of periodontitis. Therefore, in this study we explored the existence of different community types in periodontitis and their relationship with host demographic, medical and disease-related clinical characteristics. Clustering analyses of microbial abundance profiles suggested two types of communities (A and B) existed in the 34 subjects with periodontitis evaluated. Type B communities harbored greater proportions of certain periodontitis-associated taxa, including species historically associated with the disease, such as Porphyromonas gingivalis, Tannerella forsythia and Treponema denticola, and taxa recently linked to periodontitis. In contrast, subjects with type A communities had increased proportions of different periodontitis-associated species, and were also enriched for health-associated species and core taxa (those equally prevalent in health and periodontitis). Periodontitis subgingival clusters were not associated with demographic, medical or disease-specific clinical parameters other than periodontitis extent (proportion of sites affected), which positively correlated with the total proportion of cluster B signature taxa. In conclusion, two types of microbial communities were detected in subjects with periodontitis. Host demographics and underlying medical conditions did not correlate with these profiles, which instead appeared to be related to periodontitis extent, with type B communities present in more widespread disease cases. The two identified periodontitis profiles may represent distinct dysbiotic processes potentially requiring community-tailored therapeutic interventions. PMID:25984952
From source to surface: Tracking magmatic boron and chlorine input into the geothermal systems of the Taupo Volcanic Zone, New Zealand

NASA Astrophysics Data System (ADS)

Bégué, Florence; Deering, Chad D.; Gravley, Darren M.; Chambefort, Isabelle; Kennedy, Ben M.

2017-10-01

The magmatic contribution into geothermal fluids in the central Taupo Volcanic Zone (TVZ), New Zealand, has been attributed to either andesitic, 'arc-type' fluids, or rhyolitic, 'rift-type' fluids to explain the compositional diversity of discharge waters. However, this model relies on outdated assumptions related to geochemical trends associated with the magma at depth of typical arc to back-arc settings. Current tectonic models have shown that the TVZ is situated within a rifting arc and hosts magmatic systems dominated by distinct rhyolite types, that are likely to have evolved under different conditions than the subordinate andesites. Therefore, a new appraisal of the existing models is required to further understand the origin of the spatial compositional diversity observed in the geothermal fluids and its relationship to the structural setting. Here, we use volatile concentrations (i.e. H2O, Cl, B) from rhyolitic and andesitic mineral-hosted melt inclusions to evaluate the magmatic contribution to the TVZ geothermal systems. The andesite and two different types of rhyolites (R1 and R2) are each distinct in Cl/H2O and B/Cl, which will affect volatile solubility and phase separation (vapor vs. hydrosaline liquid) of the exsolved volatile phase. Ultimately, these key differences in the magmatic volatile constituents will play a significant role in governing the concentration of Cl discharged into geothermal systems. We estimate bulk fluid compositions (B and Cl) in equilibrium with the different melt types to show the potential contribution of 'parent' fluids to the geothermal systems throughout the TVZ. The results of this analysis show that the variability in fluid compositions partly reflects degassing from previously unaccounted for distinct magma source compositions. We suggest the geothermal systems that appear to have an 'arc-type' andesitic fluid contribution are actually derived from a rhyolite melt in equilibrium with a highly crystalline andesite magma. This model is in better agreement with the current understanding of magma petrogenesis in the central TVZ and its atypical rifted-arc tectonic setting, and show that the central TVZ records an arc, not back-arc, fluid signature.
Individual Distinctiveness in Call Types of Wild Western Female Gorillas

PubMed Central

Salmi, Roberta; Hammerschmidt, Kurt; Doran-Sheehy, Diane M.

2014-01-01

Individually distinct vocalizations play an important role in animal communication, allowing call recipients to respond differentially based on caller identity. However, which of the many calls in a species' repertoire should have more acoustic variability and be more recognizable is less apparent. One proposed hypothesis is that calls used over long distances should be more distinct because visual cues are not available to identify the caller. An alternative hypothesis proposes that close calls should be more recognizable because of their importance in social interactions. To examine which hypothesis garners more support, the acoustic variation and individual distinctiveness of eight call types of six wild western gorilla (Gorilla gorilla) females were investigated. Acoustic recordings of gorilla calls were collected at the Mondika Research Center (Republic of Congo). Acoustic variability was high in all gorilla calls. Similar high inter-individual variation and potential for identity coding (PIC) was found for all call types. Discriminant function analyses confirmed that all call types were individually distinct (although for call types with lowest sample size - hum, grumble and scream - this result cannot be generalized), suggesting that neither the distance at which communication occurs nor the call social function alone can explain the evolution of identity signaling in western gorilla communication. PMID:25029238
Framing life and death on YouTube: the strategic communication of organ donation messages by organ procurement organizations.

PubMed

VanderKnyff, Jeremy; Friedman, Daniela B; Tanner, Andrea

2015-01-01

Using a sample of YouTube videos posted on the YouTube channels of organ procurement organizations, a content analysis was conducted to identify the frames used to strategically communicate prodonation messages. A total of 377 videos were coded for general characteristics, format, speaker characteristics, organs discussed, structure, problem definition, and treatment. Principal components analysis identified message frames, and k-means cluster analysis established distinct groupings of videos on the basis of the strength of their relationship to message frames. Analysis of these frames and clusters found that organ procurement organizations present multiple, and sometimes competing, video types and message frames on YouTube. This study serves as important formative research that will inform future studies to measure the effectiveness of the distinct message frames and clusters identified.

Using Vocal Dialects to Assess the Population Structure of Bigg's Killer Whales in Alaska

NASA Astrophysics Data System (ADS)

Sharpe, D. L.; Wade, P. R.; Castellote, M.; Cornick, L. A.

2016-02-01

Apex predators are important indicators of ecosystem health, but little is known about the population structure of Bigg's killer whales (Orcinus orca; i.e. "transient" ecotype) in western Alaska. Currently, all Bigg's killer whales in western Alaska are ascribed to a single broad stock for management under the US Marine Mammal Protection Act. However, recent nuclear microsatellite and mitochondrial DNA analyses indicate that this stock is likely comprised of genetically distinct sub-populations. In accordance with what is known about group-specific killer whale vocal dialects in other locations, we sought to evaluate and refine Bigg's killer whale population structure by using acoustic recordings to examine the spatial distribution of call types in western Alaska. Digital audio recordings were collected from 34 encounters with Bigg's killer whales throughout the Aleutian and Pribilof Islands in the summers of 2001-2007 and 2009-2010, then visually and aurally reviewed using the software Adobe Audition. High quality calls were identified and classified into discrete call types based on spectrographic characteristics and aural uniqueness. A comparative analysis of call types recorded throughout the study area revealed spatial segregation of call types, corresponding well with proposed genetic delineations. These results suggest that Bigg's killer whales exhibit regional vocal dialects, which can be used to help refine the putative sub-populations that have been genetically identified throughout western Alaska. Our findings support the proposal to restructure current stock designations.
Structural Studies of E. coli Topoisomerase III-DNA Complexes Reveal A Novel Type IA Topoisomerase-DNA Conformational Intermediate

PubMed Central

Changela, Anita; DiGate, Russell J.; Mondragón, Alfonso

2007-01-01

Summary E. coli DNA topoisomerase III belongs to the type IA family of DNA topoisomerases, which transiently cleave single-stranded DNA (ssDNA) via a 5′ phosphotyrosine intermediate. We have solved crystal structures of wild-type E. coli topoisomerase III bound to an 8-base ssDNA molecule in three different pH environments. The structures reveal the enzyme in three distinct conformational states while bound to DNA. One conformation resembles the one observed previously with a DNA-bound, catalytically inactive mutant of topoisomerase III where DNA binding realigns catalytic residues to form a functional active site. Another conformation represents a novel intermediate in which DNA is bound along the ssDNA-binding groove but does not enter the active site, which remains in a catalytically inactive, closed state. A third conformation shows an intermediate state where the enzyme is still in a closed state, but the ssDNA is starting to invade the active site. For the first time, the active site region in the presence of both the catalytic tyrosine and ssDNA substrate is revealed for a type IA DNA topoisomerase, although there is no evidence of ssDNA cleavage. Comparative analysis of the various conformational states suggests a sequence of domain movements undertaken by the enzyme upon substrate binding. PMID:17331537
Qualitative photoluminescence study of defect activation in telecommunication fibers and Bragg gratings in hydrogen-loaded fibers

NASA Astrophysics Data System (ADS)

Bastola, B.; Fischer, B.; Roths, J.; Ruediger, A.

2018-07-01

Despite the relevance of glass fibers and integrated optical circuits for an increasing number of cutting-edge applications ranging from telecommunication to sensing and quantum photonics, the knowledge about their structural and chemical properties is still in its infancy. Optical spectroscopy techniques are challenged due to the intrinsically low cross-sections for inelastic processes. Our approach is to detect these properties along the core, extending the interaction to the fiber length. We report on in-situ temperature-dependent photoluminescence (PL) measurements in transmission geometry of a) pristine optical glass fibers (standard commercial telecom grade and different types of photosensitive fibers) and b) type I fiber Bragg grating (FBG) in hydrogen-loaded fibers of the same type. A laser with 473 nm wavelength and TEM 00 mode is coupled to an optical spectrometer through different fibers. The fibers are thermally cycled between room temperature and 950° Celsius. As a first observation, we detect a clearly visible red emission from the uncoated fibers at the location of the fiber Bragg grating. Fitting the luminescence spectra with a single Gaussian and monitoring the intensity as a function of temperature reveals an irreversible, thermally activated degradation of the luminescence associated to the fiber Bragg gratings. A closer inspection of pristine glass fibers without FBG revealed a faint, yet thermally stable luminescence with similar spectral characteristics. Analyzing qualitative data for two consecutive heating cycles confirmed two distinct activation energies. This may be due to several reasons such as different defects at the basis of this emission or different structural or chemical environments for the same defect. Further experiment will be carried out in the future to investigate the main reason of two distinct activation energies.
Molecular cloning of NILE glycoprotein and evidence for its continued expression in mature rat CNS.

PubMed

Prince, J T; Alberti, L; Healy, P A; Nauman, S J; Stallcup, W B

1991-11-01

The NILE glycoprotein is a rat neuronal cell adhesion molecule which has been reported to be very similar in structure, function, and distribution to the mouse L1 glycoprotein. Here we report the complete nucleotide sequence of the NILE message (5,208 nucleotides) and the deduced amino acid sequence of the NILE polypeptide (1,257 amino acids). The predicted NILE protein is 96% identical to L1 at the amino acid level, confirming that the two molecules are homologues. The sequence information shows that NILE is a transmembrane molecule with an extensive ectodomain and a much smaller cytoplasmic domain. The extracellular portion of the molecule contains six immunoglobulin C-2 type domains followed by five fibronectin type III repeats. These two structural motifs are characteristic of several other cell adhesion molecules. The cytoplasmic tails of NILE and L1 are identical to each other and distinct from the cytoplasmic regions of all other cell adhesion molecules except Ng-CAM and neuroglian. Several possible sites for phosphorylation are present in the cytoplasmic tail of NILE. Antisera were produced against two NILE-beta-galactosidase fusion proteins containing distinct segments of the NILE polypeptide: the cytoplasmic domain and the segment containing fibronectin type III repeats. Immunoblots with these antisera and Northern blots with a NILE cDNA probe indicate that NILE continues to be expressed in most areas of the mature rat brain. This contradicts previous immunofluorescence data, which suggested that NILE was substantially down-regulated in maturing nerve fiber tracts. This raises the possibility that NILE could be masked in situ by interactions with other cell surface molecules.
Structural basis of glycan specificity in neonate-specific bovine-human reassortant rotavirus

DOE PAGES

Hu, Liya; Ramani, Sasirekha; Czako, Rita; ...

2015-09-30

We report that strain-dependent variation of glycan recognition during initial cell attachment of viruses is a critical determinant of host specificity, tissue-tropism and zoonosis. Rotaviruses (RVs), which cause life-threatening gastroenteritis in infants and children, display significant genotype-dependent variations in glycan recognition resulting from sequence alterations in the VP8* domain of the spike protein VP4. The structural basis of this genotype-dependent glycan specificity, particularly in human RVs, remains poorly understood. Here, from crystallographic studies, we show how genotypic variations configure a novel binding site in the VP8* of a neonate-specific bovine-human reassortant to uniquely recognize either type I or type IImore » precursor glycans, and to restrict type II glycan binding in the bovine counterpart. In conclusion, such a distinct glycan-binding site that allows differential recognition of the precursor glycans, which are developmentally regulated in the neonate gut and abundant in bovine and human milk provides a basis for age-restricted tropism and zoonotic transmission of G10P[11] rotaviruses.« less
Structural basis of glycan specificity in neonate-specific bovine-human reassortant rotavirus

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

Hu, Liya; Ramani, Sasirekha; Czako, Rita

We report that strain-dependent variation of glycan recognition during initial cell attachment of viruses is a critical determinant of host specificity, tissue-tropism and zoonosis. Rotaviruses (RVs), which cause life-threatening gastroenteritis in infants and children, display significant genotype-dependent variations in glycan recognition resulting from sequence alterations in the VP8* domain of the spike protein VP4. The structural basis of this genotype-dependent glycan specificity, particularly in human RVs, remains poorly understood. Here, from crystallographic studies, we show how genotypic variations configure a novel binding site in the VP8* of a neonate-specific bovine-human reassortant to uniquely recognize either type I or type IImore » precursor glycans, and to restrict type II glycan binding in the bovine counterpart. In conclusion, such a distinct glycan-binding site that allows differential recognition of the precursor glycans, which are developmentally regulated in the neonate gut and abundant in bovine and human milk provides a basis for age-restricted tropism and zoonotic transmission of G10P[11] rotaviruses.« less
Crystal Structure of a Type IV Pilus Assembly ATPase: Insights into the Molecular Mechanism of PilB from Thermus thermophilus

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

Mancl, Jordan M.; Black, Wesley P.; Robinson, Howard

Type IV pili (T4P) mediate bacterial motility and virulence. The PilB/GspE family ATPases power the assembly of T4P and type 2 secretion systems. We determined the structure of the ATPase region of PilB (PilB ATP) in complex with ATPγS to provide a model of a T4P assembly ATPase and a view of a PilB/GspE family hexamer at better than 3-Å resolution. Spatial positioning and conformations of the protomers suggest a mechanism of force generation. All six PilB ATP protomers contain bound ATPγS. Two protomers form a closed conformation poised for ATP hydrolysis. The other four molecules assume an open conformationmore » but separate into two pairs with distinct active-site accessibilities. We propose that one pair represents the post-hydrolysis phase while the other pair appears poised for ADP/ATP exchange. In conclusion, collectively, the data suggest that T4P assembly is powered by coordinating concurrent substrate binding with ATP hydrolysis across the PilB hexamer.« less
Crystal Structure of a Type IV Pilus Assembly ATPase: Insights into the Molecular Mechanism of PilB from Thermus thermophilus

DOE PAGES

Mancl, Jordan M.; Black, Wesley P.; Robinson, Howard; ...

2016-09-22

Type IV pili (T4P) mediate bacterial motility and virulence. The PilB/GspE family ATPases power the assembly of T4P and type 2 secretion systems. We determined the structure of the ATPase region of PilB (PilB ATP) in complex with ATPγS to provide a model of a T4P assembly ATPase and a view of a PilB/GspE family hexamer at better than 3-Å resolution. Spatial positioning and conformations of the protomers suggest a mechanism of force generation. All six PilB ATP protomers contain bound ATPγS. Two protomers form a closed conformation poised for ATP hydrolysis. The other four molecules assume an open conformationmore » but separate into two pairs with distinct active-site accessibilities. We propose that one pair represents the post-hydrolysis phase while the other pair appears poised for ADP/ATP exchange. In conclusion, collectively, the data suggest that T4P assembly is powered by coordinating concurrent substrate binding with ATP hydrolysis across the PilB hexamer.« less
Reduction of virion-associated σ1 fibers on oncolytic reovirus variants promotes adaptation toward tumorigenic cells.

PubMed

Mohamed, Adil; Teicher, Carmit; Haefliger, Sarah; Shmulevitz, Maya

2015-04-01

Wild-type mammalian orthoreovirus serotype 3 Dearing (T3wt) is nonpathogenic in humans but preferentially infects and kills cancer cells in culture and demonstrates promising antitumor activity in vivo. Using forward genetics, we previously isolated two variants of reovirus, T3v1 and T3v2, with increased infectivity toward a panel of cancer cell lines and improved in vivo oncolysis in a murine melanoma model relative to that of T3wt. Our current study explored how mutations in T3v1 and T3v2 promote infectivity. Reovirions contain trimers of σ1, the reovirus cell attachment protein, at icosahedral capsid vertices. Quantitative Western blot analysis showed that purified T3v1 and T3v2 virions had ∼ 2- and 4-fold-lower levels of σ1 fiber than did T3wt virions. Importantly, using RNA interference to reduce σ1 levels during T3wt production, we were able to generate wild-type reovirus with reduced levels of σ1 per virion. As σ1 levels were reduced, virion infectivity increased by 2- to 5-fold per cell-bound particle, demonstrating a causal relationship between virion σ1 levels and the infectivity of incoming virions. During infection of tumorigenic L929 cells, T3wt, T3v1, and T3v2 uncoated the outer capsid proteins σ3 and μ1C at similar rates. However, having started with fewer σ1 molecules, a complete loss of σ1 was achieved sooner for T3v1 and T3v2. Distinct from intracellular uncoating, chymotrypsin digestion, as a mimic of natural enteric infection, resulted in more rapid σ3 and μ1C removal, unique disassembly intermediates, and a rapid loss of infectivity for T3v1 and T3v2 compared to T3wt. Optimal infectivity toward natural versus therapeutic niches may therefore require distinct reovirus structures and σ1 levels. Wild-type reovirus is currently in clinical trials as a potential cancer therapy. Our molecular studies on variants of reovirus with enhanced oncolytic activity in vitro and in vivo now show that distinct reovirus structures promote adaptation toward cancer cells and away from conditions that mimic natural routes of infection. Specifically, we found that reovirus particles with fewer molecules of the cell attachment protein σ1 became more infectious toward transformed cells. Reduced σ1 levels conferred a benefit to incoming particles only, resulting in an earlier depletion of σ1 and a higher probability of establishing productive infection. Conversely, reovirus variants with fewer σ1 molecules showed reduced stability and infectivity and distinct disassembly when exposed to conditions that mimic natural intestinal proteolysis. These findings support a model where the mode of infection dictates the precise optimum of reovirus structure and provide a molecular rationale for considering alternative reovirus structures during oncolytic therapy. Copyright © 2015, American Society for Microbiology. All Rights Reserved.
PRISM 3: expanded prediction of natural product chemical structures from microbial genomes.

PubMed

Skinnider, Michael A; Merwin, Nishanth J; Johnston, Chad W; Magarvey, Nathan A

2017-07-03

Microbial natural products represent a rich resource of pharmaceutically and industrially important compounds. Genome sequencing has revealed that the majority of natural products remain undiscovered, and computational methods to connect biosynthetic gene clusters to their corresponding natural products therefore have the potential to revitalize natural product discovery. Previously, we described PRediction Informatics for Secondary Metabolomes (PRISM), a combinatorial approach to chemical structure prediction for genetically encoded nonribosomal peptides and type I and II polyketides. Here, we present a ground-up rewrite of the PRISM structure prediction algorithm to derive prediction of natural products arising from non-modular biosynthetic paradigms. Within this new version, PRISM 3, natural product scaffolds are modeled as chemical graphs, permitting structure prediction for aminocoumarins, antimetabolites, bisindoles and phosphonate natural products, and building upon the addition of ribosomally synthesized and post-translationally modified peptides. Further, with the addition of cluster detection for 11 new cluster types, PRISM 3 expands to detect 22 distinct natural product cluster types. Other major modifications to PRISM include improved sequence input and ORF detection, user-friendliness and output. Distribution of PRISM 3 over a 300-core server grid improves the speed and capacity of the web application. PRISM 3 is available at http://magarveylab.ca/prism/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.
Land-use changes influence soil bacterial communities in a meadow grassland in Northeast China

NASA Astrophysics Data System (ADS)

Cao, Chengyou; Zhang, Ying; Qian, Wei; Liang, Caiping; Wang, Congmin; Tao, Shuang

2017-10-01

The conversion of natural grassland into agricultural fields is an intensive anthropogenic perturbation commonly occurring in semiarid regions, and this perturbation strongly affects soil microbiota. In this study, the influences of land-use conversion on the soil properties and bacterial communities in the Horqin Grasslands in Northeast China were assessed. This study aimed to investigate (1) how the abundances of soil bacteria changed across land-use types, (2) how the structure of the soil bacterial community was altered in each land-use type, and (3) how these variations were correlated with soil physical and chemical properties. Variations in the diversities and compositions of bacterial communities and the relative abundances of dominant taxa were detected in four distinct land-use systems, namely, natural meadow grassland, paddy field, upland field, and poplar plantation, through the high-throughput Illumina MiSeq sequencing technique. The results indicated that land-use changes primarily affected the soil physical and chemical properties and bacterial community structure. Soil properties, namely, organic matter, pH, total N, total P, available N and P, and microbial biomass C, N, and P, influenced the bacterial community structure. The dominant phyla and genera were almost the same among the land-use types, but their relative abundances were significantly different. The effects of land-use changes on the structure of soil bacterial communities were more quantitative than qualitative.
Fragment structure from vapor explosions during the impact of molten metal droplets into a liquid pool

NASA Astrophysics Data System (ADS)

Kouraytem, Nadia; Li, Er Qiang; Vakarelski, Ivan Uriev; Thoroddsen, Sigurdur

2015-11-01

High-speed video imaging is used in order to look at the impact of a molten metal drop falling into a liquid pool. The interaction regimes are three: film boiling, nucleate boiling or vapor explosion. Following the vapor explosion, the metal fragments and different textures are observed. It was seen that, using a tin alloy, a porous structure results whereas using a distinctive eutectic metal, Field's metal, micro beads are formed. Different parameters such as the metal type, molten metal temperature, pool surface tension and pool boiling temperature have been altered in order to assess the role they play on the explosion dynamics and the molten metal's by product.
Discovery of Novel Tricyclic Heterocycles as Potent and Selective DPP-4 Inhibitors for the Treatment of Type 2 Diabetes

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

Wu, Wen-Lian; Hao, Jinsong; Domalski, Martin

In our efforts to develop second generation DPP-4 inhibitors, we endeavored to identify distinct structures with long-acting (once weekly) potential. Taking advantage of X-ray cocrystal structures of sitagliptin and other DPP-4 inhibitors, such as alogliptin and linagliptin bound to DPP-4, and aided by molecular modeling, we designed several series of heterocyclic compounds as initial targets. During their synthesis, an unexpected chemical transformation provided a novel tricyclic scaffold that was beyond our original design. Capitalizing on this serendipitous discovery, we have elaborated this scaffold into a very potent and selective DPP-4 inhibitor lead series, as highlighted by compound 17c.
Phases of a fermionic model with chiral condensates and Cooper pairs in 1+1 dimensions

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

Mihaila, Bogdan; Blagoev, Krastan B.; MIND Institute, Albuquerque, New Mexico 87131

2006-01-01

We study the phase structure of a 4-fermi model with three bare coupling constants, which potentially has three types of bound states. This model is a generalization of the model discussed previously by [A. Chodos, F. Cooper, W. Mao, H. Minakata, and A. Singh, Phys. Rev. D 61, 045011 (2000).], which contained both chiral condensates and Cooper pairs. For this generalization we find that there are two independent renormalized coupling constants which determine the phase structure at finite density and temperature. We find that the vacuum can be in one of three distinct phases depending on the value of thesemore » two renormalized coupling constants.« less
Crystal structure of langbeinite-related Rb0.743K0.845Co0.293Ti1.707(PO4)3

PubMed Central

Strutynska, Nataliia Yu.; Bondarenko, Marina A.; Ogorodnyk, Ivan V.; Baumer, Vyacheslav N.; Slobodyanik, Nikolay S.

2015-01-01

Potassium rubidium cobalt(II)/titanium(IV) tris(orthophosphate), Rb0.743K0.845Co0.293Ti1.707(PO4)3, has been obtained using a high-temperature crystallization method. The obtained compound has a langbeinite-type structure. The three-dimensional framework is built up from mixed-occupied (Co/TiIV)O6 octahedra (point group symmetry .3.) and PO4 tetrahedra. The K+ and Rb+ cations are statistically distributed over two distinct sites (both with site symmetry .3.) in the large cavities of the framework. They are surrounded by 12 O atoms. PMID:25844179
The endoplasmic reticulum: structure, function and response to cellular signaling.

PubMed

Schwarz, Dianne S; Blower, Michael D

2016-01-01

The endoplasmic reticulum (ER) is a large, dynamic structure that serves many roles in the cell including calcium storage, protein synthesis and lipid metabolism. The diverse functions of the ER are performed by distinct domains; consisting of tubules, sheets and the nuclear envelope. Several proteins that contribute to the overall architecture and dynamics of the ER have been identified, but many questions remain as to how the ER changes shape in response to cellular cues, cell type, cell cycle state and during development of the organism. Here we discuss what is known about the dynamics of the ER, what questions remain, and how coordinated responses add to the layers of regulation in this dynamic organelle.
“Playing around” with Field-Effect Sensors on the Basis of EIS Structures, LAPS and ISFETs

PubMed Central

Schöning, Michael J.

2005-01-01

Microfabricated semiconductor devices are becoming increasingly relevant, also for the detection of biological and chemical quantities. Especially, the “marriage” of biomolecules and silicon technology often yields successful new sensor concepts. The fabrication techniques of such silicon-based chemical sensors and biosensors, respectively, will have a distinct impact in different fields of application such as medicine, food technology, environment, chemistry and biotechnology as well as information processing. Moreover, scientists and engineers are interested in the analytical benefits of miniaturised and microfabricated sensor devices. This paper gives a survey on different types of semiconductor-based field-effect structures that have been recently developed in our laboratory.
Characterization of starch polymorphic structures using vibrational sum frequency generation spectroscopy.

PubMed

Kong, Lingyan; Lee, Christopher; Kim, Seong H; Ziegler, Gregory R

2014-02-20

The polymorphic structures of starch were characterized with vibrational sum frequency generation (SFG) spectroscopy. The noncentrosymmetry requirement of SFG spectroscopy allows for the detection of the ordered domains without spectral interferences from the amorphous phase and also the distinction of the symmetric elements among crystalline polymorphs. The V-type amylose was SFG-inactive due to the antiparallel packing of single helices in crystal unit cells, whereas the A- and B-type starches showed strong SFG peaks at 2904 cm(-1) and 2952-2968 cm(-1), which were assigned to CH stretching of the axial methine group in the ring and CH2 stretching of the exocyclic CH2OH side group, respectively. The CH2/CH intensity ratios of the A- and B-type starches are significantly different, indicating that the conformation of hydroxymethyl groups in these two polymorphs may be different. Cyclodextrin inclusion complexes were also analyzed as a comparison to the V-type amylose and showed that the head-to-tail and head-to-head stacking patterns of cyclodextrin molecules govern their SFG signals and peak positions. Although the molecular packing is different between V-type amylose and cyclodextrin inclusion complexes, both crystals show the annihilation of SFG signals when the functional group dipoles are arranged pointing in opposite directions.
Distinct Motion of GFP-Tagged Histone Expressing Cells Under AC Electrokinetics in Electrode-Multilayered Microfluidic Device.

PubMed

Yao, Jiafeng; Sugawara, Michiko; Obara, Hiromichi; Mizutani, Takeomi; Takei, Masahiro

2017-12-01

The distinct motion of GFP-tagged histone expressing cells (Histone-GFP type cells) has been investigated under ac electrokinetics in an electrode-multilayered microfluidic device as compared with Wild type cells and GFP type cells in terms of different intracellular components. The Histone-GFP type cells were modified by the transfection of green fluorescent protein-fused histone from the human lung fibroblast cell line. The velocity of the Histone-GFP type cells obtained by particle tracking velocimetry technique is faster than Wild type cells by 24.9% and GFP type cells by 57.1%. This phenomenon is caused by the more amount of proteins in the intracellular of single Histone-GFP type cell than that of the Wild type and GFP type cells. The more amount of proteins in the Histone-GFP type cells corresponds to a lower electric permittivity ϵ c of the cells, which generates a lower dielectrophoretic force exerting on the cells. The velocity of Histone-GFP type cells is well agreed with Eulerian-Lagrangian two-phase flow simulation by 4.2% mean error, which proves that the fluid motion driven by thermal buoyancy and electrothermal force dominates the direction of cells motion, while the distinct motion of Histone-GFP type cells is caused by dielectrophoretic force. The fluid motion does not generate a distinct drag motion for Histone-GFP type cells because the Histone-GFP type cells have the same size to the Wild type and GFP type cells. These results clarified the mechanism of cells motion in terms of intracellular components, which helps to improve the cell manipulation efficiency with electrokinetics.
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.
Type I clathrates as novel silicon anodes: An electrochemical and structural investigation

DOE PAGES

Li, Ying; Raghavan, Rahul; Wagner, Nicholas A.; ...

2015-05-05

In this study, silicon clathrates contain cage-like structures that can encapsulate various guest atoms or molecules. Here we present an electrochemical evaluation of type I silicon clathrates based on Ba 8Al ySi 46-y for the anode material in lithium-ion batteries. Post-cycling characterization with NMR and XRD show no discernible structural or volume changes even after electrochemical insertion of 44 Li into the clathrate structure. The observed properties are in stark contrast with lithiation of other silicon anodes, which become amorphous and suffer from larger volume changes. The lithiation/delithiation processes are proposed to occur in single phase reactions at approximately 0.2more » and 0.4 V vs. Li/Li +, respectively, distinct from other diamond cubic or amorphous silicon anodes. Reversible capacities as high as 499 mAh g -1 at a 5 mA g -1 rate were observed for silicon clathrate with composition Ba 8Al 8.54S i37.46, corresponding to Li:Si of 1.18:1. The results show that silicon clathrates could be promising durable anodes for lithium-ion batteries.« less
Type I clathrates as novel silicon anodes: An electrochemical and structural investigation

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

Li, Ying; Raghavan, Rahul; Wagner, Nicholas A.

In this study, silicon clathrates contain cage-like structures that can encapsulate various guest atoms or molecules. Here we present an electrochemical evaluation of type I silicon clathrates based on Ba 8Al ySi 46-y for the anode material in lithium-ion batteries. Post-cycling characterization with NMR and XRD show no discernible structural or volume changes even after electrochemical insertion of 44 Li into the clathrate structure. The observed properties are in stark contrast with lithiation of other silicon anodes, which become amorphous and suffer from larger volume changes. The lithiation/delithiation processes are proposed to occur in single phase reactions at approximately 0.2more » and 0.4 V vs. Li/Li +, respectively, distinct from other diamond cubic or amorphous silicon anodes. Reversible capacities as high as 499 mAh g -1 at a 5 mA g -1 rate were observed for silicon clathrate with composition Ba 8Al 8.54S i37.46, corresponding to Li:Si of 1.18:1. The results show that silicon clathrates could be promising durable anodes for lithium-ion batteries.« less
Novel Afferent Terminal Structure in the Crista Ampullaris of the Goldfish, Carassius auratus

NASA Technical Reports Server (NTRS)

Lanford, Pamela J.; Popper, Arthur N.

1996-01-01

Using transmission electron microscopy, we have identified a new type of afferent terminal structure in the crista ampullaris of the goldfish Carassius auratus. In addition to the bouton-type afferent terminals previously described in the ear of this species, the crista also contained enlarged afferent terminals that enveloped a portion of the basolateral hair cell membrane. The hair cell membrane was evaginated and protruded into the afferent terminal in a glove-and-finger configuration. The membranes of the two cells were regularly aligned in the protruded region of the contact and had a distinct symmetrical electron density. The electron-dense profiles of these contacts were easily identified and were present in every crista sampled. In some cases, efferent terminals synapsed onto the afferents at a point where the hair cell protruded into the terminal. The ultrastructural similarities of the goldfish crista afferents to calyx afferents found in amniotes (birds, reptiles, and mammals) are discussed. The results of the study support the hypothesis that structural variation in the vertebrate inner ear may have evolved much earlier in evolution than previously supposed.
Distinct localization of peripheral and central types of choline acetyltransferase in the rat cochlea.

PubMed

Kitanishi, Tsuyoshi; Aimi, Yoshinari; Kitano, Hiroya; Suzuki, Mikio; Kimura, Hiroshi; Saito, Atsushi; Shimizu, Takeshi; Tooyama, Ikuo

2013-10-30

We previously discovered a splice variant of choline acetyltransferase (ChAT) mRNA, and designated the variant protein pChAT because of its preferential expression in peripheral neuronal structures. In this study, we examined the immunohistochemical localization of pChAT in rat cochlea and compared the distribution pattern to those of common ChAT (cChAT) and acetylcholinesterase. Some neuronal cell bodies and fibers in the spiral ganglia showed immunoreactivity for pChAT, predominantly the small spiral ganglion cells, indicating outer hair cell type II neurons. In contrast, cChAT- and acetylcholinesterase-positive structures were localized to fibers and not apparent in ganglion cells. After ablation of the cochlear nuclei, many pChAT-positive cochlear nerve fibers became clearly visible, whereas fibers immunopositive for cChAT and acetylcholine esterase disappeared. These results suggested that pChAT and cChAT are localized in different systems of the rat cochlea; pChAT in the afferent and cChAT in the efferent structures.
Distinct Localization of Peripheral and Central Types of Choline Acetyltransferase in the Rat Cochlea

PubMed Central

Kitanishi, Tsuyoshi; Aimi, Yoshinari; Kitano, Hiroya; Suzuki, Mikio; Kimura, Hiroshi; Saito, Atsushi; Shimizu, Takeshi; Tooyama, Ikuo

2013-01-01

We previously discovered a splice variant of choline acetyltransferase (ChAT) mRNA, and designated the variant protein pChAT because of its preferential expression in peripheral neuronal structures. In this study, we examined the immunohistochemical localization of pChAT in rat cochlea and compared the distribution pattern to those of common ChAT (cChAT) and acetylcholinesterase. Some neuronal cell bodies and fibers in the spiral ganglia showed immunoreactivity for pChAT, predominantly the small spiral ganglion cells, indicating outer hair cell type II neurons. In contrast, cChAT- and acetylcholinesterase-positive structures were localized to fibers and not apparent in ganglion cells. After ablation of the cochlear nuclei, many pChAT-positive cochlear nerve fibers became clearly visible, whereas fibers immunopositive for cChAT and acetylcholine esterase disappeared. These results suggested that pChAT and cChAT are localized in different systems of the rat cochlea; pChAT in the afferent and cChAT in the efferent structures. PMID:24194628
Complex Stoichiometry reordering of PTCDA on Ag(111) upon K Intercalation

NASA Astrophysics Data System (ADS)

Brivio, G. P.; Baby, A.; Zwick, C.; Gruenewald, M.; Forker, R.; Fritz, T.; Fratesi, G.; Hofmann, O. T.; Zojer, E.

Alkali metal atoms are a simple yet efficient n-type dopant of organic semiconductors. However, the molecular crystal structures need be controlled and well understood in order to optimize the electronic properties (charge carrier density and mobility) of the target material. Here, we report that potassium intercalation into PTCDA monolayer domains on a Ag(111) substrate induces distinct stoichiometry-dependent structural reordering processes, resulting in highly ordered and large KxPTCDA domains. The emerging structures are analyzed by low temperature scanning tunneling microscopy (STM), scanning tunneling hydrogen microscopy (STHM), and low-energy electron diffraction (LEED) as a function of the stoichiometry and by density functional theory (DFT) calculations. Large stable monolayer domains are found for x=2,4. The epitaxy types for all intercalated stages are determined as point-on-line. The K atoms adsorb in the vicinity of the oxygen atoms of the PTCDA molecules, and their positions are determined with sub-Angstrom precision. This is a crucial prerequisite for the prospective assessment of the electronic properties of such composite films, as they depend on the mutual alignment between donor atoms and acceptor molecules.
Stabilization of non-productive conformations underpins rapid electron transfer to electron-transferring flavoprotein.

PubMed

Toogood, Helen S; van Thiel, Adam; Scrutton, Nigel S; Leys, David

2005-08-26

Crystal structures of protein complexes with electron-transferring flavoprotein (ETF) have revealed a dual protein-protein interface with one region serving as anchor while the ETF FAD domain samples available space within the complex. We show that mutation of the conserved Glu-165beta in human ETF leads to drastically modulated rates of interprotein electron transfer with both medium chain acyl-CoA dehydrogenase and dimethylglycine dehydrogenase. The crystal structure of free E165betaA ETF is essentially identical to that of wild-type ETF, but the crystal structure of the E165betaA ETF.medium chain acyl-CoA dehydrogenase complex reveals clear electron density for the FAD domain in a position optimal for fast interprotein electron transfer. Based on our observations, we present a dynamic multistate model for conformational sampling that for the wild-type ETF. medium chain acyl-CoA dehydrogenase complex involves random motion between three distinct positions for the ETF FAD domain. ETF Glu-165beta plays a key role in stabilizing positions incompatible with fast interprotein electron transfer, thus ensuring high rates of complex dissociation.
Crystal Structure of Dengue Virus Type 1 Envelope Protein in the Postfusion Conformation and Its Implications for Membrane Fusion

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

Nayak, Vinod; Dessau, Moshe; Kucera, Kaury

Dengue virus relies on a conformational change in its envelope protein, E, to fuse the viral lipid membrane with the endosomal membrane and thereby deliver the viral genome into the cytosol. We have determined the crystal structure of a soluble fragment E (sE) of dengue virus type 1 (DEN-1). The protein is in the postfusion conformation even though it was not exposed to a lipid membrane or detergent. At the domain I-domain III interface, 4 polar residues form a tight cluster that is absent in other flaviviral postfusion structures. Two of these residues, His-282 and His-317, are conserved in flavivirusesmore » and are part of the 'pH sensor' that triggers the fusogenic conformational change in E, at the reduced pH of the endosome. In the fusion loop, Phe-108 adopts a distinct conformation, forming additional trimer contacts and filling the bowl-shaped concavity observed at the tip of the DEN-2 sE trimer.« less
Crystal Structure of Dengue Type 1 Envelope Protein in the Postfusion Conformation and its Implication for Receptor Binding, Membrane Fusion and Antibody Recognition

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

Nayak, V.; Dessau, M; Kucera, K

Dengue virus relies on a conformational change in its envelope protein, E, to fuse the viral lipid membrane with the endosomal membrane and thereby deliver the viral genome into the cytosol. We have determined the crystal structure of a soluble fragment E (sE) of dengue virus type 1 (DEN-1). The protein is in the postfusion conformation even though it was not exposed to a lipid membrane or detergent. At the domain I-domain III interface, 4 polar residues form a tight cluster that is absent in other flaviviral postfusion structures. Two of these residues, His-282 and His-317, are conserved in flavivirusesmore » and are part of the pH sensor that triggers the fusogenic conformational change in E, at the reduced pH of the endosome. In the fusion loop, Phe-108 adopts a distinct conformation, forming additional trimer contacts and filling the bowl-shaped concavity observed at the tip of the DEN-2 sE trimer.« less
The Evolution of Globular Cluster Systems In Early-Type Galaxies

NASA Astrophysics Data System (ADS)

Grillmair, Carl

1999-07-01

We will measure structural parameters {core radii and concentrations} of globular clusters in three early-type galaxies using deep, four-point dithered observations. We have chosen globular cluster systems which have young, medium-age and old cluster populations, as indicated by cluster colors and luminosities. Our primary goal is to test the hypothesis that globular cluster luminosity functions evolve towards a ``universal'' form. Previous observations have shown that young cluster systems have exponential luminosity functions rather than the characteristic log-normal luminosity function of old cluster systems. We will test to see whether such young system exhibits a wider range of structural parameters than an old systems, and whether and at what rate plausible disruption mechanisms will cause the luminosity function to evolve towards a log-normal form. A simple observational comparison of structural parameters between different age cluster populations and between diff er ent sub-populations within the same galaxy will also provide clues concerning both the formation and destruction mechanisms of star clusters, the distinction between open and globular clusters, and the advisability of using globular cluster luminosity functions as distance indicators.
Expression patterns of ion channels and structural proteins in a multimodal cell type of the avian optic tectum.

PubMed

Lischka, Katharina; Ladel, Simone; Luksch, Harald; Weigel, Stefan

2018-02-15

The midbrain is an important subcortical area involved in distinct functions such as multimodal integration, movement initiation, bottom-up, and top-down attention. Our group is particularly interested in cellular computation of multisensory integration. We focus on the visual part of the avian midbrain, the optic tectum (TeO, counterpart to mammalian superior colliculus). This area has a layered structure with the great advantage of distinct input and output regions. In chicken, the TeO is organized in 15 layers where visual input targets the superficial layers while auditory input terminates in deeper layers. One specific cell type, the Shepherd's crook neuron (SCN), extends dendrites in both input regions. The characteristic feature of these neurons is the axon origin at the apical dendrite. The molecular identity of this characteristic region and thus, the site of action potential generation are of particular importance to understand signal flow and cellular computation in this neuron. We present immunohistochemical data of structural proteins (NF200, Ankyrin G, and Myelin) and ion channels (Pan-Na v , Na v 1.6, and K v 3.1b). NF200 is strongly expressed in the axon. Ankyrin G is mainly expressed at the axon initial segment (AIS). Myelination starts after the AIS as well as the distribution of Na v channels on the axon. The subtype Na v 1.6 has a high density in this region. K v 3.1b is restricted to the soma, the primary neurite and the axon branch. The distribution of functional molecules in SCNs provides insight into the information flow and the integration of sensory modalities in the TeO of the avian midbrain. © 2017 Wiley Periodicals, Inc.
In silico analysis of surface structure variation of PCV2 capsid resulting from loop mutations of its capsid protein (Cap)

PubMed Central

Wang, Aibing; Zhang, Lijie; Khayat, Reza

2016-01-01

Outbreaks of porcine circovirus (PCV) type 2 (PCV2)-associated diseases have caused substantial economic losses worldwide in the last 20 years. The PCV capsid protein (Cap) is the sole structural protein and main antigenic determinant of this virus. In this study, not only were phylogenetic trees reconstructed, but variations of surface structure of the PCV capsid were analysed in the course of evolution. Unique surface patterns of the icosahedral fivefold axes of the PCV2 capsid were identified and characterized, all of which were absent in PCV type 1 (PCV1). Icosahedral fivefold axes, decorated with Loops BC, HI and DE, were distinctly different between PCV2 and PCV1. Loops BC, determining the outermost surface around the fivefold axes of PCV capsids, had limited homology between Caps of PCV1 and PCV2. A conserved tyrosine phosphorylation motif in Loop HI that might be recognized by non-receptor tyrosine kinase(s) in vivo was present only in PCV2. Particularly, the concurrent presence of 60 pairs of the conserved tyrosine and a canonical PXXP motif on the PCV2 capsid surface could be a mechanism for PXXP motif binding to and activation of an SH3-domain-containing tyrosine kinase in host cells. Additionally, a conserved cysteine in Loop DE of the PCV2 Cap was substituted by an arginine in PCV1, indicating potentially distinct assembly mechanisms of the capsid in vitro between PCV1 and PCV2. Therefore, these unique patterns on the PCV2 capsid surface, absent in PCV1 isolates, might be related to cell entry, virus function and pathogenesis. PMID:27902320
In silico analysis of surface structure variation of PCV2 capsid resulting from loop mutations of its capsid protein (Cap).

PubMed

Wang, Naidong; Zhan, Yang; Wang, Aibing; Zhang, Lijie; Khayat, Reza; Yang, Yi

2016-12-01

Outbreaks of porcine circovirus (PCV) type 2 (PCV2)-associated diseases have caused substantial economic losses worldwide in the last 20 years. The PCV capsid protein (Cap) is the sole structural protein and main antigenic determinant of this virus. In this study, not only were phylogenetic trees reconstructed, but variations of surface structure of the PCV capsid were analysed in the course of evolution. Unique surface patterns of the icosahedral fivefold axes of the PCV2 capsid were identified and characterized, all of which were absent in PCV type 1 (PCV1). Icosahedral fivefold axes, decorated with Loops BC, HI and DE, were distinctly different between PCV2 and PCV1. Loops BC, determining the outermost surface around the fivefold axes of PCV capsids, had limited homology between Caps of PCV1 and PCV2. A conserved tyrosine phosphorylation motif in Loop HI that might be recognized by non-receptor tyrosine kinase(s) in vivo was present only in PCV2. Particularly, the concurrent presence of 60 pairs of the conserved tyrosine and a canonical PXXP motif on the PCV2 capsid surface could be a mechanism for PXXP motif binding to and activation of an SH3-domain-containing tyrosine kinase in host cells. Additionally, a conserved cysteine in Loop DE of the PCV2 Cap was substituted by an arginine in PCV1, indicating potentially distinct assembly mechanisms of the capsid in vitro between PCV1 and PCV2. Therefore, these unique patterns on the PCV2 capsid surface, absent in PCV1 isolates, might be related to cell entry, virus function and pathogenesis.
Genetic divergence between two phenotypically distinct bottlenose dolphin ecotypes suggests separate evolutionary trajectories.

PubMed

Fruet, Pedro F; Secchi, Eduardo R; Di Tullio, Juliana C; Simões-Lopes, Paulo César; Daura-Jorge, Fábio; Costa, Ana P B; Vermeulen, Els; Flores, Paulo A C; Genoves, Rodrigo Cezar; Laporta, Paula; Beheregaray, Luciano B; Möller, Luciana M

2017-11-01

Due to their worldwide distribution and occupancy of different types of environments, bottlenose dolphins display considerable morphological variation. Despite limited understanding about the taxonomic identity of such forms and connectivity among them at global scale, coastal (or inshore) and offshore (or oceanic) ecotypes have been widely recognized in several ocean regions. In the Southwest Atlantic Ocean (SWA), however, there are scarce records of bottlenose dolphins differing in external morphology according to habitat preferences that resemble the coastal-offshore pattern observed elsewhere. The main aim of this study was to analyze the genetic variability, and test for population structure between coastal ( n = 127) and offshore ( n = 45) bottlenose dolphins sampled in the SWA to assess whether their external morphological distinction is consistent with genetic differentiation. We used a combination of mtDNA control region sequences and microsatellite genotypes to infer population structure and levels of genetic diversity. Our results from both molecular marker types were congruent and revealed strong levels of structuring (microsatellites F ST = 0.385, p < .001; mtDNA F ST = 0.183, p < .001; Φ ST = 0.385, p < .001) and much lower genetic diversity in the coastal than the offshore ecotype, supporting patterns found in previous studies elsewhere. Despite the opportunity for gene flow in potential "contact zones", we found minimal current and historical connectivity between ecotypes, suggesting they are following discrete evolutionary trajectories. Based on our molecular findings, which seem to be consistent with morphological differentiations recently described for bottlenose dolphins in our study area, we recommend recognizing the offshore bottlenose dolphin ecotype as an additional Evolutionarily Significant Unit (ESU) in the SWA. Implications of these results for the conservation of bottlenose dolphins in SWA are also discussed.
The Structural Basis for Activation and Inhibition of ZAP-70 Kinase Domain.

PubMed

Huber, Roland G; Fan, Hao; Bond, Peter J

2015-10-01

ZAP-70 (Zeta-chain-associated protein kinase 70) is a tyrosine kinase that interacts directly with the activated T-cell receptor to transduce downstream signals, and is hence a major player in the regulation of the adaptive immune response. Dysfunction of ZAP-70 causes selective T cell deficiency that in turn results in persistent infections. ZAP-70 is activated by a variety of signals including phosphorylation of the kinase domain (KD), and binding of its regulatory tandem Src homology 2 (SH2) domains to the T cell receptor. The present study investigates molecular mechanisms of activation and inhibition of ZAP-70 via atomically detailed molecular dynamics simulation approaches. We report microsecond timescale simulations of five distinct states of the ZAP-70 KD, comprising apo, inhibited and three phosphorylated variants. Extensive analysis of local flexibility and correlated motions reveal crucial transitions between the states, thus elucidating crucial steps in the activation mechanism of the ZAP-70 KD. Furthermore, we rationalize previously observed staurosporine-bound crystal structures, suggesting that whilst the KD superficially resembles an "active-like" conformation, the inhibitor modulates the underlying protein dynamics and restricts it in a compact, rigid state inaccessible to ligands or cofactors. Finally, our analysis reveals a novel, potentially druggable pocket in close proximity to the activation loop of the kinase, and we subsequently use its structure in fragment-based virtual screening to develop a pharmacophore model. The pocket is distinct from classical type I or type II kinase pockets, and its discovery offers promise in future design of specific kinase inhibitors, whilst mutations in residues associated with this pocket are implicated in immunodeficiency in humans.
The Structural Basis for Activation and Inhibition of ZAP-70 Kinase Domain

PubMed Central

Huber, Roland G.; Fan, Hao; Bond, Peter J.

2015-01-01

ZAP–70 (Zeta-chain-associated protein kinase 70) is a tyrosine kinase that interacts directly with the activated T-cell receptor to transduce downstream signals, and is hence a major player in the regulation of the adaptive immune response. Dysfunction of ZAP–70 causes selective T cell deficiency that in turn results in persistent infections. ZAP–70 is activated by a variety of signals including phosphorylation of the kinase domain (KD), and binding of its regulatory tandem Src homology 2 (SH2) domains to the T cell receptor. The present study investigates molecular mechanisms of activation and inhibition of ZAP–70 via atomically detailed molecular dynamics simulation approaches. We report microsecond timescale simulations of five distinct states of the ZAP–70 KD, comprising apo, inhibited and three phosphorylated variants. Extensive analysis of local flexibility and correlated motions reveal crucial transitions between the states, thus elucidating crucial steps in the activation mechanism of the ZAP–70 KD. Furthermore, we rationalize previously observed staurosporine-bound crystal structures, suggesting that whilst the KD superficially resembles an “active-like” conformation, the inhibitor modulates the underlying protein dynamics and restricts it in a compact, rigid state inaccessible to ligands or cofactors. Finally, our analysis reveals a novel, potentially druggable pocket in close proximity to the activation loop of the kinase, and we subsequently use its structure in fragment-based virtual screening to develop a pharmacophore model. The pocket is distinct from classical type I or type II kinase pockets, and its discovery offers promise in future design of specific kinase inhibitors, whilst mutations in residues associated with this pocket are implicated in immunodeficiency in humans. PMID:26473606
Quantitative fine structure of capillaries in subregions of the rat subfornical organ.

PubMed

Shaver, S W; Sposito, N M; Gross, P M

1990-04-01

The differentiated cytology across subregions of the rat subfornical organ (SFO) prompted our hypothesis that ultrastructural features of capillary endothelial cells would vary topographically and quantitatively within this small nucleus. We used electron microscopic and computer-based morphometric methods to assess fine structural dimensions of the capillary endothelium in four distinct subregions of the SFO from Long-Evans and homozygous Brattleboro rats. Three types of capillary were present. Type III capillaries (resembling those of endocrine glands) had an average wall thickness of 0.17 microns, 54% thinner than those of Type I and II capillaries. Pericapillary spaces around Type III capillaries measured 56 microns2, 100% larger than for Type I vessels (resembling those of skeletal muscle). Only Type III capillaries contained fenestrations (9 per microns2 of endothelial cell) and were the predominant type of capillary in central and caudal subregions of the SFO. Type I capillaries, prevalent in the transitional subregion between the central and rostral parts of the SFO, had 10 cytoplasmic vesicles per micron2 of endothelial cell area, a number not different from that of Type III capillaries but 3x the frequency found in Type II vessels. Type II capillaries (those typical of "blood-brain barrier" endothelium) had low vesicular density (3 per microns2), no fenestrations, and no pericapillary spaces. Luminal diameters and the densities of mitochondria and intercellular junctions were not different among capillary types or subregions in the SFO. Furthermore, there were no morphometric differences for any capillary dimensions between Long-Evans and Brattleboro rats.(ABSTRACT TRUNCATED AT 250 WORDS)
Extensive Genetic Diversity, Unique Population Structure and Evidence of Genetic Exchange in the Sexually Transmitted Parasite Trichomonas vaginalis

PubMed Central

Conrad, Melissa D.; Gorman, Andrew W.; Schillinger, Julia A.; Fiori, Pier Luigi; Arroyo, Rossana; Malla, Nancy; Dubey, Mohan Lal; Gonzalez, Jorge; Blank, Susan; Secor, William E.; Carlton, Jane M.

2012-01-01

Background Trichomonas vaginalis is the causative agent of human trichomoniasis, the most common non-viral sexually transmitted infection world-wide. Despite its prevalence, little is known about the genetic diversity and population structure of this haploid parasite due to the lack of appropriate tools. The development of a panel of microsatellite makers and SNPs from mining the parasite's genome sequence has paved the way to a global analysis of the genetic structure of the pathogen and association with clinical phenotypes. Methodology/Principal Findings Here we utilize a panel of T. vaginalis-specific genetic markers to genotype 235 isolates from Mexico, Chile, India, Australia, Papua New Guinea, Italy, Africa and the United States, including 19 clinical isolates recently collected from 270 women attending New York City sexually transmitted disease clinics. Using population genetic analysis, we show that T. vaginalis is a genetically diverse parasite with a unique population structure consisting of two types present in equal proportions world-wide. Parasites belonging to the two types (type 1 and type 2) differ significantly in the rate at which they harbor the T. vaginalis virus, a dsRNA virus implicated in parasite pathogenesis, and in their sensitivity to the widely-used drug, metronidazole. We also uncover evidence of genetic exchange, indicating a sexual life-cycle of the parasite despite an absence of morphologically-distinct sexual stages. Conclusions/Significance Our study represents the first robust and comprehensive evaluation of global T. vaginalis genetic diversity and population structure. Our identification of a unique two-type structure, and the clinically relevant phenotypes associated with them, provides a new dimension for understanding T. vaginalis pathogenesis. In addition, our demonstration of the possibility of genetic exchange in the parasite has important implications for genetic research and control of the disease. PMID:22479659
Population Structure of Two Rabies Hosts Relative to the Known Distribution of Rabies Virus Variants in Alaska

PubMed Central

Goldsmith, Elizabeth W.; Renshaw, Benjamin; Clement, Christopher J.; Himschoot, Elizabeth A.; Hundertmark, Kris J.; Hueffer, Karsten

2015-01-01

For pathogens that infect multiple species the distinction between reservoir hosts and spillover hosts is often difficult. In Alaska, three variants of the arctic rabies virus exist with distinct spatial distributions. We test the hypothesis that rabies virus variant distribution corresponds to the population structure of the primary rabies hosts in Alaska, arctic foxes (Vulpes lagopus) and red foxes (V. vulpes) in order to possibly distinguish reservoir and spill over hosts. We used mitochondrial DNA (mtDNA) sequence and nine microsatellites to assess population structure in those two species. mtDNA structure did not correspond to rabies virus variant structure in either species. Microsatellite analyses gave varying results. Bayesian clustering found 2 groups of arctic foxes in the coastal tundra region, but for red foxes it identified tundra and boreal types. Spatial Bayesian clustering and spatial principal components analysis identified 3 and 4 groups of arctic foxes, respectively, closely matching the distribution of rabies virus variants in the state. Red foxes, conversely, showed eight clusters comprising 2 regions (boreal and tundra) with much admixture. These results run contrary to previous beliefs that arctic fox show no fine-scale spatial population structure. While we cannot rule out that the red fox is part of the maintenance host community for rabies in Alaska, the distribution of virus variants appears to be driven primarily by the artic fox Therefore we show that host population genetics can be utilized to distinguish between maintenance and spillover hosts when used in conjunction with other approaches. PMID:26661691

Population structure of two rabies hosts relative to the known distribution of rabies virus variants in Alaska.

PubMed

Goldsmith, Elizabeth W; Renshaw, Benjamin; Clement, Christopher J; Himschoot, Elizabeth A; Hundertmark, Kris J; Hueffer, Karsten

2016-02-01

For pathogens that infect multiple species, the distinction between reservoir hosts and spillover hosts is often difficult. In Alaska, three variants of the arctic rabies virus exist with distinct spatial distributions. We tested the hypothesis that rabies virus variant distribution corresponds to the population structure of the primary rabies hosts in Alaska, arctic foxes (Vulpes lagopus) and red foxes (Vulpes vulpes) to possibly distinguish reservoir and spillover hosts. We used mitochondrial DNA (mtDNA) sequence and nine microsatellites to assess population structure in those two species. mtDNA structure did not correspond to rabies virus variant structure in either species. Microsatellite analyses gave varying results. Bayesian clustering found two groups of arctic foxes in the coastal tundra region, but for red foxes it identified tundra and boreal types. Spatial Bayesian clustering and spatial principal components analysis identified 3 and 4 groups of arctic foxes, respectively, closely matching the distribution of rabies virus variants in the state. Red foxes, conversely, showed eight clusters comprising two regions (boreal and tundra) with much admixture. These results run contrary to previous beliefs that arctic fox show no fine-scale spatial population structure. While we cannot rule out that the red fox is part of the maintenance host community for rabies in Alaska, the distribution of virus variants appears to be driven primarily by the arctic fox. Therefore, we show that host population genetics can be utilized to distinguish between maintenance and spillover hosts when used in conjunction with other approaches. © 2015 John Wiley & Sons Ltd.
Solution structure and backbone dynamics of the N-terminal region of the calcium regulatory domain from soybean calcium-dependent protein kinase alpha.

PubMed

Weljie, Aalim M; Gagné, Stéphane M; Vogel, Hans J

2004-12-07

Ca(2+)-dependent protein kinases (CDPKs) are vital Ca(2+)-signaling proteins in plants and protists which have both a kinase domain and a self-contained calcium regulatory calmodulin-like domain (CLD). Despite being very similar to CaM (>40% identity) and sharing the same fold, recent biochemical and structural evidence suggests that the behavior of CLD is distinct from its namesake, calmodulin. In this study, NMR spectroscopy is employed to examine the structure and backbone dynamics of a 168 amino acid Ca(2+)-saturated construct of the CLD (NtH-CLD) in which almost the entire C-terminal domain is exchange broadened and not visible in the NMR spectra. Structural characterization of the N-terminal domain indicates that the first Ca(2+)-binding loop is significantly more open than in a recently reported structure of the CLD complexed with a putative intramolecular binding region (JD) in the CDPK. Backbone dynamics suggest that parts of the third helix exhibit unusually high mobility, and significant exchange, consistent with previous findings that this helix interacts with the C-terminal domain. Dynamics data also show that the "tether" region, consisting of the first 11 amino acids of CLD, is highly mobile and these residues exhibit distinctive beta-type secondary structure, which may help to position the JD and CLD. Finally, the unusual global dynamic behavior of the protein is rationalized on the basis of possible interdomain rearrangements and the highly variable environments of the C- and N-terminal domains.
Probing the structural flexibility of MOFs by constructing metal oxide@MOF-based heterostructures for size-selective photoelectrochemical response

NASA Astrophysics Data System (ADS)

Zhan, Wenwen; He, Yue; Guo, Jiangbin; Chen, Luning; Kong, Xiangjian; Zhao, Haixia; Kuang, Qin; Xie, Zhaoxiong; Zheng, Lansun

2016-07-01

It is becoming a challenge to achieve simpler characterization and wider application of flexible metal organic frameworks (MOFs) exhibiting the gate-opening or breathing behavior. Herein, we designed an intelligent MOF-based system where the gate-opening or breathing behavior of MOFs can be facially visualized in solution. Two types of metal oxide@MOF core-shell heterostructures, ZnO@ZIF-7 and ZnO@ZIF-71, were prepared using ZnO nanorods as self-sacrificial templates. The structural flexibility of both the MOFs can be easily judged from the distinct molecular-size-related formation modes and photoelectrochemical performances between the two ZnO@ZIF heterostructures. Moreover, the rotational dynamics of the flexible parts of ZIF-7 were studied by analyzing the intrinsic physical properties, such as dielectric constants, of the structure. The present work reminds us to pay particular attention to the influences of the structural flexibility of MOFs on the structure and properties of MOF-involved heterostructures in future studies.It is becoming a challenge to achieve simpler characterization and wider application of flexible metal organic frameworks (MOFs) exhibiting the gate-opening or breathing behavior. Herein, we designed an intelligent MOF-based system where the gate-opening or breathing behavior of MOFs can be facially visualized in solution. Two types of metal oxide@MOF core-shell heterostructures, ZnO@ZIF-7 and ZnO@ZIF-71, were prepared using ZnO nanorods as self-sacrificial templates. The structural flexibility of both the MOFs can be easily judged from the distinct molecular-size-related formation modes and photoelectrochemical performances between the two ZnO@ZIF heterostructures. Moreover, the rotational dynamics of the flexible parts of ZIF-7 were studied by analyzing the intrinsic physical properties, such as dielectric constants, of the structure. The present work reminds us to pay particular attention to the influences of the structural flexibility of MOFs on the structure and properties of MOF-involved heterostructures in future studies. Electronic supplementary information (ESI) available: Experimental details, XRD patterns and SEM images of products in other reactions, concentration-dependent photocurrent responses, and supplementary data of dielectric measurements. See DOI: 10.1039/c6nr02257j
Distinct Morphology of Human T-Cell Leukemia Virus Type 1-Like Particles

PubMed Central

Maldonado, José O.; Cao, Sheng; Zhang, Wei; Mansky, Louis M.

2016-01-01

The Gag polyprotein is the main retroviral structural protein and is essential for the assembly and release of virus particles. In this study, we have analyzed the morphology and Gag stoichiometry of human T-cell leukemia virus type 1 (HTLV-1)-like particles and authentic, mature HTLV-1 particles by using cryogenic transmission electron microscopy (cryo-TEM) and scanning transmission electron microscopy (STEM). HTLV-1-like particles mimicked the morphology of immature authentic HTLV-1 virions. Importantly, we have observed for the first time that the morphology of these virus-like particles (VLPs) has the unique local feature of a flat Gag lattice that does not follow the curvature of the viral membrane, resulting in an enlarged distance between the Gag lattice and the viral membrane. Other morphological features that have been previously observed with other retroviruses include: (1) a Gag lattice with multiple discontinuities; (2) membrane regions associated with the Gag lattice that exhibited a string of bead-like densities at the inner leaflet; and (3) an arrangement of the Gag lattice resembling a railroad track. Measurement of the average size and mass of VLPs and authentic HTLV-1 particles suggested a consistent range of size and Gag copy numbers in these two groups of particles. The unique local flat Gag lattice morphological feature observed suggests that HTLV-1 Gag could be arranged in a lattice structure that is distinct from that of other retroviruses characterized to date. PMID:27187442
Computational study of the structure-free radical scavenging relationship of procyanidins.

PubMed

Mendoza-Wilson, Ana María; Castro-Arredondo, Sergio Ivan; Balandrán-Quintana, René Renato

2014-10-15

Procyanidins (PCs) are effective free radical scavengers, however, their antioxidant ability is variable because they have different degrees of polymerisation, are composed by distinct types of subunits and are very susceptible to changes in conformation. In this work the structure-free radical scavenging relationship of monomers, dimers and trimers of PCs was studied through the hydrogen atom transfer (HAT), sequential proton-loss electron-transfer (SPLET) and single electron transfer followed by proton transfer (SET-PT) mechanisms in aqueous phase, employing the Density Functional Theory (DFT) computational method. The structure-free radical scavenging relationship of PCs showed a very similar behaviour in HAT and SET-PT mechanisms, but very different in the SPLET mechanism. The structural factor that showed more effects on the ability of PCs to scavenge free radicals in aqueous phase was the conformation. Copyright © 2014 Elsevier Ltd. All rights reserved.
Development of lamellar structures in natural waxes - an electron diffraction investigation

NASA Astrophysics Data System (ADS)

Dorset, Douglas L.

1999-06-01

When they are recrystallized from the melt, natural plant or insect waxes tend to form solid phases with a nematic-like structure (i.e. a parallel array of polymethylene chains with little or no aggregation of the molecules into distinct layers). An electron diffraction study of carnauba wax and two types of beeswax has shown that the degree of molecular organization into lamellar structures can be enhanced by annealing in the presence of benzoic acid, which also acts as an epitaxial substrate. Nevertheless, the resultant layer structure in the annealed solid is not the same as that found for paraffin wax fractions refined from petroleum. Probably because of a small but significant fraction of a very long chain ingredient, the lamellar separation is incomplete, incorporating a number of `bridging molecules' that span the nascent lamellar interface.The same phenomenon has been described recently for a low molecular weight polyethylene.
Bipolar disorder type I and II show distinct relationships between cortical thickness and executive function.

PubMed

Abé, C; Rolstad, S; Petrovic, P; Ekman, C-J; Sparding, T; Ingvar, M; Landén, M

2018-06-15

Frontal cortical abnormalities and executive function impairment co-occur in bipolar disorder. Recent studies have shown that bipolar subtypes differ in the degree of structural and functional impairments. The relationships between cognitive performance and cortical integrity have not been clarified and might differ across patients with bipolar disorder type I, II, and healthy subjects. Using a vertex-wise whole-brain analysis, we investigated how cortical integrity, as measured by cortical thickness, correlates with executive performance in patients with bipolar disorder type I, II, and controls (N = 160). We found focal associations between executive function and cortical thickness in the medial prefrontal cortex in bipolar II patients and controls, but not in bipolar I disorder. In bipolar II patients, we observed additional correlations in lateral prefrontal and occipital regions. Our findings suggest that bipolar disorder patients show altered structure-function relationships, and importantly that those relationships may differ between bipolar subtypes. The findings are line with studies suggesting subtype-specific neurobiological and cognitive profiles. This study contributes to a better understanding of brain structure-function relationships in bipolar disorder and gives important insights into the neuropathophysiology of diagnostic subtypes. © 2018 The Authors Acta Psychiatrica Scandinavica Published by John Wiley & Sons Ltd.
An updated evolutionary classification of CRISPR–Cas systems

PubMed Central

Makarova, Kira S.; Wolf, Yuri I.; Alkhnbashi, Omer S.; Costa, Fabrizio; Shah, Shiraz A.; Saunders, Sita J.; Barrangou, Rodolphe; Brouns, Stan J. J.; Charpentier, Emmanuelle; Haft, Daniel H.; Horvath, Philippe; Moineau, Sylvain; Mojica, Francisco J. M.; Terns, Rebecca M.; Terns, Michael P.; White, Malcolm F.; Yakunin, Alexander F.; Garrett, Roger A.; van der Oost, John; Backofen, Rolf; Koonin, Eugene V.

2017-01-01

The evolution of CRISPR–cas loci, which encode adaptive immune systems in archaea and bacteria, involves rapid changes, in particular numerous rearrangements of the locus architecture and horizontal transfer of complete loci or individual modules. These dynamics complicate straightforward phylogenetic classification, but here we present an approach combining the analysis of signature protein families and features of the architecture of cas loci that unambiguously partitions most CRISPR–cas loci into distinct classes, types and subtypes. The new classification retains the overall structure of the previous version but is expanded to now encompass two classes, five types and 16 subtypes. The relative stability of the classification suggests that the most prevalent variants of CRISPR–Cas systems are already known. However, the existence of rare, currently unclassifiable variants implies that additional types and subtypes remain to be characterized. PMID:26411297
High-mobility field-effect transistor based on crystalline ZnSnO3 thin films

NASA Astrophysics Data System (ADS)

Minato, Hiroya; Fujiwara, Kohei; Tsukazaki, Atsushi

2018-05-01

We propose crystalline ZnSnO3 as a new channel material for field-effect transistors. By molecular-beam epitaxy on LiNbO3(0001) substrates, we synthesized films of ZnSnO3, which crystallizes in the LiNbO3-type polar structure. Field-effect transistors on ZnSnO3 exhibit n-type operation with field-effect mobility of as high as 45 cm2V-1s-1 at room temperature. Systematic examination of the transistor operation for channels with different Zn/Sn compositional ratios revealed that the observed high-mobility reflects the nature of stoichiometric ZnSnO3 phase. Moreover, we found an indication of coupling of transistor characteristics with intrinsic spontaneous polarization in ZnSnO3, potentially leading to a distinct type of polarization-induced conduction.
Occurrence and distribution of Giardia species in wild rodents in Germany.

PubMed

Helmy, Yosra A; Spierling, Nastasja G; Schmidt, Sabrina; Rosenfeld, Ulrike M; Reil, Daniela; Imholt, Christian; Jacob, Jens; Ulrich, Rainer G; Aebischer, Toni; Klotz, Christian

2018-03-27

Giardiasis is an important gastrointestinal parasitic disease in humans and other mammals caused by the protozoan Giardia duodenalis. This species complex is represented by genetically distinct groups (assemblages A-H) with varying zoonotic potential and host preferences. Wild rodents can harbor potentially zoonotic assemblages A and B, and the rodent-specific assemblage G. Other Giardia spp. found in these animals are Giardia muris and Giardia microti. For the latter, only limited information on genetic typing is available. It has been speculated that wild rodents might represent an important reservoir for parasites causing human giardiasis. The aim of this study was to investigate the occurrence and distribution of Giardia spp. and assemblage types in wild rodents from different study sites in Germany. Screening of 577 wild rodents of the genera Apodemus, Microtus and Myodes, sampled at eleven study sites in Germany, revealed a high overall Giardia prevalence. Giardia species determination at the SSU rDNA gene locus revealed that Apodemus mice, depending on species, were predominantly infected with one of two distinct G. muris sequence types. Giardia microti was the predominant parasite species found in voles of the genera Microtus and Myodes. Only a few animals were positive for potentially zoonotic G. duodenalis. Subtyping at the beta-giardin (bg) and glutamine dehydrogenase (gdh) genes strongly supported the existence of different phylogenetic subgroups of G. microti that are preferentially harbored by distinct host species. The present study highlights the preference of G. muris for Apodemus, and G. microti for Microtus and Myodes hosts and argues for a very low prevalence of zoonotic G. duodenalis assemblages in wild rodents in Germany. It also provides evidence that G. muris and G. microti subdivide into several phylogenetically distinguishable subgroups, each of which appears to be preferentially harbored by species of a particular rodent host genus. Finally, the study expands the database of sequences relevant for sequence typing of G. muris and G. microti isolates which will greatly help future analyses of these parasites' population structure.
Evolution of nuclear rDNA ITS sequences in the Cladophora albida/sericea clade (Chlorophyta).

PubMed

Bakker, F T; Olsen, J L; Stam, W T

1995-06-01

Ribosomal DNA ITS sequences were compared among 13 different species and biogeographic isolates from the monophyletic "albida/sericea clade" in the green algal genus Cladophora. Six distinct ITS sequence types were found, characterized by multiple insertions and deletions and high levels of nucleotide substitution. Conserved domains within the ITS regions indicate the presence of ITS secondary structure. Low transition/transversion ratios among the six types and nearly symmetrical tree-length frequency distributions indicate some saturation, and low phylogenetic signal. Although branching order among five of the six ITS sequence types could not be resolved, estimates of ITS sequence divergence as compared with 18S divergence in a subset of the taxa suggests that the origin of the different ITS types is probably in the mid-Miocene (12 Ma ago) but that biogeographic isolates within a single ITS type (including both Pacific and Atlantic representatives) have probably dispersed on a time scale of thousands rather than millions of years.
Immunolocalization of Collagens (I and III) and Cartilage Oligomeric Matrix Protein in the Normal and Injured Equine Superficial Digital Flexor Tendon

PubMed Central

2013-01-01

This is a descriptive study of tendon pathology with different structural appearances of repair tissue correlated to immunolocalization of cartilage oligomeric matrix protein (COMP) and type I and III collagens and expression of COMP mRNA. The material consists of nine tendons from seven horses (5–25 years old; mean age of 10 years) with clinical tendinopathy and three normal tendons from horses (3, 3, and 13 years old) euthanized for non-orthopedic reasons. The injured tendons displayed different repair-tissue appearances with organized and disorganized fibroblastic regions as well as areas of necrosis. The normal tendons presented distinct immunoreactivity for COMP and expression of COMP mRNA and type I collagen in the normal aligned fiber structures, but no immunolabeling of type III collagen. However, immunoreactivity for type III collagen was present in the endotenon surrounding the fiber bundles, where no expression of COMP could be seen. Immunostaining for type I and III collagens was present in all of the pathologic regions indicating repair tissue. Interestingly, the granulation tissues showed immunostaining for COMP and expression of COMP mRNA, indicating a role for COMP in repair and remodeling of the tendon after fiber degeneration and rupture. The present results suggest that not only type III collagen but also COMP is involved in the repair and remodeling processes of the tendon. PMID:23020676
Investigating the origins of nanostructural variations in differential ethnic hair types using X-ray scattering techniques.

PubMed

Wade, M; Tucker, I; Cunningham, P; Skinner, R; Bell, F; Lyons, T; Patten, K; Gonzalez, L; Wess, T

2013-10-01

Human hair is a major determinant of visual ethnic differentiation. Although hair types are celebrated as part of our ethnic diversity, the approach to hair care has made the assumption that hair types are structurally and chemically similar. Although this is clearly not the case at the macroscopic level, the intervention of many hair treatments is at the nanoscopic and molecular levels. The purpose of the work presented here is to identify the main nanoscopic and molecular hierarchical differences across five different ethnic hair types from hair fibres taken exclusively from the scalp. These are Afro (subdivided into elastic 'rubber' and softer non-elastic 'soft'), Chinese, European and Mullato (mixed race). Small angle X-Ray scattering (SAXS) is a technique capable of resolving nanostructural variations in complex materials. Individual hair fibres from different ethnic hair types were used to investigate structural features found in common and also specific to each type. Simultaneous wide angle X-Ray scattering (WAXS) was used to analyse the submolecular level structure of the fibrous keratin present. The data sets from both techniques were analysed with principal component analysis (PCA) to identify underlying variables. Principal component analysis of both SAXS and WAXS data was shown to discriminate the scattering signal between different hair types. The X-ray scattering results show a common underlying keratin intermediate filament (KIF) structure. However, distinct differences were observed in the preferential orientation and intensity signal from the lipid component of the hair. In addition, differences were observed in the intensity distribution of the very low-angle sample-dependent diffuse scatter surrounding the 'beamstop.' The results indicate that the fibrous keratin scaffold remains consistent between ethnic hair types. The hierarchies made by these may be modulated by variation in the content of keratin-associated proteins (KAPs) and lipids that alter the interfacial structures and lead to macroscopic differences in hair morphology. © 2013 Society of Cosmetic Scientists and the Société Française de Cosmétologie.
Policing starter unit selection of the enterocin type II polyketide synthase by the type II thioesterase EncL.

PubMed

Kalaitzis, John A; Cheng, Qian; Meluzzi, Dario; Xiang, Longkuan; Izumikawa, Miho; Dorrestein, Pieter C; Moore, Bradley S

2011-11-15

Enterocin is an atypical type II polyketide synthase (PKS) product from the marine actinomycete 'Streptomyces maritimus'. The enterocin biosynthesis gene cluster (enc) codes for proteins involved in the assembly and attachment of the rare benzoate primer that initiates polyketide assembly with the addition of seven malonate molecules and culminates in a Favorskii-like rearrangement of the linear poly-β-ketone to give its distinctive non-aromatic, caged core structure. Fundamental to enterocin biosynthesis, which utilizes a single acyl carrier protein (ACP), EncC, for both priming with benzoate and elongating with malonate, involves maintaining the correct balance of acyl-EncC substrates for efficient polyketide assembly. Here, we report the characterization of EncL as a type II thioesterase that functions to edit starter unit (mis)priming of EncC. We performed a series of in vivo mutational studies, heterologous expression experiments, in vitro reconstitution studies, and Fourier-transform mass spectrometry-monitored competitive enzyme assays that together support the proposed selective hydrolase activity of EncL toward misprimed acetyl-ACP over benzoyl-ACP to facilitate benzoyl priming of the enterocin PKS complex. While this system resembles the R1128 PKS that also utilizes an editing thioesterase (ZhuC) to purge acetate molecules from its initiation module ACP in favor of alkylacyl groups, the enterocin system is distinct in its usage of a single ACP for both priming and elongating reactions with different substrates. Copyright © 2011 Elsevier Ltd. All rights reserved.
Policing Starter Unit Selection of the Enterocin Type II Polyketide Synthase by the Type II Thioesterase EncL

PubMed Central

Kalaitzis, John A.; Cheng, Qian; Meluzzi, Dario; Xiang, Longkuan; Izumikawa, Miho; Dorrestein, Pieter C.; Moore, Bradley S.

2011-01-01

Enterocin is an atypical type II polyketide synthase (PKS) product from the marine actinomycete “Streptomyces maritimus”. The enterocin biosynthesis gene cluster (enc) codes for proteins involved in the assembly and attachment of the rare benzoate primer that initiates polyketide assembly with the addition of seven malonate molecules and culminates in a Favorskii-like rearrangement of the linear poly-β-ketone to give its distinctive non-aromatic, caged core structure. Fundamental to enterocin biosynthesis, which utilizes a single acyl carrier protein (ACP), EncC, for both priming with benzoate and elongating with malonate, involves maintaining the correct balance of acyl-EncC substrates for efficient polyketide assembly. Here we report the characterization of EncL as a type II thioesterase that functions to edit starter unit (mis)priming of EncC. We performed a series of in vivo mutational studies, heterologous expression experiments, in vitro reconstitution studies, and Fourier-transform mass spectrometry-monitored competitive enzyme assays that together support the proposed selective hydrolase activity of EncL toward misprimed acetyl-ACP over benzoyl-ACP to facilitate benzoyl priming of the enterocin PKS complex. While this system resembles the R1128 PKS that also utilizes an editing thioesterase (ZhuC) to purge acetate molecules from its initiation module ACP in favor of alkylacyl groups, the enterocin system is distinct in its usage of a single ACP for both priming and elongating reactions with different substrates. PMID:21531566
Effect of tacticity on the structure and glass transition temperature of polystyrene adsorbed onto solid surfaces

NASA Astrophysics Data System (ADS)

Negash, Solomon; Tatek, Yergou B.; Tsige, Mesfin

2018-04-01

We have carried out atomistic (all-atom) molecular dynamics simulations to investigate the effect of tacticity on the structure and glass transition temperature (Tg) of polystyrene (PS) thin films adsorbed on two distinct types of solid substrates. The systems consist of thin films made of atactic, isotactic, and syndiotactic PS chains supported by graphite or hydroxylated α-quartz substrates, which are known to be atomically flat but chemically and structurally different. We have observed a marked dependence of the film structure on substrate type as well as on tacticity. For instance, rings' orientation near substrate surfaces depends on substrate type for atactic PS and isotactic PS films, while no such dependence is observed for syndiotactic PS films whose interfacial structure seems to result from their propensity to adopt the trans conformation rather than their specific interaction with the substrates. Moreover, our results indicate that glass transition temperatures of substrate supported polystyrene films are higher compared to those of the corresponding free-standing films. More specifically, PS films on graphite exhibit larger Tg values than those on α-quartz, and we have noticed that syndiotactic PS has the largest Tg irrespective of the substrate type. Furthermore, the local Tg in the region of the film in contact with the substrates shows a strong tacticity and substrate dependence, whereas no dependencies were found for the local Tg in the middle of the film. Substrate-film interaction energy and chains' dynamics near substrate-film interfaces were subsequently investigated in order to substantiate the obtained Tgs, and it was found that films with higher Tgs are strongly adsorbed on the substrates and/or exhibit smaller interfacial chains' dynamics essentially due to steric hindrance.
Peptide models XLV: conformational properties of N-formyl-L-methioninamide and its relevance to methionine in proteins.

PubMed

Láng, András; Csizmadia, Imre G; Perczel, András

2005-02-15

The conformational space of the most biologically significant backbone folds of a suitable methionine peptide model was explored by density functional computational method. Using a medium [6-31G(d)] and a larger basis set [6-311++G(2d,2p)], the systematic exploration of low-energy backbone structures restricted for the "L-region" in the Ramachandran map of N-formyl-L-methioninamide results in conformers corresponding to the building units of an extended backbone structure (betaL), an inverse gamma-turn (gammaL), or a right-handed helical structure (alphaL). However, no poly-proline II type (epsilonL) fold was found, indicating that this conformer has no intrinsic stability, and highlighting the effect of molecular environment in stabilizing this backbone structure. This is in agreement with the abundance of the epsilonL-type backbone conformation of methionine found in proteins. Stability properties (DeltaE) and distinct backbone-side-chain interactions support the idea that specific intramolecular contacts are operative in the selection of the lowest energy conformers. Apart from the number of different folds, all stable conformers are within a 10 kcal x mol(-1) energy range, indicating the highly flexible behavior of methionine. This conformational feature can be important in supporting catalytic processes, facilitating protein folding and dimerization via metal ion binding. In both of the biological examples discussed (HIV-1 reverse transcriptase and PcoC copper-resistant protein), the conformational properties of Met residues were found to be of key importance. Spatial proximity to other types of residues or the same type of residue seems to be crucial for the structural integrity of a protein, whether Met is buried or exposed.
Structure of the Angiotensin Receptor Revealed by Serial Femtosecond Crystallography

DOE PAGES

Zhang, Haitao; Unal, Hamiyet; Gati, Cornelius; ...

2015-05-07

We report that angiotensin II type 1 receptor (AT 1R) is a G protein-coupled receptor that serves as a primary regulator for blood pressure maintenance. Although several anti-hypertensive drugs have been developed as AT 1R blockers (ARBs), the structural basis for AT 1R ligand-binding and regulation has remained elusive, mostly due to the difficulties of growing high quality crystals for structure determination using synchrotron radiation. By applying the recently developed method of serial femtosecond crystallography at an X-ray free-electron laser, we successfully determined the room-temperature crystal structure of the human AT 1R in complex with its selective antagonist ZD7155 atmore » 2.9 Å resolution. The AT 1R-ZD7155 complex structure revealed key structural features ofAT 1R and critical interactions for ZD7155 binding. Finally, docking simulations of the clinically used ARBs into the AT 1R structure further elucidated both the common and distinct binding modes for these anti-hypertensive drugs. Our results thereby provide fundamental insights into AT 1R structure-function relationship and structure-based drug design.« less
Structure of the Angiotensin Receptor Revealed by Serial Femtosecond Crystallography

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

Zhang, Haitao; Unal, Hamiyet; Gati, Cornelius

We report that angiotensin II type 1 receptor (AT 1R) is a G protein-coupled receptor that serves as a primary regulator for blood pressure maintenance. Although several anti-hypertensive drugs have been developed as AT 1R blockers (ARBs), the structural basis for AT 1R ligand-binding and regulation has remained elusive, mostly due to the difficulties of growing high quality crystals for structure determination using synchrotron radiation. By applying the recently developed method of serial femtosecond crystallography at an X-ray free-electron laser, we successfully determined the room-temperature crystal structure of the human AT 1R in complex with its selective antagonist ZD7155 atmore » 2.9 Å resolution. The AT 1R-ZD7155 complex structure revealed key structural features ofAT 1R and critical interactions for ZD7155 binding. Finally, docking simulations of the clinically used ARBs into the AT 1R structure further elucidated both the common and distinct binding modes for these anti-hypertensive drugs. Our results thereby provide fundamental insights into AT 1R structure-function relationship and structure-based drug design.« less
Perception of initial obstruent voicing is influenced by gestural organization

PubMed Central

Best, Catherine T.; Hallé, Pierre A.

2009-01-01

Cross-language differences in phonetic settings for phonological contrasts of stop voicing have posed a challenge for attempts to relate specific phonological features to specific phonetic details. We probe the phonetic-phonological relationship for voicing contrasts more broadly, analyzing in particular their relevance to nonnative speech perception, from two theoretical perspectives: feature geometry and articulatory phonology. Because these perspectives differ in assumptions about temporal/phasing relationships among features/gestures within syllable onsets, we undertook a cross-language investigation on perception of obstruent (stop, fricative) voicing contrasts in three nonnative onsets that use a common set of features/gestures but with differing time-coupling. Listeners of English and French, which differ in their phonetic settings for word-initial stop voicing distinctions, were tested on perception of three onset types, all nonnative to both English and French, that differ in how initial obstruent voicing is coordinated with a lateral feature/gesture and additional obstruent features/gestures. The targets, listed from least complex to most complex onsets, were: a lateral fricative voicing distinction (Zulu /ɬ/-ɮ/), a laterally-released affricate voicing distinction (Tlingit /tɬ/-/dɮ/), and a coronal stop voicing distinction in stop+/l/ clusters (Hebrew /tl/-/dl/). English and French listeners' performance reflected the differences in their native languages' stop voicing distinctions, compatible with prior perceptual studies on singleton consonant onsets. However, both groups' abilities to perceive voicing as a separable parameter also varied systematically with the structure of the target onsets, supporting the notion that the gestural organization of syllable onsets systematically affects perception of initial voicing distinctions. PMID:20228878

Distinction of Neurons, Glia and Endothelial Cells in the Cerebral Cortex: An Algorithm Based on Cytological Features

PubMed Central

García-Cabezas, Miguel Á.; John, Yohan J.; Barbas, Helen; Zikopoulos, Basilis

2016-01-01

The estimation of the number or density of neurons and types of glial cells and their relative proportions in different brain areas are at the core of rigorous quantitative neuroanatomical studies. Unfortunately, the lack of detailed, updated, systematic and well-illustrated descriptions of the cytology of neurons and glial cell types, especially in the primate brain, makes such studies especially demanding, often limiting their scope and broad use. Here, following an extensive analysis of histological materials and the review of current and classical literature, we compile a list of precise morphological criteria that can facilitate and standardize identification of cells in stained sections examined under the microscope. We describe systematically and in detail the cytological features of neurons and glial cell types in the cerebral cortex of the macaque monkey and the human using semithin and thick sections stained for Nissl. We used this classical staining technique because it labels all cells in the brain in distinct ways. In addition, we corroborate key distinguishing characteristics of different cell types in sections immunolabeled for specific markers counterstained for Nissl and in ultrathin sections processed for electron microscopy. Finally, we summarize the core features that distinguish each cell type in easy-to-use tables and sketches, and structure these key features in an algorithm that can be used to systematically distinguish cellular types in the cerebral cortex. Moreover, we report high inter-observer algorithm reliability, which is a crucial test for obtaining consistent and reproducible cell counts in unbiased stereological studies. This protocol establishes a consistent framework that can be used to reliably identify and quantify cells in the cerebral cortex of primates as well as other mammalian species in health and disease. PMID:27847469
Design of ternary alkaline-earth metal Sn(II) oxides with potential good p-type conductivity

DOE PAGES

Du, Mao -Hua; Singh, David J.; Zhang, Lijun; ...

2016-04-19

Oxides with good p-type conductivity have been long sought after to achieve high performance all-oxide optoelectronic devices. Divalent Sn(II) based oxides are promising candidates because of their rather dispersive upper valence bands caused by the Sn-5s/O-2p anti-bonding hybridization. There are so far few known Sn(II) oxides being p-type conductive suitable for device applications. Here, we present via first-principles global optimization structure searches a material design study for a hitherto unexplored Sn(II)-based system, ternary alkaline-earth metal Sn(II) oxides in the stoichiometry of MSn 2O 3 (M = Mg, Ca, Sr, Ba). We identify two stable compounds of SrSn 2O 3 andmore » BaSn 2O 3, which can be stabilized by Sn-rich conditions in phase stability diagrams. Their structures follow the Zintl behaviour and consist of basic structural motifs of SnO 3 tetrahedra. Unexpectedly they show distinct electronic properties with band gaps ranging from 1.90 (BaSn 2O 3) to 3.15 (SrSn 2O 3) eV, and hole effective masses ranging from 0.87 (BaSn 2O 3) to above 6.0 (SrSn 2O 3) m0. Further exploration of metastable phases indicates a wide tunability of electronic properties controlled by the details of the bonding between the basic structural motifs. Lastly, this suggests further exploration of alkaline-earth metal Sn(II) oxides for potential applications requiring good p-type conductivity such as transparent conductors and photovoltaic absorbers.« less
Using Intact Iron Microbial Mats to Gain Insights Into Mat Ecology and Geochemical Niche at the Microbial Scale

NASA Astrophysics Data System (ADS)

Glazer, B. T.; Chan, C. S. Y.; Mcallister, S.; Leavitt, A.; Emerson, D.

2015-12-01

Microbial mats are formed by microorganisms working in coordinated symbiosis, often benefitting the community by controlling the local geochemical or physical environment. Thus, the ecology of the mat depends on the individual roles of microbes organized into niches within a larger architecture. Chemolithotrophic Fe-oxidizing bacteria (FeOB) form distinctive Fe oxyhydroxide biominerals which constitute the building blocks of the mat. However, the majority of our progress has been in understanding the overall community structure. Understanding the physical mat structure on the microbial scale is important to unraveling FeOB evolution, the biogeochemistry and ecology of Fe-rich habitats, and ultimately interpreting FeOB biosignatures in the rock record. Mats in freshwater and marine environments contain strikingly similar biomineral morphologies, yet they are formed by phylogenetically distinct microorganisms. This suggests that the overall architecture and underlying genetics of freshwater and marine mats has evolved to serve particular roles specific to Fe oxidation. Thus, we conducted a comparative study of Fe seep freshwater mats and marine hydrothermal mats. We have developed a new approach to sampling Fe mats in order to preserve the delicate structure for analysis by confocal and scanning electron microscopy. Our analyses of these intact mats show that freshwater and marine mats are similarly initiated by a single type of structure-former. These ecosystem engineers form either a hollow sheath or a twisted stalk biomineral during mat formation, with a highly directional structure. These microbes appear to be the vanguard organisms that anchor the community within oxygen/Fe(II) gradients, further allowing for community succession in the mat interior as evidenced by other mineralized morphologies. Patterns in biomineral thickness and directionality were indicative of redox gradients and temporal changes in the geochemical environment. These observations show that the FeOB create the structure of the environment for the entire microbial community, acting as environmental engineers. Furthermore, they leave behind distinctive signatures of environmental conditions (e.g. presence of oxygen, hydrothermal pulsing), which can be recorded in the rock record.
Structures of Human CCL18, CCL3, and CCL4 Reveal Molecular Determinants for Quaternary Structures and Sensitivity to Insulin-Degrading Enzyme

DOE PAGES

Liang, Wenguang G.; Ren, Min; Zhao, Fan; ...

2015-01-27

CC chemokine ligands (CCL) are 8-14 kDa signaling proteins involved in diverse immune functions. While CCLs share similar tertiary structures, oligomerization produces highly diverse quaternary structures that protect chemokines from proteolytic degradation and modulate their functions. CCL18 is closely related to CCL3 and CCL4 with respect to both protein sequence and genomic location, yet CCL18 has distinct biochemical and biophysical properties. Here in this paper, we report a crystal structure of human CCL18 and its oligomerization states in solution based on crystallographic and small angle X-ray scattering (SAXS) analyses. Our data shows that CCL18 adopts an α-helical conformation at itsmore » N-terminus that weakens its dimerization, explaining CCL18’s preference for the monomeric state. Multiple contacts between monomers allow CCL18 to reversibly form a unique open-ended oligomer different from those of CCL3, CCL4, and CCL5. Furthermore, these differences hinge on proline 8, which is conserved in CCL3 and CCL4, but is replaced by lysine in human CCL18. Our structural analyses suggest that a proline 8 to alanine mutation stabilizes a type I β-turn at the N-terminus of CCL4 to prevent dimerization but prevents dimers from making key contacts with each other in CCL3. Thus, the P8A mutation induces depolymerization of CCL3 and CCL4 by distinct mechanisms. Finally, we used structural, biochemical, and functional analyses to unravel why insulin-degrading enzyme (IDE) degrades CCL3 and CCL4 but not CCL18. Lastly, our results elucidate the molecular basis for the oligomerization of three closely related CC chemokines and suggest how oligomerization shapes CCL chemokine function.« less
Structures of human CCL18, CCL3, and CCL4 reveal molecular determinants for quaternary structures and sensitivity to insulin-degrading enzyme.

PubMed

Liang, Wenguang G; Ren, Min; Zhao, Fan; Tang, Wei-Jen

2015-03-27

CC chemokine ligands (CCLs) are 8- to 14-kDa signaling proteins involved in diverse immune functions. While CCLs share similar tertiary structures, oligomerization produces highly diverse quaternary structures that protect chemokines from proteolytic degradation and modulate their functions. CCL18 is closely related to CCL3 and CCL4 with respect to both protein sequence and genomic location, yet CCL18 has distinct biochemical and biophysical properties. Here, we report a crystal structure of human CCL18 and its oligomerization states in solution based on crystallographic and small-angle X-ray scattering analyses. Our data show that CCL18 adopts an α-helical conformation at its N-terminus that weakens its dimerization, explaining CCL18's preference for the monomeric state. Multiple contacts between monomers allow CCL18 to reversibly form a unique open-ended oligomer different from those of CCL3, CCL4, and CCL5. Furthermore, these differences hinge on proline 8, which is conserved in CCL3 and CCL4 but is replaced by lysine in human CCL18. Our structural analyses suggest that a mutation of proline 8 to alanine stabilizes a type 1 β-turn at the N-terminus of CCL4 to prevent dimerization but prevents dimers from making key contacts with each other in CCL3. Thus, the P8A mutation induces depolymerization of CCL3 and CCL4 by distinct mechanisms. Finally, we used structural, biochemical, and functional analyses to unravel why insulin-degrading enzyme degrades CCL3 and CCL4 but not CCL18. Our results elucidate the molecular basis for the oligomerization of three closely related CC chemokines and suggest how oligomerization shapes CCL chemokine function. Copyright © 2015 Elsevier Ltd. All rights reserved.
Structure-Activity Relationships of the Human Immunodeficiency Virus Type 1 Maturation Inhibitor PF-46396.

PubMed

Murgatroyd, Christopher; Pirrie, Lisa; Tran, Fanny; Smith, Terry K; Westwood, Nicholas J; Adamson, Catherine S

2016-09-15

HIV-1 maturation inhibitors are a novel class of antiretroviral compounds that consist of two structurally distinct chemical classes: betulinic acid derivatives and the pyridone-based compound PF-46396. It is currently believed that both classes act by similar modes of action to generate aberrant noninfectious particles via inhibition of CA-SP1 cleavage during Gag proteolytic processing. In this study, we utilized a series of novel analogues with decreasing similarity to PF-46396 to determine the chemical groups within PF-46396 that contribute to antiviral activity, Gag binding, and the relationship between these essential properties. A spectrum of antiviral activity (active, intermediate, and inactive) was observed across the analogue series with respect to CA-SP1 cleavage and HIV-1 (NL4-3) replication kinetics in Jurkat T cells. We demonstrate that selected inactive analogues are incorporated into wild-type (WT) immature particles and that one inactive analogue is capable of interfering with PF-46396 inhibition of CA-SP1 cleavage. Mutations that confer PF-46396 resistance can impose a defective phenotype on HIV-1 that can be rescued in a compound-dependent manner. Some inactive analogues retained the capacity to rescue PF-46396-dependent mutants (SP1-A3V, SP1-A3T, and CA-P157S), implying that they can also interact with mutant Gag. The structure-activity relationships observed in this study demonstrate that (i) the tert-butyl group is essential for antiviral activity but is not an absolute requirement for Gag binding, (ii) the trifluoromethyl group is optimal but not essential for antiviral activity, and (iii) the 2-aminoindan group is important for antiviral activity and Gag binding but is not essential, as its replacement is tolerated. Combinations of antiretroviral drugs successfully treat HIV/AIDS patients; however, drug resistance problems make the development of new mechanistic drug classes an ongoing priority. HIV-1 maturation inhibitors are novel as they target the Gag protein, specifically by inhibiting CA-SP1 proteolytic cleavage. The lack of high-resolution structural information of the CA-SP1 target in Gag has hindered our understanding of the inhibitor-binding pocket and maturation inhibitor mode of action. Therefore, we utilized analogues of the maturation inhibitor PF-46396 as chemical tools to determine the chemical components of PF-46396 that contribute to antiviral activity and Gag binding and the relationship between these essential properties. This is the first study to report structure-activity relationships of the maturation inhibitor PF-46396. PF-46396 is chemically distinct from betulinic acid-derived maturation inhibitors; therefore, our data provide a foundation of knowledge that will aid our understanding of how structurally distinct maturation inhibitors act by similar modes of action. Copyright © 2016 Murgatroyd et al.
Modular synchronization in complex networks.

PubMed

Oh, E; Rho, K; Hong, H; Kahng, B

2005-10-01

We study the synchronization transition (ST) of a modified Kuramoto model on two different types of modular complex networks. It is found that the ST depends on the type of intermodular connections. For the network with decentralized (centralized) intermodular connections, the ST occurs at finite coupling constant (behaves abnormally). Such distinct features are found in the yeast protein interaction network and the Internet, respectively. Moreover, by applying the finite-size scaling analysis to an artificial network with decentralized intermodular connections, we obtain the exponent associated with the order parameter of the ST to be beta approximately 1 different from beta(MF) approximately 1/2 obtained from the scale-free network with the same degree distribution but the absence of modular structure, corresponding to the mean field value.
Depinning transition of a domain wall in ferromagnetic films

DOE PAGES

Xi, Bin; Luo, Meng -Bo; Vinokur, Valerii M.; ...

2015-09-14

Here, we report first principle numerical study of domain wall (DW) depinning in two-dimensional magnetic film, which is modeled by 2D random-field Ising system with the dipole-dipole interaction. We observe non-conventional activation-type motion of DW and reveal the fractal structure of DW near the depinning transition. We determine scaling functions describing critical dynamics near the transition and obtain universal exponents establishing connection between thermal softening of pinning potential and critical dynamics. In addition, we observe that tuning the strength of the dipole-dipole interaction switches DW dynamics between two different universality classes, corresponding to two distinct dynamic regimes characterized by non-Arrheniusmore » and conventional Arrhenius-type DW motions.« less
Doping of silicon by carbon during laser ablation process

NASA Astrophysics Data System (ADS)

Raciukaitis, G.; Brikas, M.; Kazlauskiene, V.; Miskinis, J.

2007-04-01

Effect of laser ablation on properties of remaining material was investigated in silicon. It was established that laser cutting of wafers in air induced doping of silicon by carbon. The effect was found to be more distinct by the use of higher laser power or UV radiation. Carbon ions created bonds with silicon in the depth of silicon. Formation of the silicon carbide type bonds was confirmed by SIMS, XPS and AES measurements. Modeling of the carbon diffusion was performed to clarify its depth profile in silicon. Photo-chemical reactions of such type changed the structure of material and could be a reason for the reduced quality of machining. A controlled atmosphere was applied to prevent carbonization of silicon during laser cutting.
Doping of silicon with carbon during laser ablation process

NASA Astrophysics Data System (ADS)

Račiukaitis, G.; Brikas, M.; Kazlauskienė, V.; Miškinis, J.

2006-12-01

The effect of laser ablation on properties of remaining material in silicon was investigated. It was found that laser cutting of wafers in the air induced the doping of silicon with carbon. The effect was more distinct when using higher laser power or UV radiation. Carbon ions created bonds with silicon atoms in the depth of the material. Formation of the silicon carbide type bonds was confirmed by SIMS, XPS and AES measurements. Modeling of the carbon diffusion to clarify its depth profile in silicon was performed. Photochemical reactions of such type changed the structure of material and could be the reason of the reduced machining quality. The controlled atmosphere was applied to prevent carbonization of silicon during laser cutting.
Comparative Anatomy of Phagocytic and Immunological Synapses

PubMed Central

Niedergang, Florence; Di Bartolo, Vincenzo; Alcover, Andrés

2016-01-01

The generation of phagocytic cups and immunological synapses are crucial events of the innate and adaptive immune responses, respectively. They are triggered by distinct immune receptors and performed by different cell types. However, growing experimental evidence shows that a very close series of molecular and cellular events control these two processes. Thus, the tight and dynamic interplay between receptor signaling, actin and microtubule cytoskeleton, and targeted vesicle traffic are all critical features to build functional phagosomes and immunological synapses. Interestingly, both phagocytic cups and immunological synapses display particular spatial and temporal patterns of receptors and signaling molecules, leading to the notion of “phagocytic synapse.” Here, we discuss both types of structures, their organization, and the mechanisms by which they are generated and regulated. PMID:26858721
Structural analysis of LaVO3 thin films under epitaxial strain

NASA Astrophysics Data System (ADS)

Meley, H.; Karandeep, Oberson, L.; de Bruijckere, J.; Alexander, D. T. L.; Triscone, J.-M.; Ghosez, Ph.; Gariglio, S.

2018-04-01

Rare earth vanadate perovskites exhibit a phase diagram in which two different types of structural distortions coexist: the strongest, the rotation of the oxygen octahedra, comes from the small tolerance factor of the perovskite cell (t = 0.88 for LaVO3) and the smaller one comes from inter-site d-orbital interactions manifesting as a cooperative Jahn-Teller effect. Epitaxial strain acts on octahedral rotations and crystal field symmetry to alter this complex lattice-orbit coupling. In this study, LaVO3 thin film structures have been investigated by X-ray diffraction and scanning transmission electron microscopy. The analysis shows two different orientations of octahedral tilt patterns, as well as two distinct temperature behaviors, for compressive and tensile film strain states. Ab initio calculations capture the strain effect on the tilt pattern orientation in agreement with experimental data.
Differences in proleptic and epicormic shoot structures in relation to water deficit and growth rate in almond trees (Prunus dulcis)

PubMed Central

Negrón, Claudia; Contador, Loreto; Lampinen, Bruce D.; Metcalf, Samuel G.; Guédon, Yann; Costes, Evelyne; DeJong, Theodore M.

2014-01-01

Background and Aims Shoot characteristics differ depending on the meristem tissue that they originate from and environmental conditions during their development. This study focused on the effects of plant water status on axillary meristem fate and flowering patterns along proleptic and epicormic shoots, as well as on shoot growth rates on ‘Nonpareil’ almond trees (Prunus dulcis). The aims were (1) to characterize the structural differences between proleptic and epicormic shoots, (2) to determine whether water deficits modify shoot structures differently depending on shoot type, and (3) to determine whether shoot structures are related to shoot growth rates. Methods A hidden semi-Markov model of the axillary meristem fate and number of flower buds per node was built for two shoot types growing on trees exposed to three plant water status treatments. The models segmented observed shoots into successive homogeneous zones, which were compared between treatments. Shoot growth rates were calculated from shoot extension measurements made during the growing season. Key Results Proleptic shoots had seven successive homogeneous zones while epicormic shoots had five zones. Shoot structures were associated with changes in growth rate over the season. Water deficit (1) affected the occurrence and lengths of the first zones of proleptic shoots, but only the occurrence of the third zone was reduced in epicormic shoots; (2) had a minor effect on zone flowering patterns and did not modify shoot or zone composition of axillary meristem fates; and (3) reduced growth rates, although patterns over the season were similar among treatments. Conclusions Two meristem types, with different latency durations, produced shoots with different growth rates and distinct structures. Differences between shoot type structure responses to water deficit appeared to reflect their ontogenetic characteristics and/or resource availability for their development. Tree water deficit appeared to stimulate a more rapid progression through ontogenetic states. PMID:24344139
Differences in proleptic and epicormic shoot structures in relation to water deficit and growth rate in almond trees (Prunus dulcis).

PubMed

Negrón, Claudia; Contador, Loreto; Lampinen, Bruce D; Metcalf, Samuel G; Guédon, Yann; Costes, Evelyne; DeJong, Theodore M

2014-02-01

Shoot characteristics differ depending on the meristem tissue that they originate from and environmental conditions during their development. This study focused on the effects of plant water status on axillary meristem fate and flowering patterns along proleptic and epicormic shoots, as well as on shoot growth rates on 'Nonpareil' almond trees (Prunus dulcis). The aims were (1) to characterize the structural differences between proleptic and epicormic shoots, (2) to determine whether water deficits modify shoot structures differently depending on shoot type, and (3) to determine whether shoot structures are related to shoot growth rates. A hidden semi-Markov model of the axillary meristem fate and number of flower buds per node was built for two shoot types growing on trees exposed to three plant water status treatments. The models segmented observed shoots into successive homogeneous zones, which were compared between treatments. Shoot growth rates were calculated from shoot extension measurements made during the growing season. Proleptic shoots had seven successive homogeneous zones while epicormic shoots had five zones. Shoot structures were associated with changes in growth rate over the season. Water deficit (1) affected the occurrence and lengths of the first zones of proleptic shoots, but only the occurrence of the third zone was reduced in epicormic shoots; (2) had a minor effect on zone flowering patterns and did not modify shoot or zone composition of axillary meristem fates; and (3) reduced growth rates, although patterns over the season were similar among treatments. Two meristem types, with different latency durations, produced shoots with different growth rates and distinct structures. Differences between shoot type structure responses to water deficit appeared to reflect their ontogenetic characteristics and/or resource availability for their development. Tree water deficit appeared to stimulate a more rapid progression through ontogenetic states.
Multimodal fluorescence microscopy of prion strain specific PrP deposits stained by thiophene-based amyloid ligands.

PubMed

Magnusson, Karin; Simon, Rozalyn; Sjölander, Daniel; Sigurdson, Christina J; Hammarström, Per; Nilsson, K Peter R

2014-01-01

The disease-associated prion protein (PrP) forms aggregates which vary in structural conformation yet share an identical primary sequence. These variations in PrP conformation are believed to manifest in prion strains exhibiting distinctly different periods of disease incubation as well as regionally specific aggregate deposition within the brain. The anionic luminescent conjugated polythiophene (LCP), polythiophene acetic acid (PTAA) has previously been used to distinguish PrP deposits associated with distinct mouse adapted strains via distinct fluorescence emission profiles from the dye. Here, we employed PTAA and 3 structurally related chemically defined luminescent conjugated oligothiophenes (LCOs) to stain brain tissue sections from mice inoculated with 2 distinct prion strains. Our results showed that in addition to emission spectra, excitation, and fluorescence lifetime imaging microscopy (FLIM) can fruitfully be assessed for optical distinction of PrP deposits associated with distinct prion strains. Our findings support the theory that alterations in LCP/LCO fluorescence are due to distinct conformational restriction of the thiophene backbone upon interaction with PrP aggregates associated with distinct prion strains. We foresee that LCP and LCO staining in combination with multimodal fluorescence microscopy might aid in detecting structural differences among discrete protein aggregates and in linking protein conformational features with disease phenotypes for a variety of neurodegenerative proteinopathies.
Multimodal fluorescence microscopy of prion strain specific PrP deposits stained by thiophene-based amyloid ligands

PubMed Central

Magnusson, Karin; Simon, Rozalyn; Sjölander, Daniel; Sigurdson, Christina J; Hammarström, Per; Nilsson, K Peter R

2014-01-01

The disease-associated prion protein (PrP) forms aggregates which vary in structural conformation yet share an identical primary sequence. These variations in PrP conformation are believed to manifest in prion strains exhibiting distinctly different periods of disease incubation as well as regionally specific aggregate deposition within the brain. The anionic luminescent conjugated polythiophene (LCP), polythiophene acetic acid (PTAA) has previously been used to distinguish PrP deposits associated with distinct mouse adapted strains via distinct fluorescence emission profiles from the dye. Here, we employed PTAA and 3 structurally related chemically defined luminescent conjugated oligothiophenes (LCOs) to stain brain tissue sections from mice inoculated with 2 distinct prion strains. Our results showed that in addition to emission spectra, excitation, and fluorescence lifetime imaging microscopy (FLIM) can fruitfully be assessed for optical distinction of PrP deposits associated with distinct prion strains. Our findings support the theory that alterations in LCP/LCO fluorescence are due to distinct conformational restriction of the thiophene backbone upon interaction with PrP aggregates associated with distinct prion strains. We foresee that LCP and LCO staining in combination with multimodal fluorescence microscopy might aid in detecting structural differences among discrete protein aggregates and in linking protein conformational features with disease phenotypes for a variety of neurodegenerative proteinopathies. PMID:25495506
Transancestral fine-mapping of four type 2 diabetes susceptibility loci highlights potential causal regulatory mechanisms.

PubMed

Horikoshi, Momoko; Pasquali, Lorenzo; Wiltshire, Steven; Huyghe, Jeroen R; Mahajan, Anubha; Asimit, Jennifer L; Ferreira, Teresa; Locke, Adam E; Robertson, Neil R; Wang, Xu; Sim, Xueling; Fujita, Hayato; Hara, Kazuo; Young, Robin; Zhang, Weihua; Choi, Sungkyoung; Chen, Han; Kaur, Ismeet; Takeuchi, Fumihiko; Fontanillas, Pierre; Thuillier, Dorothée; Yengo, Loic; Below, Jennifer E; Tam, Claudia H T; Wu, Ying; Abecasis, Gonçalo; Altshuler, David; Bell, Graeme I; Blangero, John; Burtt, Noél P; Duggirala, Ravindranath; Florez, Jose C; Hanis, Craig L; Seielstad, Mark; Atzmon, Gil; Chan, Juliana C N; Ma, Ronald C W; Froguel, Philippe; Wilson, James G; Bharadwaj, Dwaipayan; Dupuis, Josee; Meigs, James B; Cho, Yoon Shin; Park, Taesung; Kooner, Jaspal S; Chambers, John C; Saleheen, Danish; Kadowaki, Takashi; Tai, E Shyong; Mohlke, Karen L; Cox, Nancy J; Ferrer, Jorge; Zeggini, Eleftheria; Kato, Norihiro; Teo, Yik Ying; Boehnke, Michael; McCarthy, Mark I; Morris, Andrew P

2016-05-15

To gain insight into potential regulatory mechanisms through which the effects of variants at four established type 2 diabetes (T2D) susceptibility loci (CDKAL1, CDKN2A-B, IGF2BP2 and KCNQ1) are mediated, we undertook transancestral fine-mapping in 22 086 cases and 42 539 controls of East Asian, European, South Asian, African American and Mexican American descent. Through high-density imputation and conditional analyses, we identified seven distinct association signals at these four loci, each with allelic effects on T2D susceptibility that were homogenous across ancestry groups. By leveraging differences in the structure of linkage disequilibrium between diverse populations, and increased sample size, we localised the variants most likely to drive each distinct association signal. We demonstrated that integration of these genetic fine-mapping data with genomic annotation can highlight potential causal regulatory elements in T2D-relevant tissues. These analyses provide insight into the mechanisms through which T2D association signals are mediated, and suggest future routes to understanding the biology of specific disease susceptibility loci. © The Author 2016. Published by Oxford University Press.
Genetic relationships and clonal population structure of serotype 2 strains of Neisseria meningitidis.

PubMed Central

Caugant, D A; Zollinger, W D; Mocca, L F; Frasch, C E; Whittam, T S; Frøholm, L O; Selander, R K

1987-01-01

Two hundred and thirty-four strains of Neisseria meningitidis, including 94 serotype 2a, 111 serotype 2b, and 19 serotype 2c isolates, together with 10 isolates that were serotyped as 2 with polyvalent antiserum but did not react with monoclonal antibodies, were characterized by the electrophoretic mobilities of 15 metabolic enzymes. Of these enzymes, 14 were polymorphic, and 56 distinctive combinations of alleles at the enzyme loci (electrophoretic types) were identified, among which the mean genetic diversity per locus was 0.413, or about 75% of that recorded for the species N. meningitidis as a whole. Mean genetic diversity among electrophoretic types of the same serotype (2a, 2b, or 2c) was, however, on average, less than half the total species diversity, and no multilocus genotypes were shared between isolates of the different serotypes, which belong to distinctive clonal lineages. Recent temporal changes in the frequencies of recovery of pathogenic strains of serotypes 2a and 2b in South Africa and North America resulted from clone replacement in these populations rather than evolutionary modification of the serotype protein of the initially dominant clones. PMID:3106223
Termites Facilitate Methane Oxidation and Shape the Methanotrophic Community

PubMed Central

Erens, Hans; Mujinya, Basile Bazirake; Boeckx, Pascal; Baert, Geert; Schneider, Bellinda; Frenzel, Peter; Van Ranst, Eric

2013-01-01

Termite-derived methane contributes 3 to 4% to the total methane budget globally. Termites are not known to harbor methane-oxidizing microorganisms (methanotrophs). However, a considerable fraction of the methane produced can be consumed by methanotrophs that inhabit the mound material, yet the methanotroph ecology in these environments is virtually unknown. The potential for methane oxidation was determined using slurry incubations under conditions with high (12%) and in situ (∼0.004%) methane concentrations through a vertical profile of a termite (Macrotermes falciger) mound and a reference soil. Interestingly, the mound material showed higher methanotrophic activity. The methanotroph community structure was determined by means of a pmoA-based diagnostic microarray. Although the methanotrophs in the mound were derived from populations in the reference soil, it appears that termite activity selected for a distinct community. Applying an indicator species analysis revealed that putative atmospheric methane oxidizers (high-indicator-value probes specific for the JR3 cluster) were indicative of the active nest area, whereas methanotrophs belonging to both type I and type II were indicative of the reference soil. We conclude that termites modify their environment, resulting in higher methane oxidation and selecting and/or enriching for a distinct methanotroph population. PMID:24038691
AUthigenic feldspar as an indicator of paleo-rock/water interactions in Permian carbonates of the Northern Calcareous Alps, Austria

USGS Publications Warehouse

Spotl, C.; Kralik, M.; Kunk, Michael J.

1996-01-01

Dolostones interbedded with Upper Permian evaporites at the base of the Northern Calcareous Alps contain abundant authigenic K-feldspar. Two petrographically, structurally, and isotopically distinct generations of K-feldspar can be distinguished: crystals composed of an inclusion-rich core and a clear rim, and optically unzoned, transparent crystals. Both feldspar types have essentially identical K-feldspar end-member compositions with ??? 99.5 mole % Or component. Low oxygen isotope ratios (+16.1??? to +18.1??? SMOW) suggest precipitation from 18O-enriched, saline fluids at temperatures in excess of ??? 140??C. 40Ar/39Ar plateau-age spectra of five samples range from 145 ?? 1 to 144 ?? 1 Ma (Early Berriasian) and suggest that both types of feldspar were formed within an interval that did not exceed ??? 2 m.y. Rb/Sr model ages range from 152 to 140 Ma, assuming that the burial diagenetic regime was buffered with respect to strontium by the associated marine Permian evaporites. Authigenic K-feldspar records two distinct events of hot brine flow, most likely triggered by tectonic movements (detachment) and by an increase in the subsurface temperature in response to thrust loading.

Informatic deconvolution of biased GPCR signaling mechanisms from in vivo pharmacological experimentation.

PubMed

Maudsley, Stuart; Martin, Bronwen; Janssens, Jonathan; Etienne, Harmonie; Jushaj, Areta; van Gastel, Jaana; Willemsen, Ann; Chen, Hongyu; Gesty-Palmer, Diane; Luttrell, Louis M

2016-01-01

Ligands possessing different physico-chemical structures productively interact with G protein-coupled receptors generating distinct downstream signaling events due to their abilities to activate/select idiosyncratic receptor entities ('receptorsomes') from the full spectrum of potential receptor partners. We have employed multiple novel informatic approaches to identify and characterize the in vivo transcriptomic signature of an arrestin-signaling biased ligand, [D-Trp(12),Tyr(34)]-bPTH(7-34), acting at the parathyroid hormone type 1 receptor (PTH1R), across six different murine tissues after chronic drug exposure. We are able to demonstrate that [D-Trp(12),Tyr(34)]-bPTH(7-34) elicits a distinctive arrestin-signaling focused transcriptomic response that is more coherently regulated, in an arrestin signaling-dependent manner, across more tissues than that of the pluripotent endogenous PTH1R ligand, hPTH(1-34). This arrestin-focused response signature is strongly linked with the transcriptional regulation of cell growth and development. Our informatic deconvolution of a conserved arrestin-dependent transcriptomic signature from wild type mice demonstrates a conceptual framework within which the in vivo outcomes of biased receptor signaling may be further investigated or predicted. Published by Elsevier Inc.
Automated extraction and classification of time-frequency contours in humpback vocalizations.

PubMed

Ou, Hui; Au, Whitlow W L; Zurk, Lisa M; Lammers, Marc O

2013-01-01

A time-frequency contour extraction and classification algorithm was created to analyze humpback whale vocalizations. The algorithm automatically extracted contours of whale vocalization units by searching for gray-level discontinuities in the spectrogram images. The unit-to-unit similarity was quantified by cross-correlating the contour lines. A library of distinctive humpback units was then generated by applying an unsupervised, cluster-based learning algorithm. The purpose of this study was to provide a fast and automated feature selection tool to describe the vocal signatures of animal groups. This approach could benefit a variety of applications such as species description, identification, and evolution of song structures. The algorithm was tested on humpback whale song data recorded at various locations in Hawaii from 2002 to 2003. Results presented in this paper showed low probability of false alarm (0%-4%) under noisy environments with small boat vessels and snapping shrimp. The classification algorithm was tested on a controlled set of 30 units forming six unit types, and all the units were correctly classified. In a case study on humpback data collected in the Auau Chanel, Hawaii, in 2002, the algorithm extracted 951 units, which were classified into 12 distinctive types.
Termites facilitate methane oxidation and shape the methanotrophic community.

PubMed

Ho, Adrian; Erens, Hans; Mujinya, Basile Bazirake; Boeckx, Pascal; Baert, Geert; Schneider, Bellinda; Frenzel, Peter; Boon, Nico; Van Ranst, Eric

2013-12-01

Termite-derived methane contributes 3 to 4% to the total methane budget globally. Termites are not known to harbor methane-oxidizing microorganisms (methanotrophs). However, a considerable fraction of the methane produced can be consumed by methanotrophs that inhabit the mound material, yet the methanotroph ecology in these environments is virtually unknown. The potential for methane oxidation was determined using slurry incubations under conditions with high (12%) and in situ (∼0.004%) methane concentrations through a vertical profile of a termite (Macrotermes falciger) mound and a reference soil. Interestingly, the mound material showed higher methanotrophic activity. The methanotroph community structure was determined by means of a pmoA-based diagnostic microarray. Although the methanotrophs in the mound were derived from populations in the reference soil, it appears that termite activity selected for a distinct community. Applying an indicator species analysis revealed that putative atmospheric methane oxidizers (high-indicator-value probes specific for the JR3 cluster) were indicative of the active nest area, whereas methanotrophs belonging to both type I and type II were indicative of the reference soil. We conclude that termites modify their environment, resulting in higher methane oxidation and selecting and/or enriching for a distinct methanotroph population.
Invasive micropapillary carcinoma: a distinct type of adenocarcinomas in the gastrointestinal tract.

PubMed

Guzińska-Ustymowicz, Katarzyna; Niewiarowska, Katarzyna; Pryczynicz, Anna

2014-04-28

Invasive micropapillary carcinoma (IMPC) is a rare histological type of tumor, first described in invasive ductal breast cancer, than in malignancies in other organs such as lungs, urinary bladder, ovaries or salivary glands. Recent literature data shows that this histological lesion has also been found in cancers of the gastrointestinal system. The micropapillary components are clusters of neoplastic cells that closely adhere to each other and are located in distinct empty spaces. Moreover, clusters of neoplastic cells do not have a fibrous-vascular core. The IMPC cells show reverse polarity resulting in typical ''inside-out'' structures that determines secretary properties, disturbs adhesion and conditions grade of malignancy in gastrointestinal (GI) tract. Invasive micropapillary carcinoma in this location is associated with metastases to local lymph nodes and lymphovascular invasion. IMPC can be a prognostic factor for patients with cancers of the stomach, pancreas and with colorectal cancer since it is related with disease-free and overall survival. The purpose of this review is to present the characterization of invasive micropapillary carcinoma in colon, rectum, stomach and others site of GI tract, and to determine the immunohistological indentification of IMPC in those localization.
Microstructure Analysis of Bismuth Absorbers for Transition-Edge Sensor X-ray Microcalorimeters

NASA Astrophysics Data System (ADS)

Yan, Daikang; Divan, Ralu; Gades, Lisa M.; Kenesei, Peter; Madden, Timothy J.; Miceli, Antonino; Park, Jun-Sang; Patel, Umeshkumar M.; Quaranta, Orlando; Sharma, Hemant; Bennett, Douglas A.; Doriese, William B.; Fowler, Joseph W.; Gard, Johnathon D.; Hays-Wehle, James P.; Morgan, Kelsey M.; Schmidt, Daniel R.; Swetz, Daniel S.; Ullom, Joel N.

2018-03-01

Given its large X-ray stopping power and low specific heat capacity, bismuth (Bi) is a promising absorber material for X-ray microcalorimeters and has been used with transition-edge sensors (TESs) in the past. However, distinct X-ray spectral features have been observed in TESs with Bi absorbers deposited with different techniques. Evaporated Bi absorbers are widely reported to have non-Gaussian low-energy tails, while electroplated ones do not show this feature. In this study, we fabricated Bi absorbers with these two methods and performed microstructure analysis using scanning electron microscopy and X-ray diffraction microscopy. The two types of material showed the same crystallographic structure, but the grain size of the electroplated Bi was about 40 times larger than that of the evaporated Bi. This distinction in grain size is likely to be the cause of their different spectral responses.
Gene-Culture Coevolution in a Social Cetacean: Integrating Acoustic and Genetic Data to Understand Population Structure in the Short-Finned Pilot Whale (Globicephala macrorhynchus)

NASA Astrophysics Data System (ADS)

Van Cise, Amy

The evolutionary ecology of a species is driven by a combination of random events, ecological and environmental mechanisms, and social behavior. Gene-culture coevolutionary theory attempts to understand the evolutionary trajectory of a species by examining the interactions between these potential drivers. Further, our choice of data type will affect the patterns we observe, therefore by integrating several types of data we achieve a holistic understanding of the various aspects of evolutionary ecology within a species. In order to understand population structure in short-finned pilot whales, I use a combination of genetic and acoustic data to examine structure on evolutionary (genetic) and cultural (acoustic) timescales. I first examine structure among geographic populations in the Pacific Ocean. Using genetic sequences from the mitochondrial control region, I show that two genetically and morphologically distinct types of short-finned pilot whale, described off the coast of Japan, have non-overlapping distributions throughout their range in the Pacific Ocean. Analysis of the acoustic features of their social calls indicates that they are acoustically differentiated, possibly due to limited communication between the two types. This evidence supports the hypothesis that the two types may be separate species or subspecies. Next, I examine structure among island communities and social groups within the Hawaiian Island population of short-finned pilot whales. Using a combination of mitochondrial and nuclear DNA, I showed that the hierarchical social structure in Hawaiian pilot whales is driven by genetic relatedness; individuals remain in groups with their immediate family members, and preferentially associate with relatives. Similarly, social structure affects genetic differentiation, likely by restricting access to mates. Acoustic differentiation among social groups indicates that social structure may also restrict the flow of cultural information, such as vocal repertoire or dialect. The qualitative correlation between social structure, cultural information transfer, and genetic structure suggest that gene-culture coevolution may be an important mechanism to the evolutionary ecology of short-finned pilot whales. Further research may reveal a similar structure in the transmission of ecological behaviors, such as diet preference, habitat use, or movements. The results of this research underscore the applicability of gene-culture coevolutionary theory to non-human taxa.
Strain distributions and their influence on electronic structures of WSe2-MoS2 laterally strained heterojunctions

NASA Astrophysics Data System (ADS)

Zhang, Chendong; Li, Ming-Yang; Tersoff, Jerry; Han, Yimo; Su, Yushan; Li, Lain-Jong; Muller, David A.; Shih, Chih-Kang

2018-02-01

Monolayer transition metal dichalcogenide heterojunctions, including vertical and lateral p-n junctions, have attracted considerable attention due to their potential applications in electronics and optoelectronics. Lattice-misfit strain in atomically abrupt lateral heterojunctions, such as WSe2-MoS2, offers a new band-engineering strategy for tailoring their electronic properties. However, this approach requires an understanding of the strain distribution and its effect on band alignment. Here, we study a WSe2-MoS2 lateral heterojunction using scanning tunnelling microscopy and image its moiré pattern to map the full two-dimensional strain tensor with high spatial resolution. Using scanning tunnelling spectroscopy, we measure both the strain and the band alignment of the WSe2-MoS2 lateral heterojunction. We find that the misfit strain induces type II to type I band alignment transformation. Scanning transmission electron microscopy reveals the dislocations at the interface that partially relieve the strain. Finally, we observe a distinctive electronic structure at the interface due to hetero-bonding.
Ridges and scarps in the equatorial belt of Mars

USGS Publications Warehouse

Lucchitta, B.K.; Klockenbrink, J.L.

1981-01-01

The morphology and distribution of ridges and scarps on Mars in the ?? 30?? latitude belt were investigated. Two distinct types of ridges were recognized. The first is long and linear, resembling mare ridges on the Moon; it occurs mostly in plains areas. The other is composed of short, anastomosing segments and occurs mostly in ancient cratered terrain and intervening plateaus. Where ridges are eroded, landscape configurations suggest that they are located along regional structures. The age of ridges is uncertain, but some are as young as the latest documented volcanic activity on Mars. The origins of ridges are probably diverse-they may result from wrinkling due to compression or from buckling due to settling over subsurface structures. The similar morphologic expressions of ridge types of various origins may be related to a similar deformation mechanism caused by two main factors: (1) most ridges are developed in thick layers of competent material and (2) ridges formed under stresses near a free surface. ?? 1981 D. Reidel Publishing Co.
A general strategy for synthesis of cyclophane-braced peptide macrocycles via palladium-catalysed intramolecular sp3 C-H arylation

NASA Astrophysics Data System (ADS)

Zhang, Xuekai; Lu, Gang; Sun, Meng; Mahankali, Madhu; Ma, Yanfei; Zhang, Mingming; Hua, Wangde; Hu, Yuting; Wang, Qingbing; Chen, Jinghuo; He, Gang; Qi, Xiangbing; Shen, Weijun; Liu, Peng; Chen, Gong

2018-05-01

New methods capable of effecting cyclization, and forming novel three-dimensional structures while maintaining favourable physicochemical properties are needed to facilitate the development of cyclic peptide-based drugs that can engage challenging biological targets, such as protein-protein interactions. Here, we report a highly efficient and generally applicable strategy for constructing new types of peptide macrocycles using palladium-catalysed intramolecular C(sp3)-H arylation reactions. Easily accessible linear peptide precursors of simple and versatile design can be selectively cyclized at the side chains of either aromatic or modified non-aromatic amino acid units to form various cyclophane-braced peptide cycles. This strategy provides a powerful tool to address the long-standing challenge of size- and composition-dependence in peptide macrocyclization, and generates novel peptide macrocycles with uniquely buttressed backbones and distinct loop-type three-dimensional structures. Preliminary cell proliferation screening of the pilot library revealed a potent lead compound with selective cytotoxicity toward proliferative Myc-dependent cancer cell lines.
Tiled Microarray Identification of Novel Viral Transcript Structures and Distinct Transcriptional Profiles during Two Modes of Productive Murine Gammaherpesvirus 68 Infection

PubMed Central

Cheng, Benson Yee Hin; Zhi, Jizu; Santana, Alexis; Khan, Sohail; Salinas, Eduardo; Forrest, J. Craig; Zheng, Yueting; Jaggi, Shirin; Leatherwood, Janet

2012-01-01

We applied a custom tiled microarray to examine murine gammaherpesvirus 68 (MHV68) polyadenylated transcript expression in a time course of de novo infection of fibroblast cells and following phorbol ester-mediated reactivation from a latently infected B cell line. During de novo infection, all open reading frames (ORFs) were transcribed and clustered into four major temporal groups that were overlapping yet distinct from clusters based on the phorbol ester-stimulated B cell reactivation time course. High-density transcript analysis at 2-h intervals during de novo infection mapped gene boundaries with a 20-nucleotide resolution, including a previously undefined ORF73 transcript and the MHV68 ORF63 homolog of Kaposi's sarcoma-associated herpesvirus vNLRP1. ORF6 transcript initiation was mapped by tiled array and confirmed by 5′ rapid amplification of cDNA ends. The ∼1.3-kb region upstream of ORF6 was responsive to lytic infection and MHV68 RTA, identifying a novel RTA-responsive promoter. Transcription in intergenic regions consistent with the previously defined expressed genomic regions was detected during both types of productive infection. We conclude that the MHV68 transcriptome is dynamic and distinct during de novo fibroblast infection and upon phorbol ester-stimulated B cell reactivation, highlighting the need to evaluate further transcript structure and the context-dependent molecular events that govern viral gene expression during chronic infection. PMID:22318145
Distinct Annular Oligomers Captured along the Assembly and Disassembly Pathways of Transthyretin Amyloid Protofibrils

PubMed Central

Pires, Ricardo H.; Karsai, Árpád; Saraiva, Maria J.; Damas, Ana M.; Kellermayer, Miklós S. Z.

2012-01-01

Background Defects in protein folding may lead to severe degenerative diseases characterized by the appearance of amyloid fibril deposits. Cytotoxicity in amyloidoses has been linked to poration of the cell membrane that may involve interactions with amyloid intermediates of annular shape. Although annular oligomers have been detected in many amyloidogenic systems, their universality, function and molecular mechanisms of appearance are debated. Methodology/Principal Findings We investigated with high-resolution in situ atomic force microscopy the assembly and disassembly of transthyretin (TTR) amyloid protofibrils formed of the native protein by pH shift. Annular oligomers were the first morphologically distinct intermediates observed in the TTR aggregation pathway. Morphological analysis suggests that they can assemble into a double-stack of octameric rings with a 16±2 nm diameter, and displaying the tendency to form linear structures. According to light scattering data coupled to AFM imaging, annular oligomers appeared to undergo a collapse type of structural transition into spheroid oligomers containing 8–16 monomers. Disassembly of TTR amyloid protofibrils also resulted in the rapid appearance of annular oligomers but with a morphology quite distinct from that observed in the assembly pathway. Conclusions/Significance Our observations indicate that annular oligomers are key dynamic intermediates not only in the assembly but also in the disassembly of TTR protofibrils. The balance between annular and more compact forms of aggregation could be relevant for cytotoxicity in amyloidogenic disorders. PMID:22984597
Cell differentiation defines acute and chronic infection cell types in Staphylococcus aureus.

PubMed

García-Betancur, Juan-Carlos; Goñi-Moreno, Angel; Horger, Thomas; Schott, Melanie; Sharan, Malvika; Eikmeier, Julian; Wohlmuth, Barbara; Zernecke, Alma; Ohlsen, Knut; Kuttler, Christina; Lopez, Daniel

2017-09-12

A central question to biology is how pathogenic bacteria initiate acute or chronic infections. Here we describe a genetic program for cell-fate decision in the opportunistic human pathogen Staphylococcus aureus , which generates the phenotypic bifurcation of the cells into two genetically identical but different cell types during the course of an infection. Whereas one cell type promotes the formation of biofilms that contribute to chronic infections, the second type is planktonic and produces the toxins that contribute to acute bacteremia. We identified a bimodal switch in the agr quorum sensing system that antagonistically regulates the differentiation of these two physiologically distinct cell types. We found that extracellular signals affect the behavior of the agr bimodal switch and modify the size of the specialized subpopulations in specific colonization niches. For instance, magnesium-enriched colonization niches causes magnesium binding to S. aureus teichoic acids and increases bacterial cell wall rigidity. This signal triggers a genetic program that ultimately downregulates the agr bimodal switch. Colonization niches with different magnesium concentrations influence the bimodal system activity, which defines a distinct ratio between these subpopulations; this in turn leads to distinct infection outcomes in vitro and in an in vivo murine infection model. Cell differentiation generates physiological heterogeneity in clonal bacterial infections and helps to determine the distinct infection types.
Cell differentiation defines acute and chronic infection cell types in Staphylococcus aureus

PubMed Central

García-Betancur, Juan-Carlos; Goñi-Moreno, Angel; Horger, Thomas; Schott, Melanie; Sharan, Malvika; Eikmeier, Julian; Wohlmuth, Barbara; Zernecke, Alma; Ohlsen, Knut; Kuttler, Christina

2017-01-01

A central question to biology is how pathogenic bacteria initiate acute or chronic infections. Here we describe a genetic program for cell-fate decision in the opportunistic human pathogen Staphylococcus aureus, which generates the phenotypic bifurcation of the cells into two genetically identical but different cell types during the course of an infection. Whereas one cell type promotes the formation of biofilms that contribute to chronic infections, the second type is planktonic and produces the toxins that contribute to acute bacteremia. We identified a bimodal switch in the agr quorum sensing system that antagonistically regulates the differentiation of these two physiologically distinct cell types. We found that extracellular signals affect the behavior of the agr bimodal switch and modify the size of the specialized subpopulations in specific colonization niches. For instance, magnesium-enriched colonization niches causes magnesium binding to S. aureusteichoic acids and increases bacterial cell wall rigidity. This signal triggers a genetic program that ultimately downregulates the agr bimodal switch. Colonization niches with different magnesium concentrations influence the bimodal system activity, which defines a distinct ratio between these subpopulations; this in turn leads to distinct infection outcomes in vitro and in an in vivo murine infection model. Cell differentiation generates physiological heterogeneity in clonal bacterial infections and helps to determine the distinct infection types. PMID:28893374
Classification and evolution of human rhinoviruses.

PubMed

Palmenberg, Ann C; Gern, James E

2015-01-01

The historical classification of human rhinoviruses (RV) by serotyping has been replaced by a logical system of comparative sequencing. Given that strains must diverge within their capsid sequenced by a reasonable degree (>12-13 % pairwise base identities) before becoming immunologically distinct, the new nomenclature system makes allowances for the addition of new, future types, without compromising historical designations. Currently, three species, the RV-A, RV-B, and RV-C, are recognized. Of these, the RV-C, discovered in 2006, are the most unusual in terms of capsid structure, receptor use, and association with severe disease in children.
Enhancing Transdisciplinary Research Through Collaborative Leadership

PubMed Central

Gray, Barbara

2008-01-01

Transcending the well-established and familiar boundaries of disciplinary silos poses challenges for even the most interpersonally competent scientists. This paper explores the challenges inherent in leading transdisciplinary projects, detailing the critical roles that leaders play in shepherding transdisciplinary scientific endeavors. Three types of leadership tasks are considered: cognitive, structural, and processual. Distinctions are made between leading small, co-located projects and large, dispersed ones. Finally, social-network analysis is proposed as a useful tool for conducting research on leadership, and, in particular, on the role of brokers, on complex transdisciplinary teams. PMID:18619392
Synchronous Seasonal Change in Fin Whale Song in the North Pacific

PubMed Central

Oleson, Erin M.; Širović, Ana; Bayless, Alexandra R.; Hildebrand, John A.

2014-01-01

Fin whale (Balaenoptera physalus) song consists of down-swept pulses arranged into stereotypic sequences that can be characterized according to the interval between successive pulses. As in blue (B. musculus) and humpback whales (Megaptera novaeangliae), these song sequences may be geographically distinct and may correlate with population boundaries in some regions. We measured inter-pulse intervals of fin whale songs within year-round acoustic datasets collected between 2000 and 2006 in three regions of the eastern North Pacific: Southern California, the Bering Sea, and Hawaii. A distinctive song type that was recorded in all three regions is characterized by singlet and doublet inter-pulse intervals that increase seasonally, then annually reset to the same shorter intervals at the beginning of each season. This song type was recorded in the Bering Sea and off Southern California from September through May and off Hawaii from December through April, with the song interval generally synchronized across all monitoring locations. The broad geographic and seasonal occurrence of this particular fin whale song type may represent a single population broadly distributed throughout the eastern Pacific with no clear seasonal migratory pattern. Previous studies attempting to infer population structure of fin whales in the North Pacific using synchronous individual song samples have been unsuccessful, likely because they did not account for the seasonal lengthening in song intervals observed here. PMID:25521493
Synchronous seasonal change in fin whale song in the North Pacific.

PubMed

Oleson, Erin M; Širović, Ana; Bayless, Alexandra R; Hildebrand, John A

2014-01-01

Fin whale (Balaenoptera physalus) song consists of down-swept pulses arranged into stereotypic sequences that can be characterized according to the interval between successive pulses. As in blue (B. musculus) and humpback whales (Megaptera novaeangliae), these song sequences may be geographically distinct and may correlate with population boundaries in some regions. We measured inter-pulse intervals of fin whale songs within year-round acoustic datasets collected between 2000 and 2006 in three regions of the eastern North Pacific: Southern California, the Bering Sea, and Hawaii. A distinctive song type that was recorded in all three regions is characterized by singlet and doublet inter-pulse intervals that increase seasonally, then annually reset to the same shorter intervals at the beginning of each season. This song type was recorded in the Bering Sea and off Southern California from September through May and off Hawaii from December through April, with the song interval generally synchronized across all monitoring locations. The broad geographic and seasonal occurrence of this particular fin whale song type may represent a single population broadly distributed throughout the eastern Pacific with no clear seasonal migratory pattern. Previous studies attempting to infer population structure of fin whales in the North Pacific using synchronous individual song samples have been unsuccessful, likely because they did not account for the seasonal lengthening in song intervals observed here.
Adrenocortical Expression Profiling of Cattle with Distinct Juvenile Temperament Types.

PubMed

Friedrich, Juliane; Brand, Bodo; Graunke, Katharina Luise; Langbein, Jan; Schwerin, Manfred; Ponsuksili, Siriluck

2017-01-01

Temperament affects ease of handling, animal welfare, and economically important production traits in cattle. The use of gene expression profiles as molecular traits provides a novel means of gaining insight into behavioural genetics. In this study, differences in adrenocortical expression profiles between 60 F 2 cows (Charolais × German Holstein) of distinct temperament types were analysed. The cows were assessed in a novel-human test at an age of 90 days. Most of the adrenal cortex transcripts which were differentially expressed (FDR <0.05) were found between temperament types of 'fearful/neophobic-alert' and all other temperament types. These transcripts belong to several biological functions like NRF2-mediated oxidative stress response, Glucocorticoid Receptor Signalling and Complement System. Overall, the present study provides new insight into transcriptional differences in the adrenal cortex between cows of distinct temperament types. Genetic regulations of such molecular traits facilitate uncovering positional and functional gene candidates for temperament type in cattle.
Insights from the structure of a smallpox virus topoisomerase-DNA transition state mimic

PubMed Central

Perry, Kay; Hwang, Young; Bushman, Frederic D.; Van Duyne, Gregory D.

2010-01-01

Summary Poxviruses encode their own type IB topoisomerases (TopIBs) which release superhelical tension generated by replication and transcription of their genomes. To investigate the reaction catalyzed viral TopIBs, we have determined the structure of a variola virus topoisomerase-DNA complex trapped as a vanadate transition state mimic. The structure reveals how the viral TopIB enzymes are likely to position the DNA duplex for ligation following relaxation of supercoils and identifies the sources of friction observed in single molecule experiments that argue against free rotation. The structure also identifies a conformational change in the leaving group sugar that must occur prior to cleavage and reveals a mechanism for promoting ligation following relaxation of supercoils that involves a novel Asp-minor groove interaction. Overall, the new structural data support a common catalytic mechanism for the TopIB superfamily but indicate distinct methods for controlling duplex rotation in the small vs. large enzyme subfamilies. PMID:20152159
New types of metacaspases in phytoplankton reveal diverse origins of cell death proteases

PubMed Central

Choi, C J; Berges, J A

2013-01-01

Metacaspases are evolutionarily distant homologs of caspases that are found outside the metazoan and are known to have key roles in programmed cell death (PCD). Two types of metacaspases (types I and II) have been defined in plants based on their domain structures; these have similarities to metazoan ‘initiator' and ‘executioner' caspases. However, we know little about metacaspases in unicellular organisms and even less about their roles in cell death. We identified a novel group of metacaspases in sequenced phytoplanktonic protists that show domain architectures distinct from either type I or II enzymes; we designate them as type III. Type III metacaspases exhibit a rearrangement of domain structures between N- and C-terminus. In addition, we found a group of metacaspase-like proteases in phytoplankton that show sequence homology with other metacaspases, but defy classification in conventional schemes. These metacaspase-like proteases exist in bacteria alongside a variant of type I metacaspases and we propose these bacterial metacaspases are the origins of eukaryotic metacaspases. Type II and III metacaspases were not detected in bacteria and they might be variants of bacterial type I metacaspases that evolved in plants and phytoplanktonic protists, respectively, during the establishment of plastids through the primary and secondary endosymbiotic events. A complete absence of metacaspases in protists that lost plastids, such as oömycetes and ciliates indicates the gene loss during the plastid-to-nucleus gene transfer. Taken together, our findings suggest endosymbiotic gene transfer (EGT) is a key mechanism resulting in the evolutionary diversity of cell death proteases. PMID:23412383

The Crystal Structure of Streptococcus pyogenes Uridine Phosphorylase Reveals a Distinct Subfamily of Nucleoside Phosphorylases

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

Tran, Timothy H.; Christoffersen, S.; Allan, Paula W.

2011-09-20

Uridine phosphorylase (UP), a key enzyme in the pyrimidine salvage pathway, catalyzes the reversible phosphorolysis of uridine or 2'-deoxyuridine to uracil and ribose 1-phosphate or 2'-deoxyribose 1-phosphate. This enzyme belongs to the nucleoside phosphorylase I superfamily whose members show diverse specificity for nucleoside substrates. Phylogenetic analysis shows Streptococcus pyogenes uridine phosphorylase (SpUP) is found in a distinct branch of the pyrimidine subfamily of nucleoside phosphorylases. To further characterize SpUP, we determined the crystal structure in complex with the products, ribose 1-phosphate and uracil, at 1.8 {angstrom} resolution. Like Escherichia coli UP (EcUP), the biological unit of SpUP is a hexamermore » with an ?/? monomeric fold. A novel feature of the active site is the presence of His169, which structurally aligns with Arg168 of the EcUP structure. A second active site residue, Lys162, is not present in previously determined UP structures and interacts with O2 of uracil. Biochemical studies of wild-type SpUP showed that its substrate specificity is similar to that of EcUP, while EcUP is {approx}7-fold more efficient than SpUP. Biochemical studies of SpUP mutants showed that mutations of His169 reduced activity, while mutation of Lys162 abolished all activity, suggesting that the negative charge in the transition state resides mostly on uracil O2. This is in contrast to EcUP for which transition state stabilization occurs mostly at O4.« less
Global population structure and adaptive evolution of aflatoxin-producing fungi.

PubMed

Moore, Geromy G; Olarte, Rodrigo A; Horn, Bruce W; Elliott, Jacalyn L; Singh, Rakhi; O'Neal, Carolyn J; Carbone, Ignazio

2017-11-01

Aflatoxins produced by several species in Aspergillus section Flavi are a significant problem in agriculture and a continuous threat to human health. To provide insights into the biology and global population structure of species in section Flavi , a total of 1,304 isolates were sampled across six species ( A. flavus, A. parasiticus, A. nomius, A. caelatus, A. tamarii, and A. alliaceus ) from single fields in major peanut-growing regions in Georgia (USA), Australia, Argentina, India, and Benin (Africa). We inferred maximum-likelihood phylogenies for six loci, both combined and separately, including two aflatoxin cluster regions ( aflM/alfN and aflW/aflX ) and four noncluster regions ( amdS, trpC, mfs and MAT ), to examine population structure and history. We also employed principal component and STRUCTURE analysis to identify genetic clusters and their associations with six different categories (geography, species, precipitation, temperature, aflatoxin chemotype profile, and mating type). Overall, seven distinct genetic clusters were inferred, some of which were more strongly structured by G chemotype diversity than geography. Populations of A. flavus S in Benin were genetically distinct from all other section Flavi species for the loci examined, which suggests genetic isolation. Evidence of trans-speciation within two noncluster regions, whereby A. flavus S BG strains from Australia share haplotypes with either A. flavus or A. parasiticus , was observed. Finally, while clay soil and precipitation may influence species richness in Aspergillus section Flavi , other region-specific environmental and genetic parameters must also be considered.
Hard X-ray Microscopic Images of the Human Hair

NASA Astrophysics Data System (ADS)

Goo, Jawoong; Jeon, Soo Young; Oh, Tak Heon; Hong, Seung Phil; Yon, Hwa Shik; Lee, Won-Soo

2007-01-01

The better visualization of the human organs or internal structure is challenging to the physicist and physicians. It can lead to more understanding of the morphology, pathophysiology and the diagnosis. Conventionally used methods to investigate cells or architectures, show limited value due to sample processing procedures and lower resolution. In this respect, Zernike type phase contrast hard x-ray microscopy using 6.95keV photon energy has advantages. We investigated hair fibers of the normal healthy persons. Coherence based phase contrast images revealed three distinct structures of hair, medulla, cortex, and cuticular layer. Some different detailed characters of each sample were noted. And further details would be shown and these results would be utilized as basic data of morphologic study of human hair.
Distinct roles of 1α and 1β heavy chains of the inner arm dynein I1 of Chlamydomonas flagella

PubMed Central

Toba, Shiori; Fox, Laura A.; Sakakibara, Hitoshi; Porter, Mary E.; Oiwa, Kazuhiro; Sale, Winfield S.

2011-01-01

The Chlamydomonas I1 dynein is a two-headed inner dynein arm important for the regulation of flagellar bending. Here we took advantage of mutant strains lacking either the 1α or 1β motor domain to distinguish the functional role of each motor domain. Single- particle electronic microscopic analysis confirmed that both the I1α and I1β complexes are single headed with similar ringlike, motor domain structures. Despite similarity in structure, however, the I1β complex has severalfold higher ATPase activity and microtubule gliding motility compared to the I1α complex. Moreover, in vivo measurement of microtubule sliding in axonemes revealed that the loss of the 1β motor results in a more severe impairment in motility and failure in regulation of microtubule sliding by the I1 dynein phosphoregulatory mechanism. The data indicate that each I1 motor domain is distinct in function: The I1β motor domain is an effective motor required for wild-type microtubule sliding, whereas the I1α motor domain may be responsible for local restraint of microtubule sliding. PMID:21148301
Molecular architecture of the ATP-dependent CodWX protease having an N-terminal serine active site

PubMed Central

Kang, Min Suk; Kim, Soon Rae; Kwack, Pyeongsu; Lim, Byung Kook; Ahn, Sung Won; Rho, Young Min; Seong, Ihn Sik; Park, Seong-Chul; Eom, Soo Hyun; Cheong, Gang-Won; Chung, Chin Ha

2003-01-01

CodWX in Bacillus subtilis is an ATP-dependent, N-terminal serine protease, consisting of CodW peptidase and CodX ATPase. Here we show that CodWX is an alkaline protease and has a distinct molecular architecture. ATP hydrolysis is required for the formation of the CodWX complex and thus for its proteolytic function. Remarkably, CodX has a ‘spool-like’ structure that is formed by interaction of the intermediate domains of two hexameric or heptameric rings. In the CodWX complex, CodW consisting of two stacked hexameric rings (WW) binds to either or both ends of a CodX double ring (XX), forming asymmetric (WWXX) or symmetric cylindrical particles (WWXXWW). CodWX can also form an elongated particle, in which an additional CodX double ring is bound to the symmetric particle (WWXXWWXX). In addition, CodWX is capable of degrading EzrA, an inhibitor of FtsZ ring formation, implicating it in the regulation of cell division. Thus, CodWX appears to constitute a new type of protease that is distinct from other ATP-dependent proteases in its structure and proteolytic mechanism. PMID:12805205
The Peculiar Characteristics of Fish Type I Interferons

PubMed Central

Boudinot, Pierre; Langevin, Christelle; Secombes, Christopher J.; Levraud, Jean-Pierre

2016-01-01

Antiviral type I interferons (IFNs) have been discovered in fish. Genomic studies revealed their considerable number in many species; some genes encode secreted and non-secreted isoforms. Based on cysteine motifs, fish type I IFNs fall in two subgroups, which use two different receptors. Mammalian type I IFN genes are intronless while type III have introns; in fish, all have introns, but structurally, both subgroups belong to type I. Type I IFNs likely appeared early in vertebrates as intron containing genes, and evolved in parallel in tetrapods and fishes. The diversity of their repertoires in fish and mammals is likely a convergent feature, selected as a response to the variety of viral strategies. Several alternative nomenclatures have been established for different taxonomic fish groups, calling for a unified system. The specific functions of each type I gene remains poorly understood, as well as their interactions in antiviral responses. However, distinct induction pathways, kinetics of response, and tissue specificity indicate that fish type I likely are highly specialized, especially in groups where they are numerous such as salmonids or cyprinids. Unravelling their functional integration constitutes the next challenge to understand how these cytokines evolved to orchestrate antiviral innate immunity in vertebrates. PMID:27827855
MAGDM linear-programming models with distinct uncertain preference structures.

PubMed

Xu, Zeshui S; Chen, Jian

2008-10-01

Group decision making with preference information on alternatives is an interesting and important research topic which has been receiving more and more attention in recent years. The purpose of this paper is to investigate multiple-attribute group decision-making (MAGDM) problems with distinct uncertain preference structures. We develop some linear-programming models for dealing with the MAGDM problems, where the information about attribute weights is incomplete, and the decision makers have their preferences on alternatives. The provided preference information can be represented in the following three distinct uncertain preference structures: 1) interval utility values; 2) interval fuzzy preference relations; and 3) interval multiplicative preference relations. We first establish some linear-programming models based on decision matrix and each of the distinct uncertain preference structures and, then, develop some linear-programming models to integrate all three structures of subjective uncertain preference information provided by the decision makers and the objective information depicted in the decision matrix. Furthermore, we propose a simple and straightforward approach in ranking and selecting the given alternatives. It is worth pointing out that the developed models can also be used to deal with the situations where the three distinct uncertain preference structures are reduced to the traditional ones, i.e., utility values, fuzzy preference relations, and multiplicative preference relations. Finally, we use a practical example to illustrate in detail the calculation process of the developed approach.
A-type Lamins Form Distinct Filamentous Networks with Differential Nuclear Pore Complex Associations.

PubMed

Xie, Wei; Chojnowski, Alexandre; Boudier, Thomas; Lim, John S Y; Ahmed, Sohail; Ser, Zheng; Stewart, Colin; Burke, Brian

2016-10-10

The nuclear lamina is a universal feature of metazoan nuclear envelopes (NEs) [1]. In mammalian cells, it appears as a 10-30 nm filamentous layer at the nuclear face of the inner nuclear membrane (INM) and is composed primarily of A- and B-type lamins, members of the intermediate filament family [2]. While providing structural integrity to the NE, the lamina also represents an important signaling and regulatory platform [3]. Two A-type lamin isoforms, lamins A and C (LaA and LaC), are expressed in most adult human cells. Encoded by a single gene, these proteins are largely identical, diverging only in their C-terminal tail domains. By contrast with that of LaC, the unique LaA tail undergoes extensive processing, including farnesylation and endo-proteolysis [4, 5]. However, functional differences between LaA and LaC are still unclear. Compounding this uncertainty, the structure of the lamina remains ill defined. In this study, we used BioID, an in vivo proximity-labeling method to identify differential interactors of A-type lamins [6]. One of these, Tpr, a nuclear pore complex (NPC) protein, is highlighted by its selective association with LaC. By employing superresolution microscopy, we demonstrate that this Tpr association is mirrored in enhanced interaction of LaC with NPCs. Further superresolution studies visualizing both endogenous A- and B-type lamins have allowed us to construct a nanometer-scale model of the mammalian nuclear lamina. Our data indicate that different A- and B-type lamin species assemble into separate filament networks that together form an extended composite structure at the nuclear periphery providing attachment sites for NPCs, thereby regulating their distribution. Copyright © 2016 Elsevier Ltd. All rights reserved.
A Bacterial Pathogen uses Distinct Type III Secretion Systems to Alternate between Host Kingdom

USDA-ARS?s Scientific Manuscript database

Gram-negative bacterial pathogens of eukaryotes often secrete proteins directly into host cells via a needle-like protein channel called a ‘type III secretion system’ (T3SS). Bacteria that are adapted to either animal or plant hosts use phylogenetically distinct T3SSs for secreting proteins. Here, ...
Neuronal migration disorders in microcephalic osteodysplastic primordial dwarfism type I/III.

PubMed

Juric-Sekhar, Gordana; Kapur, Raj P; Glass, Ian A; Murray, Mitzi L; Parnell, Shawn E; Hevner, Robert F

2011-04-01

Microcephalic osteodysplastic primordial dwarfism (MOPD) is a rare microlissencephaly syndrome, with at least two distinct phenotypic and genetic types. MOPD type II is caused by pericentrin mutations, while types I and III appear to represent a distinct entity (MOPD I/III) with variably penetrant phenotypes and unknown genetic basis. The neuropathology of MOPD I/III is little understood, especially in comparison to other forms of lissencephaly. Here, we report postmortem brain findings in an 11-month-old female infant with MOPD I/III. The cerebral cortex was diffusely pachygyric, with a right parietal porencephalic lesion. Histologically, the cortex was abnormally thick and disorganized. Distinct malformations were observed in different cerebral lobes, as characterized using layer-specific neuronal markers. Frontal cortex was severely disorganized and coated with extensive leptomeningeal glioneuronal heterotopia. Temporal cortex had a relatively normal 6-layered pattern, despite cortical thickening. Occipital cortex was variably affected. The corpus callosum was extremely hypoplastic. Brainstem and cerebellar malformations were also present, as well as old necrotic foci. Findings in this case suggest that the cortical malformation in MOPD I/III is distinct from other forms of pachygyria-lissencephaly.
Discovery of the leinamycin family of natural products by mining actinobacterial genomes

PubMed Central

Xu, Zhengren; Guo, Zhikai; Hindra; Ma, Ming; Zhou, Hao; Gansemans, Yannick; Zhu, Xiangcheng; Huang, Yong; Zhao, Li-Xing; Jiang, Yi; Cheng, Jinhua; Van Nieuwerburgh, Filip; Suh, Joo-Won; Duan, Yanwen

2017-01-01

Nature’s ability to generate diverse natural products from simple building blocks has inspired combinatorial biosynthesis. The knowledge-based approach to combinatorial biosynthesis has allowed the production of designer analogs by rational metabolic pathway engineering. While successful, structural alterations are limited, with designer analogs often produced in compromised titers. The discovery-based approach to combinatorial biosynthesis complements the knowledge-based approach by exploring the vast combinatorial biosynthesis repertoire found in Nature. Here we showcase the discovery-based approach to combinatorial biosynthesis by targeting the domain of unknown function and cysteine lyase domain (DUF–SH) didomain, specific for sulfur incorporation from the leinamycin (LNM) biosynthetic machinery, to discover the LNM family of natural products. By mining bacterial genomes from public databases and the actinomycetes strain collection at The Scripps Research Institute, we discovered 49 potential producers that could be grouped into 18 distinct clades based on phylogenetic analysis of the DUF–SH didomains. Further analysis of the representative genomes from each of the clades identified 28 lnm-type gene clusters. Structural diversities encoded by the LNM-type biosynthetic machineries were predicted based on bioinformatics and confirmed by in vitro characterization of selected adenylation proteins and isolation and structural elucidation of the guangnanmycins and weishanmycins. These findings demonstrate the power of the discovery-based approach to combinatorial biosynthesis for natural product discovery and structural diversity and highlight Nature’s rich biosynthetic repertoire. Comparative analysis of the LNM-type biosynthetic machineries provides outstanding opportunities to dissect Nature’s biosynthetic strategies and apply these findings to combinatorial biosynthesis for natural product discovery and structural diversity. PMID:29229819
Discovery of the leinamycin family of natural products by mining actinobacterial genomes.

PubMed

Pan, Guohui; Xu, Zhengren; Guo, Zhikai; Hindra; Ma, Ming; Yang, Dong; Zhou, Hao; Gansemans, Yannick; Zhu, Xiangcheng; Huang, Yong; Zhao, Li-Xing; Jiang, Yi; Cheng, Jinhua; Van Nieuwerburgh, Filip; Suh, Joo-Won; Duan, Yanwen; Shen, Ben

2017-12-26

Nature's ability to generate diverse natural products from simple building blocks has inspired combinatorial biosynthesis. The knowledge-based approach to combinatorial biosynthesis has allowed the production of designer analogs by rational metabolic pathway engineering. While successful, structural alterations are limited, with designer analogs often produced in compromised titers. The discovery-based approach to combinatorial biosynthesis complements the knowledge-based approach by exploring the vast combinatorial biosynthesis repertoire found in Nature. Here we showcase the discovery-based approach to combinatorial biosynthesis by targeting the domain of unknown function and cysteine lyase domain (DUF-SH) didomain, specific for sulfur incorporation from the leinamycin (LNM) biosynthetic machinery, to discover the LNM family of natural products. By mining bacterial genomes from public databases and the actinomycetes strain collection at The Scripps Research Institute, we discovered 49 potential producers that could be grouped into 18 distinct clades based on phylogenetic analysis of the DUF-SH didomains. Further analysis of the representative genomes from each of the clades identified 28 lnm -type gene clusters. Structural diversities encoded by the LNM-type biosynthetic machineries were predicted based on bioinformatics and confirmed by in vitro characterization of selected adenylation proteins and isolation and structural elucidation of the guangnanmycins and weishanmycins. These findings demonstrate the power of the discovery-based approach to combinatorial biosynthesis for natural product discovery and structural diversity and highlight Nature's rich biosynthetic repertoire. Comparative analysis of the LNM-type biosynthetic machineries provides outstanding opportunities to dissect Nature's biosynthetic strategies and apply these findings to combinatorial biosynthesis for natural product discovery and structural diversity.
Structural Biology and Evolution of the TGF-β Family

PubMed Central

Hinck, Andrew P.; Mueller, Thomas D.; Springer, Timothy A.

2017-01-01

We review the evolution and structure of members of the transforming growth factor β (TGF-β) family, antagonistic or agonistic modulators, and receptors that regulate TGF-β signaling in extracellular environments. The growth factor (GF) domain common to all family members and many of their antagonists evolved from a common cystine knot growth factor (CKGF) domain. The CKGF superfamily comprises six distinct families in primitive metazoans, including the TGF-β and Dan families. Compared with Wnt/Frizzled and Notch/Delta families that also specify body axes, cell fate, tissues, and other families that contain CKGF domains that evolved in parallel, the TGF-β family was the most fruitful in evolution. Complexes between the prodomains and GFs of the TGF-β family suggest a new paradigm for regulating GF release by conversion from closed- to open-arm procomplex conformations. Ternary complexes of the final step in extracellular signaling show how TGF-β GF dimers bind type I and type II receptors on the cell surface, and enable understanding of much of the specificity and promiscuity in extracellular signaling. However, structures suggest that when GFs bind repulsive guidance molecule (RGM) family coreceptors, type I receptors do not bind until reaching an intracellular, membrane-enveloped compartment, blurring the line between extra- and intracellular signaling. Modulator protein structures show how structurally diverse antagonists including follistatins, noggin, and members of the chordin family bind GFs to regulate signaling; complexes with the Dan family remain elusive. Much work is needed to understand how these molecular components assemble to form signaling hubs in extracellular environments in vivo. PMID:27638177
DOE Office of Scientific and Technical Information (OSTI.GOV)

Du, Mao -Hua; Singh, David J.; Zhang, Lijun

Oxides with good p-type conductivity have been long sought after to achieve high performance all-oxide optoelectronic devices. Divalent Sn(II) based oxides are promising candidates because of their rather dispersive upper valence bands caused by the Sn-5s/O-2p anti-bonding hybridization. There are so far few known Sn(II) oxides being p-type conductive suitable for device applications. Here, we present via first-principles global optimization structure searches a material design study for a hitherto unexplored Sn(II)-based system, ternary alkaline-earth metal Sn(II) oxides in the stoichiometry of MSn 2O 3 (M = Mg, Ca, Sr, Ba). We identify two stable compounds of SrSn 2O 3 andmore » BaSn 2O 3, which can be stabilized by Sn-rich conditions in phase stability diagrams. Their structures follow the Zintl behaviour and consist of basic structural motifs of SnO 3 tetrahedra. Unexpectedly they show distinct electronic properties with band gaps ranging from 1.90 (BaSn 2O 3) to 3.15 (SrSn 2O 3) eV, and hole effective masses ranging from 0.87 (BaSn 2O 3) to above 6.0 (SrSn 2O 3) m0. Further exploration of metastable phases indicates a wide tunability of electronic properties controlled by the details of the bonding between the basic structural motifs. Lastly, this suggests further exploration of alkaline-earth metal Sn(II) oxides for potential applications requiring good p-type conductivity such as transparent conductors and photovoltaic absorbers.« less
Exploring Stability of General Relativistic Accretion Disks

NASA Astrophysics Data System (ADS)

Korobkin, Oleg; Abdikamalov, Ernazar; Schnetter, Erik; Stergioulas, Nikolaos; Zink, Burkhard

2011-04-01

Self-gravitating relativistic disks around black holes can form as transient structures in a number of astrophysical scenarios, involving core collapse of massive stars and mergers of compact ob jects. I will present results on our recent study of the stability of such disks against runaway and non-axisymmetric instabilities, which we explore using three-dimensional hydrodynamics simulations in full general relativity. All of our models develop unstable non-axisymmetric modes on a dynamical timescale. We observe two distinct types of instabilities: the Papaloizou-Pringle and the so-called intermediate type instabilities. The development of the non-axisymmetric mode with azimuthal number m=1 is accompanied by an outspiraling motion of the black hole, which significantly amplifies the growth rate of the m=1 mode in some cases. We will discuss the types, growth rates and pattern speeds of the unstable modes, as well as the detectability of the gravitational waves from such objects.
Lagrangian coherent structures during combustion instability in a premixed-flame backward-step combustor.

PubMed

Sampath, Ramgopal; Mathur, Manikandan; Chakravarthy, Satyanarayanan R

2016-12-01

This paper quantitatively examines the occurrence of large-scale coherent structures in the flow field during combustion instability in comparison with the flow-combustion-acoustic system when it is stable. For this purpose, the features in the recirculation zone of the confined flow past a backward-facing step are studied in terms of Lagrangian coherent structures. The experiments are conducted at a Reynolds number of 18600 and an equivalence ratio of 0.9 of the premixed fuel-air mixture for two combustor lengths, the long duct corresponding to instability and the short one to the stable case. Simultaneous measurements of the velocity field using time-resolved particle image velocimetry and the CH^{*} chemiluminescence of the flame along with pressure time traces are obtained. The extracted ridges of the finite-time Lyapunov exponent (FTLE) fields delineate dynamically distinct regions of the flow field. The presence of large-scale vortical structures and their modulation over different time instants are well captured by the FTLE ridges for the long combustor where high-amplitude acoustic oscillations are self-excited. In contrast, small-scale vortices signifying Kelvin-Helmholtz instability are observed in the short duct case. Saddle-type flow features are found to separate the distinct flow structures for both combustor lengths. The FTLE ridges are found to align with the flame boundaries in the upstream regions, whereas farther downstream, the alignment is weaker due to dilatation of the flow by the flame's heat release. Specifically, the FTLE ridges encompass the flame curl-up for both the combustor lengths, and thus act as the surrogate flame boundaries. The flame is found to propagate upstream from an earlier vortex roll-up to a newer one along the backward-time FTLE ridge connecting the two structures.
Unique hyper-thermal composting process in Kagoshima City forms distinct bacterial community structures.

PubMed

Tashiro, Yukihiro; Tabata, Hanae; Itahara, Asuka; Shimizu, Natsuki; Tashiro, Kosuke; Sakai, Kenji

2016-11-01

A unique compost, Satsuma soil, is produced from three types of wastewater sludge using hyper-thermal processes at temperatures much higher than that of general thermophilic processes in Kagoshima City, Japan. We analyzed the bacterial community structures of this hyper-thermal compost sample and other sludges and composts by a high-throughput barcoded pyrosequencing method targeting the 16S rRNA gene. In total, 621,076 reads were derived from 17 samples and filtered. Artificial sequences were deleted and the reads were clustered based on the operational taxonomic units (OTUs) at 97% similarity. Phylum-level analysis of the hyper-thermal compost revealed drastic changes of the sludge structures (each relative abundance) from Firmicutes (average 47.8%), Proteobacteria (average 22.3%), and Bacteroidetes (average 10.1%) to two main phyla including Firmicutes (73.6%) and Actinobacteria (25.0%) with less Proteobacteria (∼0.3%) and Bacteroidetes (∼0.1%). Furthermore, we determined the predominant species (each relative abundance) of the hyper-thermal compost including Firmicutes related to Staphylococcus cohnii (13.8%), Jeotgalicoccus coquinae (8.01%), and Staphylococcus lentus (5.96%), and Actinobacteria related to Corynebacterium stationis (6.41%), and found that these species were not predominant in wastewater sludge. In contrast, we did not observe any common structures among eight other composts produced, using the hyper-thermal composts as the inoculums, under thermophilic conditions from different materials. Principle coordinate analysis of the hyper-thermal compost indicated a large difference in bacterial community structures from material sludge and other composts. These results suggested that a distinct bacterial community structure was formed by hyper-thermal composting. Copyright © 2016 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.
Structure-function relationships in tendons: a review

PubMed Central

Benjamin, M; Kaiser, E; Milz, S

2008-01-01

The purpose of the current review is to highlight the structure-function relationship of tendons and related structures to provide an overview for readers whose interest in tendons needs to be underpinned by anatomy. Because of the availability of several recent reviews on tendon development and entheses, the focus of the current work is primarily directed towards what can best be described as the ‘tendon proper’ or the ‘mid-substance’ of tendons. The review covers all levels of tendon structure from the molecular to the gross and deals both with the extracellular matrix and with tendon cells. The latter are often called ‘tenocytes’ and are increasingly recognized as a defined cell population that is functionally and phenotypically distinct from other fibroblast-like cells. This is illustrated by their response to different types of mechanical stress. However, it is not only tendon cells, but tendons as a whole that exhibit distinct structure-function relationships geared to the changing mechanical stresses to which they are subject. This aspect of tendon biology is considered in some detail. Attention is briefly directed to the blood and nerve supply of tendons, for this is an important issue that relates to the intrinsic healing capacity of tendons. Structures closely related to tendons (joint capsules, tendon sheaths, pulleys, retinacula, fat pads and bursae) are also covered and the concept of a ‘supertendon’ is introduced to describe a collection of tendons in which the function of the whole complex exceeds that of its individual members. Finally, attention is drawn to the important relationship between tendons and fascia, highlighted by Wood Jones in his concept of an ‘ectoskeleton’ over half a century ago – work that is often forgotten today. PMID:18304204
Small bowel carcinomas in celiac or Crohn's disease: distinctive histophenotypic, molecular and histogenetic patterns.

PubMed

Vanoli, Alessandro; Di Sabatino, Antonio; Martino, Michele; Klersy, Catherine; Grillo, Federica; Mescoli, Claudia; Nesi, Gabriella; Volta, Umberto; Fornino, Daniele; Luinetti, Ombretta; Fociani, Paolo; Villanacci, Vincenzo; D'Armiento, Francesco P; Cannizzaro, Renato; Latella, Giovanni; Ciacci, Carolina; Biancone, Livia; Paulli, Marco; Sessa, Fausto; Rugge, Massimo; Fiocca, Roberto; Corazza, Gino R; Solcia, Enrico

2017-10-01

Non-familial small bowel carcinomas are relatively rare and have a poor prognosis. Two small bowel carcinoma subsets may arise in distinct immune-inflammatory diseases (celiac disease and Crohn's disease) and have been recently suggested to differ in prognosis, celiac disease-associated carcinoma cases showing a better outcome, possibly due to their higher DNA microsatellite instability and tumor-infiltrating T lymphocytes. In this study, we investigated the histological structure (glandular vs diffuse/poorly cohesive, mixed or solid), cell phenotype (intestinal vs gastric/pancreatobiliary duct type) and Wnt signaling activation (β-catenin and/or SOX-9 nuclear expression) in a series of 26 celiac disease-associated small bowel carcinoma, 25 Crohn's disease-associated small bowel carcinoma and 25 sporadic small bowel carcinoma cases, searching for new prognostic parameters. In addition, non-tumor mucosa of celiac and Crohn's disease patients was investigated for epithelial precursor changes (hyperplastic, metaplastic or dysplastic) to help clarify carcinoma histogenesis. When compared with non-glandular structure and non-intestinal phenotype, both glandular structure and intestinal phenotype were associated with a more favorable outcome at univariable or stage- and microsatellite instability/tumor-infiltrating lymphocyte-inclusive multivariable analysis. The prognostic power of histological structure was independent of the clinical groups while the non-intestinal phenotype, associated with poor outcome, was dominant among Crohn's disease-associated carcinoma. Both nuclear β-catenin and SOX-9 were preferably expressed among celiac disease-associated carcinomas; however, they were devoid, per se, of prognostic value. We obtained findings supporting an origin of celiac disease-associated carcinoma in SOX-9-positive immature hyperplastic crypts, partly through flat β-catenin-positive dysplasia, and of Crohn's disease-associated carcinoma in a metaplastic (gastric and/or pancreatobiliary-type) mucosa, often through dysplastic polypoid growths of metaplastic phenotype. In conclusion, despite their common origin in a chronically inflamed mucosa, celiac disease-associated and Crohn's disease-associated small bowel carcinomas differ substantially in histological structure, phenotype, microsatellite instability/tumor-infiltrating lymphocyte status, Wnt pathway activation, mucosal precursor lesions and prognosis.
The structure of graphene oxide membranes in liquid water, ethanol and water-ethanol mixtures

NASA Astrophysics Data System (ADS)

Talyzin, Alexandr V.; Hausmaninger, Tomas; You, Shujie; Szabó, Tamás

2013-12-01

The structure of graphene oxide (GO) membranes was studied in situ in liquid solvents using synchrotron radiation X-ray diffraction in a broad temperature interval. GO membranes are hydrated by water similarly to precursor graphite oxide powders but intercalation of alcohols is strongly hindered, which explains why the GO membranes are permeated by water and not by ethanol. Insertion of ethanol into the membrane structure is limited to only one monolayer in the whole studied temperature range, in contrast to precursor graphite oxide powders, which are intercalated with up to two ethanol monolayers (Brodie) and four ethanol monolayers (Hummers). As a result, GO membranes demonstrate the absence of ``negative thermal expansion'' and phase transitions connected to insertion/de-insertion of alcohols upon temperature variations reported earlier for graphite oxide powders. Therefore, GO membranes are a distinct type of material with unique solvation properties compared to parent graphite oxides even if they are composed of the same graphene oxide flakes.The structure of graphene oxide (GO) membranes was studied in situ in liquid solvents using synchrotron radiation X-ray diffraction in a broad temperature interval. GO membranes are hydrated by water similarly to precursor graphite oxide powders but intercalation of alcohols is strongly hindered, which explains why the GO membranes are permeated by water and not by ethanol. Insertion of ethanol into the membrane structure is limited to only one monolayer in the whole studied temperature range, in contrast to precursor graphite oxide powders, which are intercalated with up to two ethanol monolayers (Brodie) and four ethanol monolayers (Hummers). As a result, GO membranes demonstrate the absence of ``negative thermal expansion'' and phase transitions connected to insertion/de-insertion of alcohols upon temperature variations reported earlier for graphite oxide powders. Therefore, GO membranes are a distinct type of material with unique solvation properties compared to parent graphite oxides even if they are composed of the same graphene oxide flakes. Electronic supplementary information (ESI) available. See DOI: 10.1039/c3nr04631a

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