PLANETESIMAL FORMATION BY GRAVITATIONAL INSTABILITY OF A POROUS DUST DISK

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

Michikoshi, Shugo; Kokubo, Eiichiro, E-mail: michikos@ccs.tsukuba.ac.jp, E-mail: kokubo@th.nao.ac.jp

2016-07-10

It has recently been proposed that porous icy dust aggregates are formed by the pairwise accretion of dust aggregates beyond the snowline. We calculate the equilibrium random velocity of porous dust aggregates, taking into account mutual gravitational scattering, collisions, gas drag, and turbulent stirring and scattering. We find that the disk of porous dust aggregates becomes gravitationally unstable as the aggregates evolve through gravitational compression in the minimum-mass solar nebula model for a reasonable range of turbulence strength, which leads to rapid formation of planetesimals.

[A case of anti-LKM 1 positive autoimmune hepatitis accompanied by systemic lupus erythematosus].

PubMed

Choi, Dae Han; Kim, Hae Kyung; Park, Tae Il; John, Byung Min; Kang, Sung Hwan; Lee, Yoon Serk; Kim, Tae Hyun; Lee, Uh Joo; Lee, Tae Seung; Yoon, Gwi Ok

2008-03-01

Overlap of autoimmune hepatitis and systemic lupus erythematosus (SLE) is a comparatively rare condition. Although both autoimmune hepatitis and SLE can share common autoimmune features such as polyarthralgia, hypergammaglobulinemia and positive ANA, it has been considered as two different entities. We report a case of anti-LKM1 positive autoimmune hepatitis who developed SLE two years later. The presence of interface hepatitis with lymphoplasma cell infiltrates and rosette formation points to the autoimmune hepatitis rather than SLE hepatitis. Autoimmune hepatitis is infrequently accompanied by SLE, therefore, it could be recommended to investigate for SLE in patients with autoimmune hepatitis.

[Activating effect of cyclophosphane at late stages of persistence of the tick-borne encephalitis virus].

PubMed

Frolova, T V; Pogodina, V V; Larina, G I; Frolova, M P; Karmysheva, V Ia

1982-01-01

Conditions of activation of persistent infection caused by subcutaneous inoculation of Syrian hamsters with the B-383 and Vasilchenko strains of tick-borne encephalitis virus (TBE) were studied. After 2 administrations of cyclophosphane (CP) on day 170 of infection clinically manifest disease developed in some animals with increasingly severe pathomorphological lesions in the CNS. Several variants of activated TBE virus were isolated from brains and spleens of CP-treated hamsters. The activation of persistent infection was observed in the presence of marked decreased of humoral immunity level, weight of the thymus, and values of spontaneous rosette-formation.

Thermal aggregation of human immunoglobulin G in arginine solutions: Contrasting effects of stabilizers and destabilizers.

PubMed

Yoshizawa, Shunsuke; Arakawa, Tsutomu; Shiraki, Kentaro

2017-11-01

Arginine is widely used as aggregation suppressor of proteins in biotechnology and pharmaceutics. However, why the effect of arginine depends on the types of proteins and stresses, including monoclonal antibodies, is still unclear. Here we investigated the precise processes of the thermal aggregation of human immunoglobulin G (IgG) in the presence of additives. As expected, arginine was the best additive to suppress the formation of insoluble aggregates during heat treatment, though it was unable to preserve the monomer content. A systematic analysis of the additives showed that sugars and kosmotropic ion inhibit the formation of soluble oligomers. These behaviors indicate that the thermal aggregation of IgG occurs by (i) the formation of soluble oligomers, which is triggered by the unfolding process that can be stabilized by typical osmolytes, and (ii) the formation of insoluble aggregates through weak cluster-cluster interactions, which can be suppressed by arginine. Understanding the detailed mechanism of arginine will provide useful information for the rational formulation design of antibodies. Copyright © 2017 Elsevier B.V. All rights reserved.

Amyloidogenic Regions and Interaction Surfaces Overlap in Globular Proteins Related to Conformational Diseases

PubMed Central

Castillo, Virginia; Ventura, Salvador

2009-01-01

Protein aggregation underlies a wide range of human disorders. The polypeptides involved in these pathologies might be intrinsically unstructured or display a defined 3D-structure. Little is known about how globular proteins aggregate into toxic assemblies under physiological conditions, where they display an initially folded conformation. Protein aggregation is, however, always initiated by the establishment of anomalous protein-protein interactions. Therefore, in the present work, we have explored the extent to which protein interaction surfaces and aggregation-prone regions overlap in globular proteins associated with conformational diseases. Computational analysis of the native complexes formed by these proteins shows that aggregation-prone regions do frequently overlap with protein interfaces. The spatial coincidence of interaction sites and aggregating regions suggests that the formation of functional complexes and the aggregation of their individual subunits might compete in the cell. Accordingly, single mutations affecting complex interface or stability usually result in the formation of toxic aggregates. It is suggested that the stabilization of existing interfaces in multimeric proteins or the formation of new complexes in monomeric polypeptides might become effective strategies to prevent disease-linked aggregation of globular proteins. PMID:19696882

Self-organization of neural tissue architectures from pluripotent stem cells.

PubMed

Karus, Michael; Blaess, Sandra; Brüstle, Oliver

2014-08-15

Despite being a subject of intensive research, the mechanisms underlying the formation of neural tissue architectures during development of the central nervous system remain largely enigmatic. So far, studies into neural pattern formation have been restricted mainly to animal experiments. With the advent of pluripotent stem cells it has become possible to explore early steps of nervous system development in vitro. These studies have unraveled a remarkable propensity of primitive neural cells to self-organize into primitive patterns such as neural tube-like rosettes in vitro. Data from more advanced 3D culture systems indicate that this intrinsic propensity for self-organization can even extend to the formation of complex architectures such as a multilayered cortical neuroepithelium or an entire optic cup. These novel experimental paradigms not only demonstrate the enormous self-organization capacity of neural stem cells, they also provide exciting prospects for studying the earliest steps of human neural tissue development and the pathogenesis of brain malformations in reductionist in vitro paradigms. © 2014 Wiley Periodicals, Inc.

The role of multiple partners in a digestive mutualism with a protocarnivorous plant

PubMed Central

Nishi, Aline Hiroko; Vasconcellos-Neto, João; Romero, Gustavo Quevedo

2013-01-01

Background and aims The protocarnivorous plant Paepalanthus bromelioides (Eriocaulaceae) is similar to bromeliads in that this plant has a rosette-like structure that allows rainwater to accumulate in leaf axils (i.e. phytotelmata). Although the rosettes of P. bromelioides are commonly inhabited by predators (e.g. spiders), their roots are wrapped by a cylindrical termite mound that grows beneath the rosette. In this study it is predicted that these plants can derive nutrients from recycling processes carried out by termites and from predation events that take place inside the rosette. It is also predicted that bacteria living in phytotelmata can accelerate nutrient cycling derived from predators. Methods The predictions were tested by surveying plants and animals, and also by performing field experiments in rocky fields from Serra do Cipó, Brazil, using natural abundance and enriched isotopes of 15N. Laboratory bioassays were also conducted to test proteolytic activities of bacteria from P. bromelioides rosettes. Key Results Analyses of 15N in natural nitrogen abundances showed that the isotopic signature of P. bromelioides is similar to that of carnivorous plants and higher than that of non-carnivorous plants in the study area. Linear mixing models showed that predatory activities on the rosettes (i.e. spider faeces and prey carcass) resulted in overall nitrogen contributions of 26·5 % (a top-down flux). Although nitrogen flux was not detected from termites to plants via decomposition of labelled cardboard, the data on 15N in natural nitrogen abundance indicated that 67 % of nitrogen from P. bromelioides is derived from termites (a bottom-up flux). Bacteria did not affect nutrient cycling or nitrogen uptake from prey carcasses and spider faeces. Conclusions The results suggest that P. bromelioides derive nitrogen from associated predators and termites, despite differences in nitrogen cycling velocities, which seem to have been higher in nitrogen derived from predators (leaves) than from termites (roots). This is the first study that demonstrates partitioning effects from multiple partners in a digestion-based mutualism. Despite most of the nitrogen being absorbed through their roots (via termites), P. bromelioides has all the attributes necessary to be considered as a carnivorous plant in the context of digestive mutualism. PMID:23131297

Investigation of microorganisms involved in biosynthesis of the kefir grain.

PubMed

Wang, Sheng-Yao; Chen, Kun-Nan; Lo, Yung-Ming; Chiang, Ming-Lun; Chen, Hsi-Chia; Liu, Je-Ruei; Chen, Ming-Ju

2012-12-01

The purpose of this study was to understand the significance of each microorganism in grain formation by evaluating their microbial aggregation and cell surface properties during co-aggregation of LAB and yeasts together with an investigation of biofilm formation. Non-grain forming strains from viili were also evaluated as a comparison. Results indicated that the kefir grain strains, Lactobacillus kefiranofaciens and Saccharomyces turicensis possess strong auto-aggregation ability and that Lactobacillus kefiri shows significant biofilm formation properties. Significant co-aggregation was noted when S. turicensis and kefir LAB strains (Lb. kefiranofaciens and Lb. kefiri) were co-cultured. Most of the tested LAB strains are hydrophilic and had a negative charge on their cell surface. Only the kefir LAB strains, Lb. kefiranofaciens HL1 and Lb. kefiri HL2, possessed very high hydrophobicity and had a positive cell surface charge at pH 4.2. In contrast, the LAB and yeasts in viili did not show any significant self-aggregation or biofilm formation. Based on the above results, we propose that grain formation begins with the self-aggregation of Lb. kefiranofaciens and S. turicensis to form small granules. At this point, the biofilm producer, Lb. kefiri, then begins to attach to the surface of granules and co-aggregates with other organisms and components in the milk to form the grains. On sub-culturing, more organisms attach to the grains resulting in grain growth. When investigated by scanning electron microscopy, it was found that short-chain lactobacilli such as Lb. kefiri occupy the surface, while long-chain lactobacilli such as Lb. kefiranofaciens have aggregated towards the center of the kefir grains. These findings agree with the above hypothesis on the formation of grains. Taken together, this study demonstrates the importance of cell surface properties together with fermentation conditions to the formation of grains in kefir. Copyright © 2012 Elsevier Ltd. All rights reserved.

Soil aggregation and aggregating agents as affected by long term contrasting management of an Anthrosol

NASA Astrophysics Data System (ADS)

Zhang, Shulan; Wang, Renjie; Yang, Xueyun; Sun, Benhua; Li, Qinghui

2016-12-01

Soil aggregation was studied in a 21-year experiment conducted on an Anthrosol. The soil management regimes consisted of cropland abandonment, bare fallow without vegetation and cropping system. The cropping system was combined with the following nutrient management treatments: control (CONTROL, no nutrient input); nitrogen, phosphorus and potassium (NPK); straw plus NPK (SNPK); and manure (M) plus NPK (MNPK). Compared with the CONTROL treatment, the abandonment treatment significantly increased the formation of large soil macroaggregates (>2 mm) and consequently improved the stability of aggregates in the surface soil layer due to enhancement of hyphal length and of soil organic matter content. However, in response to long-term bare fallow treatment aggregate stability was low, as were the levels of aggregating agents. Long term fertilization significantly redistributed macroaggregates; this could be mainly ascribed to soil organic matter contributing to the formation of 0.5-2 mm classes of aggregates and a decrease in the formation of the >2 mm class of aggregates, especially in the MNPK treatment. Overall, hyphae represented a major aggregating agent in both of the systems tested, while soil organic compounds played significantly different roles in stabilizing aggregates in Anthrosol when the cropping system and the soil management regimes were compared.

The chaperonin CCT promotes the formation of fibrillar aggregates of γ-tubulin.

PubMed

Pouchucq, Luis; Lobos-Ruiz, Pablo; Araya, Gissela; Valpuesta, José María; Monasterio, Octavio

2018-04-01

The type II chaperonin CCT is involved in the prevention of the pathogenesis of numerous human misfolding disorders, as it sequesters misfolded proteins, blocks their aggregation and helps them to achieve their native state. In addition, it has been reported that CCT can prevent the toxicity of non-client amyloidogenic proteins by the induction of non-toxic aggregates, leading to new insight in chaperonin function as an aggregate remodeling factor. Here we add experimental evidence to this alternative mechanism by which CCT actively promotes the formation of conformationally different aggregates of γ-tubulin, a non-amyloidogenic CCT client protein, which are mediated by specific CCT-γ-tubulin interactions. The in vitro-induced aggregates were in some cases long fiber polymers, which compete with the amorphous aggregates. Direct injection of unfolded purified γ-tubulin into single-cell zebra fish embryos allowed us to relate this in vitro activity with the in vivo formation of intracellular aggregates. Injection of a CCT-binding deficient γ-tubulin mutant dramatically diminished the size of the intracellular aggregates, increasing the toxicity of the misfolded protein. These results point to CCT having a role in the remodeling of aggregates, constituting one of its many functions in cellular proteostasis. Copyright © 2018. Published by Elsevier B.V.

Fiber Optic Rosette Strain Gauge Development and Application on a Large-Scale Composite Structure

NASA Technical Reports Server (NTRS)

Moore, Jason P.; Przekop, Adam; Juarez, Peter D.; Roth, Mark C.

2015-01-01

A detailed description of the construction, application, and measurement of 196 FO rosette strain gauges that measured multi-axis strain across the outside upper surface of the forward bulkhead component of a multibay composite fuselage test article is presented. A background of the FO strain gauge and the FO measurement system as utilized in this application is given and results for the higher load cases of the testing sequence are shown.

Soil aggregation and aggregating agents as affected by long term contrasting management of an Anthrosol

PubMed Central

Zhang, Shulan; Wang, Renjie; Yang, Xueyun; Sun, Benhua; Li, Qinghui

2016-01-01

Soil aggregation was studied in a 21-year experiment conducted on an Anthrosol. The soil management regimes consisted of cropland abandonment, bare fallow without vegetation and cropping system. The cropping system was combined with the following nutrient management treatments: control (CONTROL, no nutrient input); nitrogen, phosphorus and potassium (NPK); straw plus NPK (SNPK); and manure (M) plus NPK (MNPK). Compared with the CONTROL treatment, the abandonment treatment significantly increased the formation of large soil macroaggregates (>2 mm) and consequently improved the stability of aggregates in the surface soil layer due to enhancement of hyphal length and of soil organic matter content. However, in response to long-term bare fallow treatment aggregate stability was low, as were the levels of aggregating agents. Long term fertilization significantly redistributed macroaggregates; this could be mainly ascribed to soil organic matter contributing to the formation of 0.5–2 mm classes of aggregates and a decrease in the formation of the >2 mm class of aggregates, especially in the MNPK treatment. Overall, hyphae represented a major aggregating agent in both of the systems tested, while soil organic compounds played significantly different roles in stabilizing aggregates in Anthrosol when the cropping system and the soil management regimes were compared. PMID:27958366

[A new entity in WHO classification of tumors of the central nervous system--embryonic tumor with abundant neuropil and true rosettes: case report and review of literature].

PubMed

Ryzhova, M V; Zheludkova, O G; Ozerov, S S; Shishkina, L V; Panina, T N; Gorelyshev, S K; Novikov, A I; Melikian, A G; Kushel', Iu V; Korshunov, A E

2011-01-01

Embryonic tumor with abundant neuropil and true rosettes (ETANTR) is a very aggressive rare tumor with unique histologic and molecular features occurring in very young children. At present approximately 80 cases of ETANTR have been documented in the literature since first description in 2000. We report seven patients with ETANTR below 4 years of age who underwent surgical resection in the Burdenko Neurosurgery Institute between 2005 and 2010. Four children have received different modality chemotherapy and radiotherapy and two patients were treated by chemotherapy alone. One child did not receive any adjuvant treatment. All children had local relapses, two of them were operated twice. A 2 year old girl underwent subtotal resection thrice. Histological examination showed that all tumors were composed of true multilayered rosettes admixed with large areas of paucicellular neuropil. By analysis of recurrences we have found that large areas of neuropil and number of true rosettes were lost and tumors acquired a resemblance to central nervous system primitive neuroectodermal tumors. In four cases frozen tumor material was available for array-based comparative genomic hybridization, which discovered trisomy of chromosome 2 and amplification at the 19q13.42 chromosome locus. Fluorescence in situ hybridization revealed amplification at the 19q13.42 chromosome locus in all cases.

Chemical modification of lysine residues in lysozyme may dramatically influence its amyloid fibrillation.

PubMed

Morshedi, Dina; Ebrahim-Habibi, Azadeh; Moosavi-Movahedi, Ali Akbar; Nemat-Gorgani, Mohsen

2010-04-01

Studies on the aggregation of mutant proteins have provided new insights into the genetics of amyloid diseases and the role of the net charge of the protein on the rate, extent, and type of aggregate formation. In the present work, hen egg white lysozyme (HEWL) was employed as the model protein. Acetylation and (separately) citraconylation were employed to neutralize the charge on lysine residues. Acetylation of the lysine residues promoted amyloid formation, resulting in more pronounced fibrils and a dramatic decline in the nucleation time. In contrast, citraconylation produced the opposite effect. In both cases, native secondary and tertiary structures appeared to be retained. Studies on the effect of pH on aggregation suggested greater possibilities for amorphous aggregate formation rather than fibrillation at pH values closer to neutrality, in which the protein is known to take up a conformation more similar to its native form. This is in accord with reports in the literature suggesting that formation of amorphous aggregates is more favored under relatively more native conditions. pH 5 provided a critical environment in which a mixture of amorphous and fibrillar structures were observed. Use of Tango and Aggrescan software which describe aggregation tendencies of different parts of a protein structure suggested critical importance of some of the lysine residues in the aggregation process. Results are discussed in terms of the importance of the net charge in control of protein-protein interactions leading to aggregate formation and possible specific roles of lysine residues 96 and 97. Copyright 2009 Elsevier B.V. All rights reserved.

Photoacoustic assay for probing amyloid formation: feasibility study

NASA Astrophysics Data System (ADS)

Petrova, Elena; Yoon, Soon Joon; Pelivanov, Ivan; O'Donnell, Matthew

2018-02-01

The formation of amyloid - aggregate of misfolded proteins - is associated with more than 50 human pathologies, including Alzheimer's disease, Parkinson's disease, and Type 2 diabetes mellitus. Investigating protein aggregation is a critical step in drug discovery and development of therapeutics targeted to these pathologies. However, screens to identify protein aggregates are challenging due to the stochastic character of aggregate nucleation. Here we employ photoacoustics (PA) to screen thermodynamic conditions and solution components leading to formation of protein aggregates. Particularly, we study the temperature dependence of the Gruneisen parameter in optically-contrasted, undersaturated and supersaturated solutions of glycoside hydrolase (lysozyme). As nucleation of protein aggregates proceeds in two steps, where the first is liquid-liquid separation (rearrangement of solute's density), the PA response from complex solutions and its temperature-dependence monitor nucleation and differentiate undersaturated and supersaturated protein solutions. We demonstrate that in the temperature range from 22 to 0° C the PA response of contrasted undersaturated protein solution behaves similar to water and exhibits zero thermal expansion at 4°C or below, while the response of contrasted supersaturated protein solution is nearly temperature independent, similar to the behavior of oils. These results can be used to develop a PA assay for high-throughput screening of multi-parametric conditions (pH, ionic strength, chaperone, etc.) for protein aggregation that can become a key tool in drug discovery, targeting aggregate formation for a variety of amyloids.

Cholinesterases and cell proliferation in "nonstratified" and "stratified" cell aggregates from chicken retina and tectum.

PubMed

Vollmer, G; Layer, P G

1987-12-01

Dissociated single cells from chicken retina or tectum kept in rotation-mediated cell culture aggregate, proliferate and establish a certain degree of histotypical cell-to-cell relationships ("sorting out"), but these systems never form highly laminated aggregates ("nonstratified" R- and T-aggregates). In contrast, a mixture of retinal plus pigment epithelial cells forms highly "stratified" aggregates ("RPE-aggregates", see Vollmer et al. 1984). The present comparative study of "stratified" and "nonstratified" aggregates enables us to investigate the process of cell proliferation uncoupled from that of tissue stratification. Here we try to relate these two basic neurogenetic processes with patterns of expression of cholinesterases (AChE, BChE) during formation of both types of aggregates. During early aggregate formation, in both "stratified" and "nonstratified" aggregates an increased butyrylcholinesterase activity is observed close to mitotically active cells. Quantitatively both phenomena show their maxima after 2-3 days in culture. In contrast, AChE-expression in all systems increases with incubation time. In nonproliferative areas, in the center of RPE-aggregates, the formation of plexiform layers is characterized initially by weak BChE- and then strong AChE-activity. These areas correspond with the inner (IPL) and outer (OPL) plexiform layers of the retina in vivo. Although by sucrose gradient centrifugation we find that the 6S- and the fiber-associated 11S-molecules of AChE are present in all types of aggregates, during the culture period the ratio of 11S/6S-forms increases only in RPE-aggregates, which again indicates the advanced degree of differentiation within these aggregates.(ABSTRACT TRUNCATED AT 250 WORDS)

Time-resolved forward-light-scattering monitoring of protein–lysozyme aggregation in precrystalline solutions

NASA Astrophysics Data System (ADS)

Wakamatsu, Takashi; Onoda, Takashi; Ogata, Makoto

2018-05-01

An in situ measurement method of monitoring protein aggregation in precrystalline solutions is presented. The method is based on a small-angle forward static light scattering (F-SLS) technique. This technique uses an accurate optical arrangement of a combination of a collimating lens and a CCD to obtain an F-SLS pattern from an aggregate-containing protein solution in one shot. The real-time observation of a crystallizing lysozyme captured the formation of fractal aggregates in the initial formation stage.

Influence of the individual or combined application of biochar and slurry on soil macro-aggregate formation under varying moisture conditions

NASA Astrophysics Data System (ADS)

Kaiser, Michael; Grunwald, Dennis; Koch, Heinz-Josef; Rauber, Rolf; Ludwig, Bernard

2017-04-01

The formation of aggregates is of large importance for the structure and the storage of organic matter (OM) in soil. Although positive effects of organic soil additives on the formation of macro-aggregates (> 250 µm) have been reported, the influence of biochar especially applied in combination with other organic amendments remains unclear. Furthermore, studies on the effect of varying soil moisture conditions in form of drying-rewetting cycles on soil aggregate dynamics in the presence of biochar are almost missing. The objectives of this study were to analyze the effects of biochar and slurry applied to the soil individually or in combination on the formation of macro-aggregates under constant and under varying moisture conditions. We sampled four silty loam soils, carefully crushed the soil macro-aggregates, and incubated the soil at 15 °C for 60 days with the following additions: (i) none (control), (ii) biochar (12 % of dry soil mass), (iii) slurry (150 kg N ha-1), (iv) biochar (6 %) + slurry (75 kg N ha-1), (v) biochar (12 %) + slurry (75 kg N ha-1), (vi) biochar (6 %) + slurry (150 kg N ha-1) and (vii) biochar (12 %) + slurry (150 kg N ha-1). The samples were further subdivided into two groups that were incubated under conditions of constant soil moisture and of three drying-rewetting cycles. The CO2 fluxes were continuously measured during the incubation period and the samples were analyzed for microbial biomass C, macro-aggregate yields and macro-aggregate-associated C after finishing the experiment. We found the application of biochar to result in lower macro-aggregate yields with or without slurry compared to the control or the individual slurry application. In contrast, similar or higher C contents in the macro-aggregate fraction of the biochar treatments as compared to the control or slurry treatments were found indicating an occlusion of biochar in macro-aggregates. Due to the sorption characteristics of biochar, we assume the aggregate formation to be partially abiotic with direct interactions between biochar, (adsorbed) slurry, and the mineral phase of the soil. Therefore, in the presence of slurry, a prolonged period of microbial processing does not seem to be necessary to render the biochar suitable to form aggregates. Drying and rewetting of the samples resulted in significantly lower aggregate yields especially for the biochar/slurry mixtures. The drying of slurry as thought to be the most important macro-aggregate binding agent in these treatments might irreversibly disrupt large amounts of the macro-aggregates formed. Additionally, the general lower microbial biomass C and CO2 emissions for the samples experiencing drying-rewetting cycles compared to the constantly moist soils point toward less microbial activity under varying moisture conditions. This might have led to less microbial derived aggregate binding agents contributing to the lower aggregate yields found for the samples from the drying-rewetting treatments. Beside the amount and type of binding agents derived from organic soil additives, the formation and stability of soil macro-aggregate seem also to be controlled by climatically controlled soil moisture conditions.

Void Points, Rosettes, and a Brief History of Planetary Astronomy

NASA Astrophysics Data System (ADS)

Kosso, Peter

2013-12-01

Almost all models of planetary orbits, from Aristotle through Newton, include void points, empty points in space that have an essential role in defining the orbit. By highlighting the role of these void points, as well as the rosette pattern of the orbit that often results, I bring out different features in the history of planetary astronomy and place a different emphasis on its revolutionary changes, different from those rendered in terms of epicycles or the location of the earth.

Computational study of aggregation mechanism in human lysozyme[D67H

PubMed Central

Patel, Dharmeshkumar

2017-01-01

Aggregation of proteins is an undesired phenomena that affects both human health and bioengineered products such as therapeutic proteins. Finding preventative measures could be facilitated by a molecular-level understanding of dimer formation, which is the first step in aggregation. Here we present a molecular dynamics (MD) study of dimer formation propensity in human lysozyme and its D67H variant. Because the latter protein aggregates while the former does not, they offer an ideal system for testing the feasibility of the proposed MD approach which comprises three stages: i) partially unfolded conformers involved in dimer formation are generated via high-temperature MD simulations, ii) potential dimer structures are searched using docking and refined with MD, iii) free energy calculations are performed to find the most stable dimer structure. Our results provide a detailed explanation for how a single mutation (D67H) turns human lysozyme from non-aggregating to an aggregating protein. Conversely, the proposed method can be used to identify the residues causing aggregation in a protein, which can be mutated to prevent it. PMID:28467454

Myosin II dynamics are regulated by tension in intercalating cells.

PubMed

Fernandez-Gonzalez, Rodrigo; Simoes, Sérgio de Matos; Röper, Jens-Christian; Eaton, Suzanne; Zallen, Jennifer A

2009-11-01

Axis elongation in Drosophila occurs through polarized cell rearrangements driven by actomyosin contractility. Myosin II promotes neighbor exchange through the contraction of single cell boundaries, while the contraction of myosin II structures spanning multiple pairs of cells leads to rosette formation. Here we show that multicellular actomyosin cables form at a higher frequency than expected by chance, indicating that cable assembly is an active process. Multicellular cables are sites of increased mechanical tension as measured by laser ablation. Fluorescence recovery after photobleaching experiments show that myosin II is stabilized at the cortex in regions of increased tension. Myosin II is recruited in response to an ectopic force and relieving tension leads to a rapid loss of myosin, indicating that tension is necessary and sufficient for cortical myosin localization. These results demonstrate that myosin II dynamics are regulated by tension in a positive feedback loop that leads to multicellular actomyosin cable formation and efficient tissue elongation.

Dynamics of micelle formation from temperature-jump Monte Carlo simulations.

PubMed

Heinzelmann, G; Seide, P; Figueiredo, W

2015-11-01

In the present work we perform temperature jumps in a surfactant solution by means of Monte Carlo simulations, investigating the dynamics of micelle formation. We use a lattice model that allows orientational freedom and hydrogen bonding for solvent molecules, which can make a connection between the different time scales of hydrogen bond formation and amphiphilic aggregation. When we perform a large jump between a high-temperature nonmicellized state and a micellized state, there is strong hysteresis between the heating and cooling processes, the latter showing the formation of premicelles that act as nucleation centers for the assembly of larger aggregates and the former is a drive for dissociation of the existing aggregates. Hysteresis is not seen when we perform a small jump between two states that can be both micellized or nonmicellized. Looking for a more detailed analysis of the hydrophobic effect that drives aggregation, we compare the time evolution of the solvent hydrogen bonds in our system close and far from micelles and how that is affected by the formation of large clusters at low temperatures. We find a strong connection between them, with the total number of hydrogen bonds in the system always increasing when micelles are formed. To gain insights into the mechanism of premicellar formation and growth, we measure the lifetime of micellized amphiphiles as a function of the aggregate size and the stage of the aggregation process. Our results indicate that the premicelles are always unstable, quickly exchanging amphiphiles with the solution due to their low probabilty in equilibrium. Furthermore, we find that the stability of individual surfactants in micelles increases with the aggregate size, with the lifetime of amphiphiles in large micelles being as much as 35 times longer than in the case of the unstable premicellar region.

Modeling Multivalent Ligand-Receptor Interactions with Steric Constraints on Configurations of Cell-Surface Receptor Aggregates

PubMed Central

Monine, Michael I.; Posner, Richard G.; Savage, Paul B.; Faeder, James R.; Hlavacek, William S.

2010-01-01

Abstract We use flow cytometry to characterize equilibrium binding of a fluorophore-labeled trivalent model antigen to bivalent IgE-FcεRI complexes on RBL cells. We find that flow cytometric measurements are consistent with an equilibrium model for ligand-receptor binding in which binding sites are assumed to be equivalent and ligand-induced receptor aggregates are assumed to be acyclic. However, this model predicts extensive receptor aggregation at antigen concentrations that yield strong cellular secretory responses, which is inconsistent with the expectation that large receptor aggregates should inhibit such responses. To investigate possible explanations for this discrepancy, we evaluate four rule-based models for interaction of a trivalent ligand with a bivalent cell-surface receptor that relax simplifying assumptions of the equilibrium model. These models are simulated using a rule-based kinetic Monte Carlo approach to investigate the kinetics of ligand-induced receptor aggregation and to study how the kinetics and equilibria of ligand-receptor interaction are affected by steric constraints on receptor aggregate configurations and by the formation of cyclic receptor aggregates. The results suggest that formation of linear chains of cyclic receptor dimers may be important for generating secretory signals. Steric effects that limit receptor aggregation and transient formation of small receptor aggregates may also be important. PMID:20085718

Zn(II)- and Cu(II)-induced non-fibrillar aggregates of amyloid-beta (1-42) peptide are transformed to amyloid fibrils, both spontaneously and under the influence of metal chelators.

PubMed

Tõugu, Vello; Karafin, Ann; Zovo, Kairit; Chung, Roger S; Howells, Claire; West, Adrian K; Palumaa, Peep

2009-09-01

Aggregation of amyloid-beta (Abeta) peptides is a central phenomenon in Alzheimer's disease. Zn(II) and Cu(II) have profound effects on Abeta aggregation; however, their impact on amyloidogenesis is unclear. Here we show that Zn(II) and Cu(II) inhibit Abeta(42) fibrillization and initiate formation of non-fibrillar Abeta(42) aggregates, and that the inhibitory effect of Zn(II) (IC(50) = 1.8 micromol/L) is three times stronger than that of Cu(II). Medium and high-affinity metal chelators including metallothioneins prevented metal-induced Abeta(42) aggregation. Moreover, their addition to preformed aggregates initiated fast Abeta(42) fibrillization. Upon prolonged incubation the metal-induced aggregates also transformed spontaneously into fibrils, that appear to represent the most stable state of Abeta(42). H13A and H14A mutations in Abeta(42) reduced the inhibitory effect of metal ions, whereas an H6A mutation had no significant impact. We suggest that metal binding by H13 and H14 prevents the formation of a cross-beta core structure within region 10-23 of the amyloid fibril. Cu(II)-Abeta(42) aggregates were neurotoxic to neurons in vitro only in the presence of ascorbate, whereas monomers and Zn(II)-Abeta(42) aggregates were non-toxic. Disturbed metal homeostasis in the vicinity of zinc-enriched neurons might pre-dispose formation of metal-induced Abeta aggregates, subsequent fibrillization of which can lead to amyloid formation. The molecular background underlying metal-chelating therapies for Alzheimer's disease is discussed in this light.

Radio observations of globulettes in the Carina nebula

NASA Astrophysics Data System (ADS)

Haikala, L. K.; Gahm, G. F.; Grenman, T.; Mäkelä, M. M.; Persson, C. M.

2017-06-01

Context. The Carina nebula hosts a large number of globulettes. An optical study of these tiny molecular clouds shows that the majority are of planetary mass, but there are also those with masses of several tens up to a few hundred Jupiter masses. Aims: We seek to search for, and hopefully detect, molecular line emission from some of the more massive objects; in case of successful detection we aim to map their motion in the Carina nebula complex and derive certain physical properties. Methods: We carried out radio observations of molecular line emission in 12CO and 13CO (2-1) and (3-2) of 12 globulettes in addition to positions in adjacent shell structures using APEX. Results: All selected objects were detected with radial velocities shifted relative to the emission from related shell structures and background molecular clouds. Globulettes along the western part of an extended dust shell show a small spread in velocity with small velocity shifts relative to the shell. This system of globulettes and shell structures in the foreground of the bright nebulosity surrounding the cluster Trumpler 14 is expanding with a few km s-1 relative to the cluster. A couple of isolated globulettes in the area move at similar speed. Compared to similar studies of the molecular line emission from globulettes in the Rosette nebula, we find that the integrated line intensity ratios and line widths are very different. The results show that the Carina objects have a different density/temperature structure than those in the Rosette nebula. In comparison the apparent size of the Carina globulettes is smaller, owing to the larger distance, and the corresponding beam filling factors are small. For this reason we were unable to carry out a more detailed modelling of the structure of the Carina objects in the way as performed for the Rosette objects. Conclusions: The Carina globulettes observed are compact and denser than objects of similar mass in the Rosette nebula. The distribution and velocities of these globulettes suggest that they have originated from eroding shells and elephant trunks. Some globulettes in the Trumpler 14 region are quite isolated and located far from any shell structures. These objects move at a similar speed as the globulettes along the shell, suggesting that they once formed from cloud fragments related to the same foreground shell. Based on observations collected with the Atacama Pathfinder Experiment (APEX), Llano Chajnantor, Chile (O-091.F-9316A and O-094.F-9312A).The final reduced radio data (FITS format) are available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/602/A61

In situ camera observations reveal major role of zooplankton in modulating marine snow formation during an upwelling-induced plankton bloom

NASA Astrophysics Data System (ADS)

Taucher, Jan; Stange, Paul; Algueró-Muñiz, María; Bach, Lennart T.; Nauendorf, Alice; Kolzenburg, Regina; Büdenbender, Jan; Riebesell, Ulf

2018-05-01

Particle aggregation and the consequent formation of marine snow alter important properties of biogenic particles (size, sinking rate, degradability), thus playing a key role in controlling the vertical flux of organic matter to the deep ocean. However, there are still large uncertainties about rates and mechanisms of particle aggregation, as well as the role of plankton community structure in modifying biomass transfer from small particles to large fast-sinking aggregates. Here we present data from a high-resolution underwater camera system that we used to observe particle size distributions and formation of marine snow (aggregates >0.5 mm) over the course of a 9-week in situ mesocosm experiment in the Eastern Subtropical North Atlantic. After an oligotrophic phase of almost 4 weeks, addition of nutrient-rich deep water (650 m) initiated the development of a pronounced diatom bloom and the subsequent formation of large marine snow aggregates in all 8 mesocosms. We observed a substantial time lag between the peaks of chlorophyll a and marine snow biovolume of 9-12 days, which is much longer than previously reported and indicates a marked temporal decoupling of phytoplankton growth and marine snow formation during our study. Despite this time lag, our observations revealed substantial transfer of biomass from small particle sizes (single phytoplankton cells and chains) to marine snow aggregates of up to 2.5 mm diameter (ESD), with most of the biovolume being contained in the 0.5-1 mm size range. Notably, the abundance and community composition of mesozooplankton had a substantial influence on the temporal development of particle size spectra and formation of marine snow aggregates: While higher copepod abundances were related to reduced aggregate formation and biomass transfer towards larger particle sizes, the presence of appendicularia and doliolids enhanced formation of large marine snow. Furthermore, we combined in situ particle size distributions with measurements of particle sinking velocity to compute instantaneous (potential) vertical mass flux. However, somewhat surprisingly, we did not find a coherent relationship between our computed flux and measured vertical mass flux (collected by sediment traps in 15 m depth). Although the onset of measured vertical flux roughly coincided with the emergence of marine snow, we found substantial variability in mass flux among mesocosms that was not related to marine snow numbers, and was instead presumably driven by zooplankton-mediated alteration of sinking biomass and export of small particles (fecal pellets). Altogether, our findings highlight the role of zooplankton community composition and feeding interactions on particle size spectra and formation of marine snow aggregates, with important implications for our understanding of particle aggregation and vertical flux of organic matter in the ocean.

Monitoring Insulin Aggregation via Capillary Electrophoresis

PubMed Central

Pryor, Elizabeth; Kotarek, Joseph A.; Moss, Melissa A.; Hestekin, Christa N.

2011-01-01

Early stages of insulin aggregation, which involve the transient formation of oligomeric aggregates, are an important aspect in the progression of Type II diabetes and in the quality control of pharmaceutical insulin production. This study is the first to utilize capillary electrophoresis (CE) with ultraviolet (UV) detection to monitor insulin oligomer formation at pH 8.0 and physiological ionic strength. The lag time to formation of the first detected species in the aggregation process was evaluated by UV-CE and thioflavin T (ThT) binding for salt concentrations from 100 mM to 250 mM. UV-CE had a significantly shorter (5–8 h) lag time than ThT binding (15–19 h). In addition, the lag time to detection of the first aggregated species via UV-CE was unaffected by salt concentration, while a trend toward an increased lag time with increased salt concentration was observed with ThT binding. This result indicates that solution ionic strength impacts early stages of aggregation and β-sheet aggregate formation differently. To observe whether CE may be applied for the analysis of biological samples containing low insulin concentrations, the limit of detection using UV and laser induced fluorescence (LIF) detection modes was determined. The limit of detection using LIF-CE, 48.4 pM, was lower than the physiological insulin concentration, verifying the utility of this technique for monitoring biological samples. LIF-CE was subsequently used to analyze the time course for fluorescein isothiocyanate (FITC)-labeled insulin oligomer formation. This study is the first to report that the FITC label prevented incorporation of insulin into oligomers, cautioning against the use of this fluorescent label as a tag for following early stages of insulin aggregation. PMID:22272138

Particle Formation and Aggregation of a Therapeutic Protein in Nanobubble Suspensions

PubMed Central

Snell, Jared R.; Zhou, Chen; Carpenter, John F.; Randolph, Theodore W.

2016-01-01

The generation of nanobubbles following reconstitution of lyophilized trehalose formulations has recently been reported.1 Here, we characterize particle formation and aggregation of recombinant human interleukin-1 receptor antagonist (rhIL-1ra) in reconstituted formulations of lyophilized trehalose. Particle characterization methods including resonant mass measurement and nanoparticle tracking analysis were used to count and size particles generated upon reconstitution of lyophilized trehalose formulations. In addition, accelerated degradation studies were conducted to monitor rhIL-1ra aggregation in solutions containing various concentrations of suspended nanobubbles. Reconstitution of lyophilized trehalose formulations with solutions containing rhIL-1ra reduced nanobubble concentrations and generated negatively buoyant particles attributed to aggregated rhIL-1ra. Furthermore, levels of rhIL-1ra aggregation following incubation in aqueous solution correlated with concentrations of suspended nanobubbles. The results of this study suggest nanobubbles may be a contributor to protein aggregation and particle formation in reconstituted, lyophilized therapeutic protein formulations. PMID:27488901

Particle Formation and Aggregation of a Therapeutic Protein in Nanobubble Suspensions.

PubMed

Snell, Jared R; Zhou, Chen; Carpenter, John F; Randolph, Theodore W

2016-10-01

The generation of nanobubbles following reconstitution of lyophilized trehalose formulations has recently been reported. Here, we characterize particle formation and aggregation of recombinant human interleukin-1 receptor antagonist (rhIL-1ra) in reconstituted formulations of lyophilized trehalose. Particle characterization methods including resonant mass measurement and nanoparticle tracking analysis were used to count and size particles generated upon reconstitution of lyophilized trehalose formulations. In addition, accelerated degradation studies were conducted to monitor rhIL-1ra aggregation in solutions containing various concentrations of suspended nanobubbles. Reconstitution of lyophilized trehalose formulations with solutions containing rhIL-1ra reduced nanobubble concentrations and generated negatively buoyant particles attributed to aggregated rhIL-1ra. Furthermore, levels of rhIL-1ra aggregation following incubation in aqueous solution correlated with concentrations of suspended nanobubbles. The results of this study suggest that nanobubbles may be a contributor to protein aggregation and particle formation in reconstituted, lyophilized therapeutic protein formulations. Copyright © 2016 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

Variation of Soil Aggregation along the Weathering Gradient: Comparison of Grain Size Distribution under Different Disruptive Forces.

PubMed

Wei, Yujie; Wu, Xinliang; Xia, Jinwen; Shen, Xue; Cai, Chongfa

2016-01-01

The formation and stabilization of soil aggregates play a key role in soil functions. To date, few studies have been performed on the variation of soil aggregation with increasing soil weathering degree. Here, soil aggregation and its influencing factors along the weathering gradient were investigated. Six typical zonal soils (derived from similar parent materials) were sampled from temperate to tropical regions. Grain size distribution (GSD) in aggregate fragmentation with increasing disruptive forces (air-dried, water dispersion and chemical dispersion) was determined by laser diffraction particle size analyzer. Different forms of sesquioxides were determined by selective chemical extraction and their contributions to soil aggregation were identified by multiple stepwise regression analysis. The high variability of sesquioxides in different forms appeared with increasing free oxide content (Fed and Ald) from the temperate to tropical soils. The transformation of GSD peak to small size varied with increasing disruptive forces (p<0.05). Although in different weathering degrees, zonal soils showed a similar fragmentation process. Aggregate water stability generally increased with increasing soil weathering (p<0.01), with higher stability in eluvium (A) horizon than in illuvium (B) horizon (p<0.01). Crystalline oxides and amorphous iron oxides (Feo), especially (Fed-Feo) contributed to the formation of air-dried macroaggregates and their stability against slaking (R2 = 55%, p<0.01), while fine particles (<50μm) and Feo (excluding the complex form Fep) played a positive role in the formation of water stable aggregates (R2 = 93%, p<0.01). Additionally, water stable aggregates (including stability, size distribution and specific surface area) were closely related with pH, organic matter, cation exchange capacity (CEC), bulk density (BD), and free oxides (including various forms) (p<0.05). The overall results indicate that soil aggregation conforms to aggregate hierarchy theory to some extent along the weathering gradient and different forms of sesquioxides perform their specific roles in the formation and stabilization of different size aggregates.

Variation of Soil Aggregation along the Weathering Gradient: Comparison of Grain Size Distribution under Different Disruptive Forces

PubMed Central

Wu, Xinliang; Xia, Jinwen; Shen, Xue; Cai, Chongfa

2016-01-01

The formation and stabilization of soil aggregates play a key role in soil functions. To date, few studies have been performed on the variation of soil aggregation with increasing soil weathering degree. Here, soil aggregation and its influencing factors along the weathering gradient were investigated. Six typical zonal soils (derived from similar parent materials) were sampled from temperate to tropical regions. Grain size distribution (GSD) in aggregate fragmentation with increasing disruptive forces (air-dried, water dispersion and chemical dispersion) was determined by laser diffraction particle size analyzer. Different forms of sesquioxides were determined by selective chemical extraction and their contributions to soil aggregation were identified by multiple stepwise regression analysis. The high variability of sesquioxides in different forms appeared with increasing free oxide content (Fed and Ald) from the temperate to tropical soils. The transformation of GSD peak to small size varied with increasing disruptive forces (p<0.05). Although in different weathering degrees, zonal soils showed a similar fragmentation process. Aggregate water stability generally increased with increasing soil weathering (p<0.01), with higher stability in eluvium (A) horizon than in illuvium (B) horizon (p<0.01). Crystalline oxides and amorphous iron oxides (Feo), especially (Fed-Feo) contributed to the formation of air-dried macroaggregates and their stability against slaking (R2 = 55%, p<0.01), while fine particles (<50μm) and Feo (excluding the complex form Fep) played a positive role in the formation of water stable aggregates (R2 = 93%, p<0.01). Additionally, water stable aggregates (including stability, size distribution and specific surface area) were closely related with pH, organic matter, cation exchange capacity (CEC), bulk density (BD), and free oxides (including various forms) (p<0.05). The overall results indicate that soil aggregation conforms to aggregate hierarchy theory to some extent along the weathering gradient and different forms of sesquioxides perform their specific roles in the formation and stabilization of different size aggregates. PMID:27529618

Aggregation work at polydisperse micellization: ideal solution and "dressed micelle" models comparing to molecular dynamics simulations.

PubMed

Burov, S V; Shchekin, A K

2010-12-28

General thermodynamic relations for the work of polydisperse micelle formation in the model of ideal solution of molecular aggregates in nonionic surfactant solution and the model of "dressed micelles" in ionic solution have been considered. In particular, the dependence of the aggregation work on the total concentration of nonionic surfactant has been analyzed. The analogous dependence for the work of formation of ionic aggregates has been examined with regard to existence of two variables of a state of an ionic aggregate, the aggregation numbers of surface active ions and counterions. To verify the thermodynamic models, the molecular dynamics simulations of micellization in nonionic and ionic surfactant solutions at two total surfactant concentrations have been performed. It was shown that for nonionic surfactants, even at relatively high total surfactant concentrations, the shape and behavior of the work of polydisperse micelle formation found within the model of the ideal solution at different total surfactant concentrations agrees fairly well with the numerical experiment. For ionic surfactant solutions, the numerical results indicate a strong screening of ionic aggregates by the bound counterions. This fact as well as independence of the coefficient in the law of mass action for ionic aggregates on total surfactant concentration and predictable behavior of the "waterfall" lines of surfaces of the aggregation work upholds the model of "dressed" ionic aggregates.

Direct fabrication of /sup 238/PuO/sub 2/ fuel forms

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

Burney, G.A.; Congdon, J.W.

1982-07-01

The current process for the fabrication of /sup 238/PuO/sub 2/ heat sources includes precipitation of small particle plutonium oxalate crystals (4 to 6 ..mu..m diameter), a calcination to PuO/sub 2/, ball milling, cold pressing, granulation (60 to 125 ..mu..m), and granule sintering prior to hot pressing the fuel pellet. A new two-step direct-strike Pu(III) oxalate precipitation method which yields mainly large well-developed rosettes (50 to 100 ..mu..m diameter) has been demonstrated in the laboratory and in the plant. These large rosettes are formed by agglomeration of small (2 to 4 ..mu..m) crystals, and after calcining and sintering, were directly hotmore » pressed into fuel forms, thus eliminating several of the powder conditioning steps. Conditions for direct hot pressing of the large heat-treated rosettes were determined and a full-scale General Purpose Heat Source pellet was fabricated. The pellet had the desired granule-type microstructure to provide dimensional stability at high temperature. 27 figures.« less

Galactose-depleted xyloglucan is dysfunctional and leads to dwarfism in Arabidopsis.

PubMed

Kong, Yingzhen; Peña, Maria J; Renna, Luciana; Avci, Utku; Pattathil, Sivakumar; Tuomivaara, Sami T; Li, Xuemei; Reiter, Wolf-Dieter; Brandizzi, Federica; Hahn, Michael G; Darvill, Alan G; York, William S; O'Neill, Malcolm A

2015-04-01

Xyloglucan is a polysaccharide that has important roles in the formation and function of the walls that surround growing land plant cells. Many of these plants synthesize xyloglucan that contains galactose in two different side chains (L and F), which exist in distinct molecular environments. However, little is known about the contribution of these side chains to xyloglucan function. Here, we show that Arabidopsis (Arabidopsis thaliana) mutants devoid of the F side chain galactosyltransferase MURUS3 (MUR3) form xyloglucan that lacks F side chains and contains much less galactosylated xylose than its wild-type counterpart. The galactose-depleted xyloglucan is dysfunctional, as it leads to mutants that are dwarfed with curled rosette leaves, short petioles, and short inflorescence stems. Moreover, cell wall matrix polysaccharides, including xyloglucan and pectin, are not properly secreted and instead accumulate within intracellular aggregates. Near-normal growth is restored by generating mur3 mutants that produce no detectable amounts of xyloglucan. Thus, cellular processes are affected more by the presence of the dysfunctional xyloglucan than by eliminating xyloglucan altogether. To identify structural features responsible for xyloglucan dysfunction, xyloglucan structure was modified in situ by generating mur3 mutants that lack specific xyloglucan xylosyltransferases (XXTs) or that overexpress the XYLOGLUCAN L-SIDE CHAIN GALACTOSYLTRANSFERASE2 (XLT2) gene. Normal growth was restored in the mur3-3 mutant overexpressing XLT2 and in mur3-3 xxt double mutants when the dysfunctional xyloglucan was modified by doubling the amounts of galactosylated side chains. Our study assigns a role for galactosylation in normal xyloglucan function and demonstrates that altering xyloglucan side chain structure disturbs diverse cellular and physiological processes. © 2015 American Society of Plant Biologists. All Rights Reserved.

A Strong Loss-of-Function Mutation in RAN1 Results in Constitutive Activation of the Ethylene Response Pathway as Well as a Rosette-Lethal Phenotype

PubMed Central

Woeste, Keith E.; Kieber, Joseph J.

2000-01-01

A recessive mutation was identified that constitutively activated the ethylene response pathway in Arabidopsis and resulted in a rosette-lethal phenotype. Positional cloning of the gene corresponding to this mutation revealed that it was allelic to responsive to antagonist1 (ran1), a mutation that causes seedlings to respond in a positive manner to what is normally a competitive inhibitor of ethylene binding. In contrast to the previously identified ran1-1 and ran1-2 alleles that are morphologically indistinguishable from wild-type plants, this ran1-3 allele results in a rosette-lethal phenotype. The predicted protein encoded by the RAN1 gene is similar to the Wilson and Menkes disease proteins and yeast Ccc2 protein, which are integral membrane cation-transporting P-type ATPases involved in copper trafficking. Genetic epistasis analysis indicated that RAN1 acts upstream of mutations in the ethylene receptor gene family. However, the rosette-lethal phenotype of ran1-3 was not suppressed by ethylene-insensitive mutants, suggesting that this mutation also affects a non-ethylene-dependent pathway regulating cell expansion. The phenotype of ran1-3 mutants is similar to loss-of-function ethylene receptor mutants, suggesting that RAN1 may be required to form functional ethylene receptors. Furthermore, these results suggest that copper is required not only for ethylene binding but also for the signaling function of the ethylene receptors. PMID:10715329

A strong loss-of-function mutation in RAN1 results in constitutive activation of the ethylene response pathway as well as a rosette-lethal phenotype

NASA Technical Reports Server (NTRS)

Woeste, K. E.; Kieber, J. J.; Evans, M. L. (Principal Investigator)

2000-01-01

A recessive mutation was identified that constitutively activated the ethylene response pathway in Arabidopsis and resulted in a rosette-lethal phenotype. Positional cloning of the gene corresponding to this mutation revealed that it was allelic to responsive to antagonist1 (ran1), a mutation that causes seedlings to respond in a positive manner to what is normally a competitive inhibitor of ethylene binding. In contrast to the previously identified ran1-1 and ran1-2 alleles that are morphologically indistinguishable from wild-type plants, this ran1-3 allele results in a rosette-lethal phenotype. The predicted protein encoded by the RAN1 gene is similar to the Wilson and Menkes disease proteins and yeast Ccc2 protein, which are integral membrane cation-transporting P-type ATPases involved in copper trafficking. Genetic epistasis analysis indicated that RAN1 acts upstream of mutations in the ethylene receptor gene family. However, the rosette-lethal phenotype of ran1-3 was not suppressed by ethylene-insensitive mutants, suggesting that this mutation also affects a non-ethylene-dependent pathway regulating cell expansion. The phenotype of ran1-3 mutants is similar to loss-of-function ethylene receptor mutants, suggesting that RAN1 may be required to form functional ethylene receptors. Furthermore, these results suggest that copper is required not only for ethylene binding but also for the signaling function of the ethylene receptors.

A mechanistic model for the evolution of multicellularity

NASA Astrophysics Data System (ADS)

Amado, André; Batista, Carlos; Campos, Paulo R. A.

2018-02-01

Through a mechanistic approach we investigate the formation of aggregates of variable sizes, accounting mechanisms of aggregation, dissociation, death and reproduction. In our model, cells can produce two metabolites, but the simultaneous production of both metabolites is costly in terms of fitness. Thus, the formation of larger groups can favor the aggregates to evolve to a configuration where division of labor arises. It is assumed that the states of the cells in a group are those that maximize organismal fitness. In the model it is considered that the groups can grow linearly, forming a chain, or compactly keeping a roughly spherical shape. Starting from a population consisting of single-celled organisms, we observe the formation of groups with variable sizes and usually much larger than two-cell aggregates. Natural selection can favor the formation of large groups, which allows the system to achieve new and larger fitness maxima.

Intrinsic Lens Forming Potential of Mouse Lens Epithelial versus Newt Iris Pigment Epithelial Cells in Three-Dimensional Culture

PubMed Central

Nakamura, Kenta; Tsonis, Panagiotis A.

2014-01-01

Adult newts (Notophthalmus viridescens) are capable of complete lens regeneration that is mediated through dorsal iris pigment epithelial (IPE) cells transdifferentiation. In contrast, higher vertebrates such as mice demonstrate only limited lens regeneration in the presence of an intact lens capsule with remaining lens epithelial cells. To compare the intrinsic lens regeneration potential of newt IPE versus mouse lens epithelial cells (MLE), we have established a novel culture method that uses cell aggregation before culture in growth factor-reduced Matrigel™. Dorsal newt IPE aggregates demonstrated complete lens formation within 1 to 2 weeks of Matrigel culture without basic fibroblast growth factor (bFGF) supplementation, including the establishment of a peripheral cuboidal epithelial cell layer, and the appearance of central lens fibers that were positive for αA-crystallin. In contrast, the lens-forming potential of MLE cell aggregates cultured in Matrigel was incomplete and resulted in the formation of defined-size lentoids with partial optical transparency. While the peripheral cell layers of MLE aggregates were nucleated, cells in the center of aggregates demonstrated a nonapoptotic nuclear loss over a time period of 3 weeks that was representative of lens fiber formation. Matrigel culture supplementation with bFGF resulted in higher transparent bigger-size MLE aggregates that demonstrated increased appearance of βB1-crystallin expression. Our study demonstrates that bFGF is not required for induction of newt IPE aggregate-dependent lens formation in Matrigel, while the addition of bFGF seems to be beneficial for the formation of MLE aggregate-derived lens-like structures. In conclusion, the three-dimensional aggregate culture of IPE and MLE in Matrigel allows to a higher extent than older models the indepth study of the intrinsic lens-forming potential and the corresponding identification of lentogenic factors. PMID:23672748

A numerical model for aggregations formation and magnetic driving of spherical particles based on OpenFOAM®.

PubMed

Karvelas, E G; Lampropoulos, N K; Sarris, I E

2017-04-01

This work presents a numerical model for the formation of particle aggregations under the influence of a permanent constant magnetic field and their driving process under a gradient magnetic field, suitably created by a Magnetic Resonance Imaging (MRI) device. The model is developed in the OpenFOAM platform and it is successfully compared to the existing experimental and numerical results in terms of aggregates size and their motion in water solutions. Furthermore, several series of simulations are performed for two common types of particles of different diameter in order to verify their aggregation and flow behaviour, under various constant and gradient magnetic fields in the usual MRI working range. Moreover, the numerical model is used to measure the mean length of aggregations, the total time needed to form and their mean velocity under different permanent and gradient magnetic fields. The present model is found to predict successfully the size, velocity and distribution of aggregates. In addition, our simulations showed that the mean length of aggregations is proportional to the permanent magnetic field magnitude and particle diameter according to the relation : l¯ a =7.5B 0 d i 3/2 . The mean velocity of the aggregations is proportional to the magnetic gradient, according to : u¯ a =6.63G˜B 0 and seems to reach a steady condition after a certain period of time. The mean time needed for particles to aggregate is proportional to permanent magnetic field magnitude, scaled by the relationship : t¯ a ∝7B 0 . A numerical model to predict the motion of magnetic particles for medical application is developed. This model is found suitable to predict the formation of aggregations and their motion under the influence of permanent and gradient magnetic fields, respectively, that are produced by an MRI device. The magnitude of the external constant magnetic field is the most important parameter for the aggregations formation and their driving. Copyright © 2017 Elsevier B.V. All rights reserved.

Calcium oxalate monohydrate aggregation induced by aggregation of desialylated Tamm-Horsfall protein

PubMed Central

Viswanathan, Pragasam; Rimer, Jeffrey D.; Kolbach, Ann M.; Kleinman, Jack G.

2011-01-01

Tamm-Horsfall protein (THP) is thought to protect against calcium oxalate monohydrate (COM) stone formation by inhibiting COM aggregation. Several studies reported that stone formers produce THP with reduced levels of glycosylation, particularly sialic acid levels, which leads to reduced negative charge. In this study, normal THP was treated with neuraminidase to remove sialic acid residues, confirmed by an isoelectric point shift to higher pH. COM aggregation assays revealed that desialylated THP (ds-THP) promoted COM aggregation, while normal THP inhibited aggregation. The appearance of protein aggregates in solutions at ds-THP concentrations ≥1 µg/mL in 150 mM NaCl correlated with COM aggregation promotion, implying that ds-THP aggregation induced COM aggregation. The aggregation-promoting effect of the ds-THP was independent of pH above its isoelectric point, but was substantially reduced at low ionic strength, where protein aggregation was much reduced. COM aggregation promotion was maximized at a ds-THP to COM mass ratio of ~0.025, which can be explained by a model wherein partial COM surface coverage by ds-THP aggregates promotes crystal aggregation by bridging opposing COM surfaces, whereas higher surface coverage leads to repulsion between adsorbed ds-THP aggregates. Thus, desialylation of THP apparently abrogates a normal defensive action of THP by inducing protein aggregation, and subsequently COM aggregation, a condition that favors kidney stone formation. PMID:21229239

Comparison of different procedures to stabilize biogas formation after process failure in a thermophilic waste digestion system: Influence of aggregate formation on process stability

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

Kleyboecker, A.; Liebrich, M.; Kasina, M.

2012-06-15

Highlights: Black-Right-Pointing-Pointer Mechanism of process recovery with calcium oxide. Black-Right-Pointing-Pointer Formation of insoluble calcium salts with long chain fatty acids and phosphate. Black-Right-Pointing-Pointer Adsorption of VFAs by the precipitates resulting in the formation of aggregates. Black-Right-Pointing-Pointer Acid uptake and phosphate release by the phosphate-accumulating organisms. Black-Right-Pointing-Pointer Microbial degradation of volatile fatty acids in the aggregates. - Abstract: Following a process failure in a full-scale biogas reactor, different counter measures were undertaken to stabilize the process of biogas formation, including the reduction of the organic loading rate, the addition of sodium hydroxide (NaOH), and the introduction of calcium oxide (CaO). Correspondingmore » to the results of the process recovery in the full-scale digester, laboratory experiments showed that CaO was more capable of stabilizing the process than NaOH. While both additives were able to raise the pH to a neutral milieu (pH > 7.0), the formation of aggregates was observed particularly when CaO was used as the additive. Scanning electron microscopy investigations revealed calcium phosphate compounds in the core of the aggregates. Phosphate seemed to be released by phosphorus-accumulating organisms, when volatile fatty acids accumulated. The calcium, which was charged by the CaO addition, formed insoluble salts with long chain fatty acids, and caused the precipitation of calcium phosphate compounds. These aggregates were surrounded by a white layer of carbon rich organic matter, probably consisting of volatile fatty acids. Thus, during the process recovery with CaO, the decrease in the amount of accumulated acids in the liquid phase was likely enabled by (1) the formation of insoluble calcium salts with long chain fatty acids, (2) the adsorption of volatile fatty acids by the precipitates, (3) the acid uptake by phosphorus-accumulating organisms and (4) the degradation of volatile fatty acids in the aggregates. Furthermore, this mechanism enabled a stable process performance after re-activation of biogas production. In contrast, during the counter measure with NaOH aggregate formation was only minor resulting in a rapid process failure subsequent the increase of the organic loading rate.« less

Effect of cobalt ions on the interaction between macrophages and titanium.

PubMed

Pettersson, Mattias; Pettersson, Jean; Thorén, Margareta Molin; Johansson, Anders

2018-04-30

Inflammation and bone reduction around dental implants are described as peri-implantitis and can be caused by an inflammatory response against bacterial products and toxins. Titanium (Ti) forms aggregates with serum proteins, which activate and cause release of the cytokine interleukin (IL-1β) from human macrophages. It was hypothesized that cobalt (Co) ions can interact in the formation of pro-inflammatory aggregates, formed by titanium. To test this hypothesis, we differentiated THP-1 cells into macrophages and exposed them to Ti ions alone or in combination with Co ions to investigate if IL-1β release and cytotoxicity were affected. We also investigated aggregate formation, cell uptake and human biopsies with inductively coupled plasma atomic emission spectroscopy (ICP-AES) and electron microscopy. Co at a concentration of 100 µM neutralized the IL-1β release from human macrophages and affected the aggregate formation. The aggregates formed by Ti could be detected in the cytosol of macrophages. In the presence of Co, the Ti-induced aggregates were located in the cytosol of the cultured macrophages, but outside the lysosomal structures. It is concluded that Co can neutralize the Ti-induced activation and release of active IL-1β from human macrophages in vitro. Also, serum proteins are needed for the formation of metal-protein aggregates in cell medium. Furthermore, the structures of the aggregates as well as the localisation after cellular uptake differ if Co is present in a Ti solution. Phagocytized aggregates with a similar appearance seen in vitro with Ti present, were also visible in a sample from human peri-implant tissue. This article is protected by copyright. All rights reserved. © 2018 Wiley Periodicals, Inc.

Non-pathogenic protein aggregates in skeletal muscle in MLF1 transgenic mice.

PubMed

Li, Zhi-Fang; Wu, Xiaohua; Jiang, Yun; Liu, Jianxiang; Wu, Chun; Inagaki, Masaki; Izawa, Ichiro; Mizisin, Andrew P; Engvall, Eva; Shelton, G Diane

2008-01-15

Protein aggregate formation in muscle is thought to be pathogenic and associated with clinical weakness. Over-expression of either wild type or a mutant form of myeloid leukemia factor 1 (MLF1) in transgenic mouse skeletal muscle and in cultured cells resulted in aggregate formation. Aggregates were detected in MLF1 transgenic mice at 6 weeks of age, and increased in size with age. However, histological examination of skeletal muscles of MLF1 transgenic mice revealed no pathological changes other than the aggregates, and RotaRod testing did not detect functional deficits. MLF1 has recently been identified as a protein that could neutralize the toxicity of intracellular protein aggregates in a Drosophila model of Huntington's disease (HD). We also demonstrate that MLF1 interacts with MRJ, a heat shock protein, which can independently neutralize the toxicity of intracellular protein aggregates in the Drosophila HD model. Our data suggest that over-expression of MLF1 has no significant impact on skeletal muscle function in mice; that progressive formation of protein aggregates in muscle are not necessarily pathogenic; and that MLF1 and MRJ may function together to ameliorate the toxic effects of polyglutamine or mutant proteins in myodegenerative diseases such as inclusion body myositis and oculopharyngeal muscular dystrophy, as well as neurodegenerative disease.

One-pot nucleation, growth, morphogenesis, and passivation of 1.4 nm Au nanoparticles on self-assembled rosette nanotubes.

PubMed

Chhabra, Rahul; Moralez, Jesus G; Raez, Jose; Yamazaki, Takeshi; Cho, Jae-Young; Myles, Andrew J; Kovalenko, Andriy; Fenniri, Hicham

2010-01-13

A one-pot strategy for the nucleation, growth, morphogenesis, and passivation of 1.4 nm Au nanoparticles (NPs) on self-assembled rosette nanotubes (RNTs) is described. Tapping-mode atomic force microscopy, transmission electron microscopy, energy-dispersive X-ray analysis, and selected-area electron diffraction were used to establish the structure and organization of this hybrid material. Notably, we found that the Au NPs formed were nearly monodisperse clusters of Au(55) (1.4-1.5 nm) nestled in pockets on the RNT surface.

Embryonal tumor with abundant neuropil and true rosettes: a systematic literature review and report of 2 new cases.

PubMed

Alexiou, George A; Stefanaki, Kalliopi; Vartholomatos, George; Sfakianos, George; Prodromou, Neofytos; Moschovi, Maria

2013-12-01

Embryonal tumor with abundant neuropil and true rosettes has been recently defined as a distinct central nervous system embryonal neoplasm, although it was initially regarded as a subtype of central nervous system primitive neuroectodermal tumor. To date 70 cases have been reported. We have performed a literature review and we present 2 new cases. Analysis of the reported data revealed that radiotherapy, tumor excision and high-dose adjuvant chemotherapy with sequential autologous hematopoietic stem cell rescue have a prognostic significance.

Chemotactic preferences govern competition and pattern formation in simulated two-strain microbial communities.

PubMed

Centler, Florian; Thullner, Martin

2015-01-01

Substrate competition is a common mode of microbial interaction in natural environments. While growth properties play an important and well-studied role in competition, we here focus on the influence of motility. In a simulated two-strain community populating a homogeneous two-dimensional environment, strains competed for a common substrate and only differed in their chemotactic preference, either responding more sensitively to a chemoattractant excreted by themselves or responding more sensitively to substrate. Starting from homogeneous distributions, three possible behaviors were observed depending on the competitors' chemotactic preferences: (i) distributions remained homogeneous, (ii) patterns formed but dissolved at a later time point, resulting in a shifted community composition, and (iii) patterns emerged and led to the extinction of one strain. When patterns formed, the more aggregating strain populated the core of microbial aggregates where starving conditions prevailed, while the less aggregating strain populated the more productive zones at the fringe or outside aggregates, leading to a competitive advantage of the less aggregating strain. The presence of a competitor was found to modulate a strain's behavior, either suppressing or promoting aggregate formation. This observation provides a potential mechanism by which an aggregated lifestyle might evolve even if it is initially disadvantageous. Adverse effects can be avoided as a competitor hinders aggregate formation by a strain which has just acquired this ability. The presented results highlight both, the importance of microbial motility for competition and pattern formation, and the importance of the temporal evolution, or history, of microbial communities when trying to explain an observed distribution.

Formation of planetesimals

NASA Technical Reports Server (NTRS)

Weidenschilling, Stuart J.

1991-01-01

Formation of planetesimals is discussed. The following subject areas are covered: (1) nebular structure; (2) aerodynamics of the solid bodies in the nebula; (3) problems with gravitational instability; (4) particle growth by coagulation; properties of fractal aggregates; and (5) coagulation and settling of fractal aggregates.

Ralstonia insidiosa induces cell aggregation by Listeria monocytogenes

USDA-ARS?s Scientific Manuscript database

Biofilm formation is an important strategy for foodborne bacterial pathogens to survive in stressful environments such as fresh produce processing facilities. Bacterial cell aggregation strongly promotes the initiation of microcolonies and the formation of biofilms on abiological surfaces. We previ...

Effects of Phytoplankton Growth Phase on the Formation and Properties of Marine Snow

NASA Astrophysics Data System (ADS)

Montgomery, Q. W.; Proctor, K. W.; Prairie, J. C.

2016-02-01

Marine snow aggregates often dominate carbon export from the upper mixed layer to the deep ocean. Thus, understanding the formation and the properties of these aggregates is essential to the study of the biological pump. Aggregate formation is determined by both the encounter rate and the stickiness of the particles that they are composed of. Stickiness of phytoplankton has been linked to production of transparent exopolymer particles (TEP), which has been previously shown to vary in concentration throughout different parts of the phytoplankton growth cycle. The objective of this study is to determine the effects of the growth phase of the diatom Thalassiosira weissflogii to both TEP production and the properties of the resulting aggregates produced. Cultures of T. weissflogii were stopped at separate phases of the phytoplankton growth curve and incubated in rotating cylindrical tanks to form aggregates. Aggregate properties such as size, density, and porosity were measured at the end of each period of roller incubation. Preliminary results describe little variation in the size of the aggregates formed from different parts of the growth phase, but show a significant effect of growth phase on aggregate density. Density is an important factor in the settling of marine aggregates. Therefore, variations in aggregate density during different growth phases may have large implications for the efficiency of the biological pump during different stages of a phytoplankton bloom. Further examination will be performed on the potential effects of TEP abundance on the properties of the aggregates formed at separate growth phases and the resulting implications for carbon flux.

Effects of surfaces and leachables on the stability of biopharmaceuticals.

PubMed

Bee, Jared S; Randolph, Theodore W; Carpenter, John F; Bishop, Steven M; Dimitrova, Mariana N

2011-10-01

Therapeutic proteins are exposed to various potential contact surfaces, particles, and leachables during manufacturing, shipping, storage, and delivery. In this review, we present published examples of interfacial- or leachable-induced aggregation or particle formation, and discuss the mitigation strategies that were successfully utilized. Adsorption to interfaces or interactions with leachables and/or particles in some cases has been reported to cause protein aggregation or particle formation. Identification of the cause(s) of particle formation involving minute amounts of protein over extended periods of time can be challenging. Various formulation strategies such as addition of a nonionic surfactant (e.g., polysorbate) have been demonstrated to effectively mitigate adsorption-induced protein aggregation. However, not all stability problems associated with interfaces or leachables are best resolved by formulation optimization. Detectable leachables do not necessarily have any adverse impact on the protein but control of the leachable source is preferred when there is a concern. In other cases, preventing protein aggregation and particle formation may require manufacturing process and/or equipment changes, use of compatible materials at contact interfaces, and so on. This review summarizes approaches that have been used to minimize protein aggregation and particle formation during manufacturing and fill-finish operations, product storage and transportation, and delivery of protein therapeutics. Copyright © 2011 Wiley-Liss, Inc.

Fluffy dust forms icy planetesimals by static compression

NASA Astrophysics Data System (ADS)

Kataoka, Akimasa; Tanaka, Hidekazu; Okuzumi, Satoshi; Wada, Koji

2013-09-01

Context. Several barriers have been proposed in planetesimal formation theory: bouncing, fragmentation, and radial drift problems. Understanding the structure evolution of dust aggregates is a key in planetesimal formation. Dust grains become fluffy by coagulation in protoplanetary disks. However, once they are fluffy, they are not sufficiently compressed by collisional compression to form compact planetesimals. Aims: We aim to reveal the pathway of dust structure evolution from dust grains to compact planetesimals. Methods: Using the compressive strength formula, we analytically investigate how fluffy dust aggregates are compressed by static compression due to ram pressure of the disk gas and self-gravity of the aggregates in protoplanetary disks. Results: We reveal the pathway of the porosity evolution from dust grains via fluffy aggregates to form planetesimals, circumventing the barriers in planetesimal formation. The aggregates are compressed by the disk gas to a density of 10-3 g/cm3 in coagulation, which is more compact than is the case with collisional compression. Then, they are compressed more by self-gravity to 10-1 g/cm3 when the radius is 10 km. Although the gas compression decelerates the growth, the aggregates grow rapidly enough to avoid the radial drift barrier when the orbital radius is ≲6 AU in a typical disk. Conclusions: We propose a fluffy dust growth scenario from grains to planetesimals. It enables icy planetesimal formation in a wide range beyond the snowline in protoplanetary disks. This result proposes a concrete initial condition of planetesimals for the later stages of the planet formation.

Influence of Calcium in Extracellular DNA Mediated Bacterial Aggregation and Biofilm Formation

PubMed Central

Koop, Leena; Wong, Yie Kuan; Ahmed, Safia; Siddiqui, Khawar Sohail; Manefield, Mike

2014-01-01

Calcium (Ca2+) has an important structural role in guaranteeing the integrity of the outer lipopolysaccharide layer and cell walls of bacterial cells. Extracellular DNA (eDNA) being part of the slimy matrix produced by bacteria promotes biofilm formation through enhanced structural integrity of the matrix. Here, the concurrent role of Ca2+ and eDNA in mediating bacterial aggregation and biofilm formation was studied for the first time using a variety of bacterial strains and the thermodynamics of DNA to Ca2+ binding. It was found that the eDNA concentrations under both planktonic and biofilm growth conditions were different among bacterial strains. Whilst Ca2+ had no influence on eDNA release, presence of eDNA by itself favours bacterial aggregation via attractive acid-base interactions in addition, its binding with Ca2+ at biologically relevant concentrations was shown further increase in bacterial aggregation via cationic bridging. Negative Gibbs free energy (ΔG) values in iTC data confirmed that the interaction between DNA and Ca2+ is thermodynamically favourable and that the binding process is spontaneous and exothermic owing to its highly negative enthalpy. Removal of eDNA through DNase I treatment revealed that Ca2+ alone did not enhance cell aggregation and biofilm formation. This discovery signifies the importance of eDNA and concludes that existence of eDNA on bacterial cell surfaces is a key facilitator in binding of Ca2+ to eDNA thereby mediating bacterial aggregation and biofilm formation. PMID:24651318

Understanding curcumin-induced modulation of protein aggregation.

PubMed

Ahmad, Basir; Borana, Mohanish S; Chaudhary, Ankur P

2017-07-01

Curcumin, a diarylheptanoid compound, found in spice turmeric is known to alter the aggregation of proteins and reduce the toxicity of the aggregates. This review looks at the molecular basis of modulating protein aggregation and toxicity of the aggregates. Foremost, we identify the interaction of curcumin and its derivatives with proteins/peptides and the effect of their interaction on the conformational stability and unfolding/folding pathway(s). The unfolding/folding processes generate partially folded/unfolded intermediate, which serve as aggregation precursor state. Secondly, we discuss the effect of curcumin binding on the kinetics parameters of the aggregation process, which give information about the mechanism of the aggregation inhibition. We describe, in addition, that curcumin can accelerate/promote fibril formation by binding to oligomeric intermediate(s) accumulated in the aggregation pathway. Finally, we discuss the correlation of curcumin-induced monomeric and/or oligomeric precursor states with aggregate structure and toxicity. On the basis of these discussions, we propose a model describing curcumin-induced inhibition/promotion of formation of amyloid-like fibrils. Copyright © 2016 Elsevier B.V. All rights reserved.

The Aggregation Paths and Products of Aβ42 Dimers Are Distinct from Those of the Aβ42 Monomer.

PubMed

O'Malley, Tiernan T; Witbold, William M; Linse, Sara; Walsh, Dominic M

2016-11-08

Extracts of Alzheimer's disease (AD) brain that contain what appear to be sodium dodecyl sulfate-stable amyloid β-protein (Aβ) dimers potently block LTP and impair memory consolidation. Brain-derived dimers can be physically separated the Aβ monomer, consist primarily of Aβ42, and resist denaturation by chaotropic agents. In nature, covalently cross-linked Aβ dimers could be generated in two ways: by the formation of a dityrosine (DiY) or an isopeptide ε-(γ-glutamyl)-lysine (Q-K) bond. We enzymatically cross-linked recombinant Aβ42 monomer to produce DiY and Q-K dimers and then used a range of biophysical methods to study their aggregation. Both Q-K and DiY dimers aggregate to form soluble assemblies distinct from the fibrillar aggregates formed by the Aβ monomer. The results suggest that the cross-links disfavor fibril formation from Aβ dimers, thereby enhancing the concentration of soluble aggregates akin to those in aqueous extracts of AD brain. Thus, it seems that Aβ dimers may play an important role in determining the formation of soluble rather than insoluble aggregates.

The aggregation paths and products of Aβ42 dimers are distinct from Aβ42 monomer

PubMed Central

O'Malley, Tiernan T.; Witbold, William M.; Linse, Sara; Walsh, Dominic M.

2017-01-01

Extracts of Alzheimer's disease (AD) brain that contain what appear to be SDS-stable amyloid β-protein (Aβ) dimers potently block LTP and impair memory consolidation. Brain-derived dimers can be physically separated from Aβ monomer, consist primarily of Aβ42 and resist denaturation by powerful chaotropic agents. In nature, covalently cross-linked Aβ dimers could be generated in only one of two different ways - either by the formation of a dityrosine (DiY) or an isopeptide ε-(γ-glutamyl)-lysine (Q-K) bond. We enzymatically cross-linked recombinant Aβ42 monomer to produce DiY and Q-K dimers and then applied a range of biophysical methods to study their aggregation. Both Q-K and DiY dimers aggregate to form soluble assemblies distinct from the fibrillar aggregates formed by Aβ monomer. These results suggest that Aβ dimers allow the formation of soluble aggregates akin to those in aqueous extracts of AD brain. Thus it seems that Aβ dimers may play an important role in determining the formation of soluble rather than insoluble aggregates. PMID:27750419

Intramolecular aggregation and optical limiting properties of triazine-linked mono-, bis- and tris-phthalocyanines.

PubMed

Chen, Jun; Zhang, Tao; Wang, Shuangqing; Hu, Rui; Li, Shayu; Ma, Jin Shi; Yang, Guoqiang

2015-10-05

A series of triazine-linked mono-, bis- and tris-phthalocyanines are synthesized, intramolecular aggregation is found in bis- and tris-phthalocyanines via π-π stacking interaction. Theoretical and experimental studies reveal the formation of the intramolecular aggregation. The spectrographic, photophysical and nonlinear optical properties of these compounds are adjusted for the formation of the intramolecular aggregation. The bis-phthalocyanine dimer presents smaller fluorescence quantum yield, lower triplet formation yield and the triplet-minus-ground state extinction coefficient, which causes poorer optical limiting performance. It is interesting that the tris-phthalocyanine is composed of a mono-phthalocyanine part and a bis-phthalocyanine part, the optical limiting property of the tris-phthalocyanine is similar to that of mono-phthalocyanine. Copyright © 2015 Elsevier B.V. All rights reserved.

Cu(II) promotes amyloid pore formation

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

Zhang, Hangyu, E-mail: hangyuz@uw.edu; Rochet, Jean-Christophe; Stanciu, Lia A.

2015-08-14

The aggregation of α-synuclein is associated with dopamine neuron death in Parkinson's disease. There is controversy in the field over the question of which species of the aggregates, fibrils or protofibrils, are toxic. Moreover, compelling evidence suggested the exposure to heavy metals to be a risk of PD. Nevertheless, the mechanism of metal ions in promoting PD remains unclear. In this research, we investigated the structural basis of Cu(II) induced aggregation of α-synuclein. Using transmission electron microscopy experiments, Cu(II) was found to promote in vitro aggregation of α-synuclein by facilitating annular protofibril formation rather than fibril formation. Furthermore, neuroprotective baicalein disaggregatedmore » annular protofibrils accompanied by considerable decrease of β-sheet content. These results strongly support the hypothesis that annular protofibrils are the toxic species, rather than fibrils, thereby inspiring us to search novel therapeutic strategies for the suppression of the toxic annular protofibril formation. - Highlights: • Cu(II) promoted the annular protofibril formation of α-synuclein in vitro. • Cu(II) postponed the in vitro fibrillization of α-synuclein. • Neuroprotective baicalein disaggregated annular protofibrils.« less

The Influence of Concentration and Temperature on the Formation of γ-Oryzanol + β-Sitosterol Tubules in Edible Oil Organogels

PubMed Central

Venema, Paul; Bot, Arjen; Flöter, Eckhard; van der Linden, Erik

2010-01-01

The gelation process of mixtures of γ-oryzanol and sitosterol structurants in sunflower oil was studied using light scattering, rheology, and micro-scanning calorimetry (Micro-DSC). The relation between temperature and the critical aggregation concentration (CAC) of tubule formation of γ-oryzanol and sitosterol was determined using these techniques. The temperature dependence of the CAC was used to estimate the binding energy and enthalpic and entropic contribution to the tubular formation process. The binding energy calculated at the corresponding temperatures and CACs were relatively low, in order of 2 RT (4.5 kJ mol−1), which is in accord with the reversibility of the tubular formation process. The formation of the tubules was associated with negative (exothermic) enthalpy change (ΔH0) compared with positive entropy term (−T ΔS0 >0), indicating that the aggregation into tubules is an enthalpy-driven process. The oryzanol–sitosterol ratio affected the aggregation process; solutions with ratio of (60 oryzanol–40 sitosterol) started aggregation at higher temperature compared with other ratios. PMID:21423326

The Influence of Concentration and Temperature on the Formation of γ-Oryzanol + β-Sitosterol Tubules in Edible Oil Organogels.

PubMed

Sawalha, Hassan; Venema, Paul; Bot, Arjen; Flöter, Eckhard; van der Linden, Erik

2011-03-01

The gelation process of mixtures of γ-oryzanol and sitosterol structurants in sunflower oil was studied using light scattering, rheology, and micro-scanning calorimetry (Micro-DSC). The relation between temperature and the critical aggregation concentration (CAC) of tubule formation of γ-oryzanol and sitosterol was determined using these techniques. The temperature dependence of the CAC was used to estimate the binding energy and enthalpic and entropic contribution to the tubular formation process. The binding energy calculated at the corresponding temperatures and CACs were relatively low, in order of 2 RT (4.5 kJ mol(-1)), which is in accord with the reversibility of the tubular formation process. The formation of the tubules was associated with negative (exothermic) enthalpy change (ΔH(0)) compared with positive entropy term (-T ΔS(0) >0), indicating that the aggregation into tubules is an enthalpy-driven process. The oryzanol-sitosterol ratio affected the aggregation process; solutions with ratio of (60 oryzanol-40 sitosterol) started aggregation at higher temperature compared with other ratios.

Effects of in vitro endochondral priming and pre-vascularisation of human MSC cellular aggregates in vivo.

PubMed

Freeman, Fiona E; Allen, Ashley B; Stevens, Hazel Y; Guldberg, Robert E; McNamara, Laoise M

2015-11-05

During endochondral ossification, both the production of a cartilage template and the subsequent vascularisation of that template are essential precursors to bone tissue formation. Recent studies have found the application of both chondrogenic and vascular priming of mesenchymal stem cells (MSCs) enhanced the mineralisation potential of MSCs in vitro whilst also allowing for immature vessel formation. However, the in vivo viability, vascularisation and mineralisation potential of MSC aggregates that have been pre-conditioned in vitro by a combination of chondrogenic and vascular priming, has yet to be established. In this study, we test the hypothesis that a tissue regeneration approach that incorporates both chondrogenic priming of MSCs, to first form a cartilage template, and subsequent pre-vascularisation of the cartilage constructs, by co-culture with human umbilical vein endothelial cells (HUVECs) in vitro, will improve vessel infiltration and thus mineral formation once implanted in vivo. Human MSCs were chondrogenically primed for 21 days, after which they were co-cultured with MSCs and HUVECs and cultured in endothelial growth medium for another 21 days. These aggregates were then implanted subcutaneously in nude rats for 4 weeks. We used a combination of bioluminescent imaging, microcomputed tomography, histology (Masson's trichrome and Alizarin Red) and immunohistochemistry (CD31, CD146, and α-smooth actin) to assess the vascularisation and mineralisation potential of these MSC aggregates in vivo. Pre-vascularised cartilaginous aggregates were found to have mature endogenous vessels (indicated by α-smooth muscle actin walls and erythrocytes) after 4 weeks subcutaneous implantation, and also viable human MSCs (detected by bioluminescent imaging) 21 days after subcutaneous implantation. In contrast, aggregates that were not pre-vascularised had no vessels within the aggregate interior and human MSCs did not remain viable beyond 14 days. Interestingly, the pre-vascularised cartilaginous aggregates were also the only group to have mineralised nodules within the cellular aggregates, whereas mineralisation occurred in the alginate surrounding the aggregates for all other groups. Taken together these results indicate that a combined chondrogenic priming and pre-vascularisation approach for in vitro culture of MSC aggregates shows enhanced vessel formation and increased mineralisation within the cellular aggregate when implanted subcutaneously in vivo.

Tectonic Deformation Pattern along the Longmen Shan Fault Zone in Eastern Tibet: Insights from Focal Mechanisms of the Wenchuan and Lushan Earthquake Sequences, Southwestern China

NASA Astrophysics Data System (ADS)

Yi, G.; Vallage, A.; Klinger, Y.; Long, F.; Wang, S.

2017-12-01

760 ML≥3.5 aftershocks of the 2008 Wenchuan earthquake, the 2013 Lushan mainshock and its 87 ML≥3.5 aftershocks were selected to obtain focal mechanism solutions from CAP waveform inversion method (Zhu and Helmberger, 1996), along with strain rosette (Amelung and King, 1997) and Areal strain (As) (Vallage et al., 2014), we aimed to analyze the tectonic deformation pattern along the Longmen Shan (LMS) fault zone, southwestern China. The As values show that 93% compressional earthquakes for the Lushan sequence are of pure thrust for the southern segment of the LMS fault zone, while only 50% compressional and nearly 40% of strike-slip and oblique-thrust events for the Wenchuan sequence reflect the strike-slip component increase on the central-northern segment of the LMS fault zone, meaning many different faults responsible for the Wenchuan aftershock activity. The strain rosettes with purely NW-trending compressional white lobe for the entire 87 aftershocks and 4 different classes of magnitudes are very similar to that of the Lushan mainshock. We infer that the geological structures for the southern segment are of thrust faulting under NW compressional deformation. The strain rosettes exhibit self-similarity in terms of orientation and shape for all classes, reflecting that the deformation pattern of the southern segment is independent with earthquake size, and suggesting that each class is representative of the overall deformation for the southern segment. We obtained EW-oriented pure compressional strain rosette of the entire 760 aftershocks and NW-oriented white lobe with small NE-oriented black lobe of the Wenchuan mainshock, and this difference may reflect different tectonic deformation pattern during the co-seismic and post-seismic stages. The deformation segmentation along the Wenchuan coseismic surface rupture is also evidenced from the different orientation of strain rosettes, i.e., NW for the southern area, NE for the central and NNW for the northern parts. The above inferences indicate a very complicated tectonic deformation pattern related to the complex geological structure. The segment of the northern aftershock area without ruptures behaves an oblique compressional deformation.

Pulsed electric field (PEF)-induced aggregation between lysozyme, ovalbumin and ovotransferrin in multi-protein system.

PubMed

Wu, Li; Zhao, Wei; Yang, Ruijin; Yan, Wenxu

2015-05-15

The aggregation of multi-proteins is of great interest in food processing and a good understanding of the formation of aggregates during PEF processing is needed for the application of the process to pasteurize protein-based foods. The aggregates formation of a multi-protein system (containing ovalbumin, ovotransferrin and lysozyme) was studied through turbidity, size exclusion chromatography and SDS-PAGE patterns for interaction studies and binding forces. Results from size exclusion chromatography indicated that there was no soluble aggregates formed during PEF processing. The existence of lysozyme was important to form insoluble aggregates in the chosen ovalbumin solution. The results of SDS-PAGE patterns indicated that lysozyme was prone to precipitate, and was relatively the higher component of aggregates. Citric acid could be effective in inhibiting lysozyme from interacting with other proteins during PEF processing. Blocking the free sulphydryl by N-ethylmaleimide (NEM) did not affect aggregation inhibition. Copyright © 2014 Elsevier Ltd. All rights reserved.

Mitochondrial enzymes are protected from stress-induced aggregation by mitochondrial chaperones and the Pim1/LON protease

PubMed Central

Bender, Tom; Lewrenz, Ilka; Franken, Sebastian; Baitzel, Catherina; Voos, Wolfgang

2011-01-01

Proteins in a natural environment are constantly challenged by stress conditions, causing their destabilization, unfolding, and, ultimately, aggregation. Protein aggregation has been associated with a wide variety of pathological conditions, especially neurodegenerative disorders, stressing the importance of adequate cellular protein quality control measures to counteract aggregate formation. To secure protein homeostasis, mitochondria contain an elaborate protein quality control system, consisting of chaperones and ATP-dependent proteases. To determine the effects of protein aggregation on the functional integrity of mitochondria, we set out to identify aggregation-prone endogenous mitochondrial proteins. We could show that major metabolic pathways in mitochondria were affected by the aggregation of key enzyme components, which were largely inactivated after heat stress. Furthermore, treatment with elevated levels of reactive oxygen species strongly influenced the aggregation behavior, in particular in combination with elevated temperatures. Using specific chaperone mutant strains, we showed a protective effect of the mitochondrial Hsp70 and Hsp60 chaperone systems. Moreover, accumulation of aggregated polypeptides was strongly decreased by the AAA-protease Pim1/LON. We therefore propose that the proteolytic breakdown of aggregation-prone polypeptides represents a major protective strategy to prevent the in vivo formation of aggregates in mitochondria. PMID:21209324

Fundus Autofluorescence and Photoreceptor Cell Rosettes in Mouse Models

PubMed Central

Flynn, Erin; Ueda, Keiko; Auran, Emily; Sullivan, Jack M.; Sparrow, Janet R.

2014-01-01

Purpose. This study was conducted to study correlations among fundus autofluorescence (AF), RPE lipofuscin accumulation, and photoreceptor cell degeneration and to investigate the structural basis of fundus AF spots. Methods. Fundus AF images (55° lens; 488-nm excitation) and spectral-domain optical coherence tomography (SD-OCT) scans were acquired in pigmented Rdh8−/−/Abca4−/− mice (ages 1–9 months) with a confocal scanning laser ophthalmoscope (cSLO). For quantitative fundus AF (qAF), gray levels (GLs) were calibrated to an internal fluorescence reference. Retinal bisretinoids were measured by quantitative HPLC. Histometric analysis of outer nuclear layer (ONL) thicknesses was performed, and cryostat sections of retina were examined by fluorescence microscopy. Results. Quantified A2E and qAF intensities increased until age 4 months in the Rdh8−/−/Abca4−/− mice. The A2E levels declined after 4 months of age, but qAF intensity values continued to rise. The decline in A2E levels in the Rdh8−/−/Abca4−/− mice paralleled reduced photoreceptor cell viability as reflected in ONL thinning. Hyperautofluorescent puncta in fundus AF images corresponded to photoreceptor cell rosettes in SD-OCT images and histological sections stained with hematoxylin and eosin. The inner segment/outer segment–containing core of the rosette emitted an autofluorescence detected by fluorescence microscopy. Conclusions. When neural retina is disordered, AF from photoreceptor cells can contribute to noninvasive fundus AF images. Hyperautofluorescent puncta in fundus AF images are attributable, in at least some cases, to photoreceptor cell rosettes. PMID:25015357

Helical structures in a Rosette elephant trunk

NASA Astrophysics Data System (ADS)

Carlqvist, Per; Kristen, Helmuth; Gahm, Gosta F.

1998-04-01

We discuss small-scale, helical, interstellar filaments on the basis of optical observations of an elephant trunk in the Rosette nebula. The trunk studied is composed of a number of sinusoidal or serpentine-like dark filaments, preferentially in the outer part of the trunk, where their wavelength is 7-9 times the trunk radius. The diameters are down to the limit of resolution of 1.0 arcsec, corresponding to 1600 au, and ranging up to about 6400 au. At some positions filament crossings give rise to enhanced extinction. We suggest that the sinusoidal filaments are helices lined up by magnetic fields. We derive average extinctions of 0.5-1.0 mag in the filaments, implying molecular densities of n_H2 ~ 10(4) cm(-3) . From existing data on the Rosette HiI region, we conclude that the surrounding kinetic and dynamic pressure and the background radiation field suffice to balance even the denser filaments and to exert drag forces on the trunk as a whole, consistent with evidence of stretching of the trunk. The helical magnetic structures imply the presence of electric currents along the trunk axis. These currents should form a nearly force-free geometry and are consistent with a model consisting of 4-7 helical cables on the surface of a cylinder and which produce the observed wavelength of the helices. We suggest that the Rosette elephant trunks form an interconnected system of rope-like structures which are relics from filamentary skeletons of magnetic fields in the primordial cloud. Based on observations collected at the Nordic Optical Telescope, La Palma, Spain

Deep sequencing reveals a novel closterovirus associated with wild rose leaf rosette disease.

PubMed

He, Yan; Yang, Zuokun; Hong, Ni; Wang, Guoping; Ning, Guogui; Xu, Wenxing

2015-06-01

A bizarre virus-like symptom of a leaf rosette formed by dense small leaves on branches of wild roses (Rosa multiflora Thunb.), designated as 'wild rose leaf rosette disease' (WRLRD), was observed in China. To investigate the presumed causal virus, a wild rose sample affected by WRLRD was subjected to deep sequencing of small interfering RNAs (siRNAs) for a complete survey of the infecting viruses and viroids. The assembly of siRNAs led to the reconstruction of the complete genomes of three known viruses, namely Apple stem grooving virus (ASGV), Blackberry chlorotic ringspot virus (BCRV) and Prunus necrotic ringspot virus (PNRSV), and of a novel virus provisionally named 'rose leaf rosette-associated virus' (RLRaV). Phylogenetic analysis clearly placed RLRaV alongside members of the genus Closterovirus, family Closteroviridae. Genome organization of RLRaV RNA (17,653 nucleotides) showed 13 open reading frames (ORFs), except ORF1 and the quintuple gene block, most of which showed no significant similarities with known viral proteins, but, instead, had detectable identities to fungal or bacterial proteins. Additional novel molecular features indicated that RLRaV seems to be the most complex virus among the known genus members. To our knowledge, this is the first report of WRLRD and its associated closterovirus, as well as two ilarviruses and one capilovirus, infecting wild roses. Our findings present novel information about the closterovirus and the aetiology of this rose disease which should facilitate its control. More importantly, the novel features of RLRaV help to clarify the molecular and evolutionary features of the closterovirus. © 2014 BSPP AND JOHN WILEY & SONS LTD.

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

Copuroglu, Oguzhan, E-mail: O.Copuroglu@CiTG.TUDelft.NL; Andic-Cakir, Ozge; Broekmans, Maarten A.T.M.

In this paper, the alkali-silica reaction performance of a basalt rock from western Anatolia, Turkey is reported. It is observed that the rock causes severe gel formation in the concrete microbar test. It appears that the main source of expansion is the reactive glassy phase of the basalt matrix having approximately 70% of SiO{sub 2}. The study presents the microstructural characteristics of unreacted and reacted basalt aggregate by optical and electron microscopy and discusses the possible reaction mechanism. Microstructural analysis revealed that the dissolution of silica is overwhelming in the matrix of the basalt and it eventually generates four consequences:more » (1) Formation of alkali-silica reaction gel at the aggregate perimeter, (2) increased porosity and permeability of the basalt matrix, (3) reduction of mechanical properties of the aggregate and (4) additional gel formation within the aggregate. It is concluded that the basalt rock is highly prone to alkali-silica reaction. As an aggregate, this rock is not suitable for concrete production.« less

Photo-processing P3HT conjugated polymers, in solution: A new route towards ordered polymeric structures.

NASA Astrophysics Data System (ADS)

Barbosa Neto, Newton; Dutra, Marcia; Araujo, Paulo; Sampaio, Renato

Solution aggregated thin films of conjugated polymers have demonstrated to be promising materials for many applications, e.g., solar cells and field-effect transistors. There are many standard methods to generate aggregates in polymeric solution, which includes poor solvent addiction and solution temperature manipulation. Here, we demonstrate a new approach to induce aggregate formation on solution of P3HT polymer. Under light excitation with 355 nm or 532 nm pulsed laser the polymer exhibit significant changes on its UV-Vis spectrum which are most known in the literature as the formation of H-J aggregates and additional new bands associated with polaron formation. Such changes in the amorphous phase of the polymers are seen in specific conditions of solvent combinations. We show also the dependency on the excitation laser power which can be identified as a threshold to ignite the formation of the new structure. We are grateful to CNPq and CAPES for financial support.

Soil factors effects on life history attributes of Leiothrix spiralis and Leiothrix vivipara (Eriocaulaceae) on rupestrian grasslands in Southeastern Brazil.

PubMed

Coelho, F F; Martins, R P; Figueira, J E C; Demetrio, G R

2014-11-01

In this study, we hypothesized that the life history traits of Leiothrix spiralis and L. vivipara would be linked to soil factors of the rupestrian grasslands and that rosette size would be influenced by soil moisture. Soil analyses were performed from five populations of L. spiralis and four populations of L. vivipara. In each area, three replicates were employed in 19 areas of occurrence of Leiothrix species, and we quantified the life history attributes. The microhabitats of these species show low favorability regarding to soil factors. During the dry season, their rosettes decreased in diameter due the loss of its most outlying leaves. The absence of seedlings indicated the low fecundity of both species. However, both species showed rapid population growth by pseudovivipary. Both L. spiralis and L. vivipara exhibit a kind of parental care that was quantified by the presence of connections between parental-rosettes and ramets. The findings of the present study show that the life history traits are linked to soil factors.

Variation in the expression of macrophage Fc epsilon receptors in relation to experimental rat schistosome infection.

PubMed

Pestel, J; Joseph, M; Dessaint, J P; Capron, A

1988-01-01

The relationship between IgE and rat peritoneal macrophages during the course of Schistosoma mansoni infection was examined. Immune macrophages exhibited an IgE-dependent schistosomulicidal activity mainly between the 5th and the 7th weeks. At this period the percentages of anti-IgE rosettes whose variations appeared consecutive to the variations in the serum IgE level were higher. Following incubation in a serum-free medium immune macrophages could release membrane-associated IgE, to a certain extent, and consequently formed rosettes with IgE-coated erythrocytes, indicating the existence of Fc epsilon receptors. Thus, in terms of rosettes, their number varied in the course of the disease. In fact IgE-rich serum (i.e. at day 42) as IgE molecules could induce this macrophage Fc epsilon receptor. Moreover when transferred to syngeneic rats in association with parasite-specific IgE Fc epsilon R2+ macrophages led to some protection against challenge infection. All the data reported here emphasize the determining role of macrophages and IgE in immunity to schistosomiasis.

Case Report: A Rosette-forming Glioneuronal Tumor in the Tectal Plate in a Patient with Neurofibromatosis Type I.

PubMed

Sieg, Emily P; Payne, Russell; Langan, Sara; Specht, Charles S

2016-11-01

We report the case of a 41-year-old female with neurofibromatosis Type 1 (NF1) who developed a rosette-forming glioneuronal tumor (RGNT) in the tectal plate. This tumor was diagnosed in 2002 when the patient presented with obstructive hydrocephalus, which was subsequently treated with a ventriculoperitoneal shunt and then an endoscopic third ventriculostomy. Initially thought to be a pilocytic astrocytoma, it was followed with serial magnetic resonance imaging (MRI) until tumor progression and development of a large fourth ventricular cystic component prompted resection via suboccipital craniotomy. Histological examination demonstrated an RGNT, a WHO Grade 1 tumor, with neurocytic rosettes, perivascular pseudorosettes, and elements resembling a pilocytic astrocytoma. Initially, the patient did well after her craniotomy, but postoperative complications set in that eventually led to her death. In this case report, we describe a relatively rare tumor that, despite its benign nature, leads to frequent complications and deficits due to its surgically challenging location. Along with previously reported examples, this cases raises the possibility of a causal relationship between NF1 and RGNT.

Developmental and environmental effects on assimilate partitioning in Canada thistle

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

Tworkoski, T.J.

1989-04-01

Canada thistle (Cirsium arvense) plants at three stages of development (rosette, bolt, and flower bud) were grown under spring-simulated or fall-simulated environments. Sucrose export from a single leaf exposed to {sup 14}CO{sub 2} was significantly greater in rosette-plants than bolt- or flower bud-plants during the first two hours after pulse. Twenty-four hours after pulse, total {sup 14}C translocation (dpm) was the same in both environments but the {sup 14}C concentration (dpm/gm) was greater in roots of fall-grown plants. Shoot meristem respiration of fall-grown plants was approximately 50% less than spring-grown plants and was a factor responsible for this trend. Concentrationsmore » of inulin and water-insoluble starch were greater in roots of fall-grown than spring-grown plants and pulsed {sup 14}C accumulated in these fractions. The results suggest that a shift in respiration and metabolism of fall-grown rosette- and bolt-plants leads to increased assimilate movement to the root which may have practical implications for control of this weed.« less

Opposed Effects of Dityrosine Formation in Soluble and Aggregated α-Synuclein on Fibril Growth.

PubMed

Wördehoff, Michael M; Shaykhalishahi, Hamed; Groß, Luca; Gremer, Lothar; Stoldt, Matthias; Buell, Alexander K; Willbold, Dieter; Hoyer, Wolfgang

2017-10-13

Parkinson's disease is the second most common neurodegenerative disease. It is characterized by aggregation of the protein α-synuclein (α-syn) in Lewy bodies, mitochondrial dysfunction, and increased oxidative stress in the substantia nigra. Oxidative stress leads to several modifications of biomolecules including dityrosine (DiY) crosslinking in proteins, which has recently been detected in α-syn in Lewy bodies from Parkinson's disease patients. Here we report that α-syn is highly susceptible to ultraviolet-induced DiY formation. We investigated DiY formation of α-syn and nine tyrosine-to-alanine mutants and monitored its effect on α-syn fibril formation in vitro. Ultraviolet irradiation of intrinsically disordered α-syn generates DiY-modified monomers and dimers, which inhibit fibril formation of unmodified α-syn by interfering with fibril elongation. The inhibition depends on both the DiY group and its integration into α-syn. When preformed α-syn fibrils are crosslinked by DiY formation, they gain increased resistance to denaturation. DiY-stabilized α-syn fibrils retain their high seeding efficiency even after being exposed to denaturant concentrations that completely depolymerize non-crosslinked seeds. Oxidative stress-associated DiY crosslinking of α-syn therefore entails two opposing effects: (i) inhibition of aggregation by DiY-modified monomers and dimers, and (ii) stabilization of fibrillar aggregates against potential degradation mechanisms, which can lead to promotion of aggregation, especially in the presence of secondary nucleation. Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Amyloidogenic behavior of different intermediate state of stem bromelain: A biophysical insight.

PubMed

Zaman, Masihuz; Ehtram, Aquib; Chaturvedi, Sumit Kumar; Nusrat, Saima; Khan, Rizwan Hasan

2016-10-01

Stem bromelain, a cysteine proteases from Ananas comosus is a widely accepted therapeutic drug with broad medicinal application. It exists as intermediate states at pH 2.0 and 10.0, where it encountered in gastrointestinal tract during adsorption (acidic pH) and in gut epithelium (alkaline pH), respectively. In this study, we monitored the thermal aggregation/amyloid formation of SB at different pH intermediate states. Thermal treatment of stem bromelain at pH 10.0 favors the fibrillation in which the extent of aggregation increases with increase in protein concentration. However, no fibril formation in stem bromelain at pH 2.0 was found at all the concentration used at pH 10.0. The fibril formation was confirmed by various techniques such as turbidity measurements, Rayleigh light scattering, dye binding assays and far UV circular dichroism. The Dynamic light scattering confirmed the formation of aggregates by measuring the hydrodynamic radii pattern. Moreover, microscopic techniques were performed to analyze the morphology of fibrils. The aggregation behavior may be due to variation in number of charged amino acid residues. The less negative charge developed at pH 10.0 may be responsible for aggregation. This work helps to overcome the aggregation related problems of stem bromelain during formulations in pharmaceutical industry. Copyright © 2016 Elsevier B.V. All rights reserved.

Enhancing Tumor Drug Delivery by Laser-Activated Vascular Barrier Disruption

DTIC Science & Technology

2009-12-01

found platelet aggregation, thrombus formation and endothelial cell rupture (Fig 1). All these findings demonstrate that PDT damages endothelial...after 0.5 mg/kg verteporfin (i.v.)). (A) 1 h after PDT showing platelet aggregation and thrombus formation; (B) 6 h after PDT showing edema...mechanisms causing thrombi formation. Other mechanisms, such as release of thromboxane from platelets (33) and von Willebrand factor from damaged

Detection of Mutant Huntingtin Aggregation Conformers and Modulation of SDS-Soluble Fibrillar Oligomers by Small Molecules

PubMed Central

Sontag, Emily Mitchell; Lotz, Gregor P.; Yang, Guocheng; Sontag, Christopher J.; Cummings, Brian J.; Glabe, Charles G.; Muchowski, Paul J.; Thompson, Leslie Michels

2012-01-01

The Huntington’s disease (HD) mutation leads to a complex process of Huntingtin (Htt) aggregation into multimeric species that eventually form visible inclusions in cytoplasm, nuclei and neuronal processes. One hypothesis is that smaller, soluble forms of amyloid proteins confer toxic effects and contribute to early cell dysfunction. However, analysis of mutant Htt aggregation intermediates to identify conformers that may represent toxic forms of the protein and represent potential drug targets remains difficult. We performed a detailed analysis of aggregation conformers in multiple in vitro, cell and ex vivo models of HD. Conformation-specific antibodies were used to identify and characterize aggregation species, allowing assessment of multiple conformers present during the aggregation process. Using a series of assays together with these antibodies, several forms could be identified. Fibrillar oligomers, defined as having a β-sheet rich conformation, are observed in vitro using recombinant protein and in protein extracts from cells in culture or mouse brain and shown to be globular, soluble and non-sedimentable structures. Compounds previously described to modulate visible inclusion body formation and reduce toxicity in HD models were also tested and consistently found to alter the formation of fibrillar oligomers. Interestingly, these compounds did not alter the rate of visible inclusion formation, indicating that fibrillar oligomers are not necessarily the rate limiting step of inclusion body formation. Taken together, we provide insights into the structure and formation of mutant Htt fibrillar oligomers that are modulated by small molecules with protective potential in HD models. PMID:24086178

The wearing characteristics of mineral aggregates in highway pavements.

DOT National Transportation Integrated Search

1970-01-01

Fifteen asphaltic concrete and seventeen portland cement concrete pavements located in Virginia were chosen for studies of aggregate wear and related wet pavement friction. Coarse aggregates from thirteen different geologic formations and quarry sour...

Quantitation of human thymus/leukemia-associated antigen by radioimmunoassay in different forms of leukemia.

PubMed

Chechik, B E; Jason, J; Shore, A; Baker, M; Dosch, H M; Gelfand, E W

1979-12-01

Using a radioimmunoassay, increased levels of a human thymus/leukemia-associated antigen (HThy-L) have been detected in leukemic cells and plasma from most patients with E-rosette-positive acute lymphoblastic leukemia (ALL) and a number of patients with E-rosette-negative ALL, acute myeloblastic leukemia (AML), acute monomyelocytic leukemia (AMML), and acute undifferentiated leukemia (AVL). Low levels of HThy-L have been demonstrated in white cells from patients with chronic myelocytic leukemia (stable phase) and in mononuclear cells from patients with chronic lymphatic leukemia. The relationship between HThy-L and differentiation of hematopoietic cells is discussed.

Melphalan, Carboplatin, Mannitol, and Sodium Thiosulfate in Treating Patients With Recurrent or Progressive CNS Embryonal or Germ Cell Tumors

ClinicalTrials.gov

2018-05-02

Adult Central Nervous System Germ Cell Tumor; Adult Embryonal Tumor With Multilayered Rosettes, C19MC-Altered; Adult Medulloblastoma; Adult Pineoblastoma; Adult Supratentorial Embryonal Tumor, Not Otherwise Specified; Atypical Teratoid/Rhabdoid Tumor; Childhood Atypical Teratoid/Rhabdoid Tumor; Childhood Central Nervous System Germ Cell Tumor; Childhood Embryonal Tumor With Multilayered Rosettes, C19MC-Altered; Medulloepithelioma; Ototoxicity; Recurrent Adult Brain Neoplasm; Recurrent Childhood Central Nervous System Embryonal Neoplasm; Recurrent Childhood Malignant Germ Cell Tumor; Recurrent Childhood Medulloblastoma; Recurrent Childhood Pineoblastoma; Recurrent Childhood Supratentorial Embryonal Tumor, Not Otherwise Specified

Development of an embedded Fabry Perot Fiber Optic Strain Rosette Sensor (FP-FOSRS)

NASA Technical Reports Server (NTRS)

Carman, Gregory P.; Lesko, John J.; Case, Scott W.; Fogg, Brian; Claus, Richard O.

1992-01-01

We investigate the feasibility of utilizing a Fabry-Perot Fiber Optic Strain Rosette Sensor (FP-FOSRS) for the evaluation of the internal strain state of a material system. We briefly describe the manufacturing process for this sensor and point out some potential problem areas. Results of an embedded FP-FOSRS in an epoxy matrix with external resistance strain gauges applied for comparative purposes are presented. We show that the internal and external strain measurements are in close agreement. This work lays the foundation for embedding this sensor in actual composite laminas.

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

Levin, Johannes; German Center for Neurodegenerative Diseases – DZNE, Site Munich, Feodor-Lynen-Str. 17, 81377 Munich; Hillmer, Andreas S.

Synucleinopathies such as dementia with Lewy bodies or Parkinson’s disease are characterized by intracellular deposition of pathologically aggregated α-synuclein. The details of the molecular pathogenesis of PD and especially the conditions that lead to intracellular aggregation of α-synuclein and the role of these aggregates in cell death remain unknown. In cell free in vitro systems considerable knowledge about the aggregation processes has been gathered. In comparison, the knowledge about these aggregation processes in cells is far behind. In cells α-synuclein aggregates can be toxic. However, the crucial particle species responsible for decisive steps in pathogenesis such as seeding a continuing aggregationmore » process and triggering cell death remain to be identified. In order to understand the complex nature of intracellular α-synuclein aggregate formation, we analyzed fluorescent particles formed by venus and α-synuclein-venus fusion proteins and α-synuclein-hemi-venus fusion proteins derived from gently lyzed cells. With these techniques we were able to identify and characterize α-synuclein oligomers formed in cells. Especially the use of α-synuclein-hemi-venus fusion proteins enabled us to identify very small α-synuclein oligomers with high sensitivity. Furthermore, we were able to study the molecular effect of heat shock protein 70, which is known to inhibit α-synuclein aggregation in cells. Heat shock protein 70 does not only influence the size of α-synuclein oligomers, but also their quantity. In summary, this approach based on fluorescence single particle spectroscopy, that is suited for high throughput measurements, can be used to detect and characterize intracellularly formed α-synuclein aggregates and characterize the effect of molecules that interfere with α-synuclein aggregate formation. - Highlights: • Single particle spectroscopy detects intracellular formed α-synuclein aggregates. • Fusion proteins allow detection of protein aggregates at the oligomer level. • The technique detects molecules inhibiting α-synuclein aggregate formation. • Single particle spectroscopy is suited for high throughput measurements.« less

Nattokinase improves blood flow by inhibiting platelet aggregation and thrombus formation

PubMed Central

Jang, Ja-Young; Kim, Tae-Su; Cai, Jingmei; Kim, Jihyun; Kim, Youngeun; Shin, Kyungha; Kim, Kwang Sei; Park, Sung Kyeong; Lee, Sung-Pyo; Choi, Ehn-Kyoung

2013-01-01

The effects of nattokinase on the in vitro platelet aggregation and in vivo thrombosis were investigated in comparison with aspirin. Rabbit platelet-rich plasma was incubated with nattokinase and aggregation inducers collagen and thrombin, and the platelet aggregation rate was analyzed. Nattokinase significantly inhibited both the collagen- and thrombin-induced platelet aggregations. Nattokinase also reduced thromboxane B2 formation from collagen-activated platelets in a concentration-dependent manner. Rats were orally administered with nattokinase for 1 week, and their carotid arteries were exposed. Arterial thrombosis was induced by applying 35% FeCl3-soaked filter paper for 10 min, and the blood flow was monitored with a laser Doppler probe. Nattokinase delayed the FeCl3-induced arterial occlusion in a dose-dependent manner, doubling the occlusion time at 160 mg/kg. In addition, a high dose (500 mg/kg) of nattokinase fully prevented the occlusion, as achieved with aspirin (30 mg/kg). The results indicate that nattokinase extracted from fermented soybean inhibit platelet aggregation by blocking thromboxane formation, and thereby delay thrombosis following oxidative arterial wall injury. Therefore, it is suggested that nattokinase could be a good candidate without adverse effects for the improvement of blood flow. PMID:24396387

Nattokinase improves blood flow by inhibiting platelet aggregation and thrombus formation.

PubMed

Jang, Ja-Young; Kim, Tae-Su; Cai, Jingmei; Kim, Jihyun; Kim, Youngeun; Shin, Kyungha; Kim, Kwang Sei; Park, Sung Kyeong; Lee, Sung-Pyo; Choi, Ehn-Kyoung; Rhee, Man Hee; Kim, Yun-Bae

2013-12-01

The effects of nattokinase on the in vitro platelet aggregation and in vivo thrombosis were investigated in comparison with aspirin. Rabbit platelet-rich plasma was incubated with nattokinase and aggregation inducers collagen and thrombin, and the platelet aggregation rate was analyzed. Nattokinase significantly inhibited both the collagen- and thrombin-induced platelet aggregations. Nattokinase also reduced thromboxane B2 formation from collagen-activated platelets in a concentration-dependent manner. Rats were orally administered with nattokinase for 1 week, and their carotid arteries were exposed. Arterial thrombosis was induced by applying 35% FeCl3-soaked filter paper for 10 min, and the blood flow was monitored with a laser Doppler probe. Nattokinase delayed the FeCl3-induced arterial occlusion in a dose-dependent manner, doubling the occlusion time at 160 mg/kg. In addition, a high dose (500 mg/kg) of nattokinase fully prevented the occlusion, as achieved with aspirin (30 mg/kg). The results indicate that nattokinase extracted from fermented soybean inhibit platelet aggregation by blocking thromboxane formation, and thereby delay thrombosis following oxidative arterial wall injury. Therefore, it is suggested that nattokinase could be a good candidate without adverse effects for the improvement of blood flow.

Aggregation Pathways of Native-Like Ubiquitin Promoted by Single-Point Mutation, Metal Ion Concentration, and Dielectric Constant of the Medium.

PubMed

Fermani, Simona; Calvaresi, Matteo; Mangini, Vincenzo; Falini, Giuseppe; Bottoni, Andrea; Natile, Giovanni; Arnesano, Fabio

2018-03-15

Ubiquitin-positive protein aggregates are biomarkers of neurodegeneration, but the molecular mechanism responsible for their formation and accumulation is still unclear. Possible aggregation pathways of human ubiquitin (hUb) promoted by both intrinsic and extrinsic factors, are here investigated. By a computational analysis, two different hUb dimers are indicated as possible precursors of amyloid-like structures, but their formation is disfavored by an electrostatic repulsion involving Glu16 and other carboxylate residues present at the dimer interface. Experimental data on the E16V mutant of hUb shows that this single-point mutation, although not affecting the overall protein conformation, promotes protein aggregation. It is sufficient to shift the same mutation by only two residues (E18V) to regain the behavior of wild-type hUb. The neutralization of Glu16 negative charge by a metal ion and a decrease of the dielectric constant of the medium by addition of trifluoroethanol (TFE), also promote hUb aggregation. The outcomes of this research have important implications for the prediction of physiological parameters that favor aggregate formation. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

The microphysical and radiative properties of tropical cirrus from the 2006 Tropical Warm Pool International Cloud Experiment (TWP-ICE)

NASA Astrophysics Data System (ADS)

Um, Jun Shik

During the 2006 Tropical Warm Pool International Cloud Experiment conducted in the region near Darwin, Australia, the Scaled Composites Proteus aircraft executed spiral profiles and flew horizontal legs through aging cirrus, fresh anvils, and cirrus of unknown origin. Data from 27 Jan., 29 Jan., and 2 Feb., when all the microphysical probes a Cloud and Aerosol Spectrometer (CAS), a Cloud Droplet Probe (CDP), a Cloud Imaging Probe (CIP), and a Cloud Particle Imager (CPI) were working, are used to investigate whether a single parameterization can be used to characterize tropical cirrus in terms of prognostic variables used in large-scale models, to calculate the single-scattering properties (scattering phase function P11 and asymmetry parameter g) of aggregates and small ice crystals that more closely match observed ice crystals, and to quantify the influences of small ice crystals on the bulk scattering properties of tropical cirrus. A combination of CDP (D < 50 mum), fits (50 < D < 125 microm), and CIP (D > 125 mum) distributions is used to represent ice crystal size distributions. The CDP measurements are used for small ice crystals because comparison between the CAS and CDP suggested the CAS was artificially amplifying small ice crystal concentrations by detecting remnants of shattered large ice crystals. Artifacts in CIP images are removed or corrected and then CIP measurements are used to represent large ice crystals. Because of the uncertainties in both the CPI and CIP for 50 < D < 125 mum, the incomplete gamma fitting method with the CDP (D < 50 mum) and CIP (D > 125 mum) measurements as input is used to characterize these distributions. A new quasi-automatic habit classification scheme is developed. For all days, small quasi-spheres dominated the contributions from all ice crystal sizes (D > 0 mum, by number) for all 3 days. The areal fraction (D > 200 mum) from bullet rosettes and their aggregates was 48% and 60% for 27 and 29 Jan., respectively, but only 7% for 2 Feb, whereas the fraction of aggregates of plates was 46.2% for 2 Feb. and only 7.2% and 1% for 27 and 29 Jan., respectively. The difference in ice crystal habits sampled on the different days is likely associated with the difference between fresh anvil cirrus on 2 Feb. and aged cirrus bands on the 27 and 29 of Jan. Because of variations in microphysical properties (i.e., number concentration, median mass dimension, and fit variables of gamma distributions) it is also shown that variables in addition to ice water content and temperature are required to represent the characteristics of cirrus with different origins in large-scale models. Aggregates of bullet rosettes and aggregates of plates are shown to scatter more light in the lateral and backward scattering region and less light in the forward scattering region compared to their component crystals, leading to a decrease in g for aggregates. To represent the three-dimensional shape of aggregates of plates, three parameters, the aggregation index ( AI), the area ratio (AR), and the normalized projected area (An), are introduced and the single-scattering properties of aggregates of plates are shown to depend heavily on AI. A new model (budding Bucky ball, 3B) for the shape of small ice crystals is developed based on the shapes of ice analogues grown in laboratory experiments. The 3B scatters more light in the lateral, and backward direction and less in the forward direction compared with other existing models currently used to describe small crystal shape (i.e., Gaussian random sphere and droxtal). The combination of the reduction in the forward scattering and enhancement in the lateral and backward scattering causes 11.13% and 8.74% decreases in g for the 3B compared with that for Gaussian random sphere and droxtal, respectively. The impacts of variations in small ice crystal shapes and concentrations on bulk scattering properties of tropical cirrus are quantified. The calculated mean asymmetry parameter ḡ for the fresh anvil (i.e., 2 Feb) is larger than that for cirrus bands of varying ages (i.e., 27 and 29 Jan.) for -60 < T < -45°C and -45 < T < -30°C where the fractional contributions of small ice crystals to total cross sectional area are small. The impact using different models for small ice crystals on ḡ is largest at lower temperatures (T < -60°C). The impact of enhanced number concentrations of small ice crystals on the bulk scattering properties depends on the assumed shapes of small ice crystals, which is largest (smallest) in the temperature ranges of -45 < T < -30 T (T < -60°C) where the CAS/CDP ratio of N of small ice crystals is maximum (minimum).

Chondrule Pyroxene Embedded in Cores of Amoeboid Olivine Aggregates from Allende: Evidence of Overlapping Formation Times of AOAs and Chondrules

NASA Astrophysics Data System (ADS)

Fagan, T. J.; Komatsu, M.; Nishijima, E.; Fukushima, H.; Yasuda, T.

2016-08-01

Coarse low-Ca pyroxene has been identified in two amoeboid olivine aggregates in the CV3 Allende. The pyroxene crystals appear to be relict chondrule phenocrysts. If so, the texture indicates overlapping formation times of AOAs and chondrules.

β-Synuclein suppresses both the initiation and amplification steps of α-synuclein aggregation via competitive binding to surfaces

NASA Astrophysics Data System (ADS)

Brown, James W. P.; Buell, Alexander K.; Michaels, Thomas C. T.; Meisl, Georg; Carozza, Jacqueline; Flagmeier, Patrick; Vendruscolo, Michele; Knowles, Tuomas P. J.; Dobson, Christopher M.; Galvagnion, Céline

2016-11-01

α-Synuclein is an intrinsically disordered protein that is associated with the pathogenesis of Parkinson’s disease through the processes involved in the formation of amyloid fibrils. α and β-synuclein are homologous proteins found at comparable levels in presynaptic terminals but β-synuclein has a greatly reduced propensity to aggregate and indeed has been found to inhibit α-synuclein aggregation. In this paper, we describe how sequence differences between α- and β-synuclein affect individual microscopic processes in amyloid formation. In particular, we show that β-synuclein strongly suppresses both lipid-induced aggregation and secondary nucleation of α-synuclein by competing for binding sites at the surfaces of lipid vesicles and fibrils, respectively. These results suggest that β-synuclein can act as a natural inhibitor of α-synuclein aggregation by reducing both the initiation of its self-assembly and the proliferation of its aggregates.

Heat-Induced Soluble Protein Aggregates from Mixed Pea Globulins and β-Lactoglobulin.

PubMed

Chihi, Mohamed-Lazhar; Mession, Jean-luc; Sok, Nicolas; Saurel, Rémi

2016-04-06

The present work investigates the formation of protein aggregates (85 °C, 60 min incubation) upon heat treatment of β-lactoglobulin (βlg)-pea globulins (Glob) mixtures at pH 7.2 and 5 mM NaCl from laboratory-prepared protein isolates. Various βlg/Glob weight ratios were applied, for a total protein concentration of 2 wt % in admixture. Different analytical methods were used to determine the aggregation behavior of "mixed" aggregates, that is, surface hydrophobicity and also sulfhydryl content, protein interactions by means of SDS-PAGE electrophoresis, and molecule size distribution by DLS and gel filtration. The production of "mixed" thermal aggregates would involve both the formation of new disulfide bonds and noncovalent interactions between the denatured βlg and Glob subunits. The majority of "mixed" soluble aggregates displayed higher molecular weight and smaller diameter than those for Glob heated in isolation. The development of pea-whey protein "mixed" aggregates may help to design new ingredients for the control of innovative food textures.

Formation and structure of stable aggregates in binary diffusion-limited cluster-cluster aggregation processes

NASA Astrophysics Data System (ADS)

López-López, J. M.; Moncho-Jordá, A.; Schmitt, A.; Hidalgo-Álvarez, R.

2005-09-01

Binary diffusion-limited cluster-cluster aggregation processes are studied as a function of the relative concentration of the two species. Both, short and long time behaviors are investigated by means of three-dimensional off-lattice Brownian Dynamics simulations. At short aggregation times, the validity of the Hogg-Healy-Fuerstenau approximation is shown. At long times, a single large cluster containing all initial particles is found to be formed when the relative concentration of the minority particles lies above a critical value. Below that value, stable aggregates remain in the system. These stable aggregates are composed by a few minority particles that are highly covered by majority ones. Our off-lattice simulations reveal a value of approximately 0.15 for the critical relative concentration. A qualitative explanation scheme for the formation and growth of the stable aggregates is developed. The simulations also explain the phenomenon of monomer discrimination that was observed recently in single cluster light scattering experiments.

Cataract-associated P23T γD-crystallin retains a native-like fold in amorphous-looking aggregates formed at physiological pH

NASA Astrophysics Data System (ADS)

Boatz, Jennifer C.; Whitley, Matthew J.; Li, Mingyue; Gronenborn, Angela M.; van der Wel, Patrick C. A.

2017-05-01

Cataracts cause vision loss through the large-scale aggregation of eye lens proteins as a result of ageing or congenital mutations. The development of new treatments is hindered by uncertainty about the nature of the aggregates and their mechanism of formation. We describe the structure and morphology of aggregates formed by the P23T human γD-crystallin mutant associated with congenital cataracts. At physiological pH, the protein forms aggregates that look amorphous and disordered by electron microscopy, reminiscent of the reported formation of amorphous deposits by other crystallin mutants. Surprisingly, solid-state NMR reveals that these amorphous deposits have a high degree of structural homogeneity at the atomic level and that the aggregated protein retains a native-like conformation, with no evidence for large-scale misfolding. Non-physiological destabilizing conditions used in many in vitro aggregation studies are shown to yield qualitatively different, highly misfolded amyloid-like fibrils.

Memantine inhibits β-amyloid aggregation and disassembles preformed β-amyloid aggregates.

PubMed

Takahashi-Ito, Kaori; Makino, Mitsuhiro; Okado, Keiko; Tomita, Taisuke

2017-11-04

Memantine, an uncompetitive glutamatergic N-methyl-d-aspartate (NMDA) receptor antagonist, is widely used as a medication for the treatment of Alzheimer's disease (AD). We previously reported that chronic treatment of AD with memantine reduces the amount of insoluble β-amyloid (Aβ) and soluble Aβ oligomers in animal models of AD. The mechanisms by which memantine reduces Aβ levels in the brain were evaluated by determining the effect of memantine on Aβ aggregation using thioflavin T and transmission electron microscopy. Memantine inhibited the formation of Aβ(1-42) aggregates in a concentration-dependent manner, whereas amantadine, a structurally similar compound, did not affect Aβ aggregation at the same concentrations. Furthermore, memantine inhibited the formation of different types of Aβ aggregates, including Aβs carrying familial AD mutations, and disaggregated preformed Aβ(1-42) fibrils. These results suggest that the inhibition of Aβ aggregation and induction of Aβ disaggregation may be involved in the mechanisms by which memantine reduces Aβ deposition in the brain. Copyright © 2017 Elsevier Inc. All rights reserved.

A review of oil-suspended particulate matter aggregation--a natural process of cleansing spilled oil in the aquatic environment.

PubMed

Sun, Juan; Zheng, Xilai

2009-10-01

It has been acknowledged that following an oil spill in coastal areas where suspended particulate matter (SPM) is rich, aggregation between oil and SPM can be naturally formed. This kind of aggregation product is termed as oil-SPM aggregates (OSAs). Because OSAs are not as sticky to the shorelines as crude oil and the oil-water contact area is greatly increased due to the formation of OSAs, both oil dispersion into the water body and oil biodegration would be significantly enhanced. In this review article, the authors (1) describe in detail the mechanism of OSA formation and controlling parameters which can influence OSA formation (the parameters discussed include the oil nature and properties, sediment types and concentrations, and the environmental factors such as salinity, temperature and mixing energy); (2) briefly review qualitative and quantitative methods used for characterization of OSA formation (two main methods used for the OSA characterization are the UV epi-fluorescence microscopy and gas chromatography equipped with flame ionization detector (GC-FID); (3) elucidate the applications of OSA formation in oil spill response strategies including natural attenuation, sediment relocation, and sediment mixing; and (4) discuss research needs in the future which would further improve our understanding of OSA formation and move towards the development of adequate oil behaviour models.

Protein aggregates as depots for the release of biologically active compounds.

PubMed

Artemova, Natalya V; Kasakov, Alexei S; Bumagina, Zoya M; Lyutova, Elena M; Gurvits, Bella Ya

2008-12-12

Protein misfolding and aggregation is one of the most serious problems in cell biology, molecular medicine, and biotechnology. Misfolded proteins interact with each other or with other proteins in non-productive or damaging ways. However, a new paradigm arises that protein aggregation may be exploited by nature to perform specific functions in different biological contexts. From this consideration, acceleration of stress-induced protein aggregation triggered by any factor resulting in the formation of soluble aggregates may have paradoxical positive consequences. Here, we suggest that amorphous aggregates can act as a source for the release of biologically active proteins after removal of stress conditions. To address this concept, we investigated the kinetics of thermal aggregation in vitro of yeast alcohol dehydrogenase (ADH) as a model substrate in the presence of two amphiphilic peptides: Arg-Phe or Ala-Phe-Lys. Using dynamic light scattering (DLS) and turbidimetry, we have demonstrated that under mild stress conditions the concentration-dependent acceleration of ADH aggregation by these peptides results in formation of large but soluble complexes of proteins prone to refolding.

Amyloid-like aggregation of provasopressin in diabetes insipidus and secretory granule sorting.

PubMed

Beuret, Nicole; Hasler, Franziska; Prescianotto-Baschong, Cristina; Birk, Julia; Rutishauser, Jonas; Spiess, Martin

2017-01-26

Aggregation of peptide hormone precursors in the trans-Golgi network is an essential process in the biogenesis of secretory granules in endocrine cells. It has recently been proposed that this aggregation corresponds to the formation of functional amyloids. Our previous finding that dominant mutations in provasopressin, which cause cell degeneration and diabetes insipidus, prevent native folding and produce fibrillar aggregates in the endoplasmic reticulum (ER) might thus reflect mislocalized amyloid formation by sequences that evolved to mediate granule sorting. Here we identified two sequences responsible for fibrillar aggregation of mutant precursors in the ER: the N-terminal vasopressin nonapeptide and the C-terminal glycopeptide. To test their role in granule sorting, the glycopeptide was deleted and/or vasopressin mutated to inactivate ER aggregation while still permitting precursor folding and ER exit. These mutations strongly reduced sorting into granules and regulated secretion in endocrine AtT20 cells. The same sequences - vasopressin and the glycopeptide - mediate physiological aggregation of the wild-type hormone precursor into secretory granules and the pathological fibrillar aggregation of disease mutants in the ER. These findings support the amyloid hypothesis for secretory granule biogenesis.

Development of long-term primary cell aggregates from Mediterranean octocorals.

PubMed

Huete-Stauffer, Carla; Valisano, Laura; Gaino, Elda; Vezzulli, Luigi; Cerrano, Carlo

2015-09-01

In lower metazoans, the aggregative properties of dissociated cells leading to in vitro stable multicellular aggregates have furnished a remarkable experimental material to carry out investigations in various research fields. One of the main expectations is to find good models for the study in vitro of the first steps of biomineralization processes. In this study, we examined five common Mediterranean gorgonians (Paramuricea clavata, Corallium rubrum, Eunicella singularis, Eunicella cavolinii, and Eunicella verrucosa) using mechanical cell aggregate production techniques. In particular, we investigated the conditions of aggregate formation, their number and survival in experimental conditions, the DNA synthesizing activity using 5'-bromo-2'-deoxyuridine (BrdU) tests, and the response to calcein addition and observed the secretion of newly formed sclerites. The BrdU tests showed that cell proliferation depends on the size of aggregates and on the presence/absence of symbiotic zooxanthellae. With epifluorescent and confocal imaging from calcein addition assays, we observed the presence of calcium ions within cells, a possible clue for prediction of sclerite formation or calcium deposition. The species-specific efficiency in production of cell aggregates is correlated to the size of polyps, showing that the higher density of polyps and their diameter correspond to higher production of cell aggregates. Regarding the long-term maintenance, we obtained the best results from E. singularis, which formed multicellular aggregates of 0.245 mm ± 0.086 mm in size and maintained symbiotic association with zooxanthellae throughout the experimental run. Formation of sclerites within aggregates opens a wide field of investigation on biomineralization, since de novo sclerites were observed around 30 d after the beginning of the experiment.

An immunohistochemical study of neuropeptides and neuronal cytoskeletal proteins in the neuroepithelial component of a spontaneous murine ovarian teratoma. Primitive neuroepithelium displays immunoreactivity for neuropeptides and neuron-associated beta-tubulin isotype.

PubMed Central

Caccamo, D. V.; Herman, M. M.; Frankfurter, A.; Katsetos, C. D.; Collins, V. P.; Rubinstein, L. J.

1989-01-01

Approximately one third of the female mice of the LTXBO strain develop spontaneous ovarian teratomas. These tumors contain a large neuroepithelial component, which includes primitive neural structures resembling embryonic neural tubes (medulloepithelial rosettes), ependymoblastic and ependymal rosettes, neuroblasts, mature ganglionic neurons, myelinated neurites, and astrocytes. The purpose of this study was to characterize these tumors according to the immunohistochemical location of some well-characterized trophic and regulatory neuropeptides and neurotransmitters, several neuronal-associated cytoskeletal proteins, and other proteins indicative of neuronal and glial differentiation. Medulloepithelial rosettes showed focal serotonin-like, opioid peptide-like and gamma-amino butyric acid-like immunoreactivity, and displayed immunostaining for the neuron-associated class III beta-tubulin isotype. The mature ganglion cells were also immunoreactive for these markers, and, in addition, for somatostatin, cholecystokinin, bombesin, glucagon, vasoactive intestinal peptide, and neuropeptide Y. Mature ganglion cells were also immunoreactive for proteins associated with the neuronal cytoskeleton (including microtubule-associated proteins, MAP2 and tau, and higher molecular weight phosphorylated and non-phosphorylated neurofilament subunits), neuron-specific enolase, and synaptophysin. Undifferentiated stem cells, ependymoblastic and ependymal rosettes, and astroglia all stained with a monoclonal antibody that recognizes all mammalian beta-tubulin isotypes, but did not react with antibodies to neuronal-associated cytoskeletal proteins or neuropeptides. Neuropeptide-like immunoreactivity and demonstration of the class III beta-tubulin isotype indicate early neuronal commitment in neoplastic primitive neuroepithelium. These patterns of immunoreactivity closely follow those encountered in the normal neurocytogenesis of the mammalian and avian forebrain, and increase the precision with which the early stages of progressive neuroepithelial differentiation can be analyzed in human embryonal tumors of the CNS. Images Figure 1 Figure 2 Figure 3 PMID:2817080

Multispectral Observations and Analysis of the Rosette Nebula

NASA Astrophysics Data System (ADS)

Huber, Jeremy

The Rosette nebula is a large, ring-shaped emission nebula with a distinctive central cavity excavated by its central cluster of OB stars. Toward understanding the three dimensional structure and fundamental physical processes of this object, we have acquired ux-calibrated, 4-degree field, deep exposures of the Rosette region through 3 nm bandwidth Halpha (656.3 nm) as well as Hbeta (486.1nm), [OIII] (500.7 nm) and [SII] (671.6 nm) filters with 4.5 nm bandwidth. The 4 arcsec/pixel images are supplemented with 4 degree field slit spectra and combined with archival data from the Galactic Evolution Explorer satellite (GALEX), Akari, the Infrared Astronomical Satellite (IRAS), the Midcourse Space Experiment (MSX), the Wide-field Infrared Survey Explorer (WISE), the Wilkinson Microwave Anisotropy Probe (WMAP) and the Planck mission, along with published single dish radio data of the hydrogen continuum at 1410, 2700, and 4750 MHz. These disparate sources have been converted to the same flux and spatial scale as our own wide field data to create a multispectral data cube which allows comparative analysis across the electromagnetic spectrum. Using ratios of data cube slices, spatial maps of extinction and ionization have been constructed to explore the spatial variation of these parameters across the nebula. Comparison of emission in different wavelengths across the data cube allows generation of a spectral energy distribution (SED) to probe dust temperature and geometry. A radial profile analysis of emission from the Rosette in each band supports a spherical shell model of three dimensional structure, and visual representations of this model have been generated in both Python and Javascript/GLSL. An investigation of anomalous dust emission in the center of the nebula via supplemental spectroscopy, conducted on the Anglo-Australian Telescope, is also presented.

Rosette iron deficiency transcript and microRNA profiling reveals links between copper and iron homeostasis in Arabidopsis thaliana

PubMed Central

Waters, Brian M.; Stein, Ricardo J.

2012-01-01

Iron (Fe) is an essential plant micronutrient, and its deficiency limits plant growth and development on alkaline soils. Under Fe deficiency, plant responses include up-regulation of genes involved in Fe uptake from the soil. However, little is known about shoot responses to Fe deficiency. Using microarrays to probe gene expression in Kas-1 and Tsu-1 ecotypes of Arabidopsis thaliana, and comparison with existing Col-0 data, revealed conserved rosette gene expression responses to Fe deficiency. Fe-regulated genes included known metal homeostasis-related genes, and a number of genes of unknown function. Several genes responded to Fe deficiency in both roots and rosettes. Fe deficiency led to up-regulation of Cu,Zn superoxide dismutase (SOD) genes CSD1 and CSD2, and down-regulation of FeSOD genes FSD1 and FSD2. Eight microRNAs were found to respond to Fe deficiency. Three of these (miR397a, miR398a, and miR398b/c) are known to regulate transcripts of Cu-containing proteins, and were down-regulated by Fe deficiency, suggesting that they could be involved in plant adaptation to Fe limitation. Indeed, Fe deficiency led to accumulation of Cu in rosettes, prior to any detectable decrease in Fe concentration. ccs1 mutants that lack functional Cu,ZnSOD proteins were prone to greater oxidative stress under Fe deficiency, indicating that increased Cu concentration under Fe limitation has an important role in oxidative stress prevention. The present results show that Cu accumulation, microRNA regulation, and associated differential expression of Fe and CuSOD genes are coordinated responses to Fe limitation. PMID:22962679

Study of early pregnancy factor (EPF) in equine (Equus caballus).

PubMed

Ohnuma, K; Yokoo, M; Ito, K; Nambo, Y; Miyake, Y I; Komatsu, M; Takahashi, J

2000-03-01

Early pregnancy factor (EPF) is an immunosuppressive protein detected in the early pregnancy serum. We have already reported that we developed the rosette inhibition test for mare EPF and detected EPF in thoroughbreds. The aim of this study was to determine whether or not our method could be used clinically. The rosette inhibition test for equine EPF was carried out on serum from six nonpregnant and six pregnant Shetland ponies, a female and a male Chinese pony, and four nonpregnant and 13 pregnant thoroughbred mares. In the thoroughbreds sera were collected during the pregnancy period. Furthermore, we measured progesterone and detected pregnant mare serum gonadotrophin (PMSG) in order to confirm pregnancy of the Chinese pony 3 and 6 months after mating. In the nonpregnant Shetland ponies, the rosette inhibition titre (RIT) was 6.0+/-1.0 and EPF was negative. In contrast, in the pregnant ponies, the RIT was 9.2+/-0.4 and EPF was positive. Based on these results, we diagnosed pregnancy of the Chinese pony. The RIT of the female Chinese pony (3 months after mating) was above 10 and EPF was positive. Furthermore, we detected PMSG and progesterone in the serum of this pony. EPF appeared in the maternal blood circulation at 24-72 hr after mating, it was detected until the second trimester, and after that it disappeared from the maternal serum. The pony's EPF was detected by using the same rosette inhibition test as in the thoroughbred and was present from 24 to 72 hr after mating until the second trimester. The results indicated that our method was useful for pregnancy diagnosis of Equine.

Dye Aggregation and Complex Formation Effects in 7-(Diethylamino)-coumarin-3-carboxylic Acid

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

Liu, Xiaogang; Cole, Jacqueline M.; Chow, Philip C. Y.

2014-06-19

7-(Diethylamino)-coumarin-3-carboxylic acid (1) has been used as a laser dye, fluorescent label, and biomedical inhibitor in many different applications. Although this dye is typically used in the solution phase, it is prone to molecular aggregation, resulting in many inconsistent optoelectronic properties being reported in the literature. In this paper, the UV—vis absorption and fluorescence spectra of 1 are investigated in three representative solvents: cyclohexane [nonpolar and non-hydrogen bonding (NHB)], ethanol (moderately polar and hydrogen-bond accepting/donating), and DMSO (strongly polar and hydrogen-bond accepting). These experimental results, in conjunction with (time-dependent) density functional theory (DFT/TDDFT) based quantum calculations, have led to themore » identification of the J-aggregates of 1, and rationalized its different aggregation characteristic in cyclohexane in contrast to that of another similar compound, coumarin 343. We show here that these aggregates are largely responsible for the anomalous optoelectronic properties of this compound. In addition, DFT calculations and 1H NMR spectroscopy measurements suggest that the intramolecular hydrogen bond in 1 could be "opened up" in hydrogen-bond accepting solvents, affording significant molecular conformational changes and complex formation effects. The comprehensive understanding of the molecular aggregation and complex formation mechanisms of 1 acquired through this work forms a foundation for the knowledge-based molecular design of organic dyes with tailored aggregation tendencies or anti-aggregation characteristics to cater for different opapplications.« less

Amyloid fibril formation by the chain B subunit of monellin occurs by a nucleation-dependent polymerization mechanism.

PubMed

Sabareesan, A T; Udgaonkar, Jayant B

2014-02-25

Proteins possessing very different structures, or even no structure, form amyloid fibrils that are very similar in internal structure. This suggests that the mechanisms by which amyloid fibrils form might be very similar, irrespective of whether the fibrils are associated with disease or with normal cellular function, or even if they have no physiological importance. In this context, it is important to have a model protein system whose amyloid fibril formation is robust in its reproducibility, which can reveal the fundamentals of the amyloid fibril reaction that may be applicable to all proteins. In this study, the aggregation mechanism of amyloid fibril formation by chain B of the heterodimeric protein monellin has been elucidated in detail. It is shown that the aggregation reaction meets all the stringent kinetic criteria of a homogeneous nucleation-dependent polymerization mechanism, which is valid over a wide range of protein concentrations. Quantitative analyses of the kinetic data using one approach based on features of the entire kinetic curve, and another based on only the initial rate of aggregation, indicate that the thermodynamic nucleus is a dimer. Spherical oligomers are observed by atomic force microscopy to form transiently early during fibril formation but are off-pathway to the direct fibril formation pathway. It is shown that amyloid fibril formation can be prevented by the addition of chain A of monellin at early stages of chain B aggregation: the two free chains combine to form native monellin, which leads to the dissociation of early aggregates.

ROCKY PLANETESIMAL FORMATION VIA FLUFFY AGGREGATES OF NANOGRAINS

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

Arakawa, Sota; Nakamoto, Taishi, E-mail: arakawa.s.ac@m.titech.ac.jp

2016-12-01

Several pieces of evidence suggest that silicate grains in primitive meteorites are not interstellar grains but condensates formed in the early solar system. Moreover, the size distribution of matrix grains in chondrites implies that these condensates might be formed as nanometer-sized grains. Therefore, we propose a novel scenario for rocky planetesimal formation in which nanometer-sized silicate grains are produced by evaporation and recondensation events in early solar nebula, and rocky planetesimals are formed via aggregation of these nanograins. We reveal that silicate nanograins can grow into rocky planetesimals via direct aggregation without catastrophic fragmentation and serious radial drift, and ourmore » results provide a suitable condition for protoplanet formation in our solar system.« less

Role of Multicellular Aggregates in Biofilm Formation

PubMed Central

Kragh, Kasper N.; Hutchison, Jaime B.; Melaugh, Gavin; Rodesney, Chris; Roberts, Aled E. L.; Irie, Yasuhiko; Jensen, Peter Ø.; Diggle, Stephen P.; Allen, Rosalind J.

2016-01-01

ABSTRACT In traditional models of in vitro biofilm development, individual bacterial cells seed a surface, multiply, and mature into multicellular, three-dimensional structures. Much research has been devoted to elucidating the mechanisms governing the initial attachment of single cells to surfaces. However, in natural environments and during infection, bacterial cells tend to clump as multicellular aggregates, and biofilms can also slough off aggregates as a part of the dispersal process. This makes it likely that biofilms are often seeded by aggregates and single cells, yet how these aggregates impact biofilm initiation and development is not known. Here we use a combination of experimental and computational approaches to determine the relative fitness of single cells and preformed aggregates during early development of Pseudomonas aeruginosa biofilms. We find that the relative fitness of aggregates depends markedly on the density of surrounding single cells, i.e., the level of competition for growth resources. When competition between aggregates and single cells is low, an aggregate has a growth disadvantage because the aggregate interior has poor access to growth resources. However, if competition is high, aggregates exhibit higher fitness, because extending vertically above the surface gives cells at the top of aggregates better access to growth resources. Other advantages of seeding by aggregates, such as earlier switching to a biofilm-like phenotype and enhanced resilience toward antibiotics and immune response, may add to this ecological benefit. Our findings suggest that current models of biofilm formation should be reconsidered to incorporate the role of aggregates in biofilm initiation. PMID:27006463

How the morphology of dusts influences packing density in small solar system bodies

NASA Astrophysics Data System (ADS)

Zangmeister, C.; Radney, J. G.; Zachariah, M. R.

2014-12-01

Large planetary seedlings, comets, and nanoscale soot particles are made from rigid, aggregated subunits that are compacted under low compression into larger structures spanning over 10 orders of magnitude in dimensional space. Here, we demonstrate that the packing density (Φf) of compacted rigid aggregates is independent of spatial scale for systems under weak compaction, a regime that includes small solar system bodies. The Φf of rigid aggregated structures across 6 orders of magnitude were measured using nanoscale spherical soot aerosol composed of aggregates with ≈ 17 nm monomeric subunits and aggregates made from uniform monomeric 6 mm spherical subunits at the macroscale. We find Φf = 0.36 ± 0.02 at both the nano- and macroscale. These values are remarkably similar to qf observed for comet nuclei and measured values of other rigid aggregated systems across a wide variety of spatial and formative conditions. We present a packing model that incorporates the aggregate morphology and show that Φf is independent of both monomer and aggregate size. These observations suggest thatqf of rigid aggregates is independent of spatial dimension across varied formative conditions ranging from interstellar space to pharmaceutical manufacturing.

Inhibition of the aggregation of lactoferrin and (-)-epigallocatechin gallate in the presence of polyphenols, oligosaccharides, and collagen peptide.

PubMed

Yang, Wei; Liu, Fuguo; Xu, Chenqi; Sun, Cuixia; Yuan, Fang; Gao, Yanxiang

2015-05-27

The aggregation of lactoferrin and (-)-epigallocatechin gallate (EGCG) was inhibited by polyphenols, oligosaccharides, and collagen peptide in this study. Polyphenols, oligosaccharides, or collagen peptide can effectively prevent the formation of lactoferrin-EGCG aggregates, respectively. The addition sequence of lactoferrin, polyphenols (oligosaccharides or collagen peptide) and EGCG can affect the turbidity and particle size of the ternary complexes in the buffer solution; however, it hardly affected the ζ-potential and fluorescence characteristics. With either positive or negative charge, polyphenols and collagen peptide disrupted the formation of lactoferrin-EGCG aggregate mainly through the mechanism of its competition with EGCG molecules which surrounded the lactoferrin molecule surface with weaker binding affinities, forming polyphenols or a collagen peptide-lactoferrin-EGCG ternary complex; for neutral oligosaccharides, the ternary complex was generated mainly through steric effects, accompanied by a change in the lactoferrin secondary structure induced by gallic acid, chlorogenic acid, and xylo-oligosaccharide. Polyphenols, oligosaccharides, or collagen peptide restraining the formation of lactoferrin-EGCG aggregate could be applied in the design of clear products in the food, pharmaceutical, and cosmetic industries.

Genipin-crosslinked microcarriers mediating hepatocellular aggregates formation and functionalities.

PubMed

Lau, Ting Ting; Wang, Chunming; Png, Sze Wei; Su, Kai; Wang, Dong-An

2011-01-01

In engineered regenerative medicine, various types of scaffolds have been customized to pursue the optimal environment for different types of therapeutic cells. In liver therapeutic research, hepatocytes require attachment to solid anchors for survival and proliferation before they could grow into cellular aggregates with enhanced functionalities. Among the various biomaterials scaffolds and vehicles, microspherical cell carriers are suited to these requirements. Individual spheres may provide two-dimensional (2D) cell-affinitive surfaces for cell adhesion and spreading; whereas multiple microcarriers may form three-dimensional (3D) matrices with inter-spherical space for cell expansion and multicellular aggregation. In this study, we culture human liver carcinoma cell line (HepG2) cells on genipin-crosslinked gelatin microspheres of two different sizes. Results suggest that both microcarriers support cell adhesion, proliferation, and spontaneous formation of hepatocellular aggregates, among which the spheres with bigger size (200-300 μm) seem more favorable than the smaller ones in terms of aggregate formation and liver specific functionalities. These findings suggest that the genipin-crosslinked microcarrier is a competent vehicle for liver cell delivery. Copyright © 2010 Wiley Periodicals, Inc.

Formation and implications of alpha-synuclein radical in Maneb- and paraquat-induced models of Parkinson’s disease

PubMed Central

Kumar, Ashutosh; Leinisch, Fabian; Kadiiska, Maria B.; Corbett, Jean; Mason, Ronald P.

2015-01-01

Parkinson’s disease (PD) is a debilitating, progressive, neurodegenerative disorder characterized by progressive loss of dopaminergic neurons and motor deficits. Alpha-synuclein-containing aggregates represent a feature of a variety of neurodegenerative disorders, including PD; however, the mechanism that initiates and promotes intraneuronal alpha-synuclein aggregation remains unknown. We hypothesized protein radical formation as an initiating mechanism for alpha-synuclein aggregation. Therefore, we used the highly sensitive immuno-spin trapping technique to investigate protein radical formation as a possible mechanism of alpha-synuclein aggregation as well as to investigate the source of protein radical formation in the midbrains of Maneb and paraquat coexposed mice. Coexposure to Maneb and paraquat for 6 weeks resulted in active microgliosis, NADPH oxidase activation, and inducible nitric oxide synthase (iNOS) induction, which culminated in protein radical formation in the midbrains of mice. Results obtained with immuno-spin trapping and immunoprecipitation experiments confirmed formation of alpha-synuclein radicals in dopaminergic neurons of exposed mice. Free radical formation requires NADPH oxidase and iNOS, as indicated by decreased protein radical formation in knockout mice (P47phox−/− and iNOS−/−) and in mice treated with inhibitors such as FeTPPS (a peroxynitrite decomposition catalyst), 1400W (an iNOS inhibitor), or apocynin (a NADPH oxidase inhibitor). Concurrence of protein radical formation with dopaminergic neuronal death indicated a link between protein radicals and disease progression. Taken together, these results show for the first time the formation and detection of the alpha-synuclein radical and suggest that NADPH oxidase and iNOS play roles in peroxynitrite-mediated protein radical formation and subsequent neuronal death in the midbrains of Maneb and paraquat coexposed mice. PMID:25952542

Environmental and genetic factors support the dissociation between α-synuclein aggregation and toxicity.

PubMed

Villar-Piqué, Anna; Lopes da Fonseca, Tomás; Sant'Anna, Ricardo; Szegö, Éva Mónika; Fonseca-Ornelas, Luis; Pinho, Raquel; Carija, Anita; Gerhardt, Ellen; Masaracchia, Caterina; Abad Gonzalez, Enrique; Rossetti, Giulia; Carloni, Paolo; Fernández, Claudio O; Foguel, Debora; Milosevic, Ira; Zweckstetter, Markus; Ventura, Salvador; Outeiro, Tiago Fleming

2016-10-18

Synucleinopathies are a group of progressive disorders characterized by the abnormal aggregation and accumulation of α-synuclein (aSyn), an abundant neuronal protein that can adopt different conformations and biological properties. Recently, aSyn pathology was shown to spread between neurons in a prion-like manner. Proteins like aSyn that exhibit self-propagating capacity appear to be able to adopt different stable conformational states, known as protein strains, which can be modulated both by environmental and by protein-intrinsic factors. Here, we analyzed these factors and found that the unique combination of the neurodegeneration-related metal copper and the pathological H50Q aSyn mutation induces a significant alteration in the aggregation properties of aSyn. We compared the aggregation of WT and H50Q aSyn with and without copper, and assessed the effects of the resultant protein species when applied to primary neuronal cultures. The presence of copper induces the formation of structurally different and less-damaging aSyn aggregates. Interestingly, these aggregates exhibit a stronger capacity to induce aSyn inclusion formation in recipient cells, which demonstrates that the structural features of aSyn species determine their effect in neuronal cells and supports a lack of correlation between toxicity and inclusion formation. In total, our study provides strong support in favor of the hypothesis that protein aggregation is not a primary cause of cytotoxicity.

Environmental and genetic factors support the dissociation between α-synuclein aggregation and toxicity

PubMed Central

Villar-Piqué, Anna; Lopes da Fonseca, Tomás; Sant’Anna, Ricardo; Szegö, Éva Mónika; Fonseca-Ornelas, Luis; Pinho, Raquel; Carija, Anita; Gerhardt, Ellen; Masaracchia, Caterina; Abad Gonzalez, Enrique; Rossetti, Giulia; Carloni, Paolo; Fernández, Claudio O.; Foguel, Debora; Milosevic, Ira; Zweckstetter, Markus; Ventura, Salvador; Outeiro, Tiago Fleming

2016-01-01

Synucleinopathies are a group of progressive disorders characterized by the abnormal aggregation and accumulation of α-synuclein (aSyn), an abundant neuronal protein that can adopt different conformations and biological properties. Recently, aSyn pathology was shown to spread between neurons in a prion-like manner. Proteins like aSyn that exhibit self-propagating capacity appear to be able to adopt different stable conformational states, known as protein strains, which can be modulated both by environmental and by protein-intrinsic factors. Here, we analyzed these factors and found that the unique combination of the neurodegeneration-related metal copper and the pathological H50Q aSyn mutation induces a significant alteration in the aggregation properties of aSyn. We compared the aggregation of WT and H50Q aSyn with and without copper, and assessed the effects of the resultant protein species when applied to primary neuronal cultures. The presence of copper induces the formation of structurally different and less-damaging aSyn aggregates. Interestingly, these aggregates exhibit a stronger capacity to induce aSyn inclusion formation in recipient cells, which demonstrates that the structural features of aSyn species determine their effect in neuronal cells and supports a lack of correlation between toxicity and inclusion formation. In total, our study provides strong support in favor of the hypothesis that protein aggregation is not a primary cause of cytotoxicity. PMID:27708160

Formation and spreading of TDP-43 aggregates in cultured neuronal and glial cells demonstrated by time-lapse imaging

PubMed Central

Ishii, Tomohiro; Kawakami, Emiko; Endo, Kentaro; Misawa, Hidemi; Watabe, Kazuhiko

2017-01-01

TAR DNA-binding protein 43 (TDP-43) is a main constituent of cytoplasmic aggregates in neuronal and glial cells in cases of amyotrophic lateral sclerosis and frontotemporal lobar degeneration. We have previously demonstrated that adenovirus-transduced artificial TDP-43 cytoplasmic aggregates formation is enhanced by proteasome inhibition in vitro and in vivo. However, the relationship between cytoplasmic aggregate formation and cell death remains unclear. In the present study, rat neural stem cell lines stably transfected with EGFP- or Sirius-expression vectors under the control of tubulin beta III, glial fibrillary acidic protein, or 2′,3′-cyclic nucleotide 3′-phosphodiesterase promoter were differentiated into neurons, astrocytes, and oligodendrocytes, respectively, in the presence of retinoic acid. The differentiated cells were then transduced with adenoviruses expressing DsRed-tagged human wild type and C-terminal fragment TDP-43 under the condition of proteasome inhibition. Time-lapse imaging analyses revealed growing cytoplasmic aggregates in the transduced neuronal and glial cells, followed by collapse of the cell. The aggregates remained insoluble in culture media, consisted of sarkosyl-insoluble granular materials, and contained phosphorylated TDP-43. Moreover, the released aggregates were incorporated into neighboring neuronal cells, suggesting cell-to-cell spreading. The present study provides a novel tool for analyzing the detailed molecular mechanisms of TDP-43 proteinopathy in vitro. PMID:28599005

ARAM: an automated image analysis software to determine rosetting parameters and parasitaemia in Plasmodium samples.

PubMed

Kudella, Patrick Wolfgang; Moll, Kirsten; Wahlgren, Mats; Wixforth, Achim; Westerhausen, Christoph

2016-04-18

Rosetting is associated with severe malaria and a primary cause of death in Plasmodium falciparum infections. Detailed understanding of this adhesive phenomenon may enable the development of new therapies interfering with rosette formation. For this, it is crucial to determine parameters such as rosetting and parasitaemia of laboratory strains or patient isolates, a bottleneck in malaria research due to the time consuming and error prone manual analysis of specimens. Here, the automated, free, stand-alone analysis software automated rosetting analyzer for micrographs (ARAM) to determine rosetting rate, rosette size distribution as well as parasitaemia with a convenient graphical user interface is presented. Automated rosetting analyzer for micrographs is an executable with two operation modes for automated identification of objects on images. The default mode detects red blood cells and fluorescently labelled parasitized red blood cells by combining an intensity-gradient with a threshold filter. The second mode determines object location and size distribution from a single contrast method. The obtained results are compared with standardized manual analysis. Automated rosetting analyzer for micrographs calculates statistical confidence probabilities for rosetting rate and parasitaemia. Automated rosetting analyzer for micrographs analyses 25 cell objects per second reliably delivering identical results compared to manual analysis. For the first time rosette size distribution is determined in a precise and quantitative manner employing ARAM in combination with established inhibition tests. Additionally ARAM measures the essential observables parasitaemia, rosetting rate and size as well as location of all detected objects and provides confidence intervals for the determined observables. No other existing software solution offers this range of function. The second, non-malaria specific, analysis mode of ARAM offers the functionality to detect arbitrary objects. Automated rosetting analyzer for micrographs has the capability to push malaria research to a more quantitative and statistically significant level with increased reliability due to operator independence. As an installation file for Windows © 7, 8.1 and 10 is available for free, ARAM offers a novel open and easy-to-use platform for the malaria community to elucidate resetting. © 7, 8.1 and 10 is available for free, ARAM offers a novel open and easy-to-use platform for the malaria community to elucidate rosetting.

Surface Mn(II) oxidation actuated by a multicopper oxidase in a soil bacterium leads to the formation of manganese oxide minerals

PubMed Central

Zhang, Zhen; Zhang, Zhongming; Chen, Hong; Liu, Jin; Liu, Chang; Ni, Hong; Zhao, Changsong; Ali, Muhammad; Liu, Fan; Li, Lin

2015-01-01

In this manuscript, we report that a bacterial multicopper oxidase (MCO266) catalyzes Mn(II) oxidation on the cell surface, resulting in the surface deposition of Mn(III) and Mn(IV) oxides and the gradual formation of bulky oxide aggregates. These aggregates serve as nucleation centers for the formation of Mn oxide micronodules and Mn-rich sediments. A soil-borne Escherichia coli with high Mn(II)-oxidizing activity formed Mn(III)/Mn(IV) oxide deposit layers and aggregates under laboratory culture conditions. We engineered MCO266 onto the cell surfaces of both an activity-negative recipient and wild-type strains. The results confirmed that MCO266 governs Mn(II) oxidation and initiates the formation of deposits and aggregates. By contrast, a cell-free substrate, heat-killed strains, and intracellularly expressed or purified MCO266 failed to catalyze Mn(II) oxidation. However, purified MCO266 exhibited Mn(II)-oxidizing activity when combined with cell outer membrane component (COMC) fractions in vitro. We demonstrated that Mn(II) oxidation and aggregate formation occurred through an oxygen-dependent biotic transformation process that requires a certain minimum Mn(II) concentration. We propose an approximate electron transfer pathway in which MCO266 transfers only one electron to convert Mn(II) to Mn(III) and then cooperates with other COMC electron transporters to transfer the other electron required to oxidize Mn(III) to Mn(IV). PMID:26039669

Surface Mn(II) oxidation actuated by a multicopper oxidase in a soil bacterium leads to the formation of manganese oxide minerals.

PubMed

Zhang, Zhen; Zhang, Zhongming; Chen, Hong; Liu, Jin; Liu, Chang; Ni, Hong; Zhao, Changsong; Ali, Muhammad; Liu, Fan; Li, Lin

2015-06-03

In this manuscript, we report that a bacterial multicopper oxidase (MCO266) catalyzes Mn(II) oxidation on the cell surface, resulting in the surface deposition of Mn(III) and Mn(IV) oxides and the gradual formation of bulky oxide aggregates. These aggregates serve as nucleation centers for the formation of Mn oxide micronodules and Mn-rich sediments. A soil-borne Escherichia coli with high Mn(II)-oxidizing activity formed Mn(III)/Mn(IV) oxide deposit layers and aggregates under laboratory culture conditions. We engineered MCO266 onto the cell surfaces of both an activity-negative recipient and wild-type strains. The results confirmed that MCO266 governs Mn(II) oxidation and initiates the formation of deposits and aggregates. By contrast, a cell-free substrate, heat-killed strains, and intracellularly expressed or purified MCO266 failed to catalyze Mn(II) oxidation. However, purified MCO266 exhibited Mn(II)-oxidizing activity when combined with cell outer membrane component (COMC) fractions in vitro. We demonstrated that Mn(II) oxidation and aggregate formation occurred through an oxygen-dependent biotic transformation process that requires a certain minimum Mn(II) concentration. We propose an approximate electron transfer pathway in which MCO266 transfers only one electron to convert Mn(II) to Mn(III) and then cooperates with other COMC electron transporters to transfer the other electron required to oxidize Mn(III) to Mn(IV).

Experimental volcanic ash aggregation: Internal structuring of accretionary lapilli and the role of liquid bonding

NASA Astrophysics Data System (ADS)

Mueller, Sebastian B.; Kueppers, Ulrich; Ayris, Paul M.; Jacob, Michael; Dingwell, Donald B.

2016-01-01

Explosive volcanic eruptions can release vast quantities of pyroclastic material into Earth's atmosphere, including volcanic ash, particles with diameters less than two millimeters. Ash particles can cluster together to form aggregates, in some cases reaching up to several centimeters in size. Aggregation alters ash transport and settling behavior compared to un-aggregated particles, influencing ash distribution and deposit stratigraphy. Accretionary lapilli, the most commonly preserved type of aggregates within the geologic record, can exhibit complex internal stratigraphy. The processes involved in the formation and preservation of these aggregates remain poorly constrained quantitatively. In this study, we simulate the variable gas-particle flow conditions which may be encountered within eruption plumes and pyroclastic density currents via laboratory experiments using the ProCell Lab System® of Glatt Ingenieurtechnik GmbH. In this apparatus, solid particles are set into motion in a fluidized bed over a range of well-controlled boundary conditions (particle concentration, air flow rate, gas temperature, humidity, liquid composition). Experiments were conducted with soda-lime glass beads and natural volcanic ash particles under a range of experimental conditions. Both glass beads and volcanic ash exhibited the capacity for aggregation, but stable aggregates could only be produced when materials were coated with high but volcanically-relevant concentrations of NaCl. The growth and structure of aggregates was dependent on the initial granulometry, while the rate of aggregate formation increased exponentially with increasing relative humidity (12-45% RH), before overwetting promoted mud droplet formation. Notably, by use of a broad granulometry, we generated spherical, internally structured aggregates similar to some accretionary pellets found in volcanic deposits. Adaptation of a powder-technology model offers an explanation for the origin of natural accretionary pellets, suggesting them to be the result of a particular granulometry and fast-acting selective aggregation processes. For such aggregates to survive deposition and be preserved in the deposits of eruption plumes and pyroclastic density currents likely requires a significant pre-existing salt load on ash surfaces, and rapid aggregate drying prior to deposition or interaction with a more energetic environment. Our results carry clear benefits for future efforts to parameterize models of ash transport and deposition in the field.

Effect of curcumin on amyloid-like aggregates generated from methionine-oxidized apolipoprotein A-I

DOE PAGES

Krishnamoorthy, Aparna; Tavoosi, Narjes; Chan, Gary K. L.; ...

2018-01-10

Curcumin is a polyphenolic phytonutrient that has antineurodegenerative properties. Here, we investigated the anti-amyloidogenic properties of curcumin. Following incubation with curcumin, intrinsic tryptophan fluorescence emission of apolipoprotein (apo) A-I was strongly quenched. At the same time, curcumin fluorescence emission was enhanced. The fluorescence emission spectra of curcumin in the presence of amyloid-like aggregates formed by methionine-oxidized (ox) apoA-I varied, depending on whether curcumin was added before, or after, aggregate formation. The impact of curcumin on the structure of the aggregating material was revealed by the lower amount of β-structure in ox-apoA-I amyloid-like aggregates formed in the presence of curcumin, comparedmore » to aggregates formed without curcumin. However, the kinetics of ox-apoA-I amyloid-like aggregate formation was not altered by the presence of curcumin. Moreover, electron microscopy analysis detected no discernable differences in amyloid morphology when ox-apoA-I amyloid-like aggregates were formed in the presence or absence of curcumin. In conclusion, curcumin interacts with apoA-I and alters the structure of ox-apoA-I amyloid-like aggregates yet does not diminish the propensity of ox-apoA-I to form aggregates.« less

Effect of curcumin on amyloid-like aggregates generated from methionine-oxidized apolipoprotein A-I

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

Krishnamoorthy, Aparna; Tavoosi, Narjes; Chan, Gary K. L.

Curcumin is a polyphenolic phytonutrient that has antineurodegenerative properties. Here, we investigated the anti-amyloidogenic properties of curcumin. Following incubation with curcumin, intrinsic tryptophan fluorescence emission of apolipoprotein (apo) A-I was strongly quenched. At the same time, curcumin fluorescence emission was enhanced. The fluorescence emission spectra of curcumin in the presence of amyloid-like aggregates formed by methionine-oxidized (ox) apoA-I varied, depending on whether curcumin was added before, or after, aggregate formation. The impact of curcumin on the structure of the aggregating material was revealed by the lower amount of β-structure in ox-apoA-I amyloid-like aggregates formed in the presence of curcumin, comparedmore » to aggregates formed without curcumin. However, the kinetics of ox-apoA-I amyloid-like aggregate formation was not altered by the presence of curcumin. Moreover, electron microscopy analysis detected no discernable differences in amyloid morphology when ox-apoA-I amyloid-like aggregates were formed in the presence or absence of curcumin. In conclusion, curcumin interacts with apoA-I and alters the structure of ox-apoA-I amyloid-like aggregates yet does not diminish the propensity of ox-apoA-I to form aggregates.« less

Mucor circinelloides induces platelet aggregation through integrin αIIbβ3 and FcγRIIA.

PubMed

Ghuman, Harlene; Shepherd-Roberts, Alicia; Watson, Stephanie; Zuidscherwoude, Malou; Watson, Steve P; Voelz, Kerstin

2018-01-03

Thrombosis is a hallmark of the fatal fungal infection mucormycosis. Yet, the platelet activation pathway in response to mucormycetes is unknown. In this study we determined the platelet aggregation potential of Mucor circinelloides (M. circinelloides) NRRL3631, characterized the signaling pathway facilitating aggregation in response to fungal spores, and identified the influence of the spore developmental stage upon platelet aggregation potential. Using impedance and light-transmission aggregometry, we showed that M. circinelloides induced platelet aggregation in whole blood and in platelet-rich plasma, respectively. The formation of large spore-platelet aggregates was confirmed by light-sheet microscopy, which showed spores dispersed throughout the aggregate. Aggregation potential was dependent on the spore's developmental stage, with the strongest platelet aggregation by spores in mid-germination. Inhibitor studies revealed platelet aggregation was mediated by the low affinity IgG receptor FcγRIIA and integrin αIIbβ3; Src and Syk tyrosine kinase signaling; and the secondary mediators TxA 2 and ADP. Flow cytometry of antibody stained platelets showed that interaction with spores increased expression of platelet surface integrin αIIbβ3 and the platelet activation marker CD62P. Together, this is the first elucidation of the signaling pathways underlying thrombosis formation during a fungal infection, highlighting targets for therapeutic intervention.

Zebrafish models of BAG3 myofibrillar myopathy suggest a toxic gain of function leading to BAG3 insufficiency.

PubMed

Ruparelia, Avnika A; Oorschot, Viola; Vaz, Raquel; Ramm, Georg; Bryson-Richardson, Robert J

2014-12-01

Mutations in the co-chaperone Bcl2-associated athanogene 3 (BAG3) can cause myofibrillar myopathy (MFM), a childhood-onset progressive muscle disease, characterized by the formation of protein aggregates and myofibrillar disintegration. In contrast to other MFM-causing proteins, BAG3 has no direct structural role, but regulates autophagy and the degradation of misfolded proteins. To investigate the mechanism of disease in BAG3-related MFM, we expressed wild-type BAG3 or the dominant MFM-causing BAG3 (BAG3(P209L)) in zebrafish. Expression of the mutant protein results in the formation of aggregates that contain wild-type BAG3. Through the stimulation and inhibition of autophagy, we tested the prevailing hypothesis that impaired autophagic function is responsible for the formation of protein aggregates. Contrary to the existing theory, our studies reveal that inhibition of autophagy is not sufficient to induce protein aggregation. Expression of the mutant protein, however, did not induce myofibrillar disintegration and we therefore examined the effect of knocking down Bag3 function. Loss of Bag3 resulted in myofibrillar disintegration, but not in the formation of protein aggregates. Remarkably, BAG3(P209L) is able to rescue the myofibrillar disintegration phenotype, further demonstrating that its function is not impaired. Together, our knockdown and overexpression experiments identify a mechanism whereby BAG3(P209L) aggregates form, gradually reducing the pool of available BAG3, which eventually results in BAG3 insufficiency and myofibrillar disintegration. This mechanism is consistent with the childhood onset and progressive nature of MFM and suggests that reducing aggregation through enhanced degradation or inhibition of nucleation would be an effective therapy for this disease.

Measurement of EPF for detection of cow pregnancy using rosette inhibition test.

PubMed

Ghaffari Laleh, V; Ghaffari Laleh, R; Pirany, N; Moghadaszadeh Ahrabi, M

2008-07-01

Early embryonic death of calves due to sub-fertility in cows is of great economic concern to dairy industry. Early pregnancy factor (EPF) is a secretory protein with pregnancy associated immunosuppressive properties. Rosette inhibition test (RIT) was used to detect EPF in inseminated dairy cows. Blood samples were collected at two intervals, 1-3 and 5-7 days after insemination from 23 inseminated and 18 non-inseminated control cows for RIT and pregnancy diagnosis performed between 42 and 45 days on palpation. The study indicates that RIT (P<0.05) has the potential to distinguish pregnant from non-pregnant dairy cows in the first week of pregnancy.

Molecular and physiological responses to titanium dioxide ...

EPA Pesticide Factsheets

- Changes in tissue transcriptomes and productivity of Arabidopsis thaliana were investigated during exposure of plants to two widely-used engineered metal oxide nanoparticles, titanium dioxide (nano-titanium) and cerium dioxide (nano-cerium). Microarray analyses confirmed that exposure to either nanoparticle altered the transcriptomes of rosette leaves and roots, with comparatively larger numbers of differentially expressed genes (DEGs) found under nano-titania exposure. Nano-titania induced more DEGs in rosette leaves, whereas roots had more DEGs under nano-ceria exposure. MapMan analyses indicated that while nano-titania up-regulated overall and secondary metabolism in both tissues, metabolic processes under nano-ceria remained mostly unchanged. Gene enrichment analysis indicated that both nanoparticles mainly enriched ontology groups such as responses to stress (abiotic and biotic), and defense responses (pathogens), and responses to endogenous stimuli (hormones). Nano-titania specifically induced genes associated with photosynthesis, whereas nano-ceria induced expression of genes related to activating transcription factors, most notably those belonging to the ethylene responsive element binding protein family. Interestingly, there were also increased numbers of rosette leaves and plant biomass under nano-ceria exposure, but not under nano-titania. Other transcriptomic responses did not clearly relate to responses observed at the organism level. This may b

A positional code and anisotropic forces control tissue remodeling in Drosophila

NASA Astrophysics Data System (ADS)

Zallen, Jennifer

A major challenge in developmental biology is to understand how tissue-scale changes in organism structure arise from events that occur on a cellular and molecular level. We are using cell biological, biophysical, and quantitative live-embryo imaging approaches to understand how genes encode the forces that shape tissues, and to identify the mechanisms that modulate cell behavior in response to local forces. In many animals, the elongated head-to-tail body axis is achieved by rapid and coordinated movements of hundreds of cells. We found that in the fruit fly, these cell movements are regulated by subcellular asymmetries in the localization of proteins that generate contractile and adhesive forces between cells. Asymmetries in the force-generating machinery are in turn controlled by a positional code of spatial information provided by an ancient family of Toll-related receptors that are widely used for pathogen recognition by the innate immune system. I will describe how this spatial system systematically orients local cell movements and collective rosette-like clusters in the Drosophila embryo. Rosettes have now also been shown to shape the body axis in chicks, frogs, and mice, demonstrating that rosette behaviors are a general mechanism linking cellular asymmetry to tissue reorganization.

Immunohistochemical characterization of neuroendocrine differentiation of canine anal sac glandular tumours.

PubMed

Suzuki, K; Morita, R; Hojo, Y; Nomura, K; Shibutani, M; Mitsumori, K

2013-01-01

Histological features and expression of neuroendocrine markers were examined in 69 samples of canine anal sac glandular carcinomas (ASGCs). The tumours were classified into solid, rosette and tubular types and mixtures of these types. Tumour-associated death in dogs with solid tumours and mixed tumours with solid components was higher than in dogs with rosette and tubular type tumours. Chromogranin A immunoreactivity was observed in 28 of 69 samples (40.6%) irrespective of histological type and was localized to the marginal areas of the tumour nest and the basal areas of the tubular and rosette structures. Neuron-specific enolase immunoreactivity in neoplastic epithelial cells was observed in 32 cases (46.4%) and was less frequently observed in the tubular type (14.3%). Synaptophysin expression was present in 15.9% of cases and was least frequent in the tubular type. Twenty-one of the 69 samples expressed more than two neuroendocrine markers and were classified as carcinomas with neuroendocrine differentiation. There was no relationship between neuroendocrine differentiation and clinical outcome. These results suggest that some ASGCs have neuroendocrine differentiation regardless of histological pattern, but clinical outcome is more related to the histological pattern than to neuroendocrine differentiation. Copyright © 2013 Elsevier Ltd. All rights reserved.

The primary vestibular projection to the cerebellar cortex in the pigeon (Columba livia)

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

Schwarz, I.E.; Schwarz, D.W.

1983-06-01

The cerebellar cortex of the pigeon receiving direct vestibular afferents was delineated by anterograde transport of (/sup 3/H)-amino acids injected into the vestibular nerve. Labelled mossy fiber rosettes in the granular layer were concentrated in lobule X (nodulus) and to a lesser extent, in the ventral portion of lobule IXd (uvula and paraflocculus). A few solitary labelled rosettes were also found in more dorsal portions of lobule IX, as well as in the anterior lobe between lobule II and IV. The lingula remained unlabelled. Discrete injections of (/sup 3/H)-leucine into the cristae of each of the three semicircular canals ormore » the utricular macula yielded a similar distribution of fewer labelled rosettes. A few primary mossy fiber terminals labelled after cochlear injections are attributed to afferents from the lagenar macula. Since effective diffusion of label from the injection site was excluded by controls, it is concluded that projection of individual canal and macula nerves to the vestibulocerebellar cortex is not topographically separated. It is proposed that this extensive convergence of various afferents is required by the cerebellum to compute precise and directionally specific control signals during head rotation in all conceivable planes.« less

Self-Assembly of Supramolecular Aggregates Based on Sector- and Cone-Shaped Dendrons and Bolaamphiphiles

NASA Astrophysics Data System (ADS)

Shcherbina, M. A.; Chvalun, S. N.

2018-06-01

Using a number of classes of such sector-shaped macromolecules as derivatives of 2,3,4- and 3,4,5- tri(dodecyloxy)benzenesulfonic acid and dendrimers based on gallic acid as an example, the main stages in the formation of supramolecular ensembles are considered: the formation of individual supramolecular aggregates due to the weak noncovalent interactions of mesogenic groups, and the subsequent ordering within these aggregates, which lowers the free energy of a system. Supramolecular aggregates are in turn organized into two- or three-dimensional supramolecular lattices. It is shown that the shape of the supramolecular aggregates and its change along with temperature are functions of the chemical structure of the mesogenic group (resulting in the controlled design of complex self-organizing systems with a given response to external stimuli).

Acceleration of thrombosis and hemolysis by fibrinolysis inhibiting factor and suppression by Ia antigen expressed on T cells in partially hepatectomized Lewis rats.

PubMed

Nakatsuji, T

1996-10-01

Partial hepatectomy (PH) of a left lateral lobe was performed on 45 Lewis rats 6.5-8.0 weeks old. Splenectomy, the injection of a fibrinolysis inhibiting (F1) factor (Gly-Pro-Arg-Pro) and both treatments were combined with the PH in 10, 11 and 9 rats, respectively. Among them, 4 males became weak with marked atrophic thymus before the 46th day after PH. All these males had massive pulmonary necrosis accompanied by platelet-rich emboli. Erythrocyte rosette formation was recognized in the mesenteric lymph nodes (MLN) of all 4 rats. The rosette erythrocytes reacted to anti-macrophage antibodies. FI factor-induced acute immune hemolysis occurred 5-9 days after PH in the 2 of the FI factor-injected and splenectomized males. Mildly to moderately atrophic thymuses were found in almost all the rats followed for 156-177 days after PH. T lymphocytes with cytoplasmic dense polysomes and desquamating endothelial cells with phagocytic erythrocytes were observed in the thymic electron micrograph of the FI factor-injected female. Positive D-D dimers were measured in the plasma of 7 rats. Increased peripheral reticulocytes (7.0 +/- 0.4%) were recognized in the males 156 days after single PH but not in the females. Ten of the 24 females and 3 of the 16 males showed an increase of peripheral Ia+ T cells to 20-30%. As well as acute pulmonary emboli, autoimmune hemolysis was induced more actively after PH in the males with CD5+ T cells that expressed the Ia antigen weakly.

Interphotoreceptor matrix components in retinal cell transplants.

PubMed

Juliusson, B; Mieziewska, K; Bergström, A; Wilke, K; Van Veen, T; Ehinger, B

1994-05-01

To further investigate the functional potential of retinal transplants we have used immunocytochemistry to study the distribution of four different interphotoreceptor matrix (IPM)-specific components in rabbit retinal transplants. The different components were: interphotoreceptor retinoid-binding protein (IRBP), chondroitin-6-sulfate, F22 antigen and peanut agglutinin (PNA) binding structures. IRBP acts as a retinoid-transport protein between the neural retina and the retinal pigment epithelium. Chondroitin-6-sulfate is a glycosaminoglycan and a part of the insoluble IPM skeleton. The identity and role of the F22 antigen is not known. However, it is a 250 kDa protein localized to specific extracellular compartments such as teh IPM. PNA is a lectin with a high binding affinity for D-galactose-beta (1-3) N-acetyl-D-galactosamine disaccharide linkages and binds to IPM domains surrounding cones, but not rods. The transplants (15-day-old embryonic rabbit retina) were placed between the neural retina and retinal pigment epithelium in adult hosts. The transplants developed the typical rosette formations with photoreceptors toward the center. IRBP labeling was distinct in the IPM in the host retina. However, no IRBP labeling could be detected in the transplants. The chondroitin-6-sulfate and F22 antibodies strongly labeled the IPM in the host retina and corresponding structures in the center of rosettes. A cone-specific labeling with PNA could be seen in the host retina. In the transplants, however, PNA labeling appeared in association with many more photoreceptors than in the host retina. There is no previous study available on the IPM in retinal cell transplants.(ABSTRACT TRUNCATED AT 250 WORDS)

Dynamics of proteins aggregation. I. Universal scaling in unbounded media

NASA Astrophysics Data System (ADS)

Zheng, Size; Javidpour, Leili; Shing, Katherine S.; Sahimi, Muhammad

2016-10-01

It is well understood that in some cases proteins do not fold correctly and, depending on their environment, even properly-folded proteins change their conformation spontaneously, taking on a misfolded state that leads to protein aggregation and formation of large aggregates. An important factor that contributes to the aggregation is the interactions between the misfolded proteins. Depending on the aggregation environment, the aggregates may take on various shapes forming larger structures, such as protein plaques that are often toxic. Their deposition in tissues is a major contributing factor to many neuro-degenerative diseases, such as Alzheimer's, Parkinson's, amyotrophic lateral sclerosis, and prion. This paper represents the first part in a series devoted to molecular simulation of protein aggregation. We use the PRIME, a meso-scale model of proteins, together with extensive discontinuous molecular dynamics simulation to study the aggregation process in an unbounded fluid system, as the first step toward MD simulation of the same phenomenon in crowded cellular environments. Various properties of the aggregates have been computed, including dynamic evolution of aggregate-size distribution, mean aggregate size, number of peptides that contribute to the formation of β sheets, number of various types of hydrogen bonds formed in the system, radius of gyration of the aggregates, and the aggregates' diffusivity. We show that many of such quantities follow dynamic scaling, similar to those for aggregation of colloidal clusters. In particular, at long times the mean aggregate size S(t) grows with time as, S(t) ˜ tz, where z is the dynamic exponent. To our knowledge, this is the first time that the qualitative similarity between aggregation of proteins and colloidal aggregates has been pointed out.

Insights in understanding aggregate formation and dissociation in cation exchange chromatography for a structurally unstable Fc-fusion protein.

PubMed

Chen, Zhiqiang; Huang, Chao; Chennamsetty, Naresh; Xu, Xuankuo; Li, Zheng Jian

2016-08-19

Cation-exchange chromatography (CEX) of a structurally unstable Fc-fusion protein exhibited multi-peak elution profile upon a salt-step elution due to protein aggregation during intra-column buffer transition where low pH and high salt coexisted. The protein exhibited a single-peak elution behavior during a pH-step elution; nevertheless, the levels of soluble aggregates (i.e. high molecular weight species, HMW) in the CEX eluate were still found up to 12-fold higher than that for the load material. The amount of the aggregates formed upon the pH-step elution was dependent on column loading with maximum HMW achieved at intermediate loading levels, supporting the hypothesis that the aggregation was the result of both the conformational changes of the bound protein and the solution concentration of the aggregation-susceptible proteins during elution. Factors such as high load pH, short protein/resin contact time, hydrophilic resin surface, and weak ionizable ligand were effective, to some extent, to reduce aggregate formation by improving the structural integrity of the bound protein. An orthogonal technique, differential scanning fluorimetry (DSF) using Sypro Orange dye confirmed that the bound protein exposed more hydrophobic area than the native molecule in free solution, especially in the pH 4-5 range. The Sypro Orange dye study of resin surface property also demonstrated that the poly[styrene-divinylbenzene]-based Poros XS with polyhydroxyl surface coating is more hydrophobic compared to the agarose-based CM Sepharose FF and SP Sepharose FF. The hydrophobic property of Poros XS contributed to stronger interactions with the partially unfolded bound protein and consequently to the higher aggregate levels seen in Poros XS eluate. This work also investigates the aggregation reversibility in CEX eluate where up to 66% of the aggregates were observed to dissociate into native monomers over a period of 120h, and links the aggregate stability to such conditions as resin surface properties and charged ligand type. Experimental data was correlated semi-quantitatively with theoretical protein charge and hydrophobicity calculations using homology modeling within the BIOVIA Discovery Studio software. Finally, an arginine-sulphopropyl (Arg-SP) agarose resin immobilized with multi-functional ligands was prepared to verify the proposed hypothesis and to eliminate the aggregate formation. The findings of this work provide general insights in understanding aggregate formation and dissociation for structurally unstable proteins in the CEX step. Copyright © 2016 Elsevier B.V. All rights reserved.

Formation and decay of charge carriers in aggregate nanofibers consisting of poly(3-hexylthiophene)-coated gold nanoparticles.

PubMed

Lee, Dongki; Lee, Jaewon; Song, Ki-Hee; Rhee, Hanju; Jang, Du-Jeon

2016-01-21

Thin nanofibers (NFs) of J-dominant aggregates with a thickness of 15 nm and thick NFs of H-dominant aggregates with a thickness of 25 nm were fabricated by the self-assembly of poly(3-hexylthiophene)-coated gold nanoparticles. The formation and decay dynamics of the charge carriers, which are dependent on the aggregate types of NFs, was investigated by time-resolved emission and transient-absorption spectroscopy. With increasing excitation energy, the fraction of the fast emission decay component decreased, suggesting that the fast formation of polaron pairs (PP), localized (LP), and delocalized polarons (DP) results from higher singlet exciton states produced by the singlet fusion. The faster decay dynamics of DP and LP in the thick NFs than in thin NFs is due to the increased delocalization of DP and LP. As the interchain aggregation is weaker than intrachain aggregation, PP decays faster in thin NFs than in thick NFs. In both thin and thick NFs, although triplet (T1) excitons were barely observed with excitation at 532 nm on a nanosecond time scale, they were observed with excitation at 355 nm, showing that T1 excitons within NFs are generated mainly through the singlet fission from a higher singlet exciton state rather than through intersystem crossing.

Dynamics of proteins aggregation. II. Dynamic scaling in confined media

NASA Astrophysics Data System (ADS)

Zheng, Size; Shing, Katherine S.; Sahimi, Muhammad

2018-03-01

In this paper, the second in a series devoted to molecular modeling of protein aggregation, a mesoscale model of proteins together with extensive discontinuous molecular dynamics simulation is used to study the phenomenon in a confined medium. The medium, as a model of a crowded cellular environment, is represented by a spherical cavity, as well as cylindrical tubes with two aspect ratios. The aggregation process leads to the formation of β sheets and eventually fibrils, whose deposition on biological tissues is believed to be a major factor contributing to many neuro-degenerative diseases, such as Alzheimer's, Parkinson's, and amyotrophic lateral sclerosis diseases. Several important properties of the aggregation process, including dynamic evolution of the total number of the aggregates, the mean aggregate size, and the number of peptides that contribute to the formation of the β sheets, have been computed. We show, similar to the unconfined media studied in Paper I [S. Zheng et al., J. Chem. Phys. 145, 134306 (2016)], that the computed properties follow dynamic scaling, characterized by power laws. The existence of such dynamic scaling in unconfined media was recently confirmed by experiments. The exponents that characterize the power-law dependence on time of the properties of the aggregation process in spherical cavities are shown to agree with those in unbounded fluids at the same protein density, while the exponents for aggregation in the cylindrical tubes exhibit sensitivity to the geometry of the system. The effects of the number of amino acids in the protein, as well as the size of the confined media, have also been studied. Similarities and differences between aggregation in confined and unconfined media are described, including the possibility of no fibril formation, if confinement is severe.

Bacterial and iron oxide aggregates mediate secondary iron mineral formation: green rust versus magnetite.

PubMed

Zegeye, A; Mustin, C; Jorand, F

2010-06-01

In the presence of methanoate as electron donor, Shewanella putrefaciens, a Gram-negative, facultative anaerobe, is able to transform lepidocrocite (gamma-FeOOH) to secondary Fe (II-III) minerals such as carbonated green rust (GR1) and magnetite. When bacterial cells were added to a gamma-FeOOH suspension, aggregates were produced consisting of both bacteria and gamma-FeOOH particles. Recently, we showed that the production of secondary minerals (GR1 vs. magnetite) was dependent on bacterial cell density and not only on iron reduction rates. Thus, gamma-FeOOH and S. putrefaciens aggregation pattern was suggested as the main mechanism driving mineralization. In this study, lepidocrocite bioreduction experiments, in the presence of anthraquinone disulfonate, were conducted by varying the [cell]/[lepidocrocite] ratio in order to determine whether different types of aggregate are formed, which may facilitate precipitation of GR1 as opposed to magnetite. Confocal laser scanning microscopy was used to analyze the relative cell surface area and lepidocrocite concentration within the aggregates and captured images were characterized by statistical methods for spatial data (i.e. variograms). These results suggest that the [cell]/[lepidocrocite] ratio influenced both the aggregate structure and the nature of the secondary iron mineral formed. Subsequently, a [cell]/[lepidocrocite] ratio above 1 x 10(7) cells mmol(-1) leads to densely packed aggregates and to the formation of GR1. Below this ratio, looser aggregates are formed and magnetite was systematically produced. The data presented in this study bring us closer to a more comprehensive understanding of the parameters governing the formation of minerals in dense bacterial suspensions and suggest that screening mineral-bacteria aggregate structure is critical to understanding (bio)mineralization pathways.

Rate Kinetics and Molecular Dynamics of the Structural Transitions in Amyloidogenic Proteins

NASA Astrophysics Data System (ADS)

Steckmann, Timothy M.

Amyloid fibril aggregation is associated with several horrific diseases such as Alzheimer's, Creutzfeld-Jacob, diabetes, Parkinson's and others. The process of amyloid aggregation involves forming myriad different metastable intermediate aggregates. Amyloid fibrils are composed of proteins that originate in an innocuous alpha-helix or random-coil structure. The alpha-helices convert their structure to beta-strands that aggregate into beta-sheets, and then into protofibrils, and ultimately into fully formed amyloid fibrils. On the basis of experimental data, I have developed a mathematical model for the kinetics of the reaction pathways and determined rate parameters for peptide secondary structural conversion and aggregation during the entire fibrillogenesis process from random coil to fibrils, including the molecular species that accelerate the conversions. The specific steps of the model and the rate constants that are determined by fitting to experimental data provide insight on the molecular species involved in the fibril formation process. To better understand the molecular basis of the protein structural transitions and aggregation, I report on molecular dynamics (MD) computational studies on the formation of amyloid protofibrillar structures in the small model protein ccbeta, which undergoes many of the structural transitions of the larger, naturally occurring amyloid forming proteins. Two different structural transition processes involving hydrogen bonds are observed for aggregation into fibrils: the breaking of intrachain hydrogen bonds to allow beta-hairpin proteins to straighten, and the subsequent formation of interchain hydrogen bonds during aggregation into amyloid fibrils. For my MD simulations, I found that the temperature dependence of these two different structural transition processes results in the existence of a temperature window that the ccbeta protein experiences during the process of forming protofibrillar structures. Both the mathematical modeling of the kinetics and the MD simulations show that molecular structural heterogeneity is a major factor in the process. The MD simulations also show that intrachain and interchain hydrogen bonds breaking and forming is strongly correlated to the process of amyloid formation.

To what extent clay mineralogy affects soil aggregation? Consequences for soil organic matter stabilization

NASA Astrophysics Data System (ADS)

Fernandez-Ugalde, O.; Barré, P.; Hubert, F.; Virto, I.; Chenu, C.; Ferrage, E.; Caner, L.

2012-12-01

Aggregation is a key process for soil functioning as it influences C storage, vulnerability to erosion and water holding capacity. While the influence of soil organic C on aggregation has been documented, much less is known about the role of soil mineralogy. Soils usually contain a mixture of clay minerals with contrasted surface properties, which should result on different abilities of clay minerals to aggregation. We took advantage of the intrinsic mineral heterogeneity of a temperate Luvisol to compare the role of clay minerals (illite, smectite, kaolinite, and mixed-layer illite-smectite) in aggregation. In a first step, grassland and tilled soil samples were fractionated in water in aggregate-size classes according to the hierarchical model of aggregation (Tisdall and Oades, 1982). Clay mineralogy and organic C in the aggregate-size classes were analyzed. The results showed that interstratified minerals containing swelling phases accumulated in aggregated fractions (>2 μm) compared to free clay fractions (<2 μm) in the two land-uses. The accumulation increased from large macro-aggregates (>500 μm) to micro-aggregates (50-250 μm). C concentration and C/N ratio followed the opposite trend. These results constitute a clay mineral-based evidence for the hierarchical model of aggregation, which postulates an increasing importance of the reactivity of clay minerals in the formation of micro-aggregates compared to larger aggregates. In the latter aggregates, formation relies on the physical enmeshment of particles by fungal hyphae, and root and microbial exudates. In a second step, micro-aggregates from the tilled soil samples were submitted to increasingly disaggregating treatments by sonication to evaluate the link between their water stability and clay mineralogy. Micro-aggregates with increasing stability showed an increase of interstratified minerals containing swelling phases and C concentration for low intensities of disaggregation (from 0 to 5 J mL-1). This suggests that swelling phases promote their stability. Swelling phases and organic C decreased for greater intensities of disaggregation. These results and the SEM images taken at different disaggregation intensities indicate that when increasing disaggregation intensity above 5 J mL-1, the recovered material consists on sand particles covered by physical coatings of illite and kaolinite. Our results show that different clay minerals have different contribution to soil aggregation. Swelling phases are especially important for water-stable aggregates formation, whereas illite and kaolinite can either contribute to aggregation or been coated to sand grains in "mineral aggregates", without porosity and organic C protection capability. In conclusion, soils with large proportion of swelling clay minerals have greater potential for carbon storage by occlusion in aggregates and greater resistance to erosion. Tisdall JM, Oades JM (1982) Organic matter and water-stable aggregates in soils. J Soil Sci 62: 141-163.

Increased Zinc Availability Enhances Initial Aggregation and Biofilm Formation of Streptococcus pneumoniae.

PubMed

Brown, Lindsey R; Caulkins, Rachel C; Schartel, Tyler E; Rosch, Jason W; Honsa, Erin S; Schultz-Cherry, Stacey; Meliopoulos, Victoria A; Cherry, Sean; Thornton, Justin A

2017-01-01

Bacteria growing within biofilms are protected from antibiotics and the immune system. Within these structures, horizontal transfer of genes encoding virulence factors, and promoting antibiotic resistance occurs, making biofilms an extremely important aspect of pneumococcal colonization and persistence. Identifying environmental cues that contribute to the formation of biofilms is critical to understanding pneumococcal colonization and infection. Iron has been shown to be essential for the formation of pneumococcal biofilms; however, the role of other physiologically important metals such as copper, zinc, and manganese has been largely neglected. In this study, we investigated the effect of metals on pneumococcal aggregation and early biofilm formation. Our results show that biofilms increase as zinc concentrations increase. The effect was found to be zinc-specific, as altering copper and manganese concentrations did not affect biofilm formation. Scanning electron microscopy analysis revealed structural differences between biofilms grown in varying concentrations of zinc. Analysis of biofilm formation in a mutant strain lacking the peroxide-generating enzyme pyruvate oxidase, SpxB, revealed that zinc does not protect against pneumococcal H 2 O 2 . Further, analysis of a mutant strain lacking the major autolysin, LytA, indicated the role of zinc as a negative regulator of LytA-dependent autolysis, which could affect biofilm formation. Additionally, analysis of cell-cell aggregation via plating and microscopy revealed that high concentrations of zinc contribute to intercellular interaction of pneumococci. The findings from this study demonstrate that metal availability contributes to the ability of pneumococci to form aggregates and subsequently, biofilms.

Effects of Grape Xylem Sap and Cell-Wall Constituents on In Vitro Growth, Biofilm Formation and Cellular Aggregation of Xylella fastidiosa

USDA-ARS?s Scientific Manuscript database

Purified cell-wall constituents or grape xylem sap added to media affected in vitro growth, biofilm formation, cell aggregation and gene expression of Xylella fastidiosa. Media containing xylem sap from Pierce’s disease (PD)-susceptible plants provided better support for bacterial growth and biofil...

Hsp25, a member of the Hsp30 family, promotes inclusion formation in response to stress.

PubMed

Katoh, Yumiko; Fujimoto, Mitsuaki; Nakamura, Kosuke; Inouye, Sachiye; Sugahara, Kazuma; Izu, Hanae; Nakai, Akira

2004-05-07

Protein aggregates are oligomeric complexes of misfolded proteins, and serve as the seeds of inclusion bodies termed aggresomes in the cells. Heat shock proteins (Hsps) prevent misfolding and aggregate formation. Here, we found that only avian Hsp25 dominantly accumulated in the aggresomes induced by proteasome inhibition. Molecular cloning of chicken Hsp25 (cHsp25) revealed that it belongs to the Hsp30 family, which is a subfamily of the alpha-crystallin/small Hsp gene family. Unexpectedly, overexpression of cHsp25 into HeLa cells promoted inclusion formation whereas overexpression of mouse Hsp27 and its chicken homologue did not. These results suggest that cHsp25 acts differently from other small Hsps on protein aggregates.

Intrinsic Determinants of Neurotoxic Aggregate Formation by the Amyloid β Peptide

PubMed Central

Brorsson, Ann-Christin; Bolognesi, Benedetta; Tartaglia, Gian Gaetano; Shammas, Sarah L.; Favrin, Giorgio; Watson, Ian; Lomas, David A.; Chiti, Fabrizio; Vendruscolo, Michele; Dobson, Christopher M.; Crowther, Damian C.; Luheshi, Leila M.

2010-01-01

Abstract The extent to which proteins aggregate into distinct structures ranging from prefibrillar oligomers to amyloid fibrils is key to the pathogenesis of many age-related degenerative diseases. We describe here for the Alzheimer's disease-related amyloid β peptide (Aβ) an investigation of the sequence-based determinants of the balance between the formation of prefibrillar aggregates and amyloid fibrils. We show that by introducing single-point mutations, it is possible to convert the normally harmless Aβ40 peptide into a pathogenic species by increasing its relative propensity to form prefibrillar but not fibrillar aggregates, and, conversely, to abolish the pathogenicity of the highly neurotoxic E22G Aβ42 peptide by reducing its relative propensity to form prefibrillar species rather than mature fibrillar ones. This observation can be rationalized by the demonstration that whereas regions of the sequence of high aggregation propensity dominate the overall tendency to aggregate, regions with low intrinsic aggregation propensities exert significant control over the balance of the prefibrillar and fibrillar species formed, and therefore play a major role in determining the neurotoxicity of the Aβ peptide. PMID:20409489

';Best' Practices for Aggregating Subset Results from Archived Datasets

NASA Astrophysics Data System (ADS)

Baskin, W. E.; Perez, J.

2013-12-01

In response to the exponential growth in science data analysis and visualization capabilities Data Centers have been developing new delivery mechanisms to package and deliver large volumes of aggregated subsets of archived data. New standards are evolving to help data providers and application programmers deal with growing needs of the science community. These standards evolve from the best practices gleaned from new products and capabilities. The NASA Atmospheric Sciences Data Center (ASDC) has developed and deployed production provider-specific search and subset web applications for the CALIPSO, CERES, TES, and MOPITT missions. This presentation explores several use cases that leverage aggregated subset results and examines the standards and formats ASDC developers applied to the delivered files as well as the implementation strategies for subsetting and processing the aggregated products. The following topics will be addressed: - Applications of NetCDF CF conventions to aggregated level 2 satellite subsets - Data-Provider-Specific format requirements vs. generalized standards - Organization of the file structure of aggregated NetCDF subset output - Global Attributes of individual subsetted files vs. aggregated results - Specific applications and framework used for subsetting and delivering derivative data files

Collision experiments between centimeter-sized protoplanetesimals in microgravity

NASA Astrophysics Data System (ADS)

Whizin, Akbar; Colwell, Joshua E.; Dove, Adrienne; Brisset, Julie; Cruz, Roberto; Foster, Zach

2016-10-01

In the early stages of planet formation in a protoplanetary disk the first coalescing bodies are weakly bound. Conditions in the disk, such as the presence of gas (drag), make further growth through centimeter and meter sized bodies difficult. For centimeter-sized aggregates self-gravity is almost non-existent and electrostatic surface forces such as van der Waals-type forces play a critical role in holding loosely bound rubble-piles together during their early formation. In order to understand how aggregates of this size grow we study the mechanical strengths, material, and collisional properties of cm-sized aggregates. The collisional outcomes between two aggregates can be determined by a set of definable collision parameters and experimental constraints on these parameters will aid in astrophysical models of planet formation. We have carried out a series of microgravity laboratory experiments in which we collide a pair of weakly bound aggregates together. In our free-fall chamber we collide two 3-cm aggregates together at collision velocities ranging from 50 to 220 cm/s and with pressure ~1 mbar. The aggregates are made of mm-sized silica bead particles and require internal cohesion to avoid fragmentation above modest collision speeds, which is supplied by adding H2O (later dehydrated) and between 0 - 0.1 g of a well-mixed liquid adhesive to simulate surface forces and bonds between particles. We measure the compressive strengths of the aggregates (0.5 - 10 kPa), find their coefficients of restitution (CoR), and determine their bouncing and fragmentation thresholds, over a range of velocities and internal strengths. We observed collisional outcomes such as bouncing, erosion (mass-loss), and fragmentation of the aggregates. We find the CoR of the aggregates to have a mean of 0.11 ± 0.1 with no dependence on velocity or strength. Impact velocities above ~2 m/s resulted in fragmentation of our aggregates, higher than the ~1 m/s threshold for porous dust aggregates of roughly the same size implying non-porous aggregates are also capable of easily dissipating energy in collisions.

Shortening of the Lactobacillus paracasei subsp. paracasei BGNJ1-64 AggLb Protein Switches Its Activity from Auto-aggregation to Biofilm Formation.

PubMed

Miljkovic, Marija; Bertani, Iris; Fira, Djordje; Jovcic, Branko; Novovic, Katarina; Venturi, Vittorio; Kojic, Milan

2016-01-01

AggLb is the largest (318.6 kDa) aggregation-promoting protein of Lactobacillus paracasei subsp. paracasei BGNJ1-64 responsible for forming large cell aggregates, which causes auto-aggregation, collagen binding and pathogen exclusion in vitro. It contains an N-terminus leader peptide, followed by six successive collagen binding domains, 20 successive repeats (CnaB-like domains) and an LPXTG sorting signal at the C-terminus for cell wall anchoring. Experimental information about the roles of the domains of AggLb is currently unknown. To define the domain that confers cell aggregation and the key domains for interactions of specific affinity between AggLb and components of the extracellular matrix, we constructed a series of variants of the aggLb gene and expressed them in Lactococcus lactis subsp. lactis BGKP1-20 using a lactococcal promoter. All of the variants contained a leader peptide, an inter collagen binding-CnaB domain region (used to raise an anti-AggLb antibody), an anchor domain and a different number of collagen binding and CnaB-like domains. The role of the collagen binding repeats of the N-terminus in auto-aggregation and binding to collagen and fibronectin was confirmed. Deletion of the collagen binding repeats II, III, and IV resulted in a loss of the strong auto-aggregation, collagen and fibronectin binding abilities whereas the biofilm formation capability was increased. The strong auto-aggregation, collagen and fibronectin binding abilities of AggLb were negatively correlated to biofilm formation.

Ecological and morphological profile of floating spherical Cladophora socialis aggregations in central Thailand.

PubMed

Tsutsui, Isao; Miyoshi, Tatsuo; Sukchai, Halethichanok; Pinphoo, Piyarat; Aue-Umneoy, Dusit; Meeanan, Chonlada; Songphatkaew, Jaruwan; Klomkling, Sirimas; Yamaguchi, Iori; Ganmanee, Monthon; Sudo, Hiroyuki; Hamano, Kaoru

2015-01-01

The unique beauty of spherical aggregation forming algae has attracted much attention from both the scientific and lay communities. Several aegagropilous seaweeds have been identified to date, including the plants of genus Cladophora and Chaetomorpha. However, this phenomenon remains poorly understood. In July 2013, a mass occurrence of spherical Cladophora aggregations was observed in a salt field reservoir in Central Thailand. The aims of the present study were to describe the habitat of the spherical aggregations and confirm the species. We performed a field survey, internal and external morphological observations, pyrenoid ultrastructure observations, and molecular sequence analysis. Floating spherical Cladophora aggregations (1-8 cm in diameter) were observed in an area ~560 m2, on the downwind side of the reservoir where there was water movement. Individual filaments in the aggregations were entangled in each other; consequently, branches growing in different directions were observed within a clump. We suggest that water movement and morphological characteristics promote the formation of spherical aggregations in this species. The molecular sequencing results revealed that the study species was highly homologous to both C. socialis and C. coelothrix. However, the diameter of the apical cells in the study species was less than that of C. coelothrix. The pyrenoid ultrastructure was more consistent with that of C. socialis. We conclude that the study species is C. socialis. This first record of spherical aggregations in this species advances our understanding of these formations. However, further detailed physical measurements are required to fully elucidate the mechanism behind these spherical formations.

Ecological and Morphological Profile of Floating Spherical Cladophora socialis Aggregations in Central Thailand

PubMed Central

Tsutsui, Isao; Miyoshi, Tatsuo; Sukchai, Halethichanok; Pinphoo, Piyarat; Aue-umneoy, Dusit; Meeanan, Chonlada; Songphatkaew, Jaruwan; Klomkling, Sirimas; Yamaguchi, Iori; Ganmanee, Monthon; Sudo, Hiroyuki; Hamano, Kaoru

2015-01-01

The unique beauty of spherical aggregation forming algae has attracted much attention from both the scientific and lay communities. Several aegagropilous seaweeds have been identified to date, including the plants of genus Cladophora and Chaetomorpha. However, this phenomenon remains poorly understood. In July 2013, a mass occurrence of spherical Cladophora aggregations was observed in a salt field reservoir in Central Thailand. The aims of the present study were to describe the habitat of the spherical aggregations and confirm the species. We performed a field survey, internal and external morphological observations, pyrenoid ultrastructure observations, and molecular sequence analysis. Floating spherical Cladophora aggregations (1–8 cm in diameter) were observed in an area ~560 m2, on the downwind side of the reservoir where there was water movement. Individual filaments in the aggregations were entangled in each other; consequently, branches growing in different directions were observed within a clump. We suggest that water movement and morphological characteristics promote the formation of spherical aggregations in this species. The molecular sequencing results revealed that the study species was highly homologous to both C. socialis and C. coelothrix. However, the diameter of the apical cells in the study species was less than that of C. coelothrix. The pyrenoid ultrastructure was more consistent with that of C. socialis. We conclude that the study species is C. socialis. This first record of spherical aggregations in this species advances our understanding of these formations. However, further detailed physical measurements are required to fully elucidate the mechanism behind these spherical formations. PMID:25898393

AGGREGATION PATHWAYS OF THE AMYLOID β(1–42) PEPTIDE DEPEND ON ITS COLLOIDAL STABILITY AND ORDERED β-SHEET STACKING

PubMed Central

Jiang, Dianlu; Rauda, Iris; Han, Shubo; Chen, Shu; Zhou, Feimeng

2012-01-01

Amyloid β (Aβ) fibrils are present as a major component in senile plaques, the hallmark of Alzheimer’s disease (AD). Diffuse plaques (non-fibrous, loosely packed Aβ aggregates) containing amorphous Aβ aggregates are also formed in brain. This work examines the influence of Cu2+ complexation by Aβ on the aggregation process in the context of charge and structural variations. Changes in the surface charges of Aβ molecules due to Cu2+ binding, measured with a zeta potential measurement device, were correlated with the aggregate morphologies examined by atomic force microscopy. As a result of the charge variation, the “colloid-like” stability of the aggregation intermediates, which is essential to the fibrillation process, is affected. Consequently Cu2+ enhances the amorphous aggregate formation. By monitoring variations in the secondary structures with circular dichroism spectroscopy, a direct transformation from the unstructured conformation to the β-sheet structure was observed for all types of aggregates observed (oligomers, fibrils, and/or amorphous aggregates). Compared to the Aβ aggregation pathway in the absence of Cu2+ and taking other factors affecting Aβ aggregation (i.e., pH and temperature) into account, our investigation indicates that formations of amorphous and fibrous aggregates diverge from the same β-sheet-containing partially folded intermediate. This study suggests that the hydrophilic domain of Aβ also plays a role in the Aβ aggregation process. A kinetic model was proposed to account for the effects of the Cu2+ binding on these two aggregation pathways in terms of charge and structural variations. PMID:22870885

Role of disulfide cross-linking of mutant SOD1 in the formation of inclusion-body-like structures.

PubMed

Roberts, Brittany L T; Patel, Kinaree; Brown, Hilda H; Borchelt, David R

2012-01-01

Pathologic aggregates of superoxide dismutase 1 (SOD1) harboring mutations linked to familial amyotrophic lateral sclerosis (fALS) have been shown to contain aberrant intermolecular disulfide cross-links. In prior studies, we observed that intermolecular bonding was not necessary in the formation of detergent- insoluble SOD1 complexes by mutant SOD1, but we were unable to assess whether this type of bonding may be important for pathologic inclusion formation. In the present study, we visually assess the formation of large inclusions by fusing mutant SOD1 to yellow fluorescent protein (YFP). Experimental constructs possessing mutations at all cysteine residues in SOD1 (sites 6, 57, 111, and 146 to F,S,Y,R or G,S,Y,R, respectively) were shown to maintain a high propensity of inclusion formation despite the inability to form disulfide cross-links. Interestingly, although aggregates form when all cysteines were mutated, double mutants of the ALS mutation C6G with an experimental mutation C111S exhibited low aggregation propensity. Overall, this study is an extension of previous work demonstrating that cysteine residues in mutant SOD1 play a role in modulating aggregation and that intermolecular disulfide bonds are not required to produce large intracellular inclusion-like structures.

NMR study on the network structure of a mixed gel of kappa and iota carrageenans.

PubMed

Hu, Bingjie; Du, Lei; Matsukawa, Shingo

2016-10-05

The temperature dependencies of the (1)H T2 and diffusion coefficient (D) of a mixed solution of kappa-carrageenan and iota-carrageenan were measured by NMR. Rheological and NMR measurements suggested an exponential formation of rigid aggregates of kappa-carrageenan and a gradual formation of fine aggregates of iota-carrageenan during two step increases of G'. The results also suggested that longer carrageenan chains are preferentially involved in aggregation, thus resulting in a decrease in the average Mw of solute carrageenans. The results of diffusion measurements for poly(ethylene oxide) (PEO) suggested that kappa-carrageenan formed thick aggregates that decreased hindrance to PEO diffusion by decreasing the solute kappa-carrageenan concentration in the voids of the aggregated chains, and that iota-carrageenan formed fine aggregates that decreased the solute iota-carrageenan concentration less. DPEO in a mixed solution of kappa-carrageenan and iota-carrageenan suggested two possibilities for the microscopic network structure: an interpenetrating network structure, or micro-phase separation. Copyright © 2016. Published by Elsevier Ltd.

Prediction of the aggregation propensity of proteins from the primary sequence: aggregation properties of proteomes.

PubMed

Castillo, Virginia; Graña-Montes, Ricardo; Sabate, Raimon; Ventura, Salvador

2011-06-01

In the cell, protein folding into stable globular conformations is in competition with aggregation into non-functional and usually toxic structures, since the biophysical properties that promote folding also tend to favor intermolecular contacts, leading to the formation of β-sheet-enriched insoluble assemblies. The formation of protein deposits is linked to at least 20 different human disorders, ranging from dementia to diabetes. Furthermore, protein deposition inside cells represents a major obstacle for the biotechnological production of polypeptides. Importantly, the aggregation behavior of polypeptides appears to be strongly influenced by the intrinsic properties encoded in their sequences and specifically by the presence of selective short regions with high aggregation propensity. This allows computational methods to be used to analyze the aggregation properties of proteins without the previous requirement for structural information. Applications range from the identification of individual amyloidogenic regions in disease-linked polypeptides to the analysis of the aggregation properties of complete proteomes. Herein, we review these theoretical approaches and illustrate how they have become important and useful tools in understanding the molecular mechanisms underlying protein aggregation. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Sulfur mustard induces the formation of keratin aggregates in human epidermal keratinocytes.

PubMed

Dillman, James F; McGary, Kriston L; Schlager, John J

2003-12-01

The vesicant sulfur mustard is an alkylating agent that has the capacity to cross-link biological molecules. We are interested in identifying specific proteins that are altered upon sulfur mustard exposure. Keratins are particularly important for the structural integrity of skin, and several genetically inherited blistering diseases have been linked to mutations in keratin 5 and keratin 14. We examined whether sulfur mustard exposure alters keratin biochemistry in cultured human epidermal keratinocytes. Western blotting with specific monoclonal antibodies revealed the formation of stable high-molecular-weight "aggregates" containing keratin 14 and/or keratin 5. These aggregates begin to form within 15 min after sulfur mustard exposure. These aggregates display a complex gel electrophoresis pattern between approximately 100 and approximately 200 kDa. Purification and analysis of these aggregates by one- and two-dimensional gel electrophoresis and mass spectrometry confirmed the presence of keratin 14 and keratin 5 and indicate that at least some of the aggregates are composed of keratin 14-keratin 14, keratin 14-keratin 5, or keratin 5-keratin 5 dimers. These studies demonstrate that sulfur mustard induces keratin aggregation in keratinocytes and support further investigation into the role of keratin aggregation in sulfur mustard-induced vesication.

Visible light-induced insulin aggregation on surfaces via photoexcitation of bound thioflavin T.

PubMed

Chouchane, Karim; Pignot-Paintrand, Isabelle; Bruckert, Franz; Weidenhaupt, Marianne

2018-04-01

Insulin is known to form amyloid aggregates when agitated in a hydrophobic container. Amyloid aggregation is routinely measured by the fluorescence of the conformational dye thioflavin T, which, when incorporated into amyloid fibers, fluoresces at 480 nm. The kinetics of amyloid aggregation in general is characterized by an initial lag-phase, during which aggregative nuclei form on the hydrophobic surface. These nuclei then lead to the formation of fibrils presenting a rapid growth during the elongation phase. Here we describe a novel mechanism of insulin amyloid aggregation which is surprisingly devoid of a lag-time for nucleation. The excitation of thioflavin T by visible light at 440 nm induces the aggregation of thioflavin T-positive insulin fibrils on hydrophobic surfaces in the presence of strong agitation and at physiological pH. This process is material surface-induced and depends on the fact that surface-adsorbed insulin can bind thioflavin T. Light-induced insulin aggregation kinetics is thioflavin T-mediated and is based on an energy transfer from visible light to the protein via thioflavin T. It relies on a constant supply of thioflavin T and insulin from the solution to the aggregate. The growth rate increases with the irradiance and with the concentration of thioflavin T. The supply of insulin seems to be the limiting factor of aggregate growth. This light-induced aggregation process allows the formation of local surface-bound aggregation patterns. Copyright © 2018 Elsevier B.V. All rights reserved.

The effects of glutamine/asparagine content on aggregation and heterologous prion induction by yeast prion-like domains.

PubMed

Shattuck, Jenifer E; Waechter, Aubrey C; Ross, Eric D

2017-07-04

Prion-like domains are low complexity, intrinsically disordered domains that compositionally resemble yeast prion domains. Many prion-like domains are involved in the formation of either functional or pathogenic protein aggregates. These aggregates range from highly dynamic liquid droplets to highly ordered detergent-insoluble amyloid-like aggregates. To better understand the amino acid sequence features that promote conversion to stable, detergent-insoluble aggregates, we used the prediction algorithm PAPA to identify predicted aggregation-prone prion-like domains with a range of compositions. While almost all of the predicted aggregation-prone domains formed foci when expressed in cells, the ability to form the detergent-insoluble aggregates was highly correlated with glutamine/asparagine (Q/N) content, suggesting that high Q/N content may specifically promote conversion to the amyloid state in vivo. We then used this data set to examine cross-seeding between prion-like proteins. The prion protein Sup35 requires the presence of a second prion, [PIN + ], to efficiently form prions, but this requirement can be circumvented by the expression of various Q/N-rich protein fragments. Interestingly, almost all of the Q/N-rich domains that formed SDS-insoluble aggregates were able to promote prion formation by Sup35, highlighting the highly promiscuous nature of these interactions.

Curcumin Attenuates Amyloid-β Aggregate Toxicity and Modulates Amyloid-β Aggregation Pathway.

PubMed

Thapa, Arjun; Jett, Stephen D; Chi, Eva Y

2016-01-20

The abnormal misfolding and aggregation of amyloid-β (Aβ) peptides into β-sheet enriched insoluble deposits initiates a cascade of events leading to pathological processes and culminating in cognitive decline in Alzheimer's disease (AD). In particular, soluble oligomeric/prefibrillar Aβ have been shown to be potent neurotoxins. The naturally occurring polyphenol curcumin has been shown to exert a neuroprotective effect against age-related neurodegenerative diseases such as AD. However, its protective mechanism remains unclear. In this study, we investigated the effects of curcumin on the aggregation of Aβ40 as well as Aβ40 aggregate induced neurotoxicity. Our results show that the curcumin does not inhibit Aβ fibril formation, but rather enriches the population of "off-pathway" soluble oligomers and prefibrillar aggregates that were nontoxic. Curcumin also exerted a nonspecific neuroprotective effect, reducing toxicities induced by a range of Aβ conformers, including monomeric, oligomeric, prefibrillar, and fibrillar Aβ. The neuroprotective effect is possibly membrane-mediated, as curcumin reduced the extent of cell membrane permeabilization induced by Aβ aggregates. Taken together, our study shows that curcumin exerts its neuroprotective effect against Aβ induced toxicity through at least two concerted pathways, modifying the Aβ aggregation pathway toward the formation of nontoxic aggregates and ameliorating Aβ-induced toxicity possibly through a nonspecific pathway.

The promoter of the Arabidopsis PIN6 auxin transporter enabled strong expression in the vasculature of roots, leaves, floral stems and reproductive organs.

PubMed

Nisar, Nazia; Cuttriss, Abby J; Pogson, Barry J; Cazzonelli, Christopher I

2014-01-01

Cellular auxin homeostasis controls many aspects of plant growth, organogenesis and development. The existence of intracellular auxin transport mediated by endoplasmic reticulum (ER)-localized PIN5, PIN6 and PIN8 proteins is a relatively recent discovery shaping a new era in understanding auxin-mediated growth processes. Here we summarize the importance of PIN6 in mediating intracellular auxin transport during root formation, leaf vein patterning and nectary production. While, it was previously shown that PIN6 was strongly expressed in rosette leaf cell types important in vein formation, here we demonstrate by use a PIN6 promoter-reporter fusion, that PIN6 is also preferentially expressed in the vasculature of the primary root, cotyledons, cauline leaves, floral stem, sepals and the main transmitting tract of the reproductive silique. The strong, vein- specific reporter gene expression patterns enabled by the PIN6 promoter emphasizes that transcriptional control is likely to be a major regulator of PIN6 protein levels, during vasculature formation, and supports the need for ER-localized PIN proteins in selecting specialized cells for vascular function in land plants.

The Carbonates in ALH 84001 Record the Evolution of the Martian Atmosphere Through Multiple Formation Events

NASA Technical Reports Server (NTRS)

Shaheen, R.; Niles, P. B.; Corrgan, C.

2012-01-01

Current Martian conditions restrict the presence of liquid water due to low temperatures (approx 210K), a thin atmosphere (approx 7mb), and intense UV radiation. However, past conditions on Mars may have been different with the possibility that the ancient Martian climate was warm and wet with a dense CO2 atmosphere. The cycling of carbon on Mars through atmospheric CO2 and carbonate minerals is critical for deciphering its climate history. In particular stable isotopes contained in carbonates can provide information of their origin and formation environment as well as possibly hinting at the composition of global reservoirs such as atmospheric CO2. Martian meteorite ALH 84001 contains widely studied carbonate rosettes that have been dated to approx. 3.9 Ga and have been used to interpret climatic conditions present at that time. However, there is mount-ing evidence for multiple episodes of carbonate formation in ALH 84001 with potentially distinct isotopic compositions. This study seeks to tease out these different carbonate assemblages using stepped phosphoric acid dissolution and analysis of carbon and triple oxygen stable isotopes. In addition, we report SIMS analyses of the delta O-18 several petrographically unusual carbonate phases in the meteorite.

Ionization impact on molecular clouds and star formation. Numerical simulations and observations

NASA Astrophysics Data System (ADS)

Tremblin, P.

2012-11-01

At all the scales of Astrophysics, the impact of the ionization from massive stars is a crucial issue. At the galactic scale, the ionization can regulate star formation by supporting molecular clouds against gravitational collapse and at the stellar scale, indications point toward a possible birth place of the Solar System close to massive stars. At the molecular cloud scale, it is clear that the hot ionized gas compresses the surrounding cold gas, leading to the formation of pillars, globules, and shells of dense gas in which some young stellar objects are observed. What are the formation mechanisms of these structures? Are the formation of these young stellar objects triggered or would have they formed anyway? Do massive stars have an impact on the distribution of the surrounding gas? Do they have an impact on the mass distribution of stars (the initial mass function, IMF)? This thesis aims at shedding some light on these questions, by focusing especially on the formation of the structures between the cold and the ionized gas. We present the state of the art of the theoretical and observational works on ionized regions (H ii regions) and we introduce the numerical tools that have been developed to model the ionization in the hydrodynamic simulations with turbulence performed with the HERACLES code. Thanks to the simulations, we present a new model for the formation of pillars based on the curvature and collapse of the dense shell on itself and a new model for the formations of cometary globules based on the turbulence of the cold gas. Several diagnostics have been developed to test these new models in the observations. If pillars are formed by the collapse of the dense shell on itself, the velocity spectrum of a nascent pillar presents a large spectra with a red-shifted and a blue-shifted components that are caused by the foreground and background parts of the shell that collapse along the line of sight. If cometary globules emerge because of the turbulence of the molecular cloud, the velocity spectrum of these globules is shifted at different velocities than the velocity of the shell, pillars and clumps that follow the global expansion of the H ii region. An other diagnostic is the impact of the compression on the probability density function (PDF) of the cold gas. The distribution is double peaked when the turbulent ram pressure is low compared to the ionized-gas pressure. This is the signature of the compression caused by the expansion of the ionized bubble. When the turbulence is high, the two peaks merge and the compression can still be identified although the signature is less clear. We have used Herschel column density maps and molecular-line data to characterize the density and velocity structures of the interface between the ionized and the cold gas in several regions: RCW 120, RCW 36, Cygnus X, the Rosette and Eagle Nebulae. In addition to the diagnostics derived from the simulations, analytical predictions of the shell and pillar parameters was tested and confronted to the observations. In all the regions, we have seen that there is a good agreement with the analytical models and with the simulation diagnostics. The velocity structure of a nascent pillar in the Rosette Nebula suggests that it has been formed by the collapse of the shell on itself and the bulk velocity of cometary globules in Cygnus X and in the Rosette Nebula tends to confirm their turbulent origin. The compression caused by the ionized gas can be seen on the PDF of the cold gas in most of the regions studied. This result is important for the link between the IMF and the global prop! erties of the cloud. If the IMF can be derived from the PDF of a cloud, the impact of the massive stars on the PDF has to be taken in account. Furthermore, we present dedicated simulations of RCW 36 that suggest that the dense clumps at the edge of the ionized gas are not pre-existing, it is likely that their formation was triggered by the compression caused by the ionization. Therefore the ionization from the massive stars is a key process that has to be taken into account for the understanding of the IMF. We also present in appendix other works that have been done in parallel of this thesis: the charge exchange in colliding planetary and stellar winds in collaboration with Prof. E. Chiang during the ISIMA summer school 2011 in Beijing; and the sub-millimeter site testing at the Concordia station in Antarctica with the CAMISTIC team.

Immunological profiles in alopecia areata.

PubMed

Galbraith, G M; Thiers, B H; Vasily, D B; Fudenberg, H H

1984-02-01

Cell-mediated immunity and auto-immune phenomena were investigated in sixty patients with active alopecia areata of various degrees of severity. Serum auto-antibodies to thyroid antigens were detected in twenty-three patients. Examination of T-lymphocyte populations, lymphocyte DNA synthesis, and lymphokine production in response to mitogen stimulation revealed no differences between the sixty patients and matched healthy control subjects. However, patients with thyroid auto-immunity and/or the presence of alopecia totalis or universalis showed significant reductions in interactive T lymphocytes (recognized by rosette formation with human B lymphoblastoid cells) and diminished production of leukocyte migration inhibition factor in response to stimulation with phytohaemagglutinin. This suggests that immune mechanisms may be involved in the pathogenesis of alopecia areata which is associated with thyroid auto-immunity or which progresses to total hair loss.

An extraneural primary anaplastic ependymoma at the subcutaneous inguinal region: Report of a rare case.

PubMed

Sayar, Hamide; Ersen, Ayca; Kurtul, Neslihan; Yazar, Mehmet Fatih; Balakan, Ozan

2015-01-01

Ependymomas commonly arise in the central nervous system. Extraneural presentation is quite rare. Herein, we describe a primary extraneural ependymoma in a young female. The mass was located in the right inguinal area. The cut surface of the 7.5 mm × 6.5 mm × 4.5 mm sized tumor was brownish-yellow in color. Histologically, it was hypercellular exhibiting pseudorosette or rosette formations and some papillary structures. Mitosis was counted as high as 10 per 10 high power fields. Neither necrosis nor vascular endothelial proliferation within the tumor was observed. Tumor cells showed strong glial fibrillary acidic protein immunoreactivity. On epithelial membrane antigen, intracytoplasmic dot-like immunostaining was observed. This is the first report presenting a primary extraneural anaplastic ependymoma arising in the inguinal subcutaneous region.

Spatiotemporal & Ecological Processes Associated With Goliath Grouper Aggregations in Southeastern Florida

NASA Astrophysics Data System (ADS)

Binder, B. M.; Boswell, K. M.

2016-02-01

The formation of Fish Spawning Aggregations (FSAs) is vital to the life history of many reef fishes, representing the only reproductive opportunity for many species. Unfortunately FSAs present a lucrative target for exploitation which has led to cases of decline and regional extirpation. However, the integration of stakeholders into the design of fisheries management strategies has led to the protection of several species throughout the Greater Caribbean; including the goliath grouper, which has shown evidence of recovery since the moratorium on harvest in 1990. Since the closure, user based and researcher driven initiatives have investigated the recovery, biology, and life history of goliath grouper, but fine scale spatiotemporal and community level aspects of aggregation formation have not been specifically addressed. Thus, we developed a novel two-tiered survey approach using scientific echosounders and diver visual surveys to characterize the spatiotemporal aspects of goliath grouper aggregations, along with the community response to aggregations at six aggregation sites near Jupiter, Florida. Acoustic transects and diver surveys were performed near peak lunar phases throughout the spawning season to quantify fluctuations in goliath grouper density and abundance during the season; and to characterize changes in local community structure in response to aggregation formation. The results from this study are being used to inform the development of resource management plans in South Florida; and addressing these questions will generate a framework to apply a novel research technique in other regions where knowledge of reproductive behavior is absent from the peer-reviewed literature.

J-aggregation in porphyrin nanoparticles induced by diphenylalanine

NASA Astrophysics Data System (ADS)

Li, Fengqing; Liu, Dongzhi; Wang, Tianyang; Hu, Jianxin; Meng, Fancui; Sun, Haiya; Shang, Zhi; Li, Pingan; Feng, Wenhui; Li, Wei; Zhou, Xueqin

2017-08-01

In this report, L-diphenylalanine-decorated tetraphenylporphyrin (TPPtFFC) was synthesized and self-assembled into regular nano-architechtures. The morphology of the assemblies varied with the concentration of TPPtFFC. The absorption spectra of the nanoparticles show the Soret band merges with the Q bands and redistributes with great red-shift, indicative of the formation of J-aggregates of the porphyrin molecules. The fluorescence emission of the nanoparticles is merged and red-shifted to near-infrared region. Studies of absorption and fluorescence spectra reveal an indispensible role of diphenylalanine group in the formation of J-aggregates. The Raman spectra disclose that diprotonation of the porphyrin core contributes to delocalized coherent excited states in the nanoparticles. The positive cotton effect in circular dichroism spectra corresponding to the Soret band of TPPtFFC in solution confirms the formation of J-aggregates with right-handed chirality of the dipole moment. This report will shed light on the rational design of porphyrin-peptide conjugates to mimic naturally light-harvesting complexes.

Kinetic Monte Carlo and cellular particle dynamics simulations of multicellular systems

NASA Astrophysics Data System (ADS)

Flenner, Elijah; Janosi, Lorant; Barz, Bogdan; Neagu, Adrian; Forgacs, Gabor; Kosztin, Ioan

2012-03-01

Computer modeling of multicellular systems has been a valuable tool for interpreting and guiding in vitro experiments relevant to embryonic morphogenesis, tumor growth, angiogenesis and, lately, structure formation following the printing of cell aggregates as bioink particles. Here we formulate two computer simulation methods: (1) a kinetic Monte Carlo (KMC) and (2) a cellular particle dynamics (CPD) method, which are capable of describing and predicting the shape evolution in time of three-dimensional multicellular systems during their biomechanical relaxation. Our work is motivated by the need of developing quantitative methods for optimizing postprinting structure formation in bioprinting-assisted tissue engineering. The KMC and CPD model parameters are determined and calibrated by using an original computational-theoretical-experimental framework applied to the fusion of two spherical cell aggregates. The two methods are used to predict the (1) formation of a toroidal structure through fusion of spherical aggregates and (2) cell sorting within an aggregate formed by two types of cells with different adhesivities.

A physical description of the adhesion and aggregation of platelets

NASA Astrophysics Data System (ADS)

Chopard, Bastien; de Sousa, Daniel Ribeiro; Lätt, Jonas; Mountrakis, Lampros; Dubois, Frank; Yourassowsky, Catherine; Van Antwerpen, Pierre; Eker, Omer; Vanhamme, Luc; Perez-Morga, David; Courbebaisse, Guy; Lorenz, Eric; Hoekstra, Alfons G.; Boudjeltia, Karim Zouaoui

2017-04-01

The early stages of clot formation in blood vessels involve platelet adhesion-aggregation. Although these mechanisms have been extensively studied, gaps in their understanding still persist. We have performed detailed in vitro experiments, using the well-known Impact-R device, and developed a numerical model to better describe and understand this phenomenon. Unlike previous studies, we took into account the differential role of pre-activated and non-activated platelets, as well as the three-dimensional nature of the aggregation process. Our investigation reveals that blood albumin is a major parameter limiting platelet aggregate formation in our experiment. Simulations are in very good agreement with observations and provide quantitative estimates of the adhesion and aggregation rates that are hard to measure experimentally. They also provide a value of the effective diffusion of platelets in blood subject to the shear rate produced by the Impact-R.

Externalized decondensed neutrophil chromatin occludes pancreatic ducts and drives pancreatitis

PubMed Central

Leppkes, Moritz; Maueröder, Christian; Hirth, Sebastian; Nowecki, Stefanie; Günther, Claudia; Billmeier, Ulrike; Paulus, Susanne; Biermann, Mona; Munoz, Luis E.; Hoffmann, Markus; Wildner, Dane; Croxford, Andrew L.; Waisman, Ari; Mowen, Kerri; Jenne, Dieter E.; Krenn, Veit; Mayerle, Julia; Lerch, Markus M.; Schett, Georg; Wirtz, Stefan; Neurath, Markus F.; Herrmann, Martin; Becker, Christoph

2016-01-01

Ductal occlusion has been postulated to precipitate focal pancreatic inflammation, while the nature of the primary occluding agents has remained elusive. Neutrophils make use of histone citrullination by peptidyl arginine deiminase-4 (PADI4) in contact to particulate agents to extrude decondensed chromatin as neutrophil extracellular traps (NETs). In high cellular density, NETs form macroscopically visible aggregates. Here we show that such aggregates form inside pancreatic ducts in humans and mice occluding pancreatic ducts and thereby driving pancreatic inflammation. Experimental models indicate that PADI4 is critical for intraductal aggregate formation and that PADI4-deficiency abrogates disease progression. Mechanistically, we identify the pancreatic juice as a strong instigator of neutrophil chromatin extrusion. Characteristic single components of pancreatic juice, such as bicarbonate ions and calcium carbonate crystals, induce aggregated NET formation. Ductal occlusion by aggregated NETs emerges as a pathomechanism with relevance in a plethora of inflammatory conditions involving secretory ducts. PMID:26964500

The amyloid interactome: Exploring protein aggregation

PubMed Central

Mastrokalou, Chara V.; Hamodrakas, Stavros J.

2017-01-01

Protein-protein interactions are the quintessence of physiological activities, but also participate in pathological conditions. Amyloid formation, an abnormal protein-protein interaction process, is a widespread phenomenon in divergent proteins and peptides, resulting in a variety of aggregation disorders. The complexity of the mechanisms underlying amyloid formation/amyloidogenicity is a matter of great scientific interest, since their revelation will provide important insight on principles governing protein misfolding, self-assembly and aggregation. The implication of more than one protein in the progression of different aggregation disorders, together with the cited synergistic occurrence between amyloidogenic proteins, highlights the necessity for a more universal approach, during the study of these proteins. In an attempt to address this pivotal need we constructed and analyzed the human amyloid interactome, a protein-protein interaction network of amyloidogenic proteins and their experimentally verified interactors. This network assembled known interconnections between well-characterized amyloidogenic proteins and proteins related to amyloid fibril formation. The consecutive extended computational analysis revealed significant topological characteristics and unraveled the functional roles of all constituent elements. This study introduces a detailed protein map of amyloidogenicity that will aid immensely towards separate intervention strategies, specifically targeting sub-networks of significant nodes, in an attempt to design possible novel therapeutics for aggregation disorders. PMID:28249044

Proteasome Failure Promotes Positioning of Lysosomes around the Aggresome via Local Block of Microtubule-Dependent Transport

PubMed Central

Zaarur, Nava; Meriin, Anatoli B.; Bejarano, Eloy; Xu, Xiaobin; Gabai, Vladimir L.; Cuervo, Ana Maria

2014-01-01

Ubiquitinated proteins aggregate upon proteasome failure, and the aggregates are transported to the aggresome. In aggresomes, protein aggregates are actively degraded by the autophagy-lysosome pathway, but why targeting the aggresome promotes degradation of aggregated species is currently unknown. Here we report that the important factor in this process is clustering of lysosomes around the aggresome via a novel mechanism. Proteasome inhibition causes formation of a zone around the centrosome where microtubular transport of lysosomes is suppressed, resulting in their entrapment and accumulation. Microtubule-dependent transport of other organelles, including autophagosomes, mitochondria, and endosomes, is also blocked in this entrapment zone (E-zone), while movement of organelles at the cell periphery remains unaffected. Following the whole-genome small interfering RNA (siRNA) screen for proteins involved in aggresome formation, we defined the pathway that regulates formation of the E-zone, including the Stk11 protein kinase, the Usp9x deubiquitinating enzyme, and their substrate kinase MARK4. Therefore, upon proteasome failure, targeting of aggregated proteins of the aggresome is coordinated with lysosome positioning around this body to facilitate degradation of the abnormal species. PMID:24469403

THE REBOUND CONDITION OF DUST AGGREGATES REVEALED BY NUMERICAL SIMULATION OF THEIR COLLISIONS

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

Wada, Koji; Tanaka, Hidekazu; Yamamoto, Tetsuo

2011-08-10

Collisional growth of dust aggregates is a plausible root of planetesimals forming in protoplanetary disks. However, a rebound of colliding dust aggregates prevents dust from growing into planetesimals. In fact, rebounding aggregates are observed in laboratory experiments but not in previous numerical simulations. Therefore, the condition of rebound between dust aggregates should be clarified to better understand the processes of dust growth and planetesimal formation. We have carried out numerical simulations of aggregate collisions for various types of aggregates and succeeded in reproducing a rebound of colliding aggregates under specific conditions. Our finding is that in the rebound process, themore » key factor of the aggregate structure is the coordination number, namely, the number of particles in contact with a particle. A rebound is governed by the energy dissipation along with restructuring of the aggregates and a large coordination number inhibits the restructuring at collisions. Results of our numerical simulation for various aggregates indicate that they stick to each other when the mean coordination number is less than 6, regardless of their materials and structures, as long as their collision velocity is less than the critical velocity for fragmentation. This criterion of the coordination number would correspond to a filling factor of {approx}0.3, which is somewhat larger than that reported in laboratory experiments. In protoplanetary disks, dust aggregates are expected to have low bulk densities (<0.1 g cm{sup -3}) during their growth, which would prevent dust aggregates from rebounding. This result supports the formation of planetesimals with direct dust growth in protoplanetary disks.« less

Protein Oxidation in Aging: Does It Play a Role in Aging Progression?

PubMed Central

Reeg, Sandra

2015-01-01

Abstract Significance: A constant accumulation of oxidized proteins takes place during aging. Oxidation of proteins leads to a partial unfolding and, therefore, to aggregation. Protein aggregates impair the activity of cellular proteolytic systems (proteasomes, lysosomes), resulting in further accumulation of oxidized proteins. In addition, the accumulation of highly crosslinked protein aggregates leads to further oxidant formation, damage to macromolecules, and, finally, to apoptotic cell death. Furthermore, protein oxidation seems to play a role in the development of various age-related diseases, for example, neurodegenerative diseases. Recent Advances: The highly oxidized lipofuscin accumulates during aging. Lipofuscin formation might cause impaired lysosomal and proteasomal degradation, metal ion accumulation, increased reactive oxygen species formation, and apoptosis. Critical Issues: It is still unclear to which extent protein oxidation is involved in the progression of aging and in the development of some age-related diseases. Future Directions: An extensive knowledge of the effects of protein oxidation on the aging process and its contribution to the development of age-related diseases could enable further strategies to reduce age-related impairments. Strategies aimed at lowering aggregate formation might be a straightforward intervention to reduce age-related malfunctions of organs. Antioxid. Redox Signal. 23, 239–255. PMID:25178482

Stochastic calculus of protein filament formation under spatial confinement

NASA Astrophysics Data System (ADS)

Michaels, Thomas C. T.; Dear, Alexander J.; Knowles, Tuomas P. J.

2018-05-01

The growth of filamentous aggregates from precursor proteins is a process of central importance to both normal and aberrant biology, for instance as the driver of devastating human disorders such as Alzheimer's and Parkinson's diseases. The conventional theoretical framework for describing this class of phenomena in bulk is based upon the mean-field limit of the law of mass action, which implicitly assumes deterministic dynamics. However, protein filament formation processes under spatial confinement, such as in microdroplets or in the cellular environment, show intrinsic variability due to the molecular noise associated with small-volume effects. To account for this effect, in this paper we introduce a stochastic differential equation approach for investigating protein filament formation processes under spatial confinement. Using this framework, we study the statistical properties of stochastic aggregation curves, as well as the distribution of reaction lag-times. Moreover, we establish the gradual breakdown of the correlation between lag-time and normalized growth rate under spatial confinement. Our results establish the key role of spatial confinement in determining the onset of stochasticity in protein filament formation and offer a formalism for studying protein aggregation kinetics in small volumes in terms of the kinetic parameters describing the aggregation dynamics in bulk.

Regulator LdhR and d-Lactate Dehydrogenase LdhA of Burkholderia multivorans Play Roles in Carbon Overflow and in Planktonic Cellular Aggregate Formation.

PubMed

Silva, Inês N; Ramires, Marcelo J; Azevedo, Lisa A; Guerreiro, Ana R; Tavares, Andreia C; Becker, Jörg D; Moreira, Leonilde M

2017-10-01

LysR-type transcriptional regulators (LTTRs) are the most commonly found regulators in Burkholderia cepacia complex, comprising opportunistic pathogens causing chronic respiratory infections in cystic fibrosis (CF) patients. Despite LTTRs being global regulators of pathogenicity in several types of bacteria, few have been characterized in Burkholderia Here, we show that gene ldhR of B. multivorans encoding an LTTR is cotranscribed with ldhA encoding a d-lactate dehydrogenase and evaluate their implication in virulence traits such as exopolysaccharide (EPS) synthesis and biofilm formation. A comparison of the wild type (WT) and its isogenic Δ ldhR mutant grown in medium with 2% d-glucose revealed a negative impact on EPS biosynthesis and on cell viability in the presence of LdhR. The loss of viability in WT cells was caused by intracellular acidification as a consequence of the cumulative secretion of organic acids, including d-lactate, which was absent from the Δ ldhR mutant supernatant. Furthermore, LdhR is implicated in the formation of planktonic cellular aggregates. WT cell aggregates reached 1,000 μm in size after 24 h in liquid cultures, in contrast to Δ ldhR mutant aggregates that never grew more than 60 μm. The overexpression of d-lactate dehydrogenase LdhA in the Δ ldhR mutant partially restored the formed aggregate size, suggesting a role for fermentation inside aggregates. Similar results were obtained for surface-attached biofilms, with WT cells producing more biofilm. A systematic evaluation of planktonic aggregates in Burkholderia CF clinical isolates showed aggregates in 40 of 74. As CF patients' lung environments are microaerophilic and bacteria are found as free aggregates/biofilms, LdhR and LdhA might have central roles in adapting to this environment. IMPORTANCE Cystic fibrosis patients often suffer from chronic respiratory infections caused by several types of microorganisms. Among them are the Burkholderia cepacia complex bacteria, which cause progressive deterioration of lung function that, in some patients, might develop into fatal necrotizing pneumoniae with bacteremia, known as "cepacia syndrome." Burkholderia pathogenesis is multifactorial as they express several virulence factors, form biofilms, and are highly resistant to antimicrobial compounds, making their eradication from the CF patients' airways very difficult. As Burkholderia is commonly found in CF lungs in the form of cell aggregates and biofilms, the need to investigate the mechanisms of cellular aggregation is obvious. In this study, we demonstrate the importance of a d-lactate dehydrogenase and a regulator in regulating carbon overflow, cellular aggregates, and surface-attached biofilm formation. This not only enhances our understanding of Burkholderia pathogenesis but can also lead to the development of drugs against these proteins to circumvent biofilm formation. Copyright © 2017 American Society for Microbiology.

Polyelectrolyte Bundles: Finite size at thermodynamic equilibrium?

NASA Astrophysics Data System (ADS)

Sayar, Mehmet

2005-03-01

Experimental observation of finite size aggregates formed by polyelectrolytes such as DNA and F-actin, as well as synthetic polymers like poly(p-phenylene), has created a lot of attention in recent years. Here, bundle formation in rigid rod-like polyelectrolytes is studied via computer simulations. For the case of hydrophobically modified polyelectrolytes finite size bundles are observed even in the presence of only monovalent counterions. Furthermore, in the absence of a hydrophobic backbone, we have also observed formation of finite size aggregates via multivalent counterion condensation. The size distribution of such aggregates and the stability is analyzed in this study.

Multiscale variability of soil aggregate stability: implications for rangeland hydrology and erosion

USDA-ARS?s Scientific Manuscript database

Conservation of soil and water resources in rangelands is a crucial step in stopping desertification processes. The formation of water-stable soil aggregates reduces soil erodibility and can increase infiltration capacity in many soils. Soil aggregate stability is highly variable at scales ranging f...

Oil-derived marine aggregates - hot spots of polysaccharide degradation by specialized bacterial communities

NASA Astrophysics Data System (ADS)

Arnosti, Carol; Ziervogel, Kai; Yang, Tingting; Teske, Andreas

2016-07-01

Aggregates generated in the laboratory from incubations of seawater and surface-water oil collected in the initial phase of the Deepwater Horizon oil spill resemble the oil-aggregates observed in situ. Here, we investigated the enzyme activities and microbial community composition of laboratory generated oil-aggregates, focusing on the abilities of these communities to degrade polysaccharides, which are major components of marine organic matter and are abundant constituents of exopolymeric substances (EPS) generated by oil-associated bacteria in response to the presence of oil. The patterns of polysaccharide-hydrolyzing enzyme activities in oil aggregates were very different from those in the water surrounding the aggregates after formation, and in the surface water that did not contain the oil. Specific oil aggregate-associated hydrolysis rates were also considerably higher than in the water surrounding the aggregates. The differences in initial hydrolysis profiles, and in evolution of these profiles with time, points to specialized metabolic abilities among the oil-aggregate communities compared to oil-water and ambient water communities. The composition of the oil-aggregate community indicates a multifunctional microbial assemblage containing primary oil-degrading and exopolysaccharide-producing members of the Gammaproteobacteria, and diverse members of the Alphaproteobacteria, Bacteroidetes and Planktomycetales that most likely participate in the breakdown of oil-derived bacterial biopolymers. Formation and aging of oil-aggregates encourages the growth and transformation of microbial communities that are specialized in degradation of petroleum, as well as their secondary degradation products.

Fluorescence dye-based detection of mAb aggregates in CHO culture supernatants.

PubMed

Paul, Albert Jesuran; Schwab, Karen; Prokoph, Nina; Haas, Elena; Handrick, René; Hesse, Friedemann

2015-06-01

Product yields, efficacy, and safety of monoclonal antibodies (mAbs) are reduced by the formation of higher molecular weight aggregates during upstream processing. In-process characterization of mAb aggregate formation is a challenge since there is a lack of a fast detection method to identify mAb aggregates in cell culture. In this work, we present a rapid method to characterize mAb aggregate-containing Chinese hamster ovary (CHO) cell culture supernatants. The fluorescence dyes thioflavin T (ThT) and 4-4-bis-1-phenylamino-8-naphthalene sulfonate (Bis-ANS) enabled the detection of soluble as well as large mAb aggregates. Partial least square (PLS) regression models were used to evaluate the linearity of the dye-based mAb aggregate detection in buffer down to a mAb aggregate concentration of 2.4 μg mL(-1). Furthermore, mAb aggregates were detected in bioprocess medium using Bis-ANS and ThT. Dye binding to aggregates was stable for 60 min, making the method robust and reliable. Finally, the developed method using 10 μmol L(-1) Bis-ANS enabled discrimination between CHO cell culture supernatants containing different levels of mAb aggregates. The method can be adapted for high-throughput screening, e.g., to screen for cell culture conditions influencing mAb product quality, and hence can contribute to the improvement of production processes of biopharmaceuticals in mammalian cell culture.

Shear-induced aggregation dynamics in a polymer microrod suspension

NASA Astrophysics Data System (ADS)

Kumar, Pramukta S.

A non-Brownian suspension of micron scale rods is found to exhibit reversible shear-driven formation of disordered aggregates resulting in dramatic viscosity enhancement at low shear rates. Aggregate formation is imaged at low magnification using a combined rheometer and fluorescence microscope system. The size and structure of these aggregates are found to depend on shear rate and concentration, with larger aggregates present at lower shear rates and higher concentrations. Quantitative measurements of the early-stage aggregation process are modeled by a collision driven growth of porous structures which show that the aggregate density increases with a shear rate. A Krieger-Dougherty type constitutive relation and steady-state viscosity measurements are used to estimate the intrinsic viscosity of complex structures developed under shear. Higher magnification images are collected and used to validate the aggregate size versus density relationship, as well as to obtain particle flow fields via PIV. The flow fields provide a tantalizing view of fluctuations involved in the aggregation process. Interaction strength is estimated via contact force measurements and JKR theory and found to be extremely strong in comparison to shear forces present in the system, estimated using hydrodynamic arguments. All of the results are then combined to produce a consistent conceptual model of aggregation in the system that features testable consequences. These results represent a direct, quantitative, experimental study of aggregation and viscosity enhancement in rod suspension, and demonstrate a strategy for inferring inaccessible microscopic geometric properties of a dynamic system through the combination of quantitative imaging and rheology.

Deep-sea lebensspuren: remarks on some echiuran traces in the Porcupine Seabight, northeast Atlantic

NASA Astrophysics Data System (ADS)

de Vaugelas, Jean

1989-06-01

During an exploration of the Porcupine Seabight aboard the French submersible Cyana, large rosettes attributed to echiurans were observed on the muddy bottom, sometimes associated with clumped mounds showing tension gashes. The intrusion of cores into the gashed mounds resulted in the creation of a fountain-like current of water flowing out of the center hole of the rosette, illustrating a direct connection. These two types of traces, which are classified under distinct generic names in recent classifications of deep-sea lebensspuren, are presumed to be produced by the echiuroid worm, being the two ends of an L-shaped burrow. A sketch of deep-sea echiurans' mode of life is proposed.

Picosecond x-ray strain rosette reveals direct laser excitation of coherent transverse acoustic phonons

PubMed Central

Lee, Sooheyong; Williams, G. Jackson; Campana, Maria I.; Walko, Donald A.; Landahl, Eric C.

2016-01-01

Using a strain-rosette, we demonstrate the existence of transverse strain using time-resolved x-ray diffraction from multiple Bragg reflections in laser-excited bulk gallium arsenide. We find that anisotropic strain is responsible for a considerable fraction of the total lattice motion at early times before thermal equilibrium is achieved. Our measurements are described by a new model where the Poisson ratio drives transverse motion, resulting in the creation of shear waves without the need for an indirect process such as mode conversion at an interface. Using the same excitation geometry with the narrow-gap semiconductor indium antimonide, we detected coherent transverse acoustic oscillations at frequencies of several GHz. PMID:26751616

Mechanisms and Kinetics of Amyloid Aggregation Investigated by a Phenomenological Coarse-Grained Model

NASA Astrophysics Data System (ADS)

Magno, Andrea; Pellarin, Riccardo; Caflisch, Amedeo

Amyloid fibrils are ordered polypeptide aggregates that have been implicated in several neurodegenerative pathologies, such as Alzheimer's, Parkinson's, Huntington's, and prion diseases, [1, 2] and, more recently, also in biological functionalities. [3, 4, 5] These findings have paved the way for a wide range of experimental and computational studies aimed at understanding the details of the fibril-formation mechanism. Computer simulations using low-resolution models, which employ a simplified representation of protein geometry and energetics, have provided insights into the basic physical principles underlying protein aggregation in general [6, 7, 8] and ordered amyloid aggregation. [9, 10, 11, 12, 13, 14, 15] For example, Dokholyan and coworkers have used the Discrete Molecular Dynamics method [16, 17] to shed light on the mechanisms of protein oligomerization [18] and the conformational changes that take place in proteins before the aggregation onset. [19, 20] One challenging observation, which is difficult to observe by computer simulations, is the wide range of aggregation scenarios emerging from a variety of biophysical measurements. [21, 22] Atomistic models have been employed to study the conformational space of amyloidogenic polypeptides in the monomeric state, [23, 24, 25] the very initial steps of amyloid formation, [26, 27, 28, 29, 30, 31, 32] and the structural stability of fibril models. [33, 34, 35) However, all-atom simulations of the kinetics of fibril formation are beyond what can be done with modern computers.

A biophysical insight into the formation of aggregates upon trifluoroethanol induced structural and conformational changes in garlic cystatin.

PubMed

Siddiqui, Mohd Faizan; Bano, Bilqees

2018-06-06

Intrinsic and extrinsic factors are responsible for the transition of soluble proteins into aggregated form. Trifluoroethanol is among such potent extrinsic factor which facilitates the formation of aggregated structure. It disrupts the interactive forces and destabilizes the native structure of the protein. The present study investigates the effect of trifluoroethanol (TFE) on garlic cystatin. Garlic cystatin was incubated with increasing concentration of TFE (0-90% v/v) for 4 h. Incubation of GPC with TFE induces structural changes thereby resulting in the formation of aggregates. Inactivation of garlic phytocystatin was confirmed by cysteine proteinase inhibitory activity. Garlic cystatin at 30% TFE exhibits native-like secondary structure and high ANS fluorescence, thus suggesting the presence of molten globule state. Circular dichroism and FTIR confirmed the transition of the native alpha-helical structure of garlic cystatin to the beta-sheet structure at 60% TFE. Furthermore, increased ThT fluorescence and redshift in Congo red absorbance assay confirmed the presence of aggregates. Rayleigh and turbidity assay was also performed to validate the aggregation results. Scanning electron microscopy was followed to analyze the morphological changes which confirm the presence of sheath-like structure at 60% TFE. The study sheds light on the conformational behavior of a plant protein when kept under stress condition induced by an extrinsic factor. Copyright © 2018 Elsevier B.V. All rights reserved.

Increased Zinc Availability Enhances Initial Aggregation and Biofilm Formation of Streptococcus pneumoniae

PubMed Central

Brown, Lindsey R.; Caulkins, Rachel C.; Schartel, Tyler E.; Rosch, Jason W.; Honsa, Erin S.; Schultz-Cherry, Stacey; Meliopoulos, Victoria A.; Cherry, Sean; Thornton, Justin A.

2017-01-01

Bacteria growing within biofilms are protected from antibiotics and the immune system. Within these structures, horizontal transfer of genes encoding virulence factors, and promoting antibiotic resistance occurs, making biofilms an extremely important aspect of pneumococcal colonization and persistence. Identifying environmental cues that contribute to the formation of biofilms is critical to understanding pneumococcal colonization and infection. Iron has been shown to be essential for the formation of pneumococcal biofilms; however, the role of other physiologically important metals such as copper, zinc, and manganese has been largely neglected. In this study, we investigated the effect of metals on pneumococcal aggregation and early biofilm formation. Our results show that biofilms increase as zinc concentrations increase. The effect was found to be zinc-specific, as altering copper and manganese concentrations did not affect biofilm formation. Scanning electron microscopy analysis revealed structural differences between biofilms grown in varying concentrations of zinc. Analysis of biofilm formation in a mutant strain lacking the peroxide-generating enzyme pyruvate oxidase, SpxB, revealed that zinc does not protect against pneumococcal H2O2. Further, analysis of a mutant strain lacking the major autolysin, LytA, indicated the role of zinc as a negative regulator of LytA-dependent autolysis, which could affect biofilm formation. Additionally, analysis of cell-cell aggregation via plating and microscopy revealed that high concentrations of zinc contribute to intercellular interaction of pneumococci. The findings from this study demonstrate that metal availability contributes to the ability of pneumococci to form aggregates and subsequently, biofilms. PMID:28638805

Transient β-hairpin formation in α-synuclein monomer revealed by coarse-grained molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Yu, Hang; Han, Wei; Ma, Wen; Schulten, Klaus

2015-12-01

Parkinson's disease, originating from the intrinsically disordered peptide α-synuclein, is a common neurodegenerative disorder that affects more than 5% of the population above age 85. It remains unclear how α-synuclein monomers undergo conformational changes leading to aggregation and formation of fibrils characteristic for the disease. In the present study, we perform molecular dynamics simulations (over 180 μs in aggregated time) using a hybrid-resolution model, Proteins with Atomic details in Coarse-grained Environment (PACE), to characterize in atomic detail structural ensembles of wild type and mutant monomeric α-synuclein in aqueous solution. The simulations reproduce structural properties of α-synuclein characterized in experiments, such as secondary structure content, long-range contacts, chemical shifts, and 3J(HNHCα)-coupling constants. Most notably, the simulations reveal that a short fragment encompassing region 38-53, adjacent to the non-amyloid-β component region, exhibits a high probability of forming a β-hairpin; this fragment, when isolated from the remainder of α-synuclein, fluctuates frequently into its β-hairpin conformation. Two disease-prone mutations, namely, A30P and A53T, significantly accelerate the formation of a β-hairpin in the stated fragment. We conclude that the formation of a β-hairpin in region 38-53 is a key event during α-synuclein aggregation. We predict further that the G47V mutation impedes the formation of a turn in the β-hairpin and slows down β-hairpin formation, thereby retarding α-synuclein aggregation.

Macroeconomic susceptibility, inflation, and aggregate supply

NASA Astrophysics Data System (ADS)

Hawkins, Raymond J.

2017-03-01

We unify aggregate-supply dynamics as a time-dependent susceptibility-mediated relationship between inflation and aggregate economic output. In addition to representing well various observations of inflation-output dynamics this parsimonious formalism provides a straightforward derivation of popular representations of aggregate-supply dynamics and a natural basis for economic-agent expectations as an element of inflation formation. Our formalism also illuminates questions of causality and time-correlation that challenge central banks for whom aggregate-supply dynamics is a key constraint in their goal of achieving macroeconomic stability.

Potential for direct interspecies electron transfer in methanogenic wastewater digester aggregates.

PubMed

Morita, Masahiko; Malvankar, Nikhil S; Franks, Ashley E; Summers, Zarath M; Giloteaux, Ludovic; Rotaru, Amelia E; Rotaru, Camelia; Lovley, Derek R

2011-01-01

Mechanisms for electron transfer within microbial aggregates derived from an upflow anaerobic sludge blanket reactor converting brewery waste to methane were investigated in order to better understand the function of methanogenic consortia. The aggregates were electrically conductive, with conductivities 3-fold higher than the conductivities previously reported for dual-species aggregates of Geobacter species in which the two species appeared to exchange electrons via interspecies electron transfer. The temperature dependence response of the aggregate conductance was characteristic of the organic metallic-like conductance previously described for the conductive pili of Geobacter sulfurreducens and was inconsistent with electron conduction through minerals. Studies in which aggregates were incubated with high concentrations of potential electron donors demonstrated that the aggregates had no significant capacity for conversion of hydrogen to methane. The aggregates converted formate to methane but at rates too low to account for the rates at which that the aggregates syntrophically metabolized ethanol, an important component of the reactor influent. Geobacter species comprised 25% of 16S rRNA gene sequences recovered from the aggregates, suggesting that Geobacter species may have contributed to some but probably not all of the aggregate conductivity. Microorganisms most closely related to the acetate-utilizing Methanosaeta concilii accounted for more than 90% of the sequences that could be assigned to methane producers, consistent with the poor capacity for hydrogen and formate utilization. These results demonstrate for the first time that methanogenic wastewater aggregates can be electrically conductive and suggest that direct interspecies electron transfer could be an important mechanism for electron exchange in some methanogenic systems.

Calcium Ions Promote Superoxide Dismutase 1 (SOD1) Aggregation into Non-fibrillar Amyloid

PubMed Central

Leal, Sónia S.; Cardoso, Isabel; Valentine, Joan S.; Gomes, Cláudio M.

2013-01-01

Imbalance in metal ion homeostasis is a hallmark in neurodegenerative conditions involving protein deposition, and amyotrophic lateral sclerosis (ALS) is no exception. In particular, Ca2+ dysregulation has been shown to correlate with superoxide dismutase-1 (SOD1) aggregation in a cellular model of ALS. Here we present evidence that SOD1 aggregation is enhanced and modulated by Ca2+. We show that at physiological pH, Ca2+ induces conformational changes that increase SOD1 β-sheet content, as probed by far UV CD and attenuated total reflectance-FTIR, and enhances SOD1 hydrophobicity, as probed by ANS fluorescence emission. Moreover, dynamic light scattering analysis showed that Ca2+ boosts the onset of SOD1 aggregation. In agreement, Ca2+ decreases SOD1 critical concentration and nucleation time during aggregation kinetics, as evidenced by thioflavin T fluorescence emission. Attenuated total reflectance FTIR analysis showed that Ca2+ induced aggregates consisting preferentially of antiparallel β-sheets, thus suggesting a modulation effect on the aggregation pathway. Transmission electron microscopy and analysis with conformational anti-fibril and anti-oligomer antibodies showed that oligomers and amyloidogenic aggregates constitute the prevalent morphology of Ca2+-induced aggregates, thus indicating that Ca2+ diverts SOD1 aggregation from fibrils toward amorphous aggregates. Interestingly, the same heterogeneity of conformations is found in ALS-derived protein inclusions. We thus hypothesize that transient variations and dysregulation of cellular Ca2+ levels contribute to the formation of SOD1 aggregates in ALS patients. In this scenario, Ca2+ may be considered as a pathogenic effector in the formation of ALS proteinaceous inclusions. PMID:23861388

Light-induced aggregation of microbial exopolymeric substances.

PubMed

Sun, Luni; Xu, Chen; Zhang, Saijin; Lin, Peng; Schwehr, Kathleen A; Quigg, Antonietta; Chiu, Meng-Hsuen; Chin, Wei-Chun; Santschi, Peter H

2017-08-01

Sunlight can inhibit or disrupt the aggregation process of marine colloids via cleavage of high molecular weight compounds into smaller, less stable fragments. In contrast, some biomolecules, such as proteins excreted from bacteria can form aggregates via cross-linking due to photo-oxidation. To examine whether light-induced aggregation can occur in the marine environment, we conducted irradiation experiments on a well-characterized protein-containing exopolymeric substance (EPS) from the marine bacterium Sagitulla stellata. Our results show that after 1 h sunlight irradiation, the turbidity level of soluble EPS was 60% higher than in the dark control. Flow cytometry also confirmed that more particles of larger sized were formed by sunlight. In addition, we determined a higher mass of aggregates collected on filter in the irradiated samples. This suggests light can induce aggregation of this bacterial EPS. Reactive oxygen species hydroxyl radical and peroxide played critical roles in the photo-oxidation process, and salts assisted the aggregation process. The observation that Sagitulla stellata EPS with relatively high protein content promoted aggregation, was in contrast to the case where no significant differences were found in the aggregation of a non-protein containing phytoplankton EPS between the dark and light conditions. This, together with the evidence that protein-to-carbohydrate ratio of aggregates formed under light condition is significantly higher than that formed under dark condition suggest that proteins are likely the important component for aggregate formation. Light-induced aggregation provides new insights into polymer assembly, marine snow formation, and the fate/transport of organic carbon and nitrogen in the ocean. Copyright © 2017 Elsevier Ltd. All rights reserved.

Catastrophic Disruption of Asteroids: First Simulations with Explicit Formation of Spinning Rigid and Semi-rigid Aggregates

NASA Astrophysics Data System (ADS)

Michel, Patrick; Richardson, D. C.

2007-10-01

We have made major improvements in simulations of asteroid disruption by computing explicitly aggregate formations during the gravitational reaccumulation of small fragments, allowing us to obtain information on their spin and shape. First results will be presented taking as examples asteroid families that we reproduced successfully with previous less sophisticated simulations. In the last years, we have simulated successfully the formation of asteroid families using a SPH hydrocode to compute the fragmentation following the impact of a projectile on the parent body, and the N-body code pkdgrav to compute the mutual interactions of the fragments. We found that fragments generated by the disruption of a km-size asteroid can have large enough masses to be attracted by each other during their ejection. Consequently, many reaccumulations take place. Eventually most large fragments correspond to gravitational aggregates formed by reaccumulation of smaller ones. Moreover, formation of satellites occurs around the largest and other big remnants. In these previous simulations, when fragments reaccumulate, they merge into a single sphere whose mass is the sum of their masses. Thus, no information is obtained on the actual shape of the aggregates, their spin, ... For the first time, we have now simulated the disruption of a family parent body by computing explicitly the formation of aggregates, along with the above-mentioned properties. Once formed these aggregates can interact and/or collide with each other and break up during their evolution. We will present these first simulations and their possible implications on properties of asteroids generated by disruption. Results can for instance be compared with data provided by the Japanese space mission Hayabusa of the asteroid Itokawa, a body now understood to be a reaccumulated fragment from a larger parent body. Acknowledgments: PM and DCR acknowledge supports from the French Programme National de Planétologie and grants NSF AST0307549&AST0708110.

Myxobacteria Fruiting Body Formation

NASA Astrophysics Data System (ADS)

Jiang, Yi

2006-03-01

Myxobacteria are social bacteria that swarm and glide on surfaces, and feed cooperatively. When starved, tens of thousands of cells change their movement pattern from outward spreading to inward concentration; they form aggregates that become fruiting bodies, inside which cells differentiate into nonmotile, environmentally resistant spores. Traditionally, cell aggregation has been considered to imply chemotaxis, a long-range cell interaction mediated by diffusing chemicals. However, myxobacteria aggregation is the consequence of direct cell-contact interactions. I will review our recent efforts in modeling the fruiting body formation of Myxobacteria, using lattice gas cellular automata models that are based on local cell-cell contact signaling. These models have reproduced the individual phases in Myxobacteria development such as the rippling, streaming, early aggregation and the final sporulation; the models can be unified to simulate the whole developmental process of Myxobacteria.

Gross anatomy and histology of the olfactory rosette of the shark Heptranchias perlo.

PubMed

Ferrando, Sara; Gallus, Lorenzo; Amaroli, Andrea; Gambardella, Chiara; Waryani, Baradi; Di Blasi, Davide; Vacchi, Marino

2017-06-01

Sharks belonging to the family Hexanchidae have six or seven gill slits, unlike all other elasmobranchs, which have five gill slits. Their olfactory organs have a round shape, which is common for holocephalans, but not for elasmobranchs. Thus, the shape of the olfactory organ represents a further, less striking, peculiarity of this family among elasmobranchs. Despite that, the microscopic anatomy and histology of the olfactory organ have not yet been studied in any species of this family. Here, an anatomical and histological description of the olfactory organ of the sharpnose sevengill shark Heptranchias perlo is given. The organ is a rosette, with a central raphe and 31-34 primary lamellae, which bear secondary lamellae with a more or less branched shape. The elastic connective capsule which envelops the olfactory rosette possibly changes its shape along with water influx. In the olfactory epithelium, the supporting cells also have a secretory function, while no specialized mucous cells are visible; regarding this feature the olfactory epithelium of H. perlo differs from that of other chondrichthyan species. The immunohistochemical investigation of the sensory epithelium shows the absence of immunoreactivity for Gαolf in receptor neurons, which confirms previous observations in Chondrichthyes. Copyright © 2017 Elsevier GmbH. All rights reserved.

Fermi/LAT study of gamma-ray emission in the direction of the monceros loop supernova remnant

DOE PAGES

Katagiri, H.; Sugiyama, S.; Ackermann, M.; ...

2016-10-31

Here, we present an analysis of the gamma-ray measurements by the Large Area Telescope on board the Fermi Gamma-ray Space Telescope in the region of the supernova remnant (SNR) Monoceros Loop (G205.5+0.5). The brightest gamma-ray peak is spatially correlated with the Rosette Nebula, which is a molecular cloud complex adjacent to the southeast edge of the SNR. After subtraction of this emission by spatial modeling, the gamma-ray emission from the SNR emerges, which is extended and fit by a Gaussian spatial template. The gamma-ray spectra are significantly better reproduced by a curved shape than a simple power law. The luminosities between 0.2 and 300 GeV aremore » $$\\sim 4\\times {10}^{34}$$ erg s -1 for the SNR and $$\\sim 3\\times {10}^{34}$$ erg s -1 for the Rosette Nebula, respectively. We also argue that the gamma-rays likely originate from the interactions of particles accelerated in the SNR. Furthermore, the decay of neutral pions produced in nucleon–nucleon interactions of accelerated hadrons with interstellar gas provides a reasonable explanation for the gamma-ray emission of both the Rosette Nebula and the Monoceros SNR.« less

Maternal vernalization and vernalization-pathway genes influence progeny seed germination.

PubMed

Auge, Gabriela A; Blair, Logan K; Neville, Hannah; Donohue, Kathleen

2017-10-01

Different life stages frequently respond to the same environmental cue to regulate development so that each life stage is matched to its appropriate season. We investigated how independently each life stage can respond to shared environmental cues, focusing on vernalization, in Arabidopsis thaliana plants. We first tested whether effects of rosette vernalization persisted to influence seed germination. To test whether genes in the vernalization flowering pathway also influence germination, we assessed germination of functional and nonfunctional alleles of these genes and measured their level of expression at different life stages in response to rosette vernalization. Rosette vernalization increased seed germination in diverse ecotypes. Genes in the vernalization flowering pathway also influenced seed germination. In the Columbia accession, functional alleles of most of these genes opposed the germination response observed in the ecotypes. Some genes influenced germination in a manner consistent with their known effects on FLOWERING LOCUS C gene regulation during the transition to flowering. Others did not, suggesting functional divergence across life stages. Despite persistent effects of environmental conditions across life stages, and despite pleiotropy of genes that affect both flowering and germination, the function of these genes can differ across life stages, potentially mitigating pleiotropic constraints and enabling independent environmental regulation of different life stages. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Function suggests nano-structure: towards a unified theory for secretion rate, a statistical mechanics approach.

PubMed

Hammel, Ilan; Meilijson, Isaac

2013-11-06

The inventory of secretory granules along the plasma membrane can be viewed as maintained in two restricted compartments. The release-ready pool represents docked granules available for an initial stage of fast, immediate secretion, followed by a second stage of granule set-aside secretion pool, with significantly slower rate. Transmission electron microscopy ultra-structural investigations correlated with electrophysiological techniques and mathematical modelling have allowed the categorization of these secretory vesicle compartments, in which vesicles can be in various states of secretory competence. Using the above-mentioned approaches, the kinetics of single vesicle exocytosis can be worked out. The ultra-fast kinetics, explored in this study, represents the immediately available release-ready pool, in which granules bound to the plasma membrane are exocytosed upon Ca(2+) influx at the SNARE rosette at the base of porosomes. Formalizing Dodge and Rahamimoff findings on the effect of calcium concentration and incorporating the effect of SNARE transient rosette size, we postulate that secretion rate (rate), the number (X) of intracellular calcium ions available for fusion, calcium capacity (0 ≤ M ≤ 5) and the fusion nano-machine size (as measured by the SNARE rosette size K) satisfy the parsimonious M-K relation rate ≈ C × [Ca(2+)](min(X,M))e(-K/2).

High Throughput Differential Scanning Fluorimetry (DSF) Formulation Screening with Complementary Dyes to Assess Protein Unfolding and Aggregation in Presence of Surfactants.

PubMed

McClure, Sean M; Ahl, Patrick L; Blue, Jeffrey T

2018-03-05

The purpose was to evaluate DSF for high throughput screening of protein thermal stability (unfolding/ aggregation) across a wide range of formulations. Particular focus was exploring PROTEOSTAT® - a commercially available fluorescent rotor dye - for detection of aggregation in surfactant containing formulations. Commonly used hydrophobic dyes (e.g. SYPRO™ Orange) interact with surfactants, complicating DSF measurements. CRM197 formulations were prepared and analyzed in standard 96-well plate rT-PCR system, using SYPRO™ Orange and PROTEOSTAT® dyes. Orthogonal techniques (DLS and IPF) are employed to confirm unfolding/aggregation in selected formulations. Selected formulations are subjected to non-thermal stresses (stirring and shaking) in plate based format to characterize aggregation with PROTEOSTAT®. Agreement is observed between SYPRO™ Orange (unfolding) and PROTEOSTAT® (aggregation) DSF melt temperatures across wide range of non-surfactant formulations. PROTEOSTAT® can clearly detect temperature induced aggregation in low concentration (0.2 mg/mL) CRM197 formulations containing surfactant. PROTEOSTAT® can be used to explore aggregation due to non-thermal stresses in plate based format amenable to high throughput screening. DSF measurements with complementary extrinsic dyes (PROTEOSTAT®, SYPRO™ Orange) are suitable for high throughput screening of antigen thermal stability, across a wide range of relevant formulation conditions - including surfactants -with standard, plate based rT-PCR instrumentation.

Temperature dependent rapid annealing effect induces amorphous aggregation of human serum albumin.

PubMed

Ishtikhar, Mohd; Ali, Mohd Sajid; Atta, Ayman M; Al-Lohedan, Hammad; Badr, Gamal; Khan, Rizwan Hasan

2016-01-01

This study represents an analysis of the thermal aggregation of human serum albumin (HSA) induced by novel rosin modified compounds. The aggregation process causes conformational alterations in the secondary and tertiary structures of the proteins. The conversion of globular protein to amorphous aggregates was carried out by spectroscopic, calorimetric and microscopic techniques to investigate the factors that are responsible for the structural, conformational and morphological alteration in the protein. Our outcome results show that the aggregation of HSA was dependent on the hydrophobicity, charge and temperature, because the formation of amorphous aggregates occurs in the presence of a novel cationic rosin compound, quaternary amine of rosin diethylaminoethyl ester (QRMAE), at 40°C and pH 7.4 (but at 25°C on similar pH value, there was no evidence of aggregate formation). In addition, the parent compound of QRMAE, i.e., abietic acid, and other derivatives such as nonionic rosin compounds [(RMPEG-750) and (RMA-MPEG-750)] do not shows the aggregating property. This work provides precise and necessary information that aid in the understanding the effects of rosin derivative compounds on HSA. This study also restrains important information for athletes, health providers, pharmaceutical companies, industries, and soft drink-processing companies. Copyright © 2015 Elsevier B.V. All rights reserved.

Distal Renal Tubules Are Deficient in Aggresome Formation and Autophagy upon Aldosterone Administration

PubMed Central

Cheema, Muhammad Umar; Damkier, Helle Hasager; Nielsen, Jakob; Poulsen, Ebbe Toftgaard; Enghild, Jan J.; Fenton, Robert A.; Praetorius, Jeppe

2014-01-01

Prolonged elevations of plasma aldosterone levels are associated with renal pathogenesis. We hypothesized that renal distress could be imposed by an augmented aldosterone-induced protein turnover challenging cellular protein degradation systems of the renal tubular cells. Cellular accumulation of specific protein aggregates in rat kidneys was assessed after 7 days of aldosterone administration. Aldosterone induced intracellular accumulation of 60 s ribosomal protein L22 in protein aggregates, specifically in the distal convoluted tubules. The mineralocorticoid receptor inhibitor spironolactone abolished aldosterone-induced accumulation of these aggregates. The aldosterone-induced protein aggregates also contained proteasome 20 s subunits. The partial de-ubiquitinase ataxin-3 was not localized to the distal renal tubule protein aggregates, and the aggregates only modestly colocalized with aggresome transfer proteins dynactin p62 and histone deacetylase 6. Intracellular protein aggregation in distal renal tubules did not lead to development of classical juxta-nuclear aggresomes or to autophagosome formation. Finally, aldosterone treatment induced foci in renal cortex of epithelial vimentin expression and a loss of E-cadherin expression, as signs of cellular stress. The cellular changes occurred within high, but physiological aldosterone concentrations. We conclude that aldosterone induces protein accumulation in distal renal tubules; these aggregates are not cleared by autophagy that may lead to early renal tubular damage. PMID:25000288

Arginine prevents thermal aggregation of hen egg white proteins.

PubMed

Hong, Taehun; Iwashita, Kazuki; Handa, Akihiro; Shiraki, Kentaro

2017-07-01

The control of aggregation and solubilization of hen egg white protein (HEWP) is an important issue for industrial applications of one of the most familiar food protein sources. Here, we investigated the effects of edible amino acids on heat-induced aggregation of HEWP. The addition of 0.6M arginine (Arg) completely suppressed the formation of insoluble aggregates of 1mgmL -1 HEWP following heat treatment, even at 90°C for 20min. In contrast, lysine (Lys), glycine (Gly), and sodium chloride (NaCl) did little to suppress the aggregation of HEWP under the same conditions. SDS-PAGE indicated that Arg suppresses the thermal aggregation of almost all types of HEWP at 1mgmL -1 . However, Arg did not suppress the thermal aggregation of HEWP at concentrations ≥10mgmL -1 and prompted the formation of aggregates. Transmission electron micrographs revealed a high-density structure of unfolded proteins in the presence of Arg. These results indicate that Arg exerts a greater suppressive effect on a protein mixture, such as HEWP, than on a single model protein. These observations may propose Arg as a safe and reasonable additive to HEWP for the elimination of microorganisms by allowing an increase in sterilization temperature. Copyright © 2017 Elsevier Ltd. All rights reserved.

Amyloid Formation by Human Carboxypeptidase D Transthyretin-like Domain under Physiological Conditions*

PubMed Central

Garcia-Pardo, Javier; Graña-Montes, Ricardo; Fernandez-Mendez, Marc; Ruyra, Angels; Roher, Nerea; Aviles, Francesc X.; Lorenzo, Julia; Ventura, Salvador

2014-01-01

Protein aggregation is linked to a growing list of diseases, but it is also an intrinsic property of polypeptides, because the formation of functional globular proteins comes at the expense of an inherent aggregation propensity. Certain proteins can access aggregation-prone states from native-like conformations without the need to cross the energy barrier for unfolding. This is the case of transthyretin (TTR), a homotetrameric protein whose dissociation into its monomers initiates the aggregation cascade. Domains with structural homology to TTR exist in a number of proteins, including the M14B subfamily carboxypeptidases. We show here that the monomeric transthyretin-like domain of human carboxypeptidase D aggregates under close to physiological conditions into amyloid structures, with the population of folded but aggregation-prone states being controlled by the conformational stability of the domain. We thus confirm that the TTR fold keeps a generic residual aggregation propensity upon folding, resulting from the presence of preformed amyloidogenic β-strands in the native state. These structural elements should serve for functional/structural purposes, because they have not been purged out by evolution, but at the same time they put proteins like carboxypeptidase D at risk of aggregation in biological environments and thus can potentially lead to deposition diseases. PMID:25294878

Real-time amyloid aggregation monitoring with a photonic crystal-based approach.

PubMed

Santi, Sara; Musi, Valeria; Descrovi, Emiliano; Paeder, Vincent; Di Francesco, Joab; Hvozdara, Lubos; van der Wal, Peter; Lashuel, Hilal A; Pastore, Annalisa; Neier, Reinhard; Herzig, Hans Peter

2013-10-21

We propose the application of a new label-free optical technique based on photonic nanostructures to real-time monitor the amyloid-beta 1-42 (Aβ(1-42)) fibrillization, including the early stages of the aggregation process, which are related to the onset of the Alzheimer's Disease (AD). The aggregation of Aβ peptides into amyloid fibrils has commonly been associated with neuronal death, which culminates in the clinical features of the incurable degenerative AD. Recent studies revealed that cell toxicity is determined by the formation of soluble oligomeric forms of Aβ peptides in the early stages of aggregation. At this phase, classical amyloid detection techniques lack in sensitivity. Upon a chemical passivation of the sensing surface by means of polyethylene glycol, the proposed approach allows an accurate, real-time monitoring of the refractive index variation of the solution, wherein Aβ(1-42) peptides are aggregating. This measurement is directly related to the aggregation state of the peptide throughout oligomerization and subsequent fibrillization. Our findings open new perspectives in the understanding of the dynamics of amyloid formation, and validate this approach as a new and powerful method to screen aggregation at early stages. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A hypothetical hierarchical mechanism of the self-assembly of the Escherichia coli RNA polymerase σ(70) subunit.

PubMed

Koroleva, O N; Dubrovin, E V; Tolstova, A P; Kuzmina, N V; Laptinskaya, T V; Yaminsky, I V; Drutsa, V L

2016-02-21

Diverse morphology of aggregates of amyloidogenic proteins has been attracting much attention in the last few years, and there is still no complete understanding of the relationships between various types of aggregates. In this work, we propose the model, which universally explains the formation of morphologically different (wormlike and rodlike) aggregates on the example of a σ(70) subunit of RNA polymerase, which has been recently shown to form amyloid fibrils. Aggregates were studied using AFM in solution and depolarized dynamic light scattering. The obtained results demonstrate comparably low Young's moduli of the wormlike structures (7.8-12.3 MPa) indicating less structured aggregation of monomeric proteins than that typical for β-sheet formation. To shed light on the molecular interaction of the protein during the aggregation, early stages of fibrillization of the σ(70) subunit were modeled using all-atom molecular dynamics. Simulations have shown that the σ(70) subunit is able to form quasi-symmetric extended dimers, which may further interact with each other and grow linearly. The proposed general model explains different pathways of σ(70) subunit aggregation and may be valid for other amyloid proteins.

A nanoscale bio-inspired light-harvesting system developed from self-assembled alkyl-functionalized metallochlorin nano-aggregates

NASA Astrophysics Data System (ADS)

Ocakoglu, Kasim; Joya, Khurram S.; Harputlu, Ersan; Tarnowska, Anna; Gryko, Daniel T.

2014-07-01

Self-assembled supramolecular organization of nano-structured biomimetic light-harvesting modules inside solid-state nano-templates can be exploited to develop excellent light-harvesting materials for artificial photosynthetic devices. We present here a hybrid light-harvesting system mimicking the chlorosomal structures of the natural photosynthetic system using synthetic zinc chlorin units (ZnChl-C6, ZnChl-C12 and ZnChl-C18) that are self-aggregated inside the anodic aluminum oxide (AAO) nano-channel membranes. AAO nano-templates were modified with a TiO2 matrix and functionalized with long hydrophobic chains to facilitate the formation of supramolecular Zn-chlorin aggregates. The transparent Zn-chlorin nano-aggregates inside the alkyl-TiO2 modified AAO nano-channels have a diameter of ~120 nm in a 60 μm length channel. UV-Vis studies and fluorescence emission spectra further confirm the formation of the supramolecular ZnChl aggregates from monomer molecules inside the alkyl-functionalized nano-channels. Our results prove that the novel and unique method can be used to produce efficient and stable light-harvesting assemblies for effective solar energy capture through transparent and stable nano-channel ceramic materials modified with bio-mimetic molecular self-assembled nano-aggregates.Self-assembled supramolecular organization of nano-structured biomimetic light-harvesting modules inside solid-state nano-templates can be exploited to develop excellent light-harvesting materials for artificial photosynthetic devices. We present here a hybrid light-harvesting system mimicking the chlorosomal structures of the natural photosynthetic system using synthetic zinc chlorin units (ZnChl-C6, ZnChl-C12 and ZnChl-C18) that are self-aggregated inside the anodic aluminum oxide (AAO) nano-channel membranes. AAO nano-templates were modified with a TiO2 matrix and functionalized with long hydrophobic chains to facilitate the formation of supramolecular Zn-chlorin aggregates. The transparent Zn-chlorin nano-aggregates inside the alkyl-TiO2 modified AAO nano-channels have a diameter of ~120 nm in a 60 μm length channel. UV-Vis studies and fluorescence emission spectra further confirm the formation of the supramolecular ZnChl aggregates from monomer molecules inside the alkyl-functionalized nano-channels. Our results prove that the novel and unique method can be used to produce efficient and stable light-harvesting assemblies for effective solar energy capture through transparent and stable nano-channel ceramic materials modified with bio-mimetic molecular self-assembled nano-aggregates. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr01661k

The effect of protein acetylation on the formation and processing of inclusion bodies and endogenous protein aggregates in Escherichia coli cells.

PubMed

Kuczyńska-Wiśnik, Dorota; Moruno-Algara, María; Stojowska-Swędrzyńska, Karolina; Laskowska, Ewa

2016-11-10

Acetylation of lysine residues is a reversible post-translational modification conserved from bacteria to humans. Several recent studies have revealed hundreds of lysine-acetylated proteins in various bacteria; however, the physiological role of these modifications remains largely unknown. Since lysine acetylation changes the size and charge of proteins and thereby may affect their conformation, we assumed that lysine acetylation can stimulate aggregation of proteins, especially for overproduced recombinant proteins that form inclusion bodies. To verify this assumption, we used Escherichia coli strains that overproduce aggregation-prone VP1GFP protein. We found that in ΔackA-pta cells, which display diminished protein acetylation, inclusion bodies were formed with a delay and processed faster than in the wild-type cells. Moreover, in ΔackA-pta cells, inclusion bodies exhibited significantly increased specific GFP fluorescence. In CobB deacetylase-deficient cells, in which protein acetylation was enhanced, the formation of inclusion bodies was increased and their processing was significantly inhibited. Similar results were obtained with regard to endogenous protein aggregates formed during the late stationary phase in ΔackA-pta and ΔcobB cells. Our studies revealed that protein acetylation affected the aggregation of endogenous E. coli proteins and the yield, solubility, and biological activity of a model recombinant protein. In general, decreased lysine acetylation inhibited the formation of protein aggregates, whereas increased lysine acetylation stabilized protein aggregates. These findings should be considered during the designing of efficient strategies for the production of recombinant proteins in E. coli cells.

Hsp70 and Antifibrillogenic Peptides Promote Degradation and Inhibit Intracellular Aggregation of Amyloidogenic Light Chains

PubMed Central

Dul, Jeanne L.; Davis, David P.; Williamson, Edward K.; Stevens, Fred J.; Argon, Yair

2001-01-01

In light chain (LC) amyloidosis an immunoglobulin LC assembles into fibrils that are deposited in various tissues. Little is known about how these fibrils form in vivo. We previously showed that a known amyloidogenic LC, SMA, can give rise to amyloid fibrils in vitro when a segment of one of its β sheets undergoes a conformational change, exposing an Hsp70 binding site. To examine SMA aggregation in vivo, we expressed it and its wild-type counterpart, LEN, in COS cells. While LEN is rapidly oxidized and subsequently secreted, newly synthesized SMA remains in the reduced state. Most SMA molecules are dislocated out of the ER into the cytosol, where they are ubiquitinylated and degraded by proteasomes. A parallel pathway for molecules that are not degraded is condensation into perinuclear aggresomes that are surrounded by vimentin-containing intermediate filaments and are dependent upon intact microtubules. Inhibition of proteasome activity shifts the balance toward aggresome formation. Intracellular aggregation is decreased and targeting to proteasomes improved by overexpression of the cytosolic chaperone Hsp70. Importantly, transduction into the cell of an Hsp70 target peptide, derived from the LC sequence, also reduces aggresome formation and increases SMA degradation. These results demonstrate that an amyloidogenic LC can aggregate intracellularly despite the common presentation of extracellular aggregates, and that a similar molecular surface mediates both in vitro fibril formation and in vivo aggregation. Furthermore, rationally designed peptides can be used to suppress this aggregation and may provide a feasible therapeutic approach. PMID:11266462

Hsp70 and antifibrillogenic peptides promote degradation and inhibit intracellular aggregation of amyloidogenic light chains.

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

Dul, J. L.; Davis, D. P.; Williamson, E. K.

2001-02-19

In light chain (LC) amyloidosis an immunoglobulin LC assembles into fibrils that are deposited in various tissues. Little is known about how these fibrils form in vivo. We previously showed that a known amyloidogenic LC, SMA, can give rise to amyloid fibrils in vitro when a segment of one of its {beta} sheets undergoes a conformational change, exposing an Hsp70 binding site. To examine SMA aggregation in vivo, we expressed it and its wild-type counterpart, LEN, in COS cells. While LEN is rapidly oxidized and subsequently secreted, newly synthesized SMA remains in the reduced state. Most SMA molecules are dislocatedmore » out of the ER into the cytosol, where they are ubiquitinylated and degraded by proteasomes. A parallel pathway for molecules that are not degraded is condensation into perinuclear aggresomes that are surrounded by vimentin-containing intermediate filaments and are dependent upon intact microtubules. Inhibition of proteasome activity shifts the balance toward aggresome formation. Intracellular aggregation is decreased and targeting to proteasomes improved by overexpression of the cytosolic chaperone Hsp70. Importantly, transduction into the cell of an Hsp70 target peptide, derived from the LC sequence, also reduces aggresome formation and increases SMA degradation. These results demonstrate that an amyloidogenic LC can aggregate intracellularly despite the common presentation of extracellular aggregates, and that a similar molecular surface mediates both in vitro fibril formation and in vivo aggregation. Furthermore, rationally designed peptides can be used to suppress this aggregation and may provide a feasible therapeutic approach.« less

Roles of biology, chemistry, and physics in soil macroaggregate formation and stabilization

USDA-ARS?s Scientific Manuscript database

Soil functions or ecosystem services depend on the distribution of macro- (= 0.25 mm) and micro- (< 0.25 mm) aggregates and open space between aggregates. It is the arrangement of the aggregates and pore space which allows air and water movement in and out of soil; reduces compaction; and stimulates...

Genome-wide RNA interference screen identifies previously undescribed regulators of polyglutamine aggregation

PubMed Central

Nollen, Ellen A. A.; Garcia, Susana M.; van Haaften, Gijs; Kim, Soojin; Chavez, Alejandro; Morimoto, Richard I.; Plasterk, Ronald H. A.

2004-01-01

Protein misfolding and the formation of aggregates are increasingly recognized components of the pathology of human genetic disease and hallmarks of many neurodegenerative disorders. As exemplified by polyglutamine diseases, the propensity for protein misfolding is associated with the length of polyglutamine expansions and age-dependent changes in protein-folding homeostasis, suggesting a critical role for a protein homeostatic buffer. To identify the complement of protein factors that protects cells against the formation of protein aggregates, we tested transgenic Caenorhabditis elegans strains expressing polyglutamine expansion yellow fluorescent protein fusion proteins at the threshold length associated with the age-dependent appearance of protein aggregation. We used genome-wide RNA interference to identify genes that, when suppressed, resulted in the premature appearance of protein aggregates. Our screen identified 186 genes corresponding to five principal classes of polyglutamine regulators: genes involved in RNA metabolism, protein synthesis, protein folding, and protein degradation; and those involved in protein trafficking. We propose that each of these classes represents a molecular machine collectively comprising the protein homeostatic buffer that responds to the expression of damaged proteins to prevent their misfolding and aggregation. PMID:15084750

N-terminal domains of fibrillin 1 and fibrillin 2 direct the formation of homodimers: a possible first step in microfibril assembly.

PubMed Central

Trask, T M; Ritty, T M; Broekelmann, T; Tisdale, C; Mecham, R P

1999-01-01

Aggregation of fibrillin molecules via disulphide bonds is postulated to be an early step in microfibril assembly. By expressing fragments of fibrillin 1 and fibrillin 2 in a mammalian expression system, we found that the N-terminal region of each protein directs the formation of homodimers and that disulphide bonds stabilize this interaction. A large fragment of fibrillin 1 containing much of the region downstream from the N-terminus remained as a monomer when expressed in the same cell system, indicating that this region of the protein lacks dimerization domains. This finding also confirms that the overexpression of fibrillin fragments does not in itself lead to spurious dimer formation. Pulse-chase analysis demonstrated that dimer formation occurred intracellularly, suggesting that the process of fibrillin aggregation is initiated early after biosynthesis of the molecules. These findings also implicate the N-terminal region of fibrillin 1 and fibrillin 2 in directing the formation of a dimer intermediate that aggregates to form the functional microfibril. PMID:10359653

Surface properties of heat-induced soluble soy protein aggregates of different molecular masses.

PubMed

Guo, Fengxian; Xiong, Youling L; Qin, Fang; Jian, Huajun; Huang, Xiaolin; Chen, Jie

2015-02-01

Suspensions (2% and 5%, w/v) of soy protein isolate (SPI) were heated at 80, 90, or 100 °C for different time periods to produce soluble aggregates of different molecular sizes to investigate the relationship between particle size and surface properties (emulsions and foams). Soluble aggregates generated in these model systems were characterized by gel permeation chromatography and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Heat treatment increased surface hydrophobicity, induced SPI aggregation via hydrophobic interaction and disulfide bonds, and formed soluble aggregates of different sizes. Heating of 5% SPI always promoted large-size aggregate (LA; >1000 kDa) formation irrespective of temperature, whereas the aggregate size distribution in 2% SPI was temperature dependent: the LA fraction progressively rose with temperature (80→90→100 °C), corresponding to the attenuation of medium-size aggregates (MA; 670 to 1000 kDa) initially abundant at 80 °C. Heated SPI with abundant LA (>50%) promoted foam stability. LA also exhibited excellent emulsifying activity and stabilized emulsions by promoting the formation of small oil droplets covered with a thick interfacial protein layer. However, despite a similar influence on emulsion stability, MA enhanced foaming capacity but were less capable of stabilizing emulsions than LA. The functionality variation between heated SPI samples is clearly related to the distribution of aggregates that differ in molecular size and surface activity. The findings may encourage further research to develop functional SPI aggregates for various commercial applications. © 2015 Institute of Food Technologists®

Influence of pH control in the formation of inclusion bodies during production of recombinant sphingomyelinase-D in Escherichia coli.

PubMed

Castellanos-Mendoza, Andrea; Castro-Acosta, Ricardo M; Olvera, Alejandro; Zavala, Guadalupe; Mendoza-Vera, Miguel; García-Hernández, Enrique; Alagón, Alejandro; Trujillo-Roldán, Mauricio A; Valdez-Cruz, Norma A

2014-09-12

Inclusion bodies (IBs) are aggregated proteins that form clusters when protein is overexpressed in heterologous expression systems. IBs have been considered as non-usable proteins, but recently they are being used as functional materials, catalytic particles, drug delivery agents, immunogenic structures, and as a raw material in recombinant therapeutic protein purification. However, few studies have been made to understand how culture conditions affect the protein aggregation and the physicochemical characteristics that lead them to cluster. The objective of our research was to understand how pH affects the physicochemical properties of IBs formed by the recombinant sphingomyelinase-D of tick expressed in E. coli BL21-Gold (DE3) by evaluating two pH culture strategies. Uncontrolled pH culture conditions favored recombinant sphingomyelinase-D aggregation and IB formation. The IBs of sphingomyelinase-D produced under controlled pH at 7.5 and after 24 h were smaller (<500 nm) than those produced under uncontrolled pH conditions (>500 nm). Furthermore, the composition, conformation and β-structure formation of the aggregates were different. Under controlled pH conditions in comparison to uncontrolled conditions, the produced IBs presented higher resistance to denaturants and proteinase-K degradation, presented β-structure, but apparently as time passes the IBs become compacted and less sensitive to amyloid dye binding. The manipulation of the pH has an impact on IB formation and their physicochemical characteristics. Particularly, uncontrolled pH conditions favored the protein aggregation and sphingomyelinase-D IB formation. The evidence may lead to find methodologies for bioprocesses to obtain biomaterials with particular characteristics, extending the application possibilities of the inclusion bodies.

Self-assembly in poly(dimethylsiloxane)-poly(ethylene oxide) block copolymer template directed synthesis of Linde type A zeolite.

PubMed

Bonaccorsi, Lucio; Calandra, Pietro; Kiselev, Mikhail A; Amenitsch, Heinz; Proverbio, Edoardo; Lombardo, Domenico

2013-06-11

We describe the hydrothermal synthesis of zeolite Linde type A (LTA) submicrometer particles using a water-soluble amphiphilic block copolymer of poly(dimethylsiloxane)-b-poly(ethylene oxide) as a template. The formation and growth of the intermediate aggregates in the presence of the diblock copolymer have been monitored by small-angle X-ray scattering (SAXS) above the critical micellar concentration at a constant temperature of 45 °C. The early stage of the growth process was characterized by the incorporation of the zeolite LTA components into the surface of the block copolymer micellar aggregates with the formation of primary units of 4.8 nm with a core-shell morphology. During this period, restricted to an initial time of 1-3 h, the core-shell structure of the particles does not show significant changes, while a subsequent aggregation process among these primary units takes place. A shape transition of the SAXS profile at the late stage of the synthesis has been connected with an aggregation process among primary units that leads to the formation of large clusters with fractal characteristics. The formation of large supramolecular assemblies was finally verified by scanning electron microscopy, which evidenced the presence of submicrometer aggregates with size ranging between 100 and 300 nm, while X-ray diffraction confirmed the presence of crystalline zeolite LTA. The main finding of our results gives novel insight into the mechanism of formation of organic-inorganic mesoporous materials based on the use of a soft interacting nanotemplate as well as stimulates the investigation of alternative protocols for the synthesis of novel hybrid materials with new characteristics and properties.

Inhibition of GNNQQNY prion peptide aggregation by trehalose: a mechanistic view.

PubMed

Katyal, Nidhi; Deep, Shashank

2017-07-26

Deposition of amyloid fibrils is the seminal event in the pathogenesis of numerous neurodegenerative diseases. The formation of this amyloid assembly is the manifestation of a cascade of structural transitions including toxic oligomer formation in the early stages of aggregation. Thus a viable therapeutic strategy involves the use of small molecular ligands to interfere with this assembly. In this perspective, we have explored the kinetics of aggregate formation of the fibril forming GNNQQNY peptide fragment from the yeast prion protein SUP35 using multiple all atom MD simulations with explicit solvent and provided mechanistic insights into the way trehalose, an experimentally known aggregation inhibitor, modulates the aggregation pathway. The results suggest that the assimilation process is impeded by different barriers at smaller and larger oligomeric sizes: the initial one being easily surpassed at higher temperatures and peptide concentrations. The kinetic profile demonstrates that trehalose delays the aggregation process by increasing both these activation barriers, specifically the latter one. It increases the sampling of small-sized aggregates that lack the beta sheet conformation. Analysis reveals that the barrier in the growth of larger stable oligomers causes the formation of multiple stable small oligomers which then fuse together bimolecularly. The PCA of 26 properties was carried out to deconvolute the events within the temporary lag phases, which suggested dynamism in lags involving an increase in interchain contacts and burial of SASA. The predominant growth route is monomer addition, which changes to condensation on account of a large number of depolymerisation events in the presence of trehalose. The favourable interaction of trehalose specifically with the sidechain of the peptide promotes crowding of trehalose molecules in its vicinity - the combination of both these factors imparts the observed behaviour. Furthermore, increasing trehalose concentration leads to faster expulsion of water molecules than interpeptide interactions. These expelled water molecules have larger translational movement, suggesting an entropy factor to favor the assembly process. Different conformations observed under this condition suggest the role of water molecules in guiding the morphology of the aggregates as well. A similar scenario exists on increasing peptide concentration.

Probing amyloid fibril formation of the NFGAIL peptide by computer simulations

NASA Astrophysics Data System (ADS)

Melquiond, Adrien; Gelly, Jean-Christophe; Mousseau, Normand; Derreumaux, Philippe

2007-02-01

Amyloid fibril formation, as observed in Alzheimer's disease and type II diabetes, is currently described by a nucleation-condensation mechanism, but the details of the process preceding the formation of the nucleus are still lacking. In this study, using an activation-relaxation technique coupled to a generic energy model, we explore the aggregation pathways of 12 chains of the hexapeptide NFGAIL. The simulations show, starting from a preformed parallel dimer and ten disordered chains, that the peptides form essentially amorphous oligomers or more rarely ordered β-sheet structures where the peptides adopt a parallel orientation within the sheets. Comparison between the simulations indicates that a dimer is not a sufficient seed for avoiding amorphous aggregates and that there is a critical threshold in the number of connections between the chains above which exploration of amorphous aggregates is preferred.

A local PDE model of aggregation formation in bacterial colonies

NASA Astrophysics Data System (ADS)

Chavy-Waddy, Paul-Christopher; Kolokolnikov, Theodore

2016-10-01

We study pattern formation in a model of cyanobacteria motion recently proposed by Galante, Wisen, Bhaya and Levy. By taking a continuum limit of their model, we derive a novel fourth-order nonlinear parabolic PDE equation that governs the behaviour of the model. This PDE is {{u}t}=-{{u}xx}-{{u}xxxx}+α {{≤ft(\\frac{{{u}x}{{u}xx}}{u}\\right)}x} . We then derive the instability thresholds for the onset of pattern formation. We also compute analytically the spatial profiles of the steady state aggregation density. These profiles are shown to be of the form \\text{sec}{{\\text{h}}p} where the exponent p is related to the parameters of the model. Full numerical simulations give a favorable comparison between the continuum and the underlying discrete system, and show that the aggregation profiles are stable above the critical threshold.

Marine Synechococcus Aggregation

NASA Astrophysics Data System (ADS)

Neuer, S.; Deng, W.; Cruz, B. N.; Monks, L.

2016-02-01

Cyanobacteria are considered to play an important role in the oceanic biological carbon pump, especially in oligotrophic regions. But as single cells are too small to sink, their carbon export has to be mediated by aggregate formation and possible consumption by zooplankton producing sinking fecal pellets. Here we report results on the aggregation of the ubiquitous marine pico-cyanobacterium Synechococcus as a model organism. We first investigated the mechanism behind such aggregation by studying the potential role of transparent exopolymeric particles (TEP) and the effects of nutrient (nitrogen or phosphorus) limitation on the TEP production and aggregate formation of these pico-cyanobacteria. We further studied the aggregation and subsequent settling in roller tanks and investigated the effects of the clays kaolinite and bentonite in a series of concentrations. Our results show that despite of the lowered growth rates, Synechococcus in nutrient limited cultures had larger cell-normalized TEP production, formed a greater volume of aggregates, and resulted in higher settling velocities compared to results from replete cultures. In addition, we found that despite their small size and lack of natural ballasting minerals, Synechococcus cells could still form aggregates and sink at measureable velocities in seawater. Clay minerals increased the number and reduced the size of aggregates, and their ballasting effects increased the sinking velocity and carbon export potential of aggregates. In comparison with the Synechococcus, we will also present results of the aggregation of the pico-cyanobacterium Prochlorococcus in roller tanks. These results contribute to our understanding in the physiology of marine Synechococcus as well as their role in the ecology and biogeochemistry in oligotrophic oceans.

Focal high cell density generates a gradient of patterns in self-organizing vascular mesenchymal cells.

PubMed

Cheng, Henry; Reddy, Aneela; Sage, Andrew; Lu, Jinxiu; Garfinkel, Alan; Tintut, Yin; Demer, Linda L

2012-01-01

In embryogenesis, structural patterns, such as vascular branching, may form via a reaction-diffusion mechanism in which activator and inhibitor morphogens guide cells into periodic aggregates. We previously found that vascular mesenchymal cells (VMCs) spontaneously aggregate into nodular structures and that morphogen pairs regulate the aggregation into patterns of spots and stripes. To test the effect of a focal change in activator morphogen on VMC pattern formation, we created a focal zone of high cell density by plating a second VMC layer within a cloning ring over a confluent monolayer. After 24 h, the ring was removed and pattern formation monitored by phase-contrast microscopy. At days 2-8, the patterns progressed from uniform distributions to swirl, labyrinthine and spot patterns. Within the focal high-density zone (HDZ) and a narrow halo zone, cells aggregated into spot patterns, whilst in the outermost zone of the plate, cells formed a labyrinthine pattern. The area occupied by aggregates was significantly greater in the outermost zone than in the HDZ or halo. The rate of pattern progression within the HDZ increased as a function of its plating density. Thus, focal differences in cell density may drive pattern formation gradients in tissue architecture, such as vascular branching. Copyright © 2012 S. Karger AG, Basel.

Large SOD1 aggregates, unlike trimeric SOD1, do not impact cell viability in a model of amyotrophic lateral sclerosis.

PubMed

Zhu, Cheng; Beck, Matthew V; Griffith, Jack D; Deshmukh, Mohanish; Dokholyan, Nikolay V

2018-05-01

Aberrant accumulation of misfolded Cu, Zn superoxide dismutase (SOD1) is a hallmark of SOD1-associated amyotrophic lateral sclerosis (ALS), an invariably fatal neurodegenerative disease. While recent discovery of nonnative trimeric SOD1-associated neurotoxicity has suggested a potential pathway for motor neuron impairment, it is yet unknown whether large, insoluble aggregates are cytotoxic. Here we designed SOD1 mutations that specifically stabilize either the fibrillar form or the trimeric state of SOD1. The designed mutants display elevated populations of fibrils or trimers correspondingly, as demonstrated by gel filtration chromatography and electron microscopy. The trimer-stabilizing mutant, G147P, promoted cell death, even more potently in comparison with the aggressive ALS-associated mutants A4V and G93A. In contrast, the fibril-stabilizing mutants, N53I and D101I, positively impacted the survival of motor neuron-like cells. Hence, we conclude the SOD1 oligomer and not the mature form of aggregated fibril is critical for the neurotoxic effects in the model of ALS. The formation of large aggregates is in competition with trimer formation, suggesting that aggregation may be a protective mechanism against formation of toxic oligomeric intermediates.

Hemin as a generic and potent protein misfolding inhibitor

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

Liu, Yanqin; Carver, John A.; Ho, Lam H.

2014-11-14

Highlights: • Hemin prevents Aβ42, α-synuclein and RCM-κ-casein forming amyloid fibrils. • Hemin inhibits the β-sheet structure formation of Aβ42. • Hemin reduces the cell toxicity caused by fibrillar Aβ42. • Hemin dissociates partially formed Aβ42 fibrils. • Hemin prevents amorphous aggregation by ADH, catalase and γs-crystallin. - Abstract: Protein misfolding causes serious biological malfunction, resulting in diseases including Alzheimer’s disease, Parkinson’s disease and cataract. Molecules which inhibit protein misfolding are a promising avenue to explore as therapeutics for the treatment of these diseases. In the present study, thioflavin T fluorescence and transmission electron microscopy experiments demonstrated that hemin preventsmore » amyloid fibril formation of kappa-casein, amyloid beta peptide and α-synuclein by blocking β-sheet structure assembly which is essential in fibril aggregation. Further, inhibition of fibril formation by hemin significantly reduces the cytotoxicity caused by fibrillar amyloid beta peptide in vitro. Interestingly, hemin degrades partially formed amyloid fibrils and prevents further aggregation to mature fibrils. Light scattering assay results revealed that hemin also prevents protein amorphous aggregation of alcohol dehydrogenase, catalase and γs-crystallin. In summary, hemin is a potent agent which generically stabilises proteins against aggregation, and has potential as a key molecule for the development of therapeutics for protein misfolding diseases.« less

Ellagic acid promotes A{beta}42 fibrillization and inhibits A{beta}42-induced neurotoxicity

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

Feng, Ying; Tsinghua University School of Medicine, Haidian District, Beijing 100084; Yang, Shi-gao

Smaller, soluble oligomers of {beta}-amyloid (A{beta}) play a critical role in the pathogenesis of Alzheimer's disease (AD). Selective inhibition of A{beta} oligomer formation provides an optimum target for AD therapy. Some polyphenols have potent anti-amyloidogenic activities and protect against A{beta} neurotoxicity. Here, we tested the effects of ellagic acid (EA), a polyphenolic compound, on A{beta}42 aggregation and neurotoxicity in vitro. EA promoted A{beta} fibril formation and significant oligomer loss, contrary to previous results that polyphenols inhibited A{beta} aggregation. The results of transmission electron microscopy (TEM) and Western blot displayed more fibrils in A{beta}42 samples co-incubated with EA in earlier phasesmore » of aggregation. Consistent with the hypothesis that plaque formation may represent a protective mechanism in which the body sequesters toxic A{beta} aggregates to render them harmless, our MTT results showed that EA could significantly reduce A{beta}42-induced neurotoxicity toward SH-SY5Y cells. Taken together, our results suggest that EA, an active ingredient in many fruits and nuts, may have therapeutic potential in AD.« less

Microscopic mechanism of nanocrystal formation from solution by cluster aggregation and coalescence

PubMed Central

Hassan, Sergio A.

2011-01-01

Solute-cluster aggregation and particle fusion have recently been suggested as alternative routes to the classical mechanism of nucleation from solution. The role of both processes in the crystallization of an aqueous electrolyte under controlled salt addition is here elucidated by molecular dynamics simulation. The time scale of the simulation allows direct observation of the entire crystallization pathway, from early events in the prenucleation stage to the formation of a nanocrystal in equilibrium with concentrated solution. The precursor originates in a small amorphous aggregate stabilized by hydration forces. The core of the nucleus becomes crystalline over time and grows by coalescence of the amorphous phase deposited at the surface. Imperfections of ion packing during coalescence promote growth of two conjoint crystallites. A parameter of order and calculated cohesive energies reflect the increasing crystalline order and stress relief at the grain boundary. Cluster aggregation plays a major role both in the formation of the nucleus and in the early stages of postnucleation growth. The mechanism identified shares common features with nucleation of solids from the melt and of liquid droplets from the vapor. PMID:21428633

Inhibitory effects of yuzu and its components on human platelet aggregation.

PubMed

Kim, Tae-Ho; Kim, Hye-Min; Park, Se Won; Jung, Yi-Sook

2015-03-01

Our previous study demonstrated that yuzu has an anti-platelet effect in rat blood. In the present study, we examined whether the anti-platelet effect of yuzu can be extended to human blood by investigating its ability to inhibit aggregations induced by various agonists in human platelet rich plasma (PRP). This study also investigated the underlying mechanism of yuzu focusing on ADP granule secretion, TXB2 formations, and PLCγ/Akt signaling. The results from this study showed that ethanolic yuzu extract (YE), and its components, hesperidin and naringin, inhibited human platelet aggregation in a concentration-dependent manner. YE, hesperidin and naringin also inhibited TXB2 formation and ADP release. The phosphorylation of PLCγ and Akt was significantly inhibited by YE, heperidin and naringin. Furthermore, we demonstrated that YE, heperidin and naringin has anti-platelet effects in rat ex vivo studies, and lower side effects in mice tail bleeding time studies. The results from this study suggest that YE, hesperidin and naringin can inhibit human platelet aggregation, at least partly through the inhibition of PLCγ and Akt, leading to a decrease in TXB2 formation and granule secretion.

An evolutionary recent neuroepithelial cell adhesion function of huntingtin implicates ADAM10-Ncadherin.

PubMed

Lo Sardo, Valentina; Zuccato, Chiara; Gaudenzi, Germano; Vitali, Barbara; Ramos, Catarina; Tartari, Marzia; Myre, Michael A; Walker, James A; Pistocchi, Anna; Conti, Luciano; Valenza, Marta; Drung, Binia; Schmidt, Boris; Gusella, James; Zeitlin, Scott; Cotelli, Franco; Cattaneo, Elena

2012-05-01

The Huntington's disease gene product, huntingtin, is indispensable for neural tube formation, but its role is obscure. We studied neurulation in htt-null embryonic stem cells and htt-morpholino zebrafish embryos and found a previously unknown, evolutionarily recent function for this ancient protein. We found that htt was essential for homotypic interactions between neuroepithelial cells; it permitted neurulation and rosette formation by regulating metalloprotease ADAM10 activity and Ncadherin cleavage. This function was embedded in the N terminus of htt and was phenocopied by treatment of htt knockdown zebrafish with an ADAM10 inhibitor. Notably, in htt-null cells, reversion of the rosetteless phenotype occurred only with expression of evolutionarily recent htt heterologues from deuterostome organisms. Conversely, all of the heterologues that we tested, including htt from Drosophila melanogaster and Dictyostelium discoideum, exhibited anti-apoptotic activity. Thus, anti-apoptosis may have been one of htt’s ancestral function(s), but, in deuterostomes, htt evolved to acquire a unique regulatory activity for controlling neural adhesion via ADAM10-Ncadherin, with implications for brain evolution and development.

Formation of wood secondary cell wall may involve two type cellulose synthase complexes in Populus.

PubMed

Xi, Wang; Song, Dongliang; Sun, Jiayan; Shen, Junhui; Li, Laigeng

2017-03-01

Cellulose biosynthesis is mediated by cellulose synthases (CesAs), which constitute into rosette-like cellulose synthase complexe (CSC) on the plasma membrane. Two types of CSCs in Arabidopsis are believed to be involved in cellulose synthesis in the primary cell wall and secondary cell walls, respectively. In this work, we found that the two type CSCs participated cellulose biosynthesis in differentiating xylem cells undergoing secondary cell wall thickening in Populus. During the cell wall thickening process, expression of one type CSC genes increased while expression of the other type CSC genes decreased. Suppression of different type CSC genes both affected the wall-thickening and disrupted the multilaminar structure of the secondary cell walls. When CesA7A was suppressed, crystalline cellulose content was reduced, which, however, showed an increase when CesA3D was suppressed. The CesA suppression also affected cellulose digestibility of the wood cell walls. The results suggest that two type CSCs are involved in coordinating the cellulose biosynthesis in formation of the multilaminar structure in Populus wood secondary cell walls.

Role of the disaggregase ClpB in processing of proteins aggregated as inclusion bodies.

PubMed

Zblewska, Kamila; Krajewska, Joanna; Zolkiewski, Michal; Kędzierska-Mieszkowska, Sabina

2014-08-01

Overproduction of heterologous proteins in bacterial systems often results in the formation of insoluble inclusion bodies (IBs), which is a major impediment in biochemical research and biotechnology. In principle, the activity of molecular chaperones could be employed to gain control over the IB formation and to improve the recombinant protein yields, but the potential of each of the major bacterial chaperones (DnaK/J, GroEL/ES, and ClpB) to process IBs has not been fully established yet. We investigated the formation of inclusion bodies (IBs) of two aggregation-prone proteins, VP1LAC and VP1GFP, overproduced in Escherichiacoli in the presence and absence of the chaperone ClpB. We found that both ClpB isoforms, ClpB95 and ClpB80 accumulated in E. coli cells during the production of IBs. The amount of IB proteins increased in the absence of ClpB. ClpB supported the resolubilization and reactivation of the aggregated VP1LAC and VP1GFP in E. coli cells. The IB disaggregation was optimal in the presence of both ClpB95 and ClpB80. Our results indicate an essential role of ClpB in controlling protein aggregation and inclusion body formation in bacteria. Copyright © 2014 Elsevier Inc. All rights reserved.

Directional reversals enable Myxococcus xanthus cells to produce collective one-dimensional streams during fruiting-body formation

PubMed Central

Thutupalli, Shashi; Sun, Mingzhai; Bunyak, Filiz; Palaniappan, Kannappan; Shaevitz, Joshua W.

2015-01-01

The formation of a collectively moving group benefits individuals within a population in a variety of ways. The surface-dwelling bacterium Myxococcus xanthus forms dynamic collective groups both to feed on prey and to aggregate during times of starvation. The latter behaviour, termed fruiting-body formation, involves a complex, coordinated series of density changes that ultimately lead to three-dimensional aggregates comprising hundreds of thousands of cells and spores. How a loose, two-dimensional sheet of motile cells produces a fixed aggregate has remained a mystery as current models of aggregation are either inconsistent with experimental data or ultimately predict unstable structures that do not remain fixed in space. Here, we use high-resolution microscopy and computer vision software to spatio-temporally track the motion of thousands of individuals during the initial stages of fruiting-body formation. We find that cells undergo a phase transition from exploratory flocking, in which unstable cell groups move rapidly and coherently over long distances, to a reversal-mediated localization into one-dimensional growing streams that are inherently stable in space. These observations identify a new phase of active collective behaviour and answer a long-standing open question in Myxococcus development by describing how motile cell groups can remain statistically fixed in a spatial location. PMID:26246416

Methylglyoxal induced glycation and aggregation of human serum albumin: Biochemical and biophysical approach.

PubMed

Ahmed, Azaj; Shamsi, Anas; Khan, Mohd Shahnawaz; Husain, Fohad Mabood; Bano, Bilqees

2018-07-01

Serum protein glycation and formation of advanced glycation end products (AGEs) correlates with many diseases viz. diabetes signifying the importance of studying the glycation pattern of serum proteins. In our present study, methylglyoxal was investigated for its effect on the structure of human serum albumin (HSA); exploring the formation of AGEs and aggregates of HSA. The analytical tools employed includes intrinsic and extrinsic fluorescence, UV spectroscopy, far UV circular dichroism, Thioflavin T fluorescence, congo red binding, polyacrylamide gel electrophoresis (PAGE). UV and fluorescence spectroscopy revealed the structural transition of native HSA evident by new peaks and increased absorbance in UV spectra and quenched fluorescence in the presence of MG. Far UV CD spectroscopy revealed MG induced secondary structural alteration evident by reduced α-helical content. AGEs formation was confirmed by AGEs specific fluorescence. Increased ThT fluorescence and CR absorbance of 10mM MG incubated HSA suggests that glycated HSA results in the formation of aggregates of HSA. SEM and TEM were reported to have an insight of these aggregates. Molecular docking was also utilized to see site specific interaction of MG-HSA. This study is clinically significant as HSA is a clinically relevant protein which plays a crucial role in many diseases. Copyright © 2018 Elsevier B.V. All rights reserved.

Aggregation of peptides in the tube model with correlated sidechain orientations

NASA Astrophysics Data System (ADS)

Hung, Nguyen Ba; Hoang, Trinh Xuan

2015-06-01

The ability of proteins and peptides to aggregate and form toxic amyloid fibrils is associated with a range of diseases including BSE (or mad cow), Alzheimer's and Parkinson's Diseases. In this study, we investigate the the role of amino acid sequence in the aggregation propensity by using a modified tube model with a new procedure for hydrophobic interaction. In this model, the amino acid sidechains are not considered explicitly, but their orientations are taken into account in the formation of hydrophobic contact. Extensive Monte Carlo simulations for systems of short peptides are carried out with the use of parallel tempering technique. Our results show that the propensity to form and the structures of the aggregates strongly depend on the amino acid sequence and the number of peptides. Some sequences may not aggregate at all at a presumable physiological temperature while other can easily form fibril-like, β-sheet struture. Our study provides an insight into the principles of how the formation of amyloid can be governed by amino acid sequence.

A discrete cell model with adaptive signalling for aggregation of Dictyostelium discoideum.

PubMed Central

Dallon, J C; Othmer, H G

1997-01-01

Dictyostelium discoideum (Dd) is a widely studied model system from which fundamental insights into cell movement, chemotaxis, aggregation and pattern formation can be gained. In this system aggregation results from the chemotactic response by dispersed amoebae to a travelling wave of the chemoattractant cAMP. We have developed a model in which the cells are treated as discrete points in a continuum field of the chemoattractant, and transduction of the extracellular cAMP signal into the intracellular signal is based on the G protein model developed by Tang & Othmer. The model reproduces a number of experimental observations and gives further insight into the aggregation process. We investigate different rules for cell movement the factors that influence stream formation the effect on aggregation of noise in the choice of the direction of movement and when spiral waves of chemoattractant and cell density are likely to occur. Our results give new insight into the origin of spiral waves and suggest that streaming is due to a finite amplitude instability. PMID:9134569

Stepwise Nucleation of Aniline: Emergence of Spectroscopic Fingerprints of the Liquid Phase.

PubMed

Leon, Iker; Usabiaga, Imanol; Arnaiz, Pedro Felipe; Lesarri, Alberto; Fernández, Jose Andres

2018-06-11

We deal here with the controlled nucleation of aniline from the isolated molecule until formation of a moderately large aggregate: aniline nonamer. The structure of the cluster at each step of the nucleation was unravelled combining mass-resolved IR spectroscopy and computational chemistry, demonstrating that aggregation is primarily guided by formation of extensive N-H···N hydrogen bond networks that give the aggregates a sort of branched backbone, in clear competition with multiple N-H/C-H···pi and pi···pi interactions. The result is the co-existence of close nucleation paths connecting relational aggregates. The delicate balance of molecular forces makes the aniline clusters a challenge for molecular orbital calculations and an ideal system to refine the present nucleation models. Noticeably, spectroscopic signatures characteristic of the condensed phase are apparent in the nanometer-size aggregates formed in this work. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Influence of Ice Particle Surface Roughening on the Global Cloud Radiative Effect

NASA Technical Reports Server (NTRS)

Yi, Bingqi; Yang, Ping; Baum, Bryan A.; LEcuyer, Tristan; Oreopoulos, Lazaros; Mlawer, Eli J.; Heymsfield, Andrew J.; Liou, Kuo-Nan

2013-01-01

Ice clouds influence the climate system by changing the radiation budget and large-scale circulation. Therefore, climate models need to have an accurate representation of ice clouds and their radiative effects. In this paper, new broadband parameterizations for ice cloud bulk scattering properties are developed for severely roughened ice particles. The parameterizations are based on a general habit mixture that includes nine habits (droxtals, hollow/solid columns, plates, solid/hollow bullet rosettes, aggregate of solid columns, and small/large aggregates of plates). The scattering properties for these individual habits incorporate recent advances in light-scattering computations. The influence of ice particle surface roughness on the ice cloud radiative effect is determined through simulations with the Fu-Liou and the GCM version of the Rapid Radiative Transfer Model (RRTMG) codes and the National Center for Atmospheric Research Community Atmosphere Model (CAM, version 5.1). The differences in shortwave (SW) and longwave (LW) radiative effect at both the top of the atmosphere and the surface are determined for smooth and severely roughened ice particles. While the influence of particle roughening on the single-scattering properties is negligible in the LW, the results indicate that ice crystal roughness can change the SW forcing locally by more than 10 W m(exp -2) over a range of effective diameters. The global-averaged SW cloud radiative effect due to ice particle surface roughness is estimated to be roughly 1-2 W m(exp -2). The CAM results indicate that ice particle roughening can result in a large regional SW radiative effect and a small but nonnegligible increase in the global LW cloud radiative effect.

Biosignatures in modern sulfates: texture, composition and depositional environments of gypsum deposits at Guerrero Negro, Baja, Mexico

NASA Astrophysics Data System (ADS)

Vogel, M. B.; Des Marais, D. J.; Jahnke, L. L.; Turk, K.; Kubo, M.

2007-12-01

Gypsum (CaSO4·H2O) is an important phase in biogeochemistry and sedimentology as a mineral sink for sulfur, a paleoclimatic indicator, and an endolithic niche for phototrophic and chemotrophic bacteria. Sulfate deposits are also important targets of exploration for evidence of habitable environments and life on Mars. Gypsum deposits from a range of sedimentary environments at the Guerrero Negro crystallizer ponds and sabkha settings were investigated for microscale structure and composition to differentiate fabrics formed under microbial influence from those formed under abiogenic conditions. Sub-sedimentary gypsum forms in sabkha environments as mm to cm scale selenite discs (termed bird beak gypsum; Warren, 2006) and selenite disc aggregates. Selenite discs and other sub-sedimentary gypsum are characterized by a sinuous axial microtexture and poikilitically enclosed detrital particles. Sub-aqueous gypsum forms as cements, granules (termed gypsooids), and massive botryoidal crusts that line the sediment water interface and margins of managed crystallizer ponds and natural anchialine pools. Sub-aqueous gypsum exhibits a wide range of textures and mineral/biofilm associations that include amorphous to euhedral, tabular, needle and lensoidal morphologies. Elemental sulfur forms rinds on prismatic, growth aligned gypsum twins and reticulate magnesian carbonate is interspersed with both twinned crystals and rosette aggregates in stratified sub-aqueous environments. Intracrystalline biofilms and cell material was observed in association with nearly all sub-aqueous morphologies but only scarce evidence has been found for intercrystalline microbial communities. Columnar microbial communities living in anchialine pools were found to host precipitation of mm scale gypsum granules in their EPS matrix. Fine scale gypsum textures are unlikely to persist through diagenetic alteration, but understanding their primary associations with sulfur and carbonates is necessary for interpreting sulfates or their replacement phases in the ancient record.

Interactions between extracellular polymeric substances and clay minerals affect soil aggregation

NASA Astrophysics Data System (ADS)

Vogel, Cordula; Rehschuh, Stephanie; Kemi Olagoke, Folasade; Redmile Gordon, Marc; Kalbiltz, Karsten

2017-04-01

Soil aggregation is crucial for carbon (C) sequestration and microbial processes have been recognised as important control of aggregate turnover (formation, stability, and destruction). However, how microorganisms contribute to these processes is still a matter of debate. An enthralling mechanism determining aggregate turnover and therefore C sequestration may be the excretion of extracellular polymeric substances (EPS) as microbial glue, but effects of EPS on aggregation is largely unknown. Moreover, interdependencies between important aggregation factors like the amount of fine-sized particles (clay content), the decomposability of organic matter and the microbial community (size and composition, as well as the excretion of EPS) are still poorly understood. Therefore, we studied the complex interactions between these factors and their role in aggregate turnover. It was hypothesized that an increase in microbial activity, induced by the input of organic substrates, will stimulate EPS production and therefore the formation and stability of aggregates. To test this hypothesis, an incubation experiment has been conducted across a gradient of clay content (montmorillonite) and substrate decomposability (starch and glucose) as main drivers of the microbial activity. A combination of aggregate separation and stability tests were applied. This results will be examined with respect to the obtained microbial parameters (amount and composition of EPS, CO2 emission, microbial biomass, phospholipid fatty acid), to disentangle the mechanisms and factors controlling aggregate turnover affected by soil microorganisms. This study is expected to provide insights on the role of EPS in the stability of aggregates. Thus, the results of this study will provide an improved understanding of the underlying processes of aggregate turnover in soils, which is necessary to implement strategies for enhanced C sequestration in agricultural soils.

Local growth of dust- and ice-mixed aggregates as cometary building blocks in the solar nebula

NASA Astrophysics Data System (ADS)

Lorek, S.; Lacerda, P.; Blum, J.

2018-03-01

Context. Comet formation by gravitational instability requires aggregates that trigger the streaming instability and cluster in pebble-clouds. These aggregates form as mixtures of dust and ice from (sub-)micrometre-sized dust and ice grains via coagulation in the solar nebula. Aim. We investigate the growth of aggregates from (sub-)micrometre-sized dust and ice monomer grains. We are interested in the properties of these aggregates: whether they might trigger the streaming instability, how they compare to pebbles found on comets, and what the implications are for comet formation in collapsing pebble-clouds. Methods: We used Monte Carlo simulations to study the growth of aggregates through coagulation locally in the comet-forming region at 30 au. We used a collision model that can accommodate sticking, bouncing, fragmentation, and porosity of dust- and ice-mixed aggregates. We compared our results to measurements of pebbles on comet 67P/Churyumov-Gerasimenko. Results: We find that aggregate growth becomes limited by radial drift towards the Sun for 1 μm sized monomers and by bouncing collisions for 0.1 μm sized monomers before the aggregates reach a Stokes number that would trigger the streaming instability (Stmin). We argue that in a bouncing-dominated system, aggregates can reach Stmin through compression in bouncing collisions if compression is faster than radial drift. In the comet-forming region ( 30 au), aggregates with Stmin have volume-filling factors of 10-2 and radii of a few millimetres. These sizes are comparable to the sizes of pebbles found on comet 67P/Churyumov-Gerasimenko. The porosity of the aggregates formed in the solar nebula would imply that comets formed in pebble-clouds with masses equivalent to planetesimals of the order of 100 km in diameter.

Protein Colloidal Aggregation Project

NASA Technical Reports Server (NTRS)

Oliva-Buisson, Yvette J. (Compiler)

2014-01-01

To investigate the pathways and kinetics of protein aggregation to allow accurate predictive modeling of the process and evaluation of potential inhibitors to prevalent diseases including cataract formation, chronic traumatic encephalopathy, Alzheimer's Disease, Parkinson's Disease and others.

Picosecond x-ray strain rosette reveals direct laser excitation of coherent transverse acoustic phonons

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

Lee, Sooheyong; Williams, G. Jackson; Campana, Maria I.

Using a strain-rosette, we demonstrate the existence of transverse strain using time-resolved x-ray diffraction from multiple Bragg reflections in laser-excited bulk gallium arsenide. We find that anisotropic strain is responsible for a considerable fraction of the total lattice motion at early times before thermal equilibrium is achieved. Our measurements are described by a new model where the Poisson ratio drives transverse motion, resulting in the creation of shear waves without the need for an indirect process such as mode conversion at an interface. Finally, using the same excitation geometry with the narrow-gap semiconductor indium antimonide, we detected coherent transverse acousticmore » oscillations at frequencies of several GHz.« less

Picosecond x-ray strain rosette reveals direct laser excitation of coherent transverse acoustic phonons

DOE PAGES

Lee, Sooheyong; Williams, G. Jackson; Campana, Maria I.; ...

2016-01-11

Using a strain-rosette, we demonstrate the existence of transverse strain using time-resolved x-ray diffraction from multiple Bragg reflections in laser-excited bulk gallium arsenide. We find that anisotropic strain is responsible for a considerable fraction of the total lattice motion at early times before thermal equilibrium is achieved. Our measurements are described by a new model where the Poisson ratio drives transverse motion, resulting in the creation of shear waves without the need for an indirect process such as mode conversion at an interface. Finally, using the same excitation geometry with the narrow-gap semiconductor indium antimonide, we detected coherent transverse acousticmore » oscillations at frequencies of several GHz.« less

Formation of J-Aggregates of an Anionic Oxacarbocyanine Dye Upon Interaction with Proteins and Polyelectrolytes

NASA Astrophysics Data System (ADS)

Pronkin, P. G.; Tatikolov, A. S.

2017-05-01

J-aggregation of the anionic oxacarbocyanine dye 3,3'-di-(γ-sulfopropyl)-5,5'-diphenyl-9-ethyloxacarbocyanine betaine was studied in aqueous solutions in the presence of proteins (collagens, immunoglobulin G, serum albumins) and polyelectrolytes (polyethyleneimine, polyvinylpyrrolidone). It was found that denaturation of human serum albumin by urea stimulated J-aggregation of the dye. The dye formed two types of J-aggregates in the presence of denatured albumin and polyethyleneimine. J-aggregates formed in the presence of polyethyleneimine rearranged over time.

Fragmentation, rings and coarsening: structure and transformations of nanocrystal aggregate networks on a liquid surface

NASA Astrophysics Data System (ADS)

Yang, Bo; Scheidtmann, Jens; Mayer, Joachim; Wuttig, Matthias; Michely, Thomas

2002-01-01

Deposition of Ag on a silicon oil surface leads to the formation of nm-sized Ag crystals floating on the oil surface. These nanocrystals mutually attract each other, forming strongly branched nanocrystal aggregates and continuous aggregate networks. Transformation processes of such nanocrystal aggregate networks are imaged in situ by optical microscopy. The observations are explained on the basis of a simple model involving diffusion of nanocrystals along aggregate edges and the rupture of branches resulting from branch width fluctuations due to edge diffusion.

The effect of molecular shape on oligomerization of hydrophobic drugs: Molecular simulations of ciprofloxacin and nutlin

NASA Astrophysics Data System (ADS)

Li, Jianguo; Beuerman, Roger; Verma, Chandra

2018-03-01

Molecular aggregation plays a significant role in modulating the solubility, permeability, and bioactivity of drugs. The propensity to aggregate depends on hydrophobicity and on molecular shape. Molecular dynamics simulations coupled with enhanced sampling methods are used to explore the early stages of oligomerization of two drug molecules which have a strong aggregation propensity, but with contrasting molecule shapes: the antibiotic ciprofloxacin and the anticancer drug Nutlin-3A. The planar shape of ciprofloxacin induces the formation of stable oligomers at all cluster sizes. The aggregation of ciprofloxacin is driven by two-body interactions, and transferring one ciprofloxacin molecule to an existing cluster involves the desolvation of two faces and the concomitant hydrophobic interactions between the two faces; thus, the corresponding free energy of oligomerization weakly depends on the oligomer size. By contrast, Nutlin-3A has a star-shape and hence can only form stable oligomers when the cluster size is greater than 8. Free energy simulations further confirmed that the free energy of oligomer formation for Nutlin-3A becomes more favorable as the oligomer becomes larger. The aggregation of star-shaped Nutlin-3A results from many-body interactions and hence the free energy of cluster formation is strongly dependent on the size. The findings of this study provide atomistic insights into how molecular shape modulates the aggregation behavior of molecules and may be factored into the design of drugs or nano-particles.

Heating of Porous Icy Dust Aggregates

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

Sirono, Sin-iti

At the beginning of planetary formation, highly porous dust aggregates are formed through coagulation of dust grains. Outside the snowline, the main component of an aggregate is H{sub 2}O ice. Because H{sub 2}O ice is formed in amorphous form, its thermal conductivity is extremely small. Therefore, the thermal conductivity of an icy dust aggregate is low. There is a possibility of heating inside an aggregate owing to the decay of radionuclides. It is shown that the temperature increases substantially inside an aggregate, leading to crystallization of amorphous ice. During the crystallization, the temperature further increases sufficiently to continue sintering. Themore » mechanical properties of icy dust aggregates change, and the collisional evolution of dust aggregates is affected by the sintering.« less

Crystallization Experiments in the MgO-CO2-H2O system: Role of Amorphous Magnesium Carbonate Precursors in Magnesium Carbonate Hydrated Phases and Morphologies in Low Temperature Hydrothermal Fluids

NASA Astrophysics Data System (ADS)

Giampouras, Manolis; Garcia-Ruiz, Juan Manuel; Garrido, Carlos J.

2017-04-01

Numerous forms of hydrated or basic magnesium carbonates occur in the complex MgO-CO2-H2O system. Mineral saturation states from low temperature hydrothermal fluids in Semail Ophiolite (Oman), Prony Bay (New Caledonia) and Lost City hydrothermal field (mid-Atlantic ridge) strongly indicate the presence of magnesium hydroxy-carbonate hydrates (e.g. hydromagnesite) and magnesium hydroxides (brucite). Study of formation mechanisms and morphological features of minerals forming in the MgO-CO2-H2O system could give insights into serpentinization-driven, hydrothermal, alkaline environments, which are related to early Earth conditions. Temperature, hydration degree, pH and fluid composition are crucial factors regarding the formation, coexistence and transformation of such mineral phases. The rate of supersaturation, on the other hand, is a fundamental parameter to understand nucleation and crystal growth processes. All these parameters can be examined in a solution using different crystallization techniques. In the present study, we applied different crystallization techniques to synthesize and monitor the crystallization of Mg-bearing carbonates and hydroxides under abiotic conditions. Various crystallization techniques (counter-diffusion, vapor diffusion and unseeded solution mixing) were used to screen the formation conditions of each phase, transformation processes and structural development. Mineral and textural characterization of the different synthesized phases were carried out by X-ray diffraction (XRD), Raman spectroscopy and scanning electron microscopy coupled to dispersive energy spectroscopy (FE-SEM-EDS). Experimental investigation of the effect of pH level and silica content under variable reactant concentrations revealed the importance of Amorphous Magnesium Carbonate (AMC) in the formation of hydroxy-carbonate phases (hydromagnesite and dypingite). Micro-structural resemblance between AMC precursors and later stage crystalline phases highlights the critical role of internal molecule re-organization to form crystalline structures. Aggregation of AMC spherulites triggers biomimetic morphologies forming curling laminar structures and rings. The size and number of nesquehonite (MgCO3.3H2O) crystals are controlled by pH and Mg2+ ions at pH < 9. As pH increases, nesquehonite transforms to spherical, rosette-like dypingite and/or hydromagnesite. Crystallization experiments within silica gel impedes the normal growth of prismatic nesquehonite crystals and generates peculiar dendritic crystalline structures. Finally, vapor diffusion techniques resulted in synthesis of NH4+-bearing hydrated compounds after ammonium incorporation when [NH4+]/[Mg2+] ≥ 1 and ≥ 0.5M [NH4+]. Funding: We acknowledge funding from the People programme (Marie Curie Actions - ITN) of the European Union FP7 under REA Grant Agreement n˚ 608001.

Pathological features of olfactory neuroblastoma in an axolotl (Ambystoma mexicanum).

PubMed

Shioda, Chieko; Uchida, Kazuyuki; Nakayama, Hiroyuki

2011-08-01

A one-year-old, female Mexican axolotl (Ambystoma mexicanum) had a rough-surfaced, polypoid, pink tumor mass of approximately 10 mm in diameter in the oral cavity. Histologically, the tumor extended from the ethmoturbinate region and into the oral cavity and had replaced some of the maxillary bone tissue. The tumor mass was composed of a lobular architecture of small round-shaped tumor cells with occasional Flexner-Wintersteiner-like rosette formation. There were no metastatic lesions in the other organs. Immunohistochemically, the tumor cells were partly positive for several neural markers (class III beta-tubulin, S-100 protein, and doublecortin) and intensely positive for an epithelial marker (cytokeratin AE1/AE3). These results suggest that the present tumor originated from neuroectodermal tissue. Considering the location and histological and immunohistochemical features of the tumor, a diagnosis of olfactory neuroblastoma was made.

Cellular Strategies for Regulating Functional and Nonfunctional Protein Aggregation

PubMed Central

Gsponer, Jörg; Babu, M. Madan

2012-01-01

Summary Growing evidence suggests that aggregation-prone proteins are both harmful and functional for a cell. How do cellular systems balance the detrimental and beneficial effect of protein aggregation? We reveal that aggregation-prone proteins are subject to differential transcriptional, translational, and degradation control compared to nonaggregation-prone proteins, which leads to their decreased synthesis, low abundance, and high turnover. Genetic modulators that enhance the aggregation phenotype are enriched in genes that influence expression homeostasis. Moreover, genes encoding aggregation-prone proteins are more likely to be harmful when overexpressed. The trends are evolutionarily conserved and suggest a strategy whereby cellular mechanisms specifically modulate the availability of aggregation-prone proteins to (1) keep concentrations below the critical ones required for aggregation and (2) shift the equilibrium between the monomeric and oligomeric/aggregate form, as explained by Le Chatelier’s principle. This strategy may prevent formation of undesirable aggregates and keep functional assemblies/aggregates under control. PMID:23168257

Thiol oxidation and di-tyrosine formation in human plasma proteins induced by inflammatory concentrations of hypochlorous acid.

PubMed

Colombo, Graziano; Clerici, Marco; Altomare, Alessandra; Rusconi, Francesco; Giustarini, Daniela; Portinaro, Nicola; Garavaglia, Maria Lisa; Rossi, Ranieri; Dalle-Donne, Isabella; Milzani, Aldo

2017-01-30

In this study, we assessed the oxidative damage occurring in plasma proteins when human blood was exposed to inflammatory concentrations of hypochlorous acid (HOCl). We used specific thiol labelling and Western blot analyses to determine protein thiol oxidation, as well as analytical gel filtration HPLC coupled to fluorescence detection to explore formation of high molecular weight (HMW) protein aggregates. Thiol-containing proteins oxidized by HOCl were identified by redox proteomics. Mass spectrometry (MS) analysis was performed to elucidate the protein composition of HMW aggregates. α1-antitrypsin, transthyretin, and haptoglobin showed thiol oxidation at HOCl concentrations higher than those causing complete oxidation of albumin. At the highest HOCl concentrations, formation of carbonylated and di-tyrosine cross-linked HMW protein aggregates also occurred. MS analysis identified fibrinogen, complement C3 and apolipoprotein A-I as components of HMW protein aggregates. These results could be relevant for human diseases characterized by inflammatory conditions in which myeloperoxidase and HOCl are involved. In this study we evaluated the oxidative damage occurring on plasma proteins when reconstituted human blood was exposed to inflammatory concentrations of hypochlorous acid (HOCl). Pathophysiological concentrations of HOCl are able to induce different modifications on plasma proteins such as carbonylation, sulfhydryl oxidation and formation of high molecular weight (HMW) protein aggregates characterized by di-tyrosine fluorescence. There are two relevant aspects emerging from this paper. The first one consists on identifying low abundant proteins undergoing sulfhydryl oxidation by biotin-maleimide derivatization followed by MALDI-TOF mass spectrometry. This approach suggests three low-abundant proteins undergoing HOCl-induced oxidation: transthyretin, α1-antitrypsin, and haptoglobin. In addition, we analysed HMW protein aggregates forming after HOCl exposure. These aggregates are characterized by carbonylation, intra- and/or intermolecular di-tyrosine bridges. After their isolation from SDS-PAGE gel electrophoresis, using electrospray tandem mass spectrometry coupled to reversed-phase nanoscale capillary liquid chromatography, we identified some protein constituents of these HMW aggregates such as α, β, γ fibrinogen chains, apolipoprotein A-I and complement C3. In particular, our work highlights how fibrinogen is an important constituent of HOCl-induced HMW protein aggregates validating the mass spectrometry result with additional experiments. Further investigations are required in order to evaluate the possibility to use carbonylated and di-Tyr cross-linked HMW protein aggregates as (early) biomarkers for disease progression in inflammatory conditions in which myeloperoxidase and HOCl are involved. Copyright © 2016 Elsevier B.V. All rights reserved.

Development of alginate-based aggregate inoculants of Methylobacterium sp. and Azospirillum brasilense tested under in vitro conditions to promote plant growth.

PubMed

Joe, M M; Saravanan, V S; Islam, M R; Sa, T

2014-02-01

To develop co-aggregated bacterial inoculant comprising of Methylobacterium oryzae CBMB20/Methylobacterium suomiense CBMB120 strains with Azospirillum brasilense (CW903) strain and testing their efficiency as inoculants for plant growth promotion (PGP). Biofilm formation and co-aggregation efficiency was studied between A. brasilense CW903 and methylobacterial strains M. oryzae CBMB20 and M. suomiense CBMB120. Survival and release of these co-aggregated bacterial strains entrapped in alginate beads were assessed. PGP attributes of the co-aggregated bacterial inoculant were tested in tomato plants under water-stressed conditions. Results suggest that the biofilm formation efficiency of the CBMB20 and CBMB120 strains increased by 15 and 34%, respectively, when co-cultivated with CW903. Co-aggregation with CW903 enhanced the survivability of CBMB20 strain in alginate beads. Water stress index score showed least stress index in plants inoculated with CW903 and CBMB20 strains maintained as a co-aggregated inoculant. This study reports the development of co-aggregated cell inoculants containing M. oryzae CBMB20 and A. brasilense CW903 strains conferred better shelf life and stress abatement in inoculated tomato plants. These findings could be extended to other PGP bacterial species to develop multigeneric bioinoculants with multiple benefits for various crops. © 2013 The Society for Applied Microbiology.

Aggregate-based sub-CMC Solubilization of Hexadecane by Surfactants.

PubMed

Zhong, Hua; Yang, Lei; Zeng, Guangming; Brusseau, Mark L; Wang, Yake; Li, Yang; Liu, Zhifeng; Yuan, Xingzhong; Tan, Fei

Solubilization of hexadecane by two surfactants, SDBS and Triton X-100, at concentrations near the critical micelle concentration (CMC) and the related aggregation behavior was investigated in this study. Solubilization was observed at surfactant concentrations lower than CMC, and the apparent solubility of hexadecane increased linearly with surfactant concentration for both surfactants. The capacity of SDBS to solubilize hexadecane is stronger at concentrations below CMC than above CMC. In contrast, Triton X-100 shows no difference. The results of dynamic light scattering (DLS) and cryogenic TEM analysis show aggregate formation at surfactant concentrations lower than CMC. DLS-based size of the aggregates ( d ) decreases with increasing surfactant concentration. Zeta potential of the SDBS aggregates decreases with increasing SDBS concentration, whereas it increases for Triton X-100. The surface excess (Γ) of SDBS calculated based on hexadecane solubility and aggregate size data increases rapidly with increasing bulk concentration, and then asymptotically approaches the maximum surface excess (Γ max ). Conversely, there is only a minor increase in Γ for Triton X-100. Comparison of Γ and d indicates that excess of surfactant molecules at aggregate surface has great impact on surface curvature. The results of this study demonstrate formation of aggregates at surfactant concentrations below CMC for hexadecane solubilization, and indicate the potential of employing low-concentration strategy for surfactant application such as remediation of HOC contaminated sites.

The second Cu(II)-binding site in a proton-rich environment interferes with the aggregation of amyloid-beta(1-40) into amyloid fibrils.

PubMed

Jun, Sangmi; Gillespie, Joel R; Shin, Byong-kyu; Saxena, Sunil

2009-11-17

The overall morphology and Cu(II) ion coordination for the aggregated amyloid-beta(1-40) [Abeta(1-40)] in N-ethylmorpholine (NEM) buffer are affected by Cu(II) ion concentration. This effect is investigated by transmission electron microscopy (TEM), atomic force microscopy (AFM), and electron spin echo envelope modulation (ESEEM) spectroscopy. At lower than equimolar concentrations of Cu(II) ions, fibrillar aggregates of Abeta(1-40) are observed. At these concentrations of Cu(II), the monomeric and fibrillar Abeta(1-40) ESEEM data indicate that the Cu(II) ion is coordinated by histidine residues. For aggregated Abeta(1-40) at a Cu(II):Abeta molar ratio of 2:1, TEM and AFM images show both linear fibrils and granular amorphous aggregates. The ESEEM spectra show that the multi-histidine coordination for Cu(II) ion partially breaks up and becomes exposed to water or exchangeable protons of the peptide at a higher Cu(II) concentration. Since the continuous-wave electron spin resonance results also suggest two copper-binding sites in Abeta(1-40), the proton ESEEM peak may arise from the second copper-binding site, which may be significantly involved in the formation of granular amorphous aggregates. Thioflavin T fluorescence and circular dichroism experiments also show that Cu(II) inhibits the formation of fibrils and induces a nonfibrillar beta-sheet conformation. Therefore, we propose that Abeta(1-40) has a second copper-binding site in a proton-rich environment and the second binding Cu(II) ion interferes with a conformational transition into amyloid fibrils, inducing the formation of granular amorphous aggregates.

Antiplatelet Activity of Morus alba Leaves Extract, Mediated via Inhibiting Granule Secretion and Blocking the Phosphorylation of Extracellular-Signal-Regulated Kinase and Akt

PubMed Central

Rhee, Man Hee; Sung, Yoon-Young; Yang, Won-Kyung; Kim, Seung Hyung; Kim, Ho-Kyoung

2014-01-01

Ethnopharmacological Relevance. Morus alba L. leaves (MAE) have been used in fork medicine for the treatment of beriberi, edema, diabetes, hypertension, and atherosclerosis. However, underlying mechanism of MAE on cardiovascular protection remains to be elucidated. Therefore, we investigated whether MAE affect platelet aggregation and thrombosis. Materials and Methods. The anti-platelet activity of MAE was studied using rat platelets. The extent of anti-platelet activity of MAE was assayed in collagen-induced platelet aggregation. ATP and serotonin release was carried out. The activation of integrin α IIb β 3 and phosphorylation of signaling molecules, including MAPK and Akt, were investigated with cytofluorometer and immunoblotting, respectively. The thrombus formation in vivo was also evaluated in arteriovenous shunt model of rats. Results. HPLC chromatographic analysis revealed that MAE contained rutin and isoquercetin. MAE dose-dependently inhibited collagen-induced platelet aggregation. MAE also attenuated serotonin secretion and thromboxane A2 formation. In addition, the extract in vivo activity showed that MAE at 100, 200, and 400 mg/kg significantly and dose-dependently attenuated thrombus formation in rat arterio-venous shunt model by 52.3% (P < 0.001), 28.3% (P < 0.01), and 19.1% (P < 0.05), respectively. Conclusions. MAE inhibit platelet activation, TXB2 formation, serotonin secretion, aggregation, and thrombus formation. The plant extract could be considered as a candidate to anti-platelet and antithrombotic agent. PMID:24701244

Insights into Clostridium phytofermentans biofilm formation: aggregation, microcolony development and the role of extracellular DNA.

PubMed

Zuroff, Trevor R; Gu, Weimin; Fore, Rachel L; Leschine, Susan B; Curtis, Wayne R

2014-06-01

Biofilm formation is a critical component to the lifestyle of many naturally occurring cellulose-degrading microbes. In this work, cellular aggregation and biofilm formation of Clostridium phytofermentans, a cellulolytic anaerobic bacterium, was investigated using a combination of microscopy and analytical techniques. Aggregates included thread-like linkages and a DNA/protein-rich extracellular matrix when grown on soluble cellobiose. Similar dense biofilms formed on the surface of the model cellulosic substrate Whatman no. 1 filter paper. Following initially dispersed attachment, microcolonies of ~500 µm diameter formed on the filter paper after 6 days. Enzymic treatment of both the biofilm and cellular aggregates with DNase and proteinase resulted in significant loss of rigidity, pointing to the key role of extracellular DNA and proteins in the biofilm structure. A high-throughput biofilm assay was adapted for studying potential regulators of biofilm formation. Various media manipulations were shown to greatly impact biofilm formation, including repression in the presence of glucose but not the β(1→4)-linked disaccharide cellobiose, implicating a balance of hydrolytic activity and assimilation to maintain biofilm integrity. Using the microtitre plate biofilm assay, DNase and proteinase dispersed ~60 and 30 % of mature biofilms, respectively, whilst RNase had no impact. This work suggests that Clostridium phytofermentans has evolved a DNA/protein-rich biofilm matrix complementing its cellulolytic nature. These insights add to our current understanding of natural ecosystems as well as strategies for efficient bioprocess design. © 2014 The Authors.

Stacking and Branching in Self-Aggregation of Caffeine in Aqueous Solution: From the Supramolecular to Atomic Scale Clustering.

PubMed

Tavagnacco, Letizia; Gerelli, Yuri; Cesàro, Attilio; Brady, John W

2016-09-22

The dynamical and structural properties of caffeine solutions at the solubility limit have been investigated as a function of temperature by means of MD simulations, static and dynamic light scattering, and small angle neutron scattering experiments. A clear picture unambiguously supported by both experiment and simulation emerges: caffeine self-aggregation promotes the formation of two distinct types of clusters: linear aggregates of stacked molecules, formed by 2-14 caffeine molecules depending on the thermodynamic conditions and disordered branched aggregates with a size in the range 1000-3000 Å. While the first type of association is well-known to occur under room temperature conditions for both caffeine and other purine systems, such as nucleotides, the presence of the supramolecular aggregates has not been reported previously. MD simulations indicate that branched structures are formed by caffeine molecules in a T-shaped arrangement. An increase of the solubility limit (higher temperature but also higher concentration) broadens the distribution of cluster sizes, promoting the formation of stacked aggregates composed by a larger number of caffeine molecules. Surprisingly, the effect on the branched aggregates is rather limited. Their internal structure and size do not change considerably in the range of solubility limits investigated.

Assembly of Huntingtin headpiece into α-helical bundles.

PubMed

Ozgur, Beytullah; Sayar, Mehmet

2017-05-24

Protein aggregation is a hallmark of neurodegenerative disorders. In this group of brain-related disorders, a disease-specific "host" protein or fragment misfolds and adopts a metastatic, aggregate-prone conformation. Often, this misfolded conformation is structurally and thermodynamically different from its native state. Intermolecular contacts, which arise in this non-native state, promote aggregation. In this regard, understanding the molecular principles and mechanisms that lead to the formation of such a non-native state and further promote the formation of the critical nucleus for fiber growth is essential. In this study, the authors analyze the aggregation propensity of Huntingtin headpiece (htt NT ), which is known to facilitate the polyQ aggregation, in relation to the helix mediated aggregation mechanism proposed by the Wetzel group. The authors demonstrate that even though htt NT displays a degenerate conformational spectrum on its own, interfaces of macroscopic or molecular origin can promote the α-helix conformation, eliminating all other alternatives in the conformational phase space. Our findings indicate that htt NT molecules do not have a strong orientational preference for parallel or antiparallel orientation of the helices within the aggregate. However, a parallel packed bundle of helices would support the idea of increased polyglutamine concentration, to pave the way for cross-β structures.

Studies of protein aggregation in A53T α-synuclein transgenic, Tg2576 transgenic, and P246L presenilin-1 knock-in cross bred mice.

PubMed

Emmer, Kristel L; Covy, Jason P; Giasson, Benoit I

2012-01-24

Synucleinopathies are a group of neurodegenerative disorders, including Parkinson disease, associated with neuronal amyloid inclusions comprised of the presynaptic protein α-synuclein (α-syn); however the biological events that initiate and lead to the formation of these inclusions are still poorly understood. There is mounting evidence that intracellular α-syn aggregation may proceed via a seeding mechanism and could spread between neurons through a prion-like mechanism that may involve other amyloidogenic proteins. Several lines of evidence suggest that Aβ peptides and/or extracellular Aβ deposits may directly or indirectly promote intracellular α-syn aggregation. To assess the effects of Aβ peptides and extracellular Aβ deposits on α-syn aggregate formation, transgenic mice (line M83) expressing A53T human α-syn that are sensitive to developing α-syn pathological inclusions were cross bred to Tg2576 transgenic mice that generated elevated levels of Aβ peptides and develop abundant Aβ plaques. In addition these mice were bred to mice with the P264L presenilin-1 knock-in mutation that further promotes Aβ plaque formation. These mice demonstrated the expected formation of Aβ plaques; however despite the accumulation of hyperphosphorylated α-syn dystrophic neurites within or surrounding Aβ plaques, no additional α-syn pathologies were observed. These studies show that Aβ amyloid deposits can cause the local aggregation of α-syn, but these did not lead to more extensive α-syn pathology. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Stimulated emission depletion microscopy to study amyloid fibril formation

NASA Astrophysics Data System (ADS)

Mahou, Pierre; Curry, Nathan; Pinotsi, Dorothea; Kaminski Schierle, Gabriele; Kaminski, Clemens

2015-03-01

Aggregation of misfolded proteins is a characteristic hallmark of many neurodegenerative disorders, such as Parkinson's, Alzheimer's and Huntington's diseases. The ability to observe these aggregation processes and the corresponding structures formed in vitro or in situ is therefore a key requirement to understand the molecular mechanisms of these diseases. We report here on the implementation and application of Stimulated Emission Depletion (STED) microscopy to visualize the formation of amyloid fibrils in vitro.

Primary and aggregate color centers in proton irradiated LiF crystals and thin films for luminescent solid state detectors

NASA Astrophysics Data System (ADS)

Piccinini, M.; Ambrosini, F.; Ampollini, A.; Bonfigli, F.; Libera, S.; Picardi, L.; Ronsivalle, C.; Vincenti, M. A.; Montereali, R. M.

2015-04-01

Proton beams of 3 MeV energy, produced by the injector of a linear accelerator for proton therapy, were used to irradiate at room temperature lithium fluoride crystals and polycrystalline thin films grown by thermal evaporation. The irradiation fluence range was 1011-1015 protons/cm2. The proton irradiation induced the stable formation of primary and aggregate color centers. Their formation was investigated by optical absorption and photoluminescence spectroscopy. The F2 and F3+ photoluminescence intensities, carefully measured in LiF crystals and thin films, show linear behaviours up to different maximum values of the irradiation fluence, after which a quenching is observed, depending on the nature of the samples (crystals and films). The Principal Component Analysis, applied to the absorption spectra of colored crystals, allowed to clearly identify the formation of more complex aggregate defects in samples irradiated at highest fluences.

Dynamics of neutrophil aggregation in couette flow revealed by videomicroscopy: effect of shear rate on two-body collision efficiency and doublet lifetime.

PubMed Central

Goldsmith, H L; Quinn, T A; Drury, G; Spanos, C; McIntosh, F A; Simon, S I

2001-01-01

During inflammation, neutrophil capture by vascular endothelial cells is dependent on L-selectin and beta(2)-integrin adhesion receptors. One of us (S.I.S.) previously demonstrated that homotypic neutrophil aggregation is analogous to this process in that it is also mediated by these receptors, thus providing a model for studying the dynamics of neutrophil adhesion. In the present work, we set out to confirm the hypothesis that cell-cell adhesion via selectins serves to increase the lifetimes of neutrophil doublets formed through shear-induced two-body collisions. In turn, this would facilitate the engagement of more stable beta(2)-integrin bonds and thus increase the two-body collision efficiency (fraction of collisions resulting in the formation of nonseparating doublets). To this end, suspensions of unstimulated neutrophils were subjected to a uniform shear field in a transparent counter-rotating cone and plate rheoscope, and the formation of doublets and growth of aggregates recorded using high-speed videomicroscopy. The dependence of neutrophil doublet lifetime and two-body collision-capture efficiency on shear rate, G, from 14 to 220 s(-1) was investigated. Bond formation during a two-body collision was indicated by doublets rotating well past the orientation predicted for break-up of doublets of inert spheres. A striking dependence of doublet lifetime on shear rate was observed. At low shear (G = 14 s(-1)), no collision capture occurred, and doublet lifetimes were no different from those of neutrophils pretreated with a blocking antibody to L-selectin, or in Ca(++)-depleted EDTA buffers. At G > or = 66 s(-1), doublet lifetimes increased, with increasing G reaching values twice those for the L-selectin-blocked controls. This correlated with capture efficiencies in excess of 20%, and, at G > or = 110 s(-1), led to the rapid formation of large aggregates, and this in the absence of exogenous chemotactic stimuli. Moreover, the aggregates almost completely broke up when the shear rate was reduced below 66 s(-1). Partial inhibition of aggregate formation was achieved by blocking beta(2)-integrin receptors with antibody. By direct observation of the shear-induced interactions between neutrophils, these data reveal that steady application of a threshold level of shear rate is sufficient to support homotypic neutrophil aggregation. PMID:11566775

Decreased stability and increased formation of soluble aggregates by immature superoxide dismutase do not account for disease severity in ALS

PubMed Central

Vassall, Kenrick A.; Stubbs, Helen R.; Primmer, Heather A.; Tong, Ming Sze; Sullivan, Sarah M.; Sobering, Ryan; Srinivasan, Saipraveen; Briere, Lee-Ann K.; Dunn, Stanley D.; Colón, Wilfredo; Meiering, Elizabeth M.

2011-01-01

Protein aggregation is a hallmark of many diseases, including amyotrophic lateral sclerosis (ALS), where aggregation of Cu/Zn superoxide dismutase (SOD1) is implicated in causing neurodegeneration. Recent studies have suggested that destabilization and aggregation of the most immature form of SOD1, the disulfide-reduced, unmetallated (apo) protein is particularly important in causing ALS. We report herein in depth analyses of the effects of chemically and structurally diverse ALS-associated mutations on the stability and aggregation of reduced apo SOD1. In contrast with previous studies, we find that various reduced apo SOD1 mutants undergo highly reversible thermal denaturation with little aggregation, enabling quantitative thermodynamic stability analyses. In the absence of ALS-associated mutations, reduced apo SOD1 is marginally stable but predominantly folded. Mutations generally result in slight decreases to substantial increases in the fraction of unfolded protein. Calorimetry, ultracentrifugation, and light scattering show that all mutations enhance aggregation propensity, with the effects varying widely, from subtle increases in most cases, to pronounced formation of 40–100 nm soluble aggregates by A4V, a mutation that is associated with particularly short disease duration. Interestingly, although there is a correlation between observed aggregation and stability, there is minimal to no correlation between observed aggregation, predicted aggregation propensity, and disease characteristics. These findings suggest that reduced apo SOD1 does not play a dominant role in modulating disease. Rather, additional and/or multiple forms of SOD1 and additional biophysical and biological factors are needed to account for the toxicity of mutant SOD1 in ALS. PMID:21257910

Regulation of aggregate size and pattern by adenosine and caffeine in cellular slime molds

PubMed Central

2012-01-01

Background Multicellularity in cellular slime molds is achieved by aggregation of several hundreds to thousands of cells. In the model slime mold Dictyostelium discoideum, adenosine is known to increase the aggregate size and its antagonist caffeine reduces the aggregate size. However, it is not clear if the actions of adenosine and caffeine are evolutionarily conserved among other slime molds known to use structurally unrelated chemoattractants. We have examined how the known factors affecting aggregate size are modulated by adenosine and caffeine. Result Adenosine and caffeine induced the formation of large and small aggregates respectively, in evolutionarily distinct slime molds known to use diverse chemoattractants for their aggregation. Due to its genetic tractability, we chose D. discoideum to further investigate the factors affecting aggregate size. The changes in aggregate size are caused by the effect of the compounds on several parameters such as cell number and size, cell-cell adhesion, cAMP signal relay and cell counting mechanisms. While some of the effects of these two compounds are opposite to each other, interestingly, both compounds increase the intracellular glucose level and strengthen cell-cell adhesion. These compounds also inhibit the synthesis of cAMP phosphodiesterase (PdsA), weakening the relay of extracellular cAMP signal. Adenosine as well as caffeine rescue mutants impaired in stream formation (pde4- and pdiA-) and colony size (smlA- and ctnA-) and restore their parental aggregate size. Conclusion Adenosine increased the cell division timings thereby making large number of cells available for aggregation and also it marginally increased the cell size contributing to large aggregate size. Reduced cell division rates and decreased cell size in the presence of caffeine makes the aggregates smaller than controls. Both the compounds altered the speed of the chemotactic amoebae causing a variation in aggregate size. Our data strongly suggests that cytosolic glucose and extracellular cAMP levels are the other major determinants regulating aggregate size and pattern. Importantly, the aggregation process is conserved among different lineages of cellular slime molds despite using unrelated signalling molecules for aggregation. PMID:22269093

Regulation of aggregate size and pattern by adenosine and caffeine in cellular slime molds.

PubMed

Jaiswal, Pundrik; Soldati, Thierry; Thewes, Sascha; Baskar, Ramamurthy

2012-01-23

Multicellularity in cellular slime molds is achieved by aggregation of several hundreds to thousands of cells. In the model slime mold Dictyostelium discoideum, adenosine is known to increase the aggregate size and its antagonist caffeine reduces the aggregate size. However, it is not clear if the actions of adenosine and caffeine are evolutionarily conserved among other slime molds known to use structurally unrelated chemoattractants. We have examined how the known factors affecting aggregate size are modulated by adenosine and caffeine. Adenosine and caffeine induced the formation of large and small aggregates respectively, in evolutionarily distinct slime molds known to use diverse chemoattractants for their aggregation. Due to its genetic tractability, we chose D. discoideum to further investigate the factors affecting aggregate size. The changes in aggregate size are caused by the effect of the compounds on several parameters such as cell number and size, cell-cell adhesion, cAMP signal relay and cell counting mechanisms. While some of the effects of these two compounds are opposite to each other, interestingly, both compounds increase the intracellular glucose level and strengthen cell-cell adhesion. These compounds also inhibit the synthesis of cAMP phosphodiesterase (PdsA), weakening the relay of extracellular cAMP signal. Adenosine as well as caffeine rescue mutants impaired in stream formation (pde4- and pdiA-) and colony size (smlA- and ctnA-) and restore their parental aggregate size. Adenosine increased the cell division timings thereby making large number of cells available for aggregation and also it marginally increased the cell size contributing to large aggregate size. Reduced cell division rates and decreased cell size in the presence of caffeine makes the aggregates smaller than controls. Both the compounds altered the speed of the chemotactic amoebae causing a variation in aggregate size. Our data strongly suggests that cytosolic glucose and extracellular cAMP levels are the other major determinants regulating aggregate size and pattern. Importantly, the aggregation process is conserved among different lineages of cellular slime molds despite using unrelated signalling molecules for aggregation.

Kinetic model for astaxanthin aggregation in water-methanol mixtures

NASA Astrophysics Data System (ADS)

Giovannetti, Rita; Alibabaei, Leila; Pucciarelli, Filippo

2009-07-01

The aggregation of astaxanthin in hydrated methanol was kinetically studied in the temperature range from 10 °C to 50 °C, at different astaxanthin concentrations and solvent composition. A kinetic model for the formation and transformation of astaxanthin aggregated has been proposed. Spectrophotometric studies showed that monomeric astaxanthin decayed to H-aggregates that after-wards formed J-aggregates when water content was 50% and the temperature lower than 20 °C; at higher temperatures, very stable J-aggregates were formed directly. Monomer formed very stable H-aggregates when the water content was greater than 60%; in these conditions H-aggregates decayed into J-aggregates only when the temperature was at least 50 °C. Through these findings it was possible to establish that the aggregation reactions took place through a two steps consecutive reaction with first order kinetic constants and that the values of these depended on the solvent composition and temperature.

Monosized aggregates -- A new model

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

Gopal, M.

1997-08-01

For applications requiring colloidal particles, it is desirable that they be monosized to better control the structure and the properties. In a number of systems, the monosized particles come together to form aggregates that are also monosized. A model is presented here to explain the formation of these monosized aggregates. This is of particular importance in the fields of ceramics, catalysis, pigments, pharmacy, photographic emulsions, etc.

From The Cover: Genome-wide RNA interference screen identifies previously undescribed regulators of polyglutamine aggregation

NASA Astrophysics Data System (ADS)

Nollen, Ellen A. A.; Garcia, Susana M.; van Haaften, Gijs; Kim, Soojin; Chavez, Alejandro; Morimoto, Richard I.; Plasterk, Ronald H. A.

2004-04-01

Protein misfolding and the formation of aggregates are increasingly recognized components of the pathology of human genetic disease and hallmarks of many neurodegenerative disorders. As exemplified by polyglutamine diseases, the propensity for protein misfolding is associated with the length of polyglutamine expansions and age-dependent changes in protein-folding homeostasis, suggesting a critical role for a protein homeostatic buffer. To identify the complement of protein factors that protects cells against the formation of protein aggregates, we tested transgenic Caenorhabditis elegans strains expressing polyglutamine expansion yellow fluorescent protein fusion proteins at the threshold length associated with the age-dependent appearance of protein aggregation. We used genome-wide RNA interference to identify genes that, when suppressed, resulted in the premature appearance of protein aggregates. Our screen identified 186 genes corresponding to five principal classes of polyglutamine regulators: genes involved in RNA metabolism, protein synthesis, protein folding, and protein degradation; and those involved in protein trafficking. We propose that each of these classes represents a molecular machine collectively comprising the protein homeostatic buffer that responds to the expression of damaged proteins to prevent their misfolding and aggregation. protein misfolding | neurodegenerative diseases

Aggregate formation and suspension culture of human pluripotent stem cells and differentiated progeny.

PubMed

Hookway, Tracy A; Butts, Jessica C; Lee, Emily; Tang, Hengli; McDevitt, Todd C

2016-05-15

Culture of human pluripotent stem cells (hPSC) as in vitro multicellular aggregates has been increasingly used as a method to model early embryonic development. Three-dimensional assemblies of hPSCs facilitate interactions between cells and their microenvironment to promote morphogenesis, analogous to the multicellular organization that accompanies embryogenesis. In this paper, we describe a method for reproducibly generating and maintaining populations of homogeneous three-dimensional hPSC aggregates using forced aggregation and rotary orbital suspension culture. We propose solutions to several challenges associated with the consistent formation and extended culture of cell spheroids generated from hPSCs and their differentiated progeny. Further, we provide examples to demonstrate how aggregation can be used as a tool to select specific subpopulations of cells to create homotypic spheroids, or as a means to introduce multiple cell types to create heterotypic tissue constructs. Finally, we demonstrate that the aggregation and rotary suspension method can be used to support culture and maintenance of hPSC-derived cell populations representing each of the three germ layers, underscoring the utility of this platform for culturing many different cell types. Copyright © 2015 Elsevier Inc. All rights reserved.

Early-Stage Aggregation of Human Islet Amyloid Polypeptide

NASA Astrophysics Data System (ADS)

Guo, Ashley; de Pablo, Juan

Human islet amyloid polypeptide (hIAPP, or human amylin) is implicated in the development of type II diabetes. hIAPP is known to aggregate into amyloid fibrils; however, it is prefibrillar oligomeric species, rather than mature fibrils, that are proposed to be cytotoxic. In order to better understand the role of hIAPP aggregation in the onset of disease, as well as to design effective diagnostics and therapeutics, it is crucial to understand the mechanism of early-stage hIAPP aggregation. In this work, we use atomistic molecular dynamics simulations combined with multiple advanced sampling techniques to examine the formation of the hIAPP dimer and trimer. Metadynamics calculations reveal a free energy landscape for the hIAPP dimer, which suggest multiple possible transition pathways. We employ finite temperature string method calculations to identify favorable pathways for dimer and trimer formation, along with relevant free energy barriers and intermediate structures. Results provide valuable insights into the mechanisms and energetics of hIAPP aggregation. In addition, this work demonstrates that the finite temperature string method is an effective tool in the study of protein aggregation. Funded by National Institute of Standards and Technology.

Phenylpropanoid profiling reveals a class of hydroxycinnamoyl glucaric acid conjugates in Isatis tinctoria leaves.

PubMed

Nguyen, Thi-Kieu-Oanh; Jamali, Arash; Grand, Eric; Morreel, Kris; Marcelo, Paulo; Gontier, Eric; Dauwe, Rebecca

2017-12-01

The brassicaceous herb, Isatis tinctoria, is an ancient medicinal plant whose rosette leaf extracts have anti-inflammatory and anti-allergic activity. Brassicaceae are known to accumulate a variety of phenylpropanoids in their rosette leaves acting as antioxidants and a UV-B shield, and these compounds often have pharmacological potential. Nevertheless, knowledge about the phenylpropanoid content of I. tinctoria leaves remains limited to the characterization of a number of flavonoids. In this research, we profiled the methanol extracts of I. tinctoria fresh leaf extracts by liquid chromatography - mass spectrometry (LC-MS) and focused on the phenylpropanoid derivatives. We report the structural characterization of 99 compounds including 18 flavonoids, 21 mono- or oligolignols, 2 benzenoids, and a wide spectrum of 58 hydroxycinnamic acid esters. Besides the sinapate esters of malate, glucose and gentiobiose, which are typical of brassicaceous plants, these conjugates comprised a large variety of glucaric acid esters that have not previously been reported in plants. Feeding with 13 C 6 -glucaric acid showed that glucaric acid is an acyl acceptor of an as yet unknown acyltransferase activity in I. tinctoria rosette leaves. The large amount of hydroxycinnamic acid derivatives changes radically our view of the woad metabolite profile and potentially contributes to the pharmacological activity of I. tinctoria leaf extracts. Copyright © 2017 Elsevier Ltd. All rights reserved.

Direct impact of the sustained decline in the photosystem II efficiency upon plant productivity at different developmental stages.

PubMed

Tian, Yonglan; Ungerer, Petra; Zhang, Huayong; Ruban, Alexander V

2017-05-01

The impact of chronic photoinhibition of photosystem II (PSII) on the productivity of plants remains unknown. The present study investigated the influences of persistent decline in the PSII yield on morphology and productivity of Arabidopsis plants that were exposed to lincomycin at two different developmental stages (seedling and rosette stage). The results indicated that, although retarded, the lincomycin treated plants were able to accomplish the entire growth period with only 50% of the maximum quantum yield of primary photochemistry (Fv/Fm) of the control plants. The decline in quantum yield limited the electron transport rate (ETR). The impact of lincomycin on NPQ was not significant in seedlings, but was pronounced in mature plants. The treated plants produced an above ground biomass of 50% compared to control plants. Moreover, a linear relationship was found between the above ground biomass and total rosette leaf area, and the slope was decreased due to photoinhibition. The starch accumulation was highly inhibited by lincomycin treatment. Lincomycin induced a significant decrease in seed yield with plants treated from the rosette state showing higher yield than those treated from the seedling stage. Our data suggest that the sustained decline of PSII efficiency decreases plant productivity by constraining the ETR, leaf development and starch production. Copyright © 2017 Elsevier GmbH. All rights reserved.

Objective definition of rosette shape variation using a combined computer vision and data mining approach.

PubMed

Camargo, Anyela; Papadopoulou, Dimitra; Spyropoulou, Zoi; Vlachonasios, Konstantinos; Doonan, John H; Gay, Alan P

2014-01-01

Computer-vision based measurements of phenotypic variation have implications for crop improvement and food security because they are intrinsically objective. It should be possible therefore to use such approaches to select robust genotypes. However, plants are morphologically complex and identification of meaningful traits from automatically acquired image data is not straightforward. Bespoke algorithms can be designed to capture and/or quantitate specific features but this approach is inflexible and is not generally applicable to a wide range of traits. In this paper, we have used industry-standard computer vision techniques to extract a wide range of features from images of genetically diverse Arabidopsis rosettes growing under non-stimulated conditions, and then used statistical analysis to identify those features that provide good discrimination between ecotypes. This analysis indicates that almost all the observed shape variation can be described by 5 principal components. We describe an easily implemented pipeline including image segmentation, feature extraction and statistical analysis. This pipeline provides a cost-effective and inherently scalable method to parameterise and analyse variation in rosette shape. The acquisition of images does not require any specialised equipment and the computer routines for image processing and data analysis have been implemented using open source software. Source code for data analysis is written using the R package. The equations to calculate image descriptors have been also provided.

A simplified strategy for sensitive detection of Rose rosette virus compatible with three RT-PCR chemistries.

PubMed

Dobhal, Shefali; Olson, Jennifer D; Arif, Mohammad; Garcia Suarez, Johnny A; Ochoa-Corona, Francisco M

2016-06-01

Rose rosette disease is a disorder associated with infection by Rose rosette virus (RRV), a pathogen of roses that causes devastating effects on most garden cultivated varieties, and the wild invasive rose especially Rosa multiflora. Reliable and sensitive detection of this disease in early phases is needed to implement proper control measures. This study assesses a single primer-set based detection method for RRV and demonstrates its application in three different chemistries: Endpoint RT-PCR, TaqMan-quantitative RT-PCR (RT-qPCR) and SYBR Green RT-qPCR with High Resolution Melting analyses. A primer set (RRV2F/2R) was designed from consensus sequences of the nucleocapsid protein gene p3 located in the RNA 3 region of RRV. The specificity of primer set RRV2F/2R was validated in silico against published GenBank sequences and in-vitro against infected plant samples and an exclusivity panel of near-neighbor and other viruses that commonly infect Rosa spp. The developed assay is sensitive with a detection limit of 1fg from infected plant tissue. Thirty rose samples from 8 different states of the United States were tested using the developed methods. The developed methods are sensitive and reliable, and can be used by diagnostic laboratories for routine testing and disease management decisions. Copyright © 2016 Elsevier B.V. All rights reserved.

Influence of polysaccharides on wine protein aggregation.

PubMed

Jaeckels, Nadine; Meier, Miriam; Dietrich, Helmut; Will, Frank; Decker, Heinz; Fronk, Petra

2016-06-01

Polysaccharides are the major high-molecular weight components of wines. In contrast, proteins occur only in small amounts in wine, but contribute to haze formation. The detailed mechanism of aggregation of these proteins, especially in combination with other wine components, remains unclear. This study demonstrates the different aggregation behavior between a buffer and a model wine system by dynamic light scattering. Arabinogalactan-protein, for example, shows an increased aggregation in the model wine system, while in the buffer system a reducing effect is observed. Thus, we could show the importance to examine the behavior of wine additives under conditions close to reality, instead of simpler buffer systems. Additional experiments on melting points of wine proteins reveal that only some isoforms of thaumatin-like proteins and chitinases are involved in haze formation. We can confirm interactions between polysaccharides and proteins, but none of these polysaccharides is able to prevent haze in wine. Copyright © 2016. Published by Elsevier Ltd.

2',5'-Dihydroxychalcone as a potent chemical mediator and cyclooxygenase inhibitor.

PubMed

Lin, C N; Lee, T H; Hsu, M F; Wang, J P; Ko, F N; Teng, C M

1997-05-01

Eleven chalcone derivatives have been tested for their inhibitory effects on platelet aggregation in rabbit platelet suspension and the activation of mast cells and neutrophils. Arachidonic acid-induced platelet aggregation was potently inhibited by almost all the compounds and some also had a potent inhibitory effect on collagen-induced platelet aggregation and cyclooxygenase. Some hydroxychalcone derivatives showed strong inhibitory effects on the release of beta-glucuronidase and lysozyme, and on superoxide formation by rat neutrophils stimulated with the peptide fMet-Leu-Phe (fMLP). We found that the anti-inflammatory effect of 2',5'-dihydroxychalcone was greater than that of trifluoperazine. 2'5'-Dihydroxy and 2',3,4,5'-tetrahydroxyl chalcones, even at low concentration (50 microM), tested in platelet-rich plasma from man almost completely inhibited secondary aggregation induced by adrenaline. These results suggest that the anti-platelet effects of the chalcones are mainly a result of inhibition of thromboxane formation.

Intermolecular interactions and aggregation of fac-tris(2-phenylpyridinato-C2,N)iridium(III) in nonpolar solvents.

PubMed

Takayasu, Satoshi; Suzuki, Takayoshi; Shinozaki, Kazuteru

2013-08-15

The intermolecular interaction and aggregation of the neutral complex fac-tris(2-phenylpyridinato-C(2),N)iridium(III) (fac-Ir(ppy)3) in solution was investigated. Intermolecular interactions were found to effectively decrease the luminescence lifetime via self-quenching with increasing fac-Ir(ppy)3 concentrations. A Stern-Volmer plot for quenching in acetonitrile was linear, due to bimolecular self-quenching, but curved in toluene as the result of excimer formation. (1)H NMR spectra demonstrated a monomer-aggregate equilibrium which resulted in spectral shifts depending on solvent polarity. X-ray crystallography provided structural information concerning the aggregate, which is based on a tetramer consisting of two Δ-fac-Ir(ppy)3-Λ-fac-Ir(ppy)3 pairs. Offset π-π stacking of ppy ligands and electrostatic dipole-dipole interactions between complex molecules play an important role in the formation of these molecular pairs.

Correlation of the protein structure and gelling properties in dried egg white products.

PubMed

Handa, A; Hayashi, K; Shidara, H; Kuroda, N

2001-08-01

The relationship between protein structure and aggregation, as well as heat-induced gelling properties, of seven dried egg white (DEW) products was investigated. Strong correlations were found between average molecular weight and hydrophobicity plus surface SH groups of DEW-soluble protein aggregate (SPA). This suggests that hydrophobic interactions and disulfide bond formation between protein molecules were involved in the aggregation. The average molecular weight of DEW products with alkaline pHs was relatively higher than those with neutral pHs and the same degree of protein unfolding, probably because of more disulfide bond formation between protein molecules. In addition, strong correlations were found between hydrophobicity, surface SH groups plus average molecular weight of DEW-SPA, and physical properties of the gels from DEW products. These data indicated that controlling the aggregation of DEW proteins in the dry state is crucial to controlling the gelling properties of DEW.

Can hydro-economic river basin models simulate water shadow prices under asymmetric access?

PubMed

Kuhn, A; Britz, W

2012-01-01

Hydro-economic river basin models (HERBM) based on mathematical programming are conventionally formulated as explicit 'aggregate optimization' problems with a single, aggregate objective function. Often unintended, this format implicitly assumes that decisions on water allocation are made via central planning or functioning markets such as to maximize social welfare. In the absence of perfect water markets, however, individually optimal decisions by water users will differ from the social optimum. Classical aggregate HERBMs cannot simulate that situation and thus might be unable to describe existing institutions governing access to water and might produce biased results for alternative ones. We propose a new solution format for HERBMs, based on the format of the mixed complementarity problem (MCP), where modified shadow price relations express spatial externalities resulting from asymmetric access to water use. This new problem format, as opposed to commonly used linear (LP) or non-linear programming (NLP) approaches, enables the simultaneous simulation of numerous 'independent optimization' decisions by multiple water users while maintaining physical interdependences based on water use and flow in the river basin. We show that the alternative problem format allows the formulation HERBMs that yield more realistic results when comparing different water management institutions.

Role of pyridoxamine in the formation of the Amadori/Heyns compounds and aggregates during the glycation of beta-lactoglobulin with galactose and tagatose.

PubMed

Corzo-Martínez, Marta; Moreno, F Javier; Olano, Agustín; Villamiel, Mar

2010-01-13

The effect of pyridoxamine on the Maillard reaction during the formation of conjugates of beta-lactoglobulin with galactose and tagatose under controlled conditions (pH 7, 0.44 aw, 40 and 50 degrees C, for 6 days) has been studied, for the first time, by means of the changes in reducing carbohydrates, formation of Amadori or Heyns compounds, and aggregates and browning development. The results showed the formation of interaction products between pyridoxamine and galactose or tagatose either in the presence or in the absence of beta-lactoglobulin, indicating that pyridoxamine competes with the free amino groups of beta-lactoglobulin for the carbonyl group of both carbohydrates. Thus, a small inhibitory effect of pyridoxamine on the initial stages of the Maillard reaction was pointed out. Furthermore, much lower aggregation and color formation rates were observed in the conjugates of beta-lactoglobulin galactose/tagatose with pyridoxamine than without this compound, supporting its potent inhibitory effect on the advanced and final stages of the Maillard reaction. These findings reveal the usefulness of food-grade inhibitors of the advanced stages of the Maillard reaction, such as pyridoxamine, that, in combination with mild storage conditions, could lead to the formation of safer neoglycoconjugates without impairing their nutritional quality.

Formation of the nitrogen aggregates in annealed diamond by neutron irradiation

NASA Astrophysics Data System (ADS)

Mita, Y.; Nisida, Y.; Okada, M.

2018-02-01

Neutron heavy irradiation was performed on synthetic diamonds contain nitrogen atoms in isolated substitutional form (called "type Ib diamond") and they were annealed under a pressure of 6 GPa. A large number of nitrogen B-aggregate which consists of four substitutional nitrogen atoms symmetrically surrounding a vacancy was formed within 30 m from single nitrogen atoms. Furthermore it is observed that, in these diamonds, single nitrogen atoms coexist with the B-aggregates, which is unexplainable by the simple nitrogen aggregation model.

Solvent tuning configurational conversion of lycopene aggregates in organic-aqueous mixing solvent

NASA Astrophysics Data System (ADS)

Dong, Jia; Zhang, Di; Wang, Xin-Yue; Wang, Peng

2018-06-01

In general cases, carotenoid aggregates are prepared in organic-water mixing solvent depending on its hydrophobic character. It is well-known that one of carotenoids, lycopene, is more likely to form typical H-aggregates. In this study, new type lycopene J-aggregates were prepared in DMSO-water mixing solvent with small amount of toluene, which was observed for the first time. We proposed a potential structure model combining with exciton model to interpret the mechanism of spectra changes. Our finding has provided new methods and novel ideas for controlling carotenoid aggregates formation.

Changes in soil aggregate dynamics following 18 years of experimentally increased precipitation in a cold desert ecosystem

NASA Astrophysics Data System (ADS)

De Graaff, M.; vanderVeen, J.; Germino, M. J.

2011-12-01

Climate change is expected to alter the amount and timing of precipitation in semiarid ecosystems of the intermountain west, which can alter soil carbon dynamics. Specifically, an increase in precipitation in arid ecosystems promotes microbial activity, which can increase soil aggregate formation and enhance sequestration of soil organic carbon within stable aggregates. This study was conducted to assess: (1) how precipitation shifts affect soil aggregate formation and associated soil organic carbon contents in semi arid ecosystems, and (2) how plants mediate precipitation impacts on soil aggregate dynamics. Soil samples were collected from a long-term ecohydrology study located in the cold desert of the Idaho National Lab, USA. Precipitation treatments delivered during the previous 18 years consist of three regimes: (1) a control (ambient precipitation), (2) 200 mm irrigation added during the growing season, and (3) 200 mm irrigation added during the cold dormant season. Experimental plots were planted with a diverse native mix of big sagebrush (Artemisia tridentate) and associated shrubs, grasses, and forbs, but had also become invaded by crested wheatgrass (Agropyron cristatum). Soils were collected in February (2011) with a 4.8 cm diameter soil corer to a depth of 15 cm. Across all precipitation treatments we sampled both directly beneath sagebrush and crested wheatgrass and from relatively bare plant-interspaces. Subsamples (100 g) were sieved (4.75 mm) and air dried. Then, the soils were fractionated into (1) macro aggregates (> 250 μm), (2) free micro aggregates (53-250 μm) and (3) free silt and clay fractions (<53 μm), using a wet sieving protocol. Further, macro aggregates were separated into particulate organic matter (POM), micro aggregates and silt and clay fractions using a micro aggregate isolator. Soil fractions were analyzed for soil organic carbon contents after removal of soil carbonates using sulfurous acid. Our preliminary results indicate that supplemental precipitation enhanced macro aggregate formation by 20% under plants and by 70% in plant interspaces. In contrast, free silt and clay fractions decreased in response to supplemental precipitation. These preliminary findings suggest that increased precipitation in a cold desert ecosystem may significantly enhance soil structure, particularly in the interspaces separating plants where surface crusting, poor infiltration and reduced fertility otherwise prevail.

Influence of l-amino acids on aggregation and biofilm formation in Azotobacter chroococcum and Trichoderma viride.

PubMed

Velmourougane, K; Prasanna, R

2017-10-01

The effects of l-amino acids on growth and biofilm formation in Azotobacter chroococcum (Az) and Trichoderma viride (Tv) as single (Az, Tv) and staggered inoculated cultures (Az-Tv, Tv-Az) were investigated. A preliminary study using a set of 20 l-amino acids, identified 6 amino acids (l-Glu, l-Gln, l-His, l-Ser, l-Thr and l-Trp) which significantly enhanced growth and biofilm formation. Supplementation of these amino acids at different concentrations revealed that 40 mmol l -1 was most effective. l-Glu and l-Gln favoured planktonic growth in both single and in staggered inoculated cultures, while l-Trp and l-Thr, enhanced aggregation and biofilm formation. Addition of l-Glu or l-Gln increased carbohydrate content and planktonic population. Principal component analysis revealed the significant role of proteins in growth and biofilm formation, particularly with supplementation of l-Trp, l-Thr and l-Ser. Azotobacter was found to function better as biofilm under staggered inoculated culture with Trichoderma. The results illustrate that amino acids play crucial roles in microbial biofilm formation, by influencing growth, aggregation and carbohydrates synthesized. The differential and specific roles of amino acids on biofilm formation are of significance for agriculturally important micro-organisms that grow as biofilms, colonize and benefit the plants more effectively. © 2017 The Society for Applied Microbiology.

Kinetics of Inclusion Body Formation and Its Correlation with the Characteristics of Protein Aggregates in Escherichia coli

PubMed Central

Upadhyay, Arun K.; Murmu, Aruna; Singh, Anupam; Panda, Amulya K.

2012-01-01

The objective of the research was to understand the structural determinants governing protein aggregation into inclusion bodies during expression of recombinant proteins in Escherichia coli. Recombinant human growth hormone (hGH) and asparaginase were expressed as inclusion bodies in E.coli and the kinetics of aggregate formation was analyzed in details. Asparaginase inclusion bodies were of smaller size (200 nm) and the size of the aggregates did not increase with induction time. In contrast, the seeding and growth behavior of hGH inclusion bodies were found to be sequential, kinetically stable and the aggregate size increased from 200 to 800 nm with induction time. Human growth hormone inclusion bodies showed higher resistance to denaturants and proteinase K degradation in comparison to those of asparaginase inclusion bodies. Asparaginase inclusion bodies were completely solubilized at 2–3 M urea concentration and could be refolded into active protein, whereas 7 M urea was required for complete solubilization of hGH inclusion bodies. Both hGH and asparaginase inclusion bodies showed binding with amyloid specific dyes. In spite of its low β-sheet content, binding with dyes was more prominent in case of hGH inclusion bodies than that of asparaginase. Arrangements of protein molecules present in the surface as well as in the core of inclusion bodies were similar. Hydrophobic interactions between partially folded amphiphillic and hydrophobic alpha-helices were found to be one of the main determinants of hGH inclusion body formation. Aggregation behavior of the protein molecules decides the nature and properties of inclusion bodies. PMID:22479486

Scaling behavior of GaAs and GaMnAs quantum rings grown by droplet epitaxy

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

Placidi, E.; Dipartimento di Fisica, Universita di Roma 'Tor Vergata,' via della Ricerca Scientifica 1, 00133 Roma Italy; Arciprete, F.

2012-10-01

The transition from the liquid phase of Ga droplets to the formation of GaAs and GaMnAs quantum rings has been studied as a function of temperature. We show that different aggregation processes involve the GaAs (GaMnAs) island and the droplet formation. Furthermore, the aspect ratio of the islands exhibits an anomalous scaling law related to a tendency to aggregate in the vertical direction.

Photosynthetic pathway types of evergreen rosette plants (Liliaceae) of the Chihuahuan desert.

PubMed

Kemp, Paul R; Gardetto, Pietra E

1982-11-01

Diurnal patterns of CO 2 exchange and titratable acidity were monitored in six species of evergreen rosette plants growing in controlled environment chambers and under outdoor environmental conditions. These patterns indicated that two of the species, Yucca baccata and Y. torreyi, were constituitive CAM plants while the other species, Y. elata, Y. campestris, Nolina microcarpa and Dasylirion wheeleri, were C 3 plants. The C 3 species did not exhibit CAM when grown in any of several different temperature, photoperiod, and moisture regimes. Both photosynthetic pathway types appear adapted to desert environments and all species show environmentally induced changes in their photosynthetic responses consistent with desert adaptation. The results of this study do not indicate that changes in the photosynthetic pathway type are an adaptation in any of these species.

Thermodynamics of aggregate formation between a non-ionic polymer and ionic surfactants: An isothermal titration calorimetric study.

PubMed

Patel, Salin Gupta; Bummer, Paul M

2017-01-10

This report examines the energetics of aggregate formation between hydroxypropyl methylcellulose (HPMC) and model ionic surfactants including sodium dodecyl sulfate (SDS) at pharmaceutically relevant concentrations using the isothermal titration calorimetry (ITC) technique and a novel treatment of calorimetric data that accounts for the various species formed. The influence of molecular weight of HPMC, temperature and ionic strength of solution on the aggregate formation process was explored. The interaction between SDS and HPMC was determined to be an endothermic process and initiated at a critical aggregation concentration (CAC). The SDS-HPMC interactions were observed to be cooperative in nature and dependent on temperature and ionic strength of the solution. Molecular weight of HPMC significantly shifted the interaction parameters between HPMC and SDS such that at the highest molecular weight (HPMC K-100M;>240kDa), although the general shape of the titration curve (enthalpogram) was observed to remain similar, the critical concentration parameters (CAC, polymer saturation concentration (C sat ) and critical micelle concentration (CMC)) were significantly altered and shifted to lower concentrations of SDS. Ionic strength was also observed to influence the critical concentration parameters for the SDS-HPMC aggregation and decreased to lower SDS concentrations with increasing ionic strength for both anionic and cationic surfactant-HPMC systems. From these data, other thermodynamic parameters of aggregation such as ΔH agg ° , ΔG agg ° , H agg ° , ΔS agg ° , and ΔC p were calculated and utilized to postulate the hydrophobic nature of SDS-HPMC aggregate formation. The type of ionic surfactant head group (anionic vs. cationic i.e., dodecyltrimethylammonium bromide (DTAB)) was found to influence the strength of HPMC-surfactant interactions wherein a distinct CAC signifying the strength of HPMC-DTAB interactions was not observed. The interpretation of the microcalorimetric data at different temperatures and ionic strengths while varying properties of polymer and surfactant was a very effective tool in investigating the nature and energetics of HPMC and ionic surfactant interactions. Copyright © 2016 Elsevier B.V. All rights reserved.

Optical Fiber Infrasound Sensor Arrays: An Improved Alternative to Arrays of Rosette Wind Filters

NASA Astrophysics Data System (ADS)

Walker, Kristoffer; Zumberge, Mark; Dewolf, Scott; Berger, Jon; Hedlin, Michael

2010-05-01

A key difficulty in infrasound signal detection is the noise created by spatially incoherent turbulence that is usually present in wind. Increasing wind speeds correlate with increasing noise levels across the entire infrasound band. Optical fiber infrasound sensors (OFIS) are line microphones that instantaneously integrate pressure along their lengths with laser interferometry. Although the sensor has a very low noise floor, the promise of the sensor is in its effectiveness at reducing wind noise without the need for a network of interconnected pipes. We have previously shown that a single 90 m OFIS (spanning a line) is just as effective at reducing wind noise as a 70 m diameter rosette (covering a circular area). We have also empirically measured the infrasound response of the OFIS as a function of back azimuth, showing that it is well predicted by an analytical solution; the response is flat for broadside signals and similar to the rosette response for endfire signals. Using that analytical solution, we have developed beamforming techniques that permit the estimation of back azimuth using an array of OFIS arms as well as an array deconvolution technique that accurately stacks weighted versions of the recordings to obtain the original infrasound signal. We show how a slight modification to traditional array processing techniques can also be used with OFIS arrays to determine back azimuth, even for signal-to-noise ratios much less than 1. Recently several improvements to the OFIS instrumentation have been achieved. We have made an important modification to our interferometric technique that makes the interferometer insensitive to ambient temperature fluctuation. We are also developing a continuous real-time calibration system, which may eliminate the need for periodic array calibration efforts. We also report progress in comparing a newly installed 270 m long OFIS at Piñon Flat Observatory (PFO) to a collocated 70 m rosette of the I57US array. Specifically, we compare hundreds of wind noise spectra and two Vandenberg rocket launch infrasound signals that were recorded by both systems. The 70-m diameter rosette (L2) was connected to a Chaparral Physics Model 50 microphone, which is usually more sensitive than the MB2000 microbarometer in the 1-10 Hz band. The data show that in low wind, the noise floor of the OFIS is the same as the Chaparral. However, in moderate wind (5 m/s) the OFIS attenuates wind noise at 1 Hz by 10 dB better than L2. Similarly, the two rocket launch signals that were recorded in the presence of 3-4 m/s wind confirm that the signal-to-noise ratio improvement is 10 dB at 1 Hz. This confirms that at each signal frequency and direction, there exists an OFIS length threshold above which an OFIS wind filter will always outperform a rosette in terms recorded signal-to-noise ratio. The OFIS technology is proven and mature for observatory installations. Work is underway to make the technology more portable for remote, DC-powered deployments. A DC-powered, ruggedized OFIS array will be installed for microbarom research in Northern California during the spring of 2010. We seek collaborations with other researchers that are interested in evaluating or assisting in the further development of the OFIS technology.

HSF1 stress response pathway regulates autophagy receptor SQSTM1/p62-associated proteostasis.

PubMed

Watanabe, Yoshihisa; Tsujimura, Atsushi; Taguchi, Katsutoshi; Tanaka, Masaki

2017-01-02

Proteostasis is important for protecting cells from harmful proteins and is mainly controlled by the HSF1 (heat shock transcription factor 1) stress response pathway. This pathway facilitates protein refolding by molecular chaperones; however, it is unclear whether it functions in autophagy or inclusion formation. The autophagy receptor SQSTM1/p62 is involved in selective autophagic clearance and inclusion formation by harmful proteins, and its phosphorylation at S349, S403, and S407 is required for binding to substrates. Here, we demonstrate that casein kinase 1 phosphorylates the SQSTM1 S349 residue when harmful proteins accumulate. Investigation of upstream factors showed that both SQSTM1 S349 and SQSTM1 S403 residues were phosphorylated in an HSF1 dependent manner. Inhibition of SQSTM1 phosphorylation suppressed inclusion formation by ubiquitinated proteins and prevented colocalization of SQSTM1 with aggregation-prone proteins. Moreover, HSF1 inhibition impaired aggregate-induced autophagosome formation and elimination of protein aggregates. Our findings indicate that HSF1 triggers SQSTM1-mediated proteostasis.

Low numeracy predicts reduced accuracy of retrospective reports of frequency of sexual behavior.

PubMed

McAuliffe, Timothy L; DiFranceisco, Wayne; Reed, Barbara R

2010-12-01

Assessment of the frequency of sexual behavior relies on participants' ability to arithmetically aggregate information over time and across partners. This study examines the effect of numeracy (arithmetic skills) on the accuracy of retrospective reports of sexual behavior. For 91 days, the participants completed daily reports about their sexual activity. Participants then completed a survey on sexual behavior over the same period. The discrepancies between the survey-based and the diary-based measures of frequency of vaginal and anal intercourse were evaluated. Multiple regression analysis showed that the discrepancy between retrospective and diary measurements of sexual intercourse increased with lower numeracy (P = 0.026), lower education (P = 0.001), aggregate question format compared to partner-by-partner format (P = 0.031) and higher frequency of intercourse occasions (P < 0.001). Lower numeracy led to a 1.5-fold increase (adjusted mean = 14.1-20.9) in the discrepancy for those using the aggregate question format and a 2.0-fold increase (adjusted mean = 3.7-7.6) for those using the partner-by-partner format.

HSF1 stress response pathway regulates autophagy receptor SQSTM1/p62-associated proteostasis

PubMed Central

Watanabe, Yoshihisa; Tsujimura, Atsushi; Taguchi, Katsutoshi; Tanaka, Masaki

2017-01-01

ABSTRACT Proteostasis is important for protecting cells from harmful proteins and is mainly controlled by the HSF1 (heat shock transcription factor 1) stress response pathway. This pathway facilitates protein refolding by molecular chaperones; however, it is unclear whether it functions in autophagy or inclusion formation. The autophagy receptor SQSTM1/p62 is involved in selective autophagic clearance and inclusion formation by harmful proteins, and its phosphorylation at S349, S403, and S407 is required for binding to substrates. Here, we demonstrate that casein kinase 1 phosphorylates the SQSTM1 S349 residue when harmful proteins accumulate. Investigation of upstream factors showed that both SQSTM1 S349 and SQSTM1 S403 residues were phosphorylated in an HSF1 dependent manner. Inhibition of SQSTM1 phosphorylation suppressed inclusion formation by ubiquitinated proteins and prevented colocalization of SQSTM1 with aggregation-prone proteins. Moreover, HSF1 inhibition impaired aggregate-induced autophagosome formation and elimination of protein aggregates. Our findings indicate that HSF1 triggers SQSTM1-mediated proteostasis. PMID:27846364

Lens protein composition, glycation and high molecular weight aggregation in aging rats.

PubMed

Swamy, M S; Abraham, E C

1987-10-01

Because of minimal or no turnover, lens proteins are subjected to substantial post-translational modifications which in turn disrupt lens architecture and change the optical properties leading to senile cataract formation. Progressive glycation is believed to have the potential to initiate the changes that are conducive to lens opacification. Fisher 344 rats were systematically followed from juvenile to older and aged phases of their life to study the relationship between lens glycation and high molecular weight (HMW) aggregate formation as well as quantitative and qualitative changes in lens crystallins. Levels of glycated proteins were quantified by affinity chromatography. Changes in lens crystallin composition and HMW aggregate formation were monitored by molecular sieve HPLC, further confirmed by SDS-PAGE and IEF techniques. As the age advances HMW and insoluble proteins increase with a concomitant disappearance of gamma-crystallins from soluble fraction. This disappearance of gamma-crystallins coincided with increased glycation (approximately 2-fold higher in insoluble fraction) and decreased sulfhydryl groups from soluble fraction. It appears that lens protein glycation, disappearance of gamma-crystallins and sulfhydryls from soluble fraction and increase of insoluble fraction and HMW aggregate are interrelated.

Inhibitory Effects of Yuzu and Its Components on Human Platelet Aggregation

PubMed Central

Kim, Tae-Ho; Kim, Hye-Min; Park, Se Won; Jung, Yi-Sook

2015-01-01

Our previous study demonstrated that yuzu has an anti-platelet effect in rat blood. In the present study, we examined whether the anti-platelet effect of yuzu can be extended to human blood by investigating its ability to inhibit aggregations induced by various agonists in human platelet rich plasma (PRP). This study also investigated the underlying mechanism of yuzu focusing on ADP granule secretion, TXB2 formations, and PLCγ/Akt signaling. The results from this study showed that ethanolic yuzu extract (YE), and its components, hesperidin and naringin, inhibited human platelet aggregation in a concentration-dependent manner. YE, hesperidin and naringin also inhibited TXB2 formation and ADP release. The phosphorylation of PLCγ and Akt was significantly inhibited by YE, heperidin and naringin. Furthermore, we demonstrated that YE, heperidin and naringin has anti-platelet effects in rat ex vivo studies, and lower side effects in mice tail bleeding time studies. The results from this study suggest that YE, hesperidin and naringin can inhibit human platelet aggregation, at least partly through the inhibition of PLCγ and Akt, leading to a decrease in TXB2 formation and granule secretion. PMID:25767683

Granular activated carbon as nucleating agent for aerobic sludge granulation: Effect of GAC size on velocity field differences (GAC versus flocs) and aggregation behavior.

PubMed

Zhou, Jia-Heng; Zhao, Hang; Hu, Miao; Yu, Hai-Tian; Xu, Xiang-Yang; Vidonish, Julia; Alvarez, Pedro J J; Zhu, Liang

2015-12-01

Initial cell aggregation plays an important role in the formation of aerobic granules. In this study, three parallel aerobic granular sludge reactors treating low-strength wastewater were established using granular activated carbon (GAC) of different sizes as the nucleating agent. A novel visual quantitative evaluation method was used to discern how GAC size affects velocity field differences (GAC versus flocs) and aggregation behavior during sludge granulation. Results showed that sludge granulation was significantly enhanced by addition of 0.2mm GAC. However, there was no obvious improvement in granulation in reactor amended with 0.6mm GAC. Hydraulic analysis revealed that increase of GAC size enhanced the velocity field difference between flocs and GAC, which decreased the lifecycle and fraction of flocs-GAC aggregates. Overall, based on analysis of aggregation behavior, GAC of suitable sizes (0.2mm) can serve as the nucleating agent to accelerate flocs-GAC coaggregation and formation of aerobic granules. Copyright © 2015 Elsevier Ltd. All rights reserved.

Factors that drive peptide assembly and fibril formation: experimental and theoretical analysis of Sup35 NNQQNY mutants.

PubMed

Do, Thanh D; Economou, Nicholas J; LaPointe, Nichole E; Kincannon, William M; Bleiholder, Christian; Feinstein, Stuart C; Teplow, David B; Buratto, Steven K; Bowers, Michael T

2013-07-18

Residue mutations have substantial effects on aggregation kinetics and propensities of amyloid peptides and their aggregate morphologies. Such effects are attributed to conformational transitions accessed by various types of oligomers such as steric zipper or single β-sheet. We have studied the aggregation propensities of six NNQQNY mutants: NVVVVY, NNVVNV, NNVVNY, VIQVVY, NVVQIY, and NVQVVY in water using a combination of ion-mobility mass spectrometry, transmission electron microscopy, atomic force microscopy, and all-atom molecular dynamics simulations. Our data show a strong correlation between the tendency to form early β-sheet oligomers and the subsequent aggregation propensity. Our molecular dynamics simulations indicate that the stability of a steric zipper structure can enhance the propensity for fibril formation. Such stability can be attained by either hydrophobic interactions in the mutant peptide or polar side-chain interdigitations in the wild-type peptide. The overall results display only modest agreement with the aggregation propensity prediction methods such as PASTA, Zyggregator, and RosettaProfile, suggesting the need for better parametrization and model peptides for these algorithms.

Barcoding heat shock proteins to human diseases: looking beyond the heat shock response.

PubMed

Kakkar, Vaishali; Meister-Broekema, Melanie; Minoia, Melania; Carra, Serena; Kampinga, Harm H

2014-04-01

There are numerous human diseases that are associated with protein misfolding and the formation of toxic protein aggregates. Activating the heat shock response (HSR)--and thus generally restoring the disturbed protein homeostasis associated with such diseases--has often been suggested as a therapeutic strategy. However, most data on activating the HSR or its downstream targets in mouse models of diseases associated with aggregate formation have been rather disappointing. The human chaperonome consists of many more heat shock proteins (HSPs) that are not regulated by the HSR, however, and researchers are now focusing on these as potential therapeutic targets. In this Review, we summarize the existing literature on a set of aggregation diseases and propose that each of them can be characterized or 'barcoded' by a different set of HSPs that can rescue specific types of aggregation. Some of these 'non-canonical' HSPs have demonstrated effectiveness in vivo, in mouse models of protein-aggregation disease. Interestingly, several of these HSPs also cause diseases when mutated--so-called chaperonopathies--which are also discussed in this Review.

Barcoding heat shock proteins to human diseases: looking beyond the heat shock response

PubMed Central

Kakkar, Vaishali; Meister-Broekema, Melanie; Minoia, Melania; Carra, Serena; Kampinga, Harm H.

2014-01-01

There are numerous human diseases that are associated with protein misfolding and the formation of toxic protein aggregates. Activating the heat shock response (HSR) – and thus generally restoring the disturbed protein homeostasis associated with such diseases – has often been suggested as a therapeutic strategy. However, most data on activating the HSR or its downstream targets in mouse models of diseases associated with aggregate formation have been rather disappointing. The human chaperonome consists of many more heat shock proteins (HSPs) that are not regulated by the HSR, however, and researchers are now focusing on these as potential therapeutic targets. In this Review, we summarize the existing literature on a set of aggregation diseases and propose that each of them can be characterized or ‘barcoded’ by a different set of HSPs that can rescue specific types of aggregation. Some of these ‘non-canonical’ HSPs have demonstrated effectiveness in vivo, in mouse models of protein-aggregation disease. Interestingly, several of these HSPs also cause diseases when mutated – so-called chaperonopathies – which are also discussed in this Review. PMID:24719117

Mutagenic analysis of the nucleation propensity of oxidized Alzheimer's beta-amyloid peptide.

PubMed

Christopeit, Tony; Hortschansky, Peter; Schroeckh, Volker; Gührs, Karlheinz; Zandomeneghi, Giorgia; Fändrich, Marcus

2005-08-01

The formation of polypeptide aggregates represents a nucleated polymerization reaction in which an initial nucleation event (lag phase) is followed by the extension of newly formed nuclei into larger aggregates, including fibrils (growth phase). The efficiencies of these reactions relate to the lag time (lag phase) and to the rate of aggregation (growth phase), which can be determined from experimental aggregation curves. Here we present a mutagenic analysis in which we replace valine 18 of the Alzheimer's Abeta (1-40) peptide with 17 different amino acids and determine its effect on the lag time, and therefore, on the propensity of nucleation. Comparison with various physico-chemical properties shows that nucleation is affected in a predictable manner depending on the beta-sheet propensity and hydrophobicity of residue 18. In addition, we observe a direct proportionality between the lag time and the rate of aggregation. These data imply that the two reactions, nucleation and polymerization, are governed by very similar physicochemical principles and that they involve the formation of the same types of noncovalent interactions.

Morphological Evolution of Nanocluster Aggregates and Single Crystals in Alkaline Zinc Electrodeposition

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

Desai, D; Turney, DE; Anantharaman, B

2014-04-24

The morphology of Zn electrodeposits is studied on carbon-coated transmission electron microscopy grids. At low over-potentials (eta = -50 mV), the morphology develops by aggregation at two distinct length scales: similar to 5 nm diameter monocrystalline nanoclusters form similar to 50 nm diameter polycrystalline aggregates, and the aggregates form a branched network. Epitaxial (00 (0) over bar2) growth above an overpotential of vertical bar eta(c)vertical bar > 125 mV leads to the formation of hexagonal single crystals up to 2 mu m in diameter. Potentiostatic current transients were used to calculate the nucleation rate from Scharifker et al.'s model. Themore » exp(eta) dependence of the nucleation rates indicates that atomistic nucleation theory explains the nucleation process better than Volmer-Weber theory. A kinetic model is provided using the rate equations of vapor solidification to simulate the evolution of the different morphologies. On solving these equations, we show that aggregation is attributed to cluster impingement and cluster diffusion while single-crystal formation is attributed to direct attachment.« less

Cooperative structural transitions in amyloid-like aggregation

NASA Astrophysics Data System (ADS)

Steckmann, Timothy; Bhandari, Yuba R.; Chapagain, Prem P.; Gerstman, Bernard S.

2017-04-01

Amyloid fibril aggregation is associated with several horrific diseases such as Alzheimer's, Creutzfeld-Jacob, diabetes, Parkinson's, and others. Although proteins that undergo aggregation vary widely in their primary structure, they all produce a cross-β motif with the proteins in β-strand conformations perpendicular to the fibril axis. The process of amyloid aggregation involves forming myriad different metastable intermediate aggregates. To better understand the molecular basis of the protein structural transitions and aggregation, we report on molecular dynamics (MD) computational studies on the formation of amyloid protofibrillar structures in the small model protein ccβ, which undergoes many of the structural transitions of the larger, naturally occurring amyloid forming proteins. Two different structural transition processes involving hydrogen bonds are observed for aggregation into fibrils: the breaking of intrachain hydrogen bonds to allow β-hairpin proteins to straighten, and the subsequent formation of interchain H-bonds during aggregation into amyloid fibrils. For our MD simulations, we found that the temperature dependence of these two different structural transition processes results in the existence of a temperature window that the ccβ protein experiences during the process of forming protofibrillar structures. This temperature dependence allows us to investigate the dynamics on a molecular level. We report on the thermodynamics and cooperativity of the transformations. The structural transitions that occurred in a specific temperature window for ccβ in our investigations may also occur in other amyloid forming proteins but with biochemical parameters controlling the dynamics rather than temperature.

Fate of small charred particles in soils - importance of aggregation

NASA Astrophysics Data System (ADS)

Mueller, C. W.; Pechenkina, N.; Grünz, G.; Kölbl, A.; Steffens, M.; Heister, K.; Kögel-Knabner, I.

2009-04-01

Historic and recent fires affect a broad range of terrestrial ecosystems and are reflected in the composition of soil organic matter (SOM). Although the assignments of different sources and pools of black carbon (BC) are still under debate, the importance of BC for carbon (C) storage, nutrient supply and contaminant sorption is well recognized. Nevertheless, how processes of encapsulation of BC into aggregates may influence fate and properties of BC still needs further research. We observed small highly aromatic particulate OM (oPOMsmall, <20 µm) exclusively occluded within aggregates in a range of soils. As these particles were absent in the inter-aggregate soil space the question of the importance of soil aggregation for the fate of these particles is raised. In the presented study we analysed intact soil aggregates and the distribution of highly aromatic micro-scale charred particles and mineral bound SOM in Haplic Chernozems from Central Russia. We fractionated the soils by means of density to obtain particulate and mineral bound SOM fractions. The chemical composition of the obtained fractions was studied by solid-state 13C-NMR spectroscopy and energy dispersive X-ray spectroscopy (EDX). For visualization of the particles and aggregates we used scanning electron microscopy (SEM) and nano-scale secondary ion mass spectrometry (NanoSIMS). The importance of oxides for aggregate formation was elucidated by analyses of extractable Fe. Furthermore, we incubated the oPOMsmall fraction at 20°C in batch experiments to study the aggregate formation of charred particles with time. To track the fate of OM on new formed aggregates, we used a labelled amino acid mixture (min. 98 atom% 13C and 15N) as readily bioavailable OM input and isotopic tracer. The matrix of the intact soil aggregates, embedded in epoxy resin, was dominated by densely packed clay particles. At all depths particulate SOM was quantitatively dominated by the aromatic oPOM fractions, inter-aggregate POM was almost absent at higher depths. The oPOMsmall showed mainly amorphous structures and very few plant tissue structures as revealed by SEM. The oPOMsmall fraction showed a drastic increase in the content of aromatic C with depth along with decreasing aliphatic C in the thick A horizons. Almost the entire OM of the oPOMsmall fraction was composed of aromatic C compounds in the AB horizons. The incubation experiment with particles from the oPOMsmall fraction revealed a fast aggregate formation in water within a few days. With the isotopic sensitivity of the NanoSIMS 50, we were able to show spatial heterogeneous enrichments in 13C and 15N on new formed aggregates of aromatic particles.

Actinobacillus pleuropneumoniae grows as aggregates in the lung of pigs: is it time to refine our in vitro biofilm assays?

PubMed

Tremblay, Yannick D N; Labrie, Josée; Chénier, Sonia; Jacques, Mario

2017-07-01

Actinobacillus pleuropneumoniae causes porcine pleuropneumonia and forms biofilms in vitro on abiotic surfaces; however, presence of biofilms during infections has not been documented. The aim of this study was to use a species-specific fluorescent oligonucleotide probe and confocal microscopy to localize A. pleuropneumoniae in the lungs of two naturally infected pigs. Actinobacillus pleuropneumoniae was detected by fluorescence in situ hybridization and observed to grow as aggregates (~30-45 μm) during a natural infection. As the A. pleuropneumoniae aggregates observed in porcine lungs differed from the biofilms grown on a solid surface obtained in vitro, we designed a new biofilm assay using agarose, a porous substrate, favouring the formation of aggregates. In this study, we described for the first time the mode of growth of A. pleuropneumoniae during a natural infection in pigs. We also propose an in vitro biofilm assay for A. pleuropneumoniae using a porous substrate which allows the formation of aggregates. This assay might be more representative of the in vivo situation, at least in terms of the size of the bacterial aggregates and the presence of a porous matrix, and could potentially be used to test the susceptibility of A. pleuropneumoniae aggregates to antibiotics and disinfectants. © 2016 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Phosphorylation of NBR1 by GSK3 modulates protein aggregation

PubMed Central

Nicot, Anne-Sophie; Lo Verso, Francesca; Ratti, Francesca; Pilot-Storck, Fanny; Streichenberger, Nathalie; Sandri, Marco; Schaeffer, Laurent; Goillot, Evelyne

2014-01-01

The autophagy receptor NBR1 (neighbor of BRCA1 gene 1) binds UB/ubiquitin and the autophagosome-conjugated MAP1LC3/LC3 (microtubule-associated protein 1 light chain 3) proteins, thereby ensuring ubiquitinated protein degradation. Numerous neurodegenerative and neuromuscular diseases are associated with inappropriate aggregation of ubiquitinated proteins and GSK3 (glycogen synthase kinase 3) activity is involved in several of these proteinopathies. Here we show that NBR1 is a substrate of GSK3. NBR1 phosphorylation by GSK3 at Thr586 prevents the aggregation of ubiquitinated proteins and their selective autophagic degradation. Indeed, NBR1 phosphorylation decreases protein aggregation induced by puromycin or by the DES/desmin N342D mutant found in desminopathy patients and stabilizes ubiquitinated proteins. Importantly, decrease of protein aggregates is due to an inhibition of their formation and not to their autophagic degradation as confirmed by data on Atg7 knockout mice. The relevance of NBR1 phosphorylation in human pathology was investigated. Analysis of muscle biopsies of sporadic inclusion body myositis (sIBM) patients revealed a strong decrease of NBR1 phosphorylation in muscles of sIBM patients that directly correlated with the severity of protein aggregation. We propose that phosphorylation of NBR1 by GSK3 modulates the formation of protein aggregates and that this regulation mechanism is defective in a human muscle proteinopathy. PMID:24879152

Considering the formation of hematite spherules on Mars by freezing aqueous hematite nanoparticle suspensions

NASA Astrophysics Data System (ADS)

Sexton, M. R.; Elwood Madden, M. E.; Swindle, A. L.; Hamilton, V. E.; Bickmore, B. R.; Elwood Madden, A. S.

2017-04-01

The enigmatic and unexpected occurrence of coarse crystalline (gray) hematite spherules at Terra Meridiani on Mars in association with deposits of jarosite-rich sediments fueled a variety of hypotheses to explain their origin. In this study, we tested the hypothesis that freezing of aqueous hematite nanoparticle suspensions, possibly produced from low-temperature weathering of jarosite-bearing deposits, could produce coarse-grained hematite aggregate spherules. We synthesized four hematite nanoparticle suspensions with a range of sizes and morphologies and performed freezing experiments. All sizes of hematite nanoparticles rapidly aggregate during freezing. Regardless of the size or shape of the initial starting material, they rapidly collect into aggregates that are then too big to push in front of a stable advancing ice front, leading to incohesive masses of particles, rather than solid spherules. We also explored the effects of "seed" silicates, a matrix of sand grains, various concentrations of NaCl and CaCl2, and varying the freezing temperature on hematite nanoparticle aggregation. However, none of these factors resulted in mm-scale spherical aggregates. By comparing our measured freezing rates with empirical and theoretical values from the literature, we conclude that the spherules on Mars could not have been produced through the freezing of aqueous hematite nanoparticle suspensions; ice crystallization front instability disrupts the aggregation process and prevents the formation of mm-scale continuous aggregates.

Modulation of mutant Huntingtin aggregates and toxicity by human myeloid leukemia factors.

PubMed

Banerjee, Manisha; Datta, Moumita; Bhattacharyya, Nitai P

2017-01-01

Increased poly glutamine (polyQ) stretch at N-terminal of Huntingtin (HTT) causes Huntington's disease. HTT interacts with large number of proteins, although the preference for such interactions with wild type or mutated HTT protein remains largely unknown. HYPK, an intrinsically unstructured protein chaperone and interactor of mutant HTT was found to interact with myeloid leukemia factor 1 (MLF1) and 2 (MLF2). To identify the role of these two proteins in mutant HTT mediated aggregate formation and toxicity in a cell model, both the proteins were found to preferentially interact with the mutated N-terminal HTT. They significantly reduced the number of cells containing mutant HTT aggregates and subsequent apoptosis in Neuro2A cells. Additionally, in FRAP assay, mobile fraction of mutant HTT aggregates was increased in the presence of MLF1 or MLF2. Further, MLF1 could release transcription factors like p53, CBP and CREB from mutant HTT aggregates. Moreover, in HeLa cell co-expressing mutant HTT exon1 and full length MLF1, p53 was released from the aggregates, leading to the recovery of the expression of the GADD45A transcript, a p53 regulated gene. Taking together, these results showed that MLF1 and MLF2 modulated the formation of aggregates and induction of apoptosis as well as the expressions of genes indirectly. Copyright © 2016 Elsevier Ltd. All rights reserved.

Geometrical frustration yields fibre formation in self-assembly

NASA Astrophysics Data System (ADS)

Lenz, Martin; Witten, Thomas A.

2017-11-01

Controlling the self-assembly of supramolecular structures is vital for living cells, and a central challenge for engineering at the nano- and microscales. Nevertheless, even particles without optimized shapes can robustly form well-defined morphologies. This is the case in numerous medical conditions where normally soluble proteins aggregate into fibres. Beyond the diversity of molecular mechanisms involved, we propose that fibres generically arise from the aggregation of irregular particles with short-range interactions. Using a minimal model of ill-fitting, sticky particles, we demonstrate robust fibre formation for a variety of particle shapes and aggregation conditions. Geometrical frustration plays a crucial role in this process, and accounts for the range of parameters in which fibres form as well as for their metastable character.

Liquid crystals from mesogens containing gold nanoparticles

NASA Astrophysics Data System (ADS)

Lewandowski, Wiktor; Gorecka, Ewa

Long-range ordered structures made of nanoparticles are perspective materials for future optical, electronic and sensing technologies. Conspicuous physicochemical features of nanoparticle aggregates originate from distant-dependent collective interactions, therefore lately a lot of attention was put to the development of assembly strategies allowing control over nanoparticle spatial distribution. In this chapter we will focus on the assembly process based on using thermotropic liquid-crystalline molecules as surface nanoparticle ligands. First, we discuss architectural parameters that inuence structure and thermal properties of the aggregates. Then, we show that this approach enables formation of assemblies with metamaterial characteristic, gives access to dynamic materials with light-, magneto- and thermo-responsive behavior and allows formation of aggregates with unique structures, which all make this strategy an attractive object of research.

Met receptor tyrosine kinase signals through a cortactin–Gab1 scaffold complex, to mediate invadopodia

PubMed Central

Rajadurai, Charles V.; Havrylov, Serhiy; Zaoui, Kossay; Vaillancourt, Richard; Stuible, Matthew; Naujokas, Monica; Zuo, Dongmei; Tremblay, Michel L.; Park, Morag

2012-01-01

Summary Invasive carcinoma cells form actin-rich matrix-degrading protrusions called invadopodia. These structures resemble podosomes produced by some normal cells and play a crucial role in extracellular matrix remodeling. In cancer, formation of invadopodia is strongly associated with invasive potential. Although deregulated signals from the receptor tyrosine kinase Met (also known as hepatocyte growth factor are linked to cancer metastasis and poor prognosis, its role in invadopodia formation is not known. Here we show that stimulation of breast cancer cells with the ligand for Met, hepatocyte growth factor, promotes invadopodia formation, and in aggressive gastric tumor cells where Met is amplified, invadopodia formation is dependent on Met activity. Using both GRB2-associated-binding protein 1 (Gab1)-null fibroblasts and specific knockdown of Gab1 in tumor cells we show that Met-mediated invadopodia formation and cell invasion requires the scaffold protein Gab1. By a structure–function approach, we demonstrate that two proline-rich motifs (P4/5) within Gab1 are essential for invadopodia formation. We identify the actin regulatory protein, cortactin, as a direct interaction partner for Gab1 and show that a Gab1–cortactin interaction is dependent on the SH3 domain of cortactin and the integrity of the P4/5 region of Gab1. Both cortactin and Gab1 localize to invadopodia rosettes in Met-transformed cells and the specific uncoupling of cortactin from Gab1 abrogates invadopodia biogenesis and cell invasion downstream from the Met receptor tyrosine kinase. Met localizes to invadopodia along with cortactin and promotes phosphorylation of cortactin. These findings provide insights into the molecular mechanisms of invadopodia formation and identify Gab1 as a scaffold protein involved in this process. PMID:22366451

Pressure effects on the structure, kinetic, and thermodynamic properties of heat-induced aggregation of protein studied by FT-IR spectroscopy

NASA Astrophysics Data System (ADS)

Taniguchi, Y.; Okuno, A.; Kato, M.

2010-03-01

Pressure can retrain the heat-induced aggregation and dissociate the heat-induced aggregates. We observed the aggregation-preventing pressure effect and the aggregates-dissociating pressure effect to characterize the heat-induced aggregation of equine serum albumin (ESA) by FT-IR spectroscopy. The results suggest the α-helical structure collapses at the beginning of heat-induced aggregation through the swollen structure, and then the rearrangement of structure to the intermolecular β-sheet takes place through partially unfolded structure. We determined the activation volume for the heat-induced aggregation (ΔV# = +93 ml/mol) and the partial molar volume difference between native state and heat-induced aggregates (ΔV=+32 ml/mol). This positive partial molar volume difference suggests that the heat-induced aggregates have larger internal voids than the native structure. Moreover, the positive volume change implies that the formation of the intermolecular β-sheet is unfavorable under high pressure.

Aggregation behavior of the southern chinch bug (Hemiptera: Blissidae)

USDA-ARS?s Scientific Manuscript database

The southern chinch bug, Blissus insularis Barber, forms dense, multigenerational aggregations in St. Augustinegrass lawns leading to grass death from sap feeding. We conducted several bioassays to better understand the signals responsible for the formation and maintenance of southern chinch bug ag...

Formation of wormlike aggregates of fluorocarbon-hydrocarbon hybrid surfactant by Langmuir-Blodgett transfer and alignment of gold nanoparticles.

PubMed

Kondo, Yukishige; Fukuoka, Hiroshi; Nakano, Shuichi; Hayashi, Kohei; Tsukagoshi, Tatsuya; Matsumoto, Mutsuyoshi; Yoshino, Norio

2007-05-22

A novel anionic fluorocarbon-hydrocarbon hybrid surfactant (SS-Hyb-Na+) with a disulfide group has been synthesized from 11-bromo-1-undecanal and perfluorohexylethyl iodide via three steps. The Langmuir-Blodgett (LB) transfer of the 1:100 (mol/mol) mixed monolayer of SS-Hyb-Na+ and stearyl alcohol (C18OH) formed on an aqueous solution containing a cationic polymer, poly(diallyldimethylammonium chloride) (PDDA+Cl-) onto a hydrophobic silicon wafer yields the formation of wormlike aggregates consisting of SS-Hyb-/PDDA+ polyion complexes. It is found that the aggregates align along the withdrawal direction of the wafer substrate. When the wafer on which the wormlike aggregates exist is immersed into the dispersion of gold nanoparticles (Au NPs) prepared by the citrate reduction method, Au NPs align along the wormlike structures. Even though the surface of the wafer is placed either vertical or parallel to the monolayer compression direction during the LB transfer, the one-dimensional (1D) array of Au NPs is observed along the withdrawal direction of the wafer. This indicates that the wormlike aggregates of SS-Hyb-/PDDA+ complexes are aligned during the LB transfer, and the aligned aggregates behave as a scaffold in the 1D array of Au NPs.

Inhibitory effects of magnolol and honokiol on human calcitonin aggregation

PubMed Central

Guo, Caiao; Ma, Liang; Zhao, Yudan; Peng, Anlin; Cheng, Biao; Zhou, Qiaoqiao; Zheng, Ling; Huang, Kun

2015-01-01

Amyloid formation is associated with multiple amyloidosis diseases. Human calcitonin (hCT) is a typical amyloidogenic peptide, its aggregation is associated with medullary carcinoma of the thyroid (MTC), and also limits its clinical application. Magnolia officinalis is a traditional Chinese herbal medicine; its two major polyphenol components, magnolol (Mag) and honokiol (Hon), have displayed multiple functions. Polyphenols like flavonoids and their derivatives have been extensively studied as amyloid inhibitors. However, the anti-amyloidogenic property of a biphenyl backbone containing polyphenols such as Mag and Hon has not been reported. In this study, these two compounds were tested for their effects on hCT aggregation. We found that Mag and Hon both inhibited the amyloid formation of hCT, whereas Mag showed a stronger inhibitory effect; moreover, they both dose-dependently disassembled preformed hCT aggregates. Further immuno-dot blot and dynamic light scattering studies suggested Mag and Hon suppressed the aggregation of hCT both at the oligomerization and the fibrillation stages, while MTT-based and dye-leakage assays demonstrated that Mag and Hon effectively reduced cytotoxicity caused by hCT aggregates. Furthermore, isothermal titration calorimetry indicated Mag and Hon both interact with hCT. Together, our study suggested a potential anti-amyloidogenic property of these two compounds and their structure related derivatives. PMID:26324190

A nanoscale bio-inspired light-harvesting system developed from self-assembled alkyl-functionalized metallochlorin nano-aggregates.

PubMed

Ocakoglu, Kasim; Joya, Khurram S; Harputlu, Ersan; Tarnowska, Anna; Gryko, Daniel T

2014-08-21

Self-assembled supramolecular organization of nano-structured biomimetic light-harvesting modules inside solid-state nano-templates can be exploited to develop excellent light-harvesting materials for artificial photosynthetic devices. We present here a hybrid light-harvesting system mimicking the chlorosomal structures of the natural photosynthetic system using synthetic zinc chlorin units (ZnChl-C6, ZnChl-C12 and ZnChl-C18) that are self-aggregated inside the anodic aluminum oxide (AAO) nano-channel membranes. AAO nano-templates were modified with a TiO2 matrix and functionalized with long hydrophobic chains to facilitate the formation of supramolecular Zn-chlorin aggregates. The transparent Zn-chlorin nano-aggregates inside the alkyl-TiO2 modified AAO nano-channels have a diameter of ∼120 nm in a 60 μm length channel. UV-Vis studies and fluorescence emission spectra further confirm the formation of the supramolecular ZnChl aggregates from monomer molecules inside the alkyl-functionalized nano-channels. Our results prove that the novel and unique method can be used to produce efficient and stable light-harvesting assemblies for effective solar energy capture through transparent and stable nano-channel ceramic materials modified with bio-mimetic molecular self-assembled nano-aggregates.

Aggregate-based sub-CMC Solubilization of n-Alkanes by Monorhamnolipid Biosurfactant.

PubMed

Zhong, Hua; Yang, Xin; Tan, Fei; Brusseau, Mark L; Yang, Lei; Liu, Zhifeng; Zeng, Guangming; Yuan, Xingzhong

2016-03-01

Solubilization of n -decane, dodecane, tetradecane and hexadecane by monorhamnolipid biosurfactant (monoRL) at concentrations near the critical micelle concentration (CMC) was investigated. The apparent solubility of all the four alkanes increases linearly with increasing monoRL concentration either below or above CMC. The capacity of solubilization presented by the molar solubilization ratio (MSR), however, is stronger at monoRL concentrations below CMC than above CMC. The MSR decreases following the order dodecane > decane > tetradecane > hexadecane at monoRL concentration below CMC. Formation of aggregates at sub-CMC monoRL concentrations was demonstrated by dynamic light scattering (DLS) and cryo-transmission electron microscopy examination. DLS-based size ( d ) and zeta potential of the aggregates decrease with increasing monoRL concentration. The surface excess ( Γ ) of monoRL calculated based on alkane solubility and aggregate size data increases rapidly with increasing bulk monoRL concentration, and then asymptotically approaches the maximum surface excess ( Γ max ). Relation between Γ and d indicates that the excess of monoRL molecules at the aggregate surface greatly impacts the surface curvature. The results demonstrate formation of aggregates for alkane solubilization at monoRL concentrations below CMC, indicating the potential of employing low-concentration rhamnolipid for enhanced solubilization of hydrophobic organic compounds.

Microstructured block copolymer surfaces for control of microbe capture and aggregation

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

Hansen, Ryan R; Shubert, Katherine R; Morrell, Jennifer L.

2014-01-01

The capture and arrangement of surface-associated microbes is influenced by biochemical and physical properties of the substrate. In this report, we develop lectin-functionalized substrates containing patterned, three-dimensional polymeric structures of varied shapes and densities and use these to investigate the effects of topology and spatial confinement on lectin-mediated microbe capture. Films of poly(glycidyl methacrylate)-block-4,4-dimethyl-2-vinylazlactone (PGMA-b-PVDMA) were patterned on silicon surfaces into line or square grid patterns with 5 m wide features and varied edge spacing. The patterned films had three-dimensional geometries with 900 nm film thickness. After surface functionalization with wheat germ agglutinin, the size of Pseudomonas fluorescens aggregates capturedmore » was dependent on the pattern dimensions. Line patterns with edge spacing of 5 m or less led to the capture of individual microbes with minimal formation of aggregates, while grid patterns with the same spacing also captured individual microbes with further reduction in aggregation. Both geometries allowed for increases in aggregate size distribution with increased in edge spacing. These engineered surfaces combine spatial confinement with affinity-based microbe capture based on exopolysaccharide content to control the degree of microbe aggregation, and can also be used as a platform to investigate intercellular interactions and biofilm formation in microbial populations of controlled sizes.« less

A microfabricated platform to form three-dimensional toroidal multicellular aggregate.

PubMed

Masuda, Taisuke; Takei, Natsuki; Nakano, Takuma; Anada, Takahisa; Suzuki, Osamu; Arai, Fumihito

2012-12-01

Techniques that allow cells to self-assemble into three-dimensional (3D) spheroid microtissues provide powerful in vitro models that are becoming increasingly popular in fields such as stem cell research, tissue engineering, and cancer biology. Appropriate simulation of the 3D environment in which tissues normally develop and function is crucial for the engineering of in vitro models that can be used for the formation of complex tissues. We have developed a unique multicellular aggregate formation platform that utilizes a maskless gray-scale photolithography. The cellular aggregate formed using this platform has a toroidal-like geometry and includes a micro lumen that facilitates the supply of oxygen and growth factors and the expulsion of waste products. As a result, this platform was capable of rapidly producing hundreds of multicellular aggregates at a time, and of regulating the diameter of aggregates with complex design. These toroidal multicellular aggregates can grow as long-term culture. In addition, the micro lumen can be used as a continuous channel and for the insertion of a vascular system or a nerve system into the assembled tissue. These platform characteristics highlight its potential to be used in a wide variety of applications, e.g. as a bioactuator, as a micro-machine component or in drug screening and tissue engineering.

A model for the kinetics of homotypic cellular aggregation under static conditions

NASA Technical Reports Server (NTRS)

Neelamegham, S.; Munn, L. L.; Zygourakis, K.; McIntire, L. V. (Principal Investigator)

1997-01-01

We present the formulation and testing of a mathematical model for the kinetics of homotypic cellular aggregation. The model considers cellular aggregation under no-flow conditions as a two-step process. Individual cells and cell aggregates 1) move on the tissue culture surface and 2) collide with other cells (or aggregates). These collisions lead to the formation of intercellular bonds. The aggregation kinetics are described by a system of coupled, nonlinear ordinary differential equations, and the collision frequency kernel is derived by extending Smoluchowski's colloidal flocculation theory to cell migration and aggregation on a two-dimensional surface. Our results indicate that aggregation rates strongly depend upon the motility of cells and cell aggregates, the frequency of cell-cell collisions, and the strength of intercellular bonds. Model predictions agree well with data from homotypic lymphocyte aggregation experiments using Jurkat cells activated by 33B6, an antibody to the beta 1 integrin. Since cell migration speeds and all the other model parameters can be independently measured, the aggregation model provides a quantitative methodology by which we can accurately evaluate the adhesivity and aggregation behavior of cells.

Plasma based formation and deposition of metal and metal oxide nanoparticles using a gas aggregation source

NASA Astrophysics Data System (ADS)

Polonskyi, Oleksandr; Ahadi, Amir Mohammad; Peter, Tilo; Fujioka, Kenji; Abraham, Jan Willem; Vasiliauskaite, Egle; Hinz, Alexander; Strunskus, Thomas; Wolf, Sebastian; Bonitz, Michael; Kersten, Holger; Faupel, Franz

2018-05-01

Metal clusters and nanoparticles (NPs) have been studied intensively due to their unique chemical, physical, electrical, and optical properties, resulting from their dimensions, which provided host of applications in nanoscience and nanotechnology. Formation of new materials by embedding NPs into various matrices (i.e. formation of nanocomposites) further expands the horizon of possible application of such nanomaterials. In the last few decades, the focus was put on the formation of metallic and metal oxide NPs via a so-called gas aggregation nanoparticle source employing magnetron sputtering (i.e. Haberland concept). In this paper, an overview is given of the recent progress in formation and deposition of NPs by the gas aggregation method. Examples range from noble metals (Ag, Au) through reactive metals (Al, Ti) to Si and the respective oxides. Emphasis is placed on the mechanism of nanoparticle growth and the resulting properties. Moreover, kinetic Monte Carlo simulations were developed to explain the growth mechanism and dynamics of nanoparticle formation depending on the experimental conditions. In addition, the role of trace amounts of reactive gases and of pulsed operation of the plasma on the nucleation process is addressed. Finally, the treatment of the NPs in the plasma environment resulting in nanoparticle charging, morphological and chemical modifications is discussed. Contribution to the Topical Issue "Fundamentals of Complex Plasmas", edited by Jürgen Meichsner, Michael Bonitz, Holger Fehske, Alexander Piel.

Entrapment of Aβ1-40 peptide in unstructured aggregates

NASA Astrophysics Data System (ADS)

Corsale, C.; Carrotta, R.; Mangione, M. R.; Vilasi, S.; Provenzano, A.; Cavallaro, G.; Bulone, D.; San Biagio, P. L.

2012-06-01

Recognizing the complexity of the fibrillogenesis process provides a solid ground for the development of therapeutic strategies aimed at preventing or inhibiting protein-protein aggregation. Under this perspective, it is meaningful to identify the possible aggregation pathways and their relative products. We found that Aβ-peptide dissolved in a pH 7.4 solution at small peptide concentration and low ionic strength forms globular aggregates without typical amyloid β-conformation. ThT binding kinetics was used to monitor aggregate formation. Circular dichroism spectroscopy, AFM imaging, static and dynamic light scattering were used for structural and morphological characterization of the aggregates. They appear stable or at least metastable with respect to fiber growth, therefore appearing as an incidental product in the pathway of fibrillogenesis.

Molecular aggregation of humic substances

USGS Publications Warehouse

Wershaw, R. L.

1999-01-01

Humic substances (HS) form molecular aggregates in solution and on mineral surfaces. Elucidation of the mechanism of formation of these aggregates is important for an understanding of the interactions of HS in soils arid natural waters. The HS are formed mainly by enzymatic depolymerization and oxidation of plant biopolymers. These reactions transform the aromatic and lipid plant components into amphiphilic molecules, that is, molecules that consist of separate hydrophobic (nonpolar) and hydrophilic (polar) parts. The nonpolar parts of the molecules are composed of relatively unaltered segments of plant polymers and the polar parts of carboxylic acid groups. These amphiphiles form membrane-like aggregates on mineral surfaces and micelle-like aggregates in solution. The exterior surfaces of these aggregates are hydrophilic, and the interiors constitute separate hydrophobic liquid-like phases.

Influence of pH and Metal Cations on Aggregative Growth of Non-Slime-forming Strains of Zoogloea ramigera

PubMed Central

Angelbeck, Donald I.; Kirsch, Edwin J.

1969-01-01

Aggregative growth of non-slime-forming strains of Zoogloea ramigera was induced by growing the organisms at a depressed pH. Calcium and magnesium ion was found to reverse aggregative growth of the organisms. Conversely, aggregation was stimulated when the available inorganic cation concentration of the growth medium was lowered by the use of a chelating agent. The aggregative effects of pH depression or cation depletion and the dispersal effects of cation supplementation were observed only during cellular growth. The data suggest that aggregate formation of non-slime-forming strains of Z. ramigera may be related to the calcium or magnesium metabolism of the organisms, or both. Images PMID:4976326

A-DROP: A predictive model for the formation of oil particle aggregates (OPAs)

USGS Publications Warehouse

Zhao, Lin; Boufadel, Michel C.; Geng, Xiaolong; Lee, Kenneth; King, Thomas; Robinson, Brian; Fitzpatrick, Faith A.

2016-01-01

Oil–particle interactions play a major role in removal of free oil from the water column. We present a new conceptual–numerical model, A-DROP, to predict oil amount trapped in oil–particle aggregates. A new conceptual formulation of oil–particle coagulation efficiency is introduced to account for the effects of oil stabilization by particles, particle hydrophobicity, and oil–particle size ratio on OPA formation. A-DROP was able to closely reproduce the oil trapping efficiency reported in experimental studies. The model was then used to simulate the OPA formation in a typical nearshore environment. Modeling results indicate that the increase of particle concentration in the swash zone would speed up the oil–particle interaction process; but the oil amount trapped in OPAs did not correspond to the increase of particle concentration. The developed A-DROP model could become an important tool in understanding the natural removal of oil and developing oil spill countermeasures by means of oil–particle aggregation.

A-DROP: A predictive model for the formation of oil particle aggregates (OPAs).

PubMed

Zhao, Lin; Boufadel, Michel C; Geng, Xiaolong; Lee, Kenneth; King, Thomas; Robinson, Brian; Fitzpatrick, Faith

2016-05-15

Oil-particle interactions play a major role in removal of free oil from the water column. We present a new conceptual-numerical model, A-DROP, to predict oil amount trapped in oil-particle aggregates. A new conceptual formulation of oil-particle coagulation efficiency is introduced to account for the effects of oil stabilization by particles, particle hydrophobicity, and oil-particle size ratio on OPA formation. A-DROP was able to closely reproduce the oil trapping efficiency reported in experimental studies. The model was then used to simulate the OPA formation in a typical nearshore environment. Modeling results indicate that the increase of particle concentration in the swash zone would speed up the oil-particle interaction process; but the oil amount trapped in OPAs did not correspond to the increase of particle concentration. The developed A-DROP model could become an important tool in understanding the natural removal of oil and developing oil spill countermeasures by means of oil-particle aggregation. Copyright © 2016 Elsevier Ltd. All rights reserved.

Monomer-dependent secondary nucleation in amyloid formation.

PubMed

Linse, Sara

2017-08-01

Secondary nucleation of monomers on the surface of an already existing aggregate that is formed from the same kind of monomers may lead to autocatalytic amplification of a self-assembly process. Such monomer-dependent secondary nucleation occurs during the crystallization of small molecules or proteins and self-assembled materials, as well as in protein self-assembly into fibrous structures. Indications of secondary nucleation may come from analyses of kinetic experiments starting from pure monomers or monomers supplemented with a low concentration of pre-formed aggregates (seeds). More firm evidence requires additional experiments, for example those employing isotope labels to distinguish new aggregates arising from the monomer from those resulting from fragmentation of the seed. In cases of amyloid formation, secondary nucleation leads to the formation of toxic oligomers, and inhibitors of secondary nucleation may serve as starting points for therapeutic developments. Secondary nucleation displays a high degree of structural specificity and may be enhanced by mutations or screening of electrostatic repulsion.

Isolation and chemical identification of lipid derivatives from avocado (Persea americana) pulp with antiplatelet and antithrombotic activities.

PubMed

Rodriguez-Sanchez, Dariana Graciela; Flores-García, Mirthala; Silva-Platas, Christian; Rizzo, Sheryl; Torre-Amione, Guillermo; De la Peña-Diaz, Aurora; Hernández-Brenes, Carmen; García-Rivas, Gerardo

2015-01-01

Platelets play a pivotal role in physiological hemostasis. However, in coronary arteries damaged by atherosclerosis, enhanced platelet aggregation, with subsequent thrombus formation, is a precipitating factor in acute ischemic events. Avocado pulp (Persea americana) is a good source of bioactive compounds, and its inclusion in the diet as a source of fatty acid has been related to reduced platelet aggregability. Nevertheless, constituents of avocado pulp with antiplatelet activity remain unknown. The present study aims to characterize the chemical nature of avocado constituents with inhibitory effects on platelet aggregation. Centrifugal partition chromatography (CPC) was used as a fractionation and purification tool, guided by an in vitro adenosine diphosphate (ADP), arachidonic acid or collagen-platelet aggregation assay. Antiplatelet activity was initially linked to seven acetogenins that were further purified, and their dose-dependent effects in the presence of various agonists were contrasted. This process led to the identification of Persenone-C (3) as the most potent antiplatelet acetogenin (IC₅₀=3.4 mM) among the evaluated compounds. In vivo evaluations with Persenone A (4) demonstrated potential protective effects against arterial thrombosis (25 mg kg⁻¹ of body weight), as coagulation times increased (2-fold with respect to the vehicle) and thrombus formation was attenuated (71% versus vehicle). From these results, avocado may be referred to as a functional food containing acetogenin compounds that inhibit platelet aggregation with a potential preventive effect on thrombus formation, such as those that occur in ischaemic diseases.

Anti-fibrillogenic properties of phthalocyanines: effect of the out-of-plane ligands.

PubMed

Kovalska, V; Cherepanov, V; Losytskyy, M; Chernii, S; Senenko, A; Chernii, V; Tretyakova, I; Yarmoluk, S; Volkov, S

2014-12-15

The axially-coordinated phthalocyanines were previously reported as agents possessing strong anti-fibrillogenic properties. In the presented study we used the atomic force microscopy to investigate the intermediates and the products of insulin aggregation reaction formed in the presence of Zr and Hf phthalocyanine complexes that contain out-of-plane ligands of different size and nature. It is shown that while phthalocyanine-free insulin generated mostly amyloid fibrils with a diameter of 2-8nm and a length of up to 5μm, the presence of phthalocyanines with spatial bulky ligands (PcZrDbm2) leads to the redirection of the fibrillization reaction to the formation of the spherical oligomer aggregates with a diameter of 4-12nm. At the same time the phthalocyanine complex PcHfCl2 having the small-volume ligands induces the formation of large size insulin aggregates with a height of about 100nm that are supposed to be amorphous species. The study of the aggregation intermediates showed the certain similarity of the reaction passing for phthalocyanine-free insulin and insulin in the presence of PcZrDbm2. The large-size amorphous species were observed at the beginning of reaction, later they dissociated, leading to the formation and growth of the smaller size particles. The amyloid-sensitive cyanine dye 7519 demonstrates the strong fluorescent response both in the presence of fibrils and spherical oligomers, while it is non-sensitive to amorphous aggregates. Copyright © 2014 Elsevier Ltd. All rights reserved.

Attachment and biofilm formation by various serotypes of Salmonella as influenced by cellulose production and thin aggregative fimbriae biosynthesis.

PubMed

Jain, Sudeep; Chen, Jinru

2007-11-01

This study was undertaken to quantify thin aggregative fimbriae and cellulose produced by Salmonella and to evaluate their roles in attachment and biofilm formation on polystyrene and glass surfaces. Thin aggregative fimbriae and cellulose produced by four wild-type and two pairs of Salmonella, representing four different colony morphotypes (rdar: red, dry, and rough; pdar: pink, dry, and rough; bdar: brown, dry, and rough; and saw: smooth and white), were quantified. The ability of the Salmonella cells to attach and form biofilms on the selected surfaces was evaluated in Luria-Bertani (LB) broth with or without salt (0.5%) or glucose (2%) at 28 degrees C during a 7-day period. The cells expressing the rdar or pdar colony morphotypes produced significantly greater amounts of thin aggregative fimbriae and cellulose on LB no salt agar, respectively. The cells expressing the rdar colony morphotype attached in higher numbers and formed more biofilm than did the cells expressing the pdar colony morphotype. The members of the pairs expressing the bdar colony morphotype attached more efficiently and formed more biofilm on the tested surfaces than did their counterparts expressing the saw colony morphotype. These results indicated that thin aggregative fimbriae impart attachment ability to Salmonella and, upon coexpression with cellulose, enhance biofilm formation on certain abiotic surfaces. The knowledge acquired in the study may help develop better cleaning strategies for food processing equipment.

Expression of Fap amyloids in Pseudomonas aeruginosa, P. fluorescens, and P. putida results in aggregation and increased biofilm formation

PubMed Central

Dueholm, Morten S; Søndergaard, Mads T; Nilsson, Martin; Christiansen, Gunna; Stensballe, Allan; Overgaard, Michael T; Givskov, Michael; Tolker-Nielsen, Tim; Otzen, Daniel E; Nielsen, Per H

2013-01-01

The fap operon, encoding functional amyloids in Pseudomonas (Fap), is present in most pseudomonads, but so far the expression and importance for biofilm formation has only been investigated for P. fluorescens strain UK4. In this study, we demonstrate the capacity of P. aeruginosa PAO1, P. fluorescens Pf-5, and P. putida F1 to express Fap fibrils, and investigated the effect of Fap expression on aggregation and biofilm formation. The fap operon in all three Pseudomonas species conferred the ability to express Fap fibrils as shown using a recombinant approach. This Fap overexpression consistently resulted in highly aggregative phenotypes and in increased biofilm formation. Detailed biophysical investigations of purified fibrils confirmed FapC as the main fibril monomer and supported the role of FapB as a minor, nucleating constituent as also indicated by bioinformatic analysis. Bioinformatics analysis suggested FapF and FapD as a potential β-barrel membrane pore and protease, respectively. Manipulation of the fap operon showed that FapA affects monomer composition of the final amyloid fibril, and that FapB is an amyloid protein, probably a nucleator for FapC polymerization. Our study highlights the fap operon as a molecular machine for functional amyloid formation. PMID:23504942

Aggregation effects on anhydrobiotic survival in the tardigrade Richtersius coronifer.

PubMed

Ivarsson, Helen; Jönsson, K Ingemar

2004-02-01

For anhydrobiotic metazoans the rate of desiccation is an important factor influencing the probability of survival in a dry anhydrobiotic state. Formation of animal aggregations, in which the exposed body surface area of individual animals is reduced, represents one way to reduce the rate of evaporation. Such aggregations have earlier been documented in e.g., nematodes. We experimentally evaluate the effect of aggregation size (number of animals in a group of desiccating animals) on anhydrobiotic survival in the eutardigrade Richtersius coronifer. The experiment shows that aggregation provides a clear improvement on anhydrobiotic survival. The most likely explanation for this is that aggregated animals were exposed to a lower rate of desiccation. Although the empirical evidence of aggregation in tardigrades is scarce, our study suggests that aggregation could potentially be an important survival factor for tardigrades living in environments characterized by periods of rapid desiccation. Copyright 2004 Wiley-Liss, Inc.

Dye-sensitized solar cell employing zinc oxide aggregates grown in the presence of lithium

DOEpatents

Zhang, Qifeng; Cao, Guozhong

2013-10-15

Provided are a novel ZnO dye-sensitized solar cell and method of fabricating the same. In one embodiment, deliberately added lithium ions are used to mediate the growth of ZnO aggregates. The use of lithium provides ZnO aggregates that have advantageous microstructure, morphology, crystallinity, and operational characteristics. Employing lithium during aggregate synthesis results in a polydisperse collection of ZnO aggregates favorable for porosity and light scattering. The resulting nanocrystallites forming the aggregates have improved crystallinity and more favorable facets for dye molecule absorption. The lithium synthesis improves the surface stability of ZnO in acidic dyes. The procedures developed and disclosed herein also help ensure the formation of an aggregate film that has a high homogeneity of thickness, a high packing density, a high specific surface area, and good electrical contact between the film and the fluorine-doped tin oxide electrode and among the aggregate particles.

Awa1p on the cell surface of sake yeast inhibits biofilm formation and the co-aggregation between sake yeasts and Lactobacillus plantarum ML11-11.

PubMed

Hirayama, Satoru; Shimizu, Masashi; Tsuchiya, Noriko; Furukawa, Soichi; Watanabe, Daisuke; Shimoi, Hitoshi; Takagi, Hiroshi; Ogihara, Hirokazu; Morinaga, Yasushi

2015-05-01

We examined mixed-species biofilm formation between Lactobacillus plantarum ML11-11 and both foaming and non-foaming mutant strains of Saccharomyces cerevisiae sake yeasts. Wild-type strains showed significantly lower levels of biofilm formation compared with the non-foaming mutants. Awa1p, a protein involved in foam formation during sake brewing, is a glycosylphosphatidylinositol (GPI)-anchored protein and is associated with the cell wall of sake yeasts. The AWA1 gene of the non-foaming mutant strain Kyokai no. 701 (K701) has lost the C-terminal sequence that includes the GPI anchor signal. Mixed-species biofilm formation and co-aggregation of wild-type strain Kyokai no. 7 (K7) were significantly lower than K701 UT-1 (K701 ura3/ura3 trp1/trp1), while the levels of strain K701 UT-1 carrying the AWA1 on a plasmid were comparable to those of K7. The levels of biofilm formation and co-aggregation of the strain K701 UT-1 harboring AWA1 with a deleted GPI anchor signal were similar to those of K701 UT-1. These results clearly demonstrate that Awa1p present on the surface of sake yeast strain K7 inhibits adhesion between yeast cells and L. plantarum ML11-11, consequently impeding mixed-species biofilm formation. Copyright © 2014 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Phase II Study of Intraventricular Methotrexate in Children With Recurrent or Progressive Malignant Brain Tumors

ClinicalTrials.gov

2018-03-01

Recurrent Childhood Medulloblastoma; Recurrent Childhood Ependymoma; Childhood Atypical Teratoid/Rhabdoid Tumor; Embryonal Tumor With Abundant Neuropil and True Rosettes; Metastatic Malignant Neoplasm to the Leptomeninges

26. Historic American Buildings Survey Albert S. Burns, Photographer September ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

26. Historic American Buildings Survey Albert S. Burns, Photographer September 30, 1935. FRAGMENTS OF PLASTER CEILING ROSETTE - MUSIC ROOM - The Maples, 630 South Carolina Avenue Southeast, Washington, District of Columbia, DC

Development of Nested PCR-Based Specific Markers for Detection of Peach Rosette Mosaic Virus in Plant Quarantine.

PubMed

Lee, S; Kim, C S; Shin, Y G; Kim, J H; Kim, Y S; Jheong, W H

2016-03-01

The Peach rosette mosaic virus (PRMV) is a plant pathogen of the genus Nepovirus, and has been designated as a controlled quarantine virus in Korea. In this study, a specific reverse transcription (RT)-PCR marker set, nested PCR marker set, and modified-plasmid positive control were developed to promptly and accurately diagnose PRMV at plant-quarantine sites. The final selected PRMV-specific RT-PCR marker was PRMV-N10/C70 (967 bp), and the nested PCR product of 419 bp was finally amplified. The modified-plasmid positive control, in which the SalI restriction-enzyme region (GTCGAC) was inserted, verified PRMV contamination in a comparison with the control, enabling a more accurate diagnosis. It is expected that the developed method will continuously contribute to the plant-quarantine process in Korea.

Retrieving the CTD:Rosette

NASA Image and Video Library

2017-12-08

On June 28, 2011, Holley Kelly, a teacher from Farragut High School, helped retrieve the CTD/Rosette ensemble from the Bering Strait, east of the Diomede Islands. The ICESCAPE mission, or "Impacts of Climate on Ecosystems and Chemistry of the Arctic Pacific Environment," is a NASA shipborne investigation to study how changing conditions in the Arctic affect the ocean's chemistry and ecosystems. The bulk of the research took place in the Beaufort and Chukchi seas in summer 2010 and 2011. Credit: NASA/Kathryn Hansen NASA image use policy. NASA Goddard Space Flight Center enables NASA’s mission through four scientific endeavors: Earth Science, Heliophysics, Solar System Exploration, and Astrophysics. Goddard plays a leading role in NASA’s accomplishments by contributing compelling scientific knowledge to advance the Agency’s mission. Follow us on Twitter Like us on Facebook Find us on Instagram

Rhizoid differentiation of Spirogyra is regulated by substratum.

PubMed

Ikegaya, Hisato; Sonobe, Seiji; Murakami, Kohei; Shimmen, Teruo

2008-11-01

Some species of Spirogyra can anchor to substratum with rod- or rosette-shaped rhizoid (hapteron). The rhizoid differentiation can be induced by cutting algal filaments in a laboratory. Requirement of contact stimulation for rhizoid differentiation has been reported (Nagata in Plant Cell Physiol 14:531-541, 1973a). However, the control mechanism of rhizoid morphology has not been elucidated. When cut filaments were incubated on the glass surface, start of tip growth, secretion of lectin-binding material and callose synthesis were observed. In the absence of contact to the glass surface, none of above phenomena was induced. Systematic analysis showed that rosette-shaped rhizoid was formed only on the hydrophobic substratum. On the hydrophobic substratum, both Bandeiraea (Griffonia) simplicifolia lectin and jacalin strongly stained the rhizoids. On the hydrophilic substratum, however, only Bandeiraea (Griffonia) simplicifolia lectin strongly stained the rhizoids.

Repression of CYSTATHIONINE γ-SYNTHASE in Seeds Recruits the S-Methylmethionine Cycle.

PubMed

Cohen, Hagai; Hacham, Yael; Panizel, Irina; Rogachev, Ilana; Aharoni, Asaph; Amir, Rachel

2017-07-01

S -Methylmethionine (SMM) was suggested previously to participate in the metabolism of methionine (Met) in seeds. To further reveal its roles, we had previously produced transgenic Arabidopsis ( Arabidopsis thaliana ) RNA interference (RNAi) seeds with lower transcript expression of CYSTATHIONINE γ-SYNTHASE ( AtCGS ), Met's main regulatory enzyme. Unexpectedly, these seeds accumulated significantly higher levels of Met compared with control seeds through an as yet unknown mechanism. Here, transcript and metabolic analyses coupled with isotope-labeled [ 13 C]SMM and [ 13 C]Met feeding experiments enabled us to reveal that SMM that was synthesized in rosette leaves of RNAi plants significantly contributed to the accumulation of Met in their seeds at late stages of development. Seed-specific repression of AtCGS in RNAi seeds triggered the induction of genes operating in the SMM cycle of rosette leaves, leading to elevated transport of SMM toward the seeds, where higher reconversion rates of SMM to Met were detected. The metabolic rearrangements in RNAi seeds resulted in an altered sulfur-associated metabolism, such as lower amounts of Cys and glutathione, as well as a differential composition of glucosinolates. Together, the data propose a novel cross talk existing between seeds and rosette leaves along with mutual effects between the Asp family and SMM pathways operating in these tissues. They also shed light on the effects of higher Met levels on seed physiology and behavior. © 2017 American Society of Plant Biologists. All Rights Reserved.

Hydrothermal venting on the flanks of Heard and McDonald islands, southern Indian Ocean

NASA Astrophysics Data System (ADS)

Lupton, J. E.; Arculus, R. J.; Coffin, M.; Bradney, A.; Baumberger, T.; Wilkinson, C.

2017-12-01

Heard Island and the nearby McDonald Islands are two sites of active volcanism associated with the so-called Kerguelen mantle plume or hot spot. In fact, it has been proposed that the Kerguelen hot spot is currently located beneath Heard Island. During its maiden maximum endurance voyage (IN2016_V01), the recently commissioned Australian R/V Investigator conducted a detailed bathymetric and water column survey of the waters around Heard Island and the McDonald Islands as well as other sites on the Kerguelen Plateau. Some 50 hydrographic profiles were completed using the CTD/rosette system equipped with trace metal sampling and a nephelometer for suspended particle concentrations. In addition to the hydrographic profiles, 244 bubble plumes were detected in the vicinity of the Heard and McDonald Islands using the ship's multibeam system. It is thought that the bubble plumes observed on sea knolls and other seafloor surrounding the McDonald Islands are likely hydrothermal in origin, while plumes northeast of Heard Island may be biogenic methane from cold seeps. At 29 of the hydrographic stations water samples for helium isotope measurements were drawn from the CTD rosette and hermetically sealed into copper tubing for subsequent shorebased mass spectrometer and gas chromatograph analysis. In this paper we report results for 3He/4He ratios and CO2 and CH4 concentrations in water samples collected with the CTD/rosette, and discuss how these results are correlated with suspended particle concentrations and temperature anomalies.

Role of streams in myxobacteria aggregate formation

NASA Astrophysics Data System (ADS)

Kiskowski, Maria A.; Jiang, Yi; Alber, Mark S.

2004-10-01

Cell contact, movement and directionality are important factors in biological development (morphogenesis), and myxobacteria are a model system for studying cell-cell interaction and cell organization preceding differentiation. When starved, thousands of myxobacteria cells align, stream and form aggregates which later develop into round, non-motile spores. Canonically, cell aggregation has been attributed to attractive chemotaxis, a long range interaction, but there is growing evidence that myxobacteria organization depends on contact-mediated cell-cell communication. We present a discrete stochastic model based on contact-mediated signaling that suggests an explanation for the initialization of early aggregates, aggregation dynamics and final aggregate distribution. Our model qualitatively reproduces the unique structures of myxobacteria aggregates and detailed stages which occur during myxobacteria aggregation: first, aggregates initialize in random positions and cells join aggregates by random walk; second, cells redistribute by moving within transient streams connecting aggregates. Streams play a critical role in final aggregate size distribution by redistributing cells among fewer, larger aggregates. The mechanism by which streams redistribute cells depends on aggregate sizes and is enhanced by noise. Our model predicts that with increased internal noise, more streams would form and streams would last longer. Simulation results suggest a series of new experiments.

Analysis of the cellulose synthase operon genes, bcsA, bcsB, and bcsC in Cronobacter species: Prevalence among species and their roles in biofilm formation and cell-cell aggregation.

PubMed

Hu, Lan; Grim, Christopher J; Franco, Augusto A; Jarvis, Karen G; Sathyamoorthy, Vengopal; Kothary, Mahendra H; McCardell, Barbara A; Tall, Ben D

2015-12-01

Cronobacter species are emerging food-borne pathogens that cause severe sepsis, meningitis, and necrotizing entercolitis in neonates and infants. Bacterial pathogens such as Escherichia coli and Salmonella species produce extracellular cellulose which has been shown to be involved in rugosity, biofilm formation, and host colonization. In this study the distribution and prevalence of cellulose synthase operon genes (bcsABZC) were determined by polymerase chain reaction (PCR) analysis in 231 Cronobacter strains isolated from clinical, food, environmental, and unknown sources. Furthermore, bcsA and bcsB isogenic mutants were constructed in Cronobacter sakazakii BAA894 to determine their roles. In calcofluor binding assays bcsA and bcsB mutants did not produce cellulose, and their colonial morphotypes were different to that of the parent strain. Biofilm formation and bacterial cell-cell aggregation were significantly reduced in bcsA and bcsB mutants compared to the parental strain. bcsA or bcsAB PCR-negative strains of C. sakazakii did not bind calcofluor, and produced less biofilm and cell-cell aggregation compared to strains possessing bcsAB genes. These data indicated that Cronobacter bcsABZC were present in all clinical isolates and most of food and environmental isolates. bcsA and bcsB genes of Cronobacter were necessary to produce cellulose, and were involved in biofilm formation and cell-cell aggregation. Published by Elsevier Ltd.

Competence formation and post-graduate education in the public water sector in Indonesia

NASA Astrophysics Data System (ADS)

Kaspersma, J. M.; Alaerts, G. J.; Slinger, J. H.

2012-07-01

The water sector is dependent on effective institutions and organisations, and, therefore, on strong competences at the individual level. In this paper we describe competence formation and competence needs in a case study of the Directorate General of Water Resources (DGWR) in the Ministry of Public Works in Indonesia. A framework is introduced for the water sector comprising three aggregate competences for technical issues, management, and governance, and a meta-competence for continuous learning and innovation. The four competences are further organised in a T-shaped competence profile. Though DGWR professionals have a firmly "technical" orientation, both surveys and interviews reveal a strong perceived requirement for other competences: in particular the learning meta-competence, as well as the aggregate competence for management. The aggregate competence for governance systematically scores lower. Further, a discrepancy appears to exist between the competences that staff perceive as needed in daily work, and those that can be acquired during post-graduate water education. In both locally-based and international post-graduate water education, the aggregate competences for management as well as governance are reportedly addressed modestly, if at all. With low competence in these fields, it is difficult for professionals to communicate and collaborate effectively in a multidisciplinary way. As a result, the horizontal bar of the T-shaped profile remains weakly developed. In international post-graduate education, this is partially compensated by the attention to continuous learning and innovation. The exposure to a different culture and learning format is experienced as fundamentally formative.

Identification of New Factors Modulating Adhesion Abilities of the Pioneer Commensal Bacterium Streptococcus salivarius

PubMed Central

Couvigny, Benoit; Kulakauskas, Saulius; Pons, Nicolas; Quinquis, Benoit; Abraham, Anne-Laure; Meylheuc, Thierry; Delorme, Christine; Renault, Pierre; Briandet, Romain; Lapaque, Nicolas; Guédon, Eric

2018-01-01

Biofilm formation is crucial for bacterial community development and host colonization by Streptococcus salivarius, a pioneer colonizer and commensal bacterium of the human gastrointestinal tract. This ability to form biofilms depends on bacterial adhesion to host surfaces, and on the intercellular aggregation contributing to biofilm cohesiveness. Many S. salivarius isolates auto-aggregate, an adhesion process mediated by cell surface proteins. To gain an insight into the genetic factors of S. salivarius that dictate host adhesion and biofilm formation, we developed a screening method, based on the differential sedimentation of bacteria in semi-liquid conditions according to their auto-aggregation capacity, which allowed us to identify twelve mutations affecting this auto-aggregation phenotype. Mutations targeted genes encoding (i) extracellular components, including the CshA surface-exposed protein, the extracellular BglB glucan-binding protein, the GtfE, GtfG and GtfH glycosyltransferases and enzymes responsible for synthesis of cell wall polysaccharides (CwpB, CwpK), (ii) proteins responsible for the extracellular localization of proteins, such as structural components of the accessory SecA2Y2 system (Asp1, Asp2, SecA2) and the SrtA sortase, and (iii) the LiaR transcriptional response regulator. These mutations also influenced biofilm architecture, revealing that similar cell-to-cell interactions govern assembly of auto-aggregates and biofilm formation. We found that BglB, CshA, GtfH and LiaR were specifically associated with bacterial auto-aggregation, whereas Asp1, Asp2, CwpB, CwpK, GtfE, GtfG, SecA2 and SrtA also contributed to adhesion to host cells and host-derived components, or to interactions with the human pathogen Fusobacterium nucleatum. Our study demonstrates that our screening method could also be used to identify genes implicated in the bacterial interactions of pathogens or probiotics, for which aggregation is either a virulence trait or an advantageous feature, respectively. PMID:29515553

Influence of surface coating on the intracellular behaviour of gold nanoparticles: a fluorescence correlation spectroscopy study.

PubMed

Silvestri, A; Di Silvio, D; Llarena, I; Murray, R A; Marelli, M; Lay, L; Polito, L; Moya, S E

2017-10-05

In the biomedical applications of nanoparticles (NPs), the proper choice of surface chemistry is a crucial aspect in their design. The nature of the coating can heavily impact the interaction of NPs with biomolecules, affect the state of aggregation, and ultimately determine their biological fate. As such, protein corona formation and the aggregation behaviour of gold NPs (Au NPs) are studied here. Au NPs are prepared with four distinct surface functionalisations, namely mercaptosuccinic acid (MSA), N-4-thiobutyroil glucosamine, HS-PEG 5000 and HS-alkyl-PEG 600 . Corona formation, aggregation, and the intracellular behaviour of the Au NPs are then investigated by means of Fluorescence Correlation Spectroscopy (FCS) in cell culture media and in live cells. To evaluate the state of aggregation and the formation of a protein corona, the Au NPs are incubated in cell media and the diffusion coefficient is determined via FCS. The in vitro behaviour is compared with the level of aggregation of the NPs in cells. Diffusion times of the NPs are estimated at different positions in the cell after a one hour incubation period. It is found that the majority of MSA and glucose-Au NPs are present inside the cell as slowly diffusing species with diffusion times (τ D ) greater than 6000 μs (hydrodynamic diameter >250 nm). PEGylated Au NPs adsorb a small amount of protein and manifest low agglomeration both in media and in living cells. In particular, the HS-alkyl-PEG 600 coating shows an excellent correlation between lower protein adsorption, 4-fold lower compared to the MSA coated NPs, and limited intracellular aggregation. In the case of single HS-alkyl-PEG 600 coated NPs, it is found that typical intracellular τ D values range from 500 to 1500 μs, indicating that these particles display reduced aggregation in the intracellular environment.

Impact of Supramolecular Aggregation on the Crystallization Kinetics of Organic Compounds from the Supercooled Liquid State.

PubMed

Kalra, Arjun; Tishmack, Patrick; Lubach, Joseph W; Munson, Eric J; Taylor, Lynne S; Byrn, Stephen R; Li, Tonglei

2017-06-05

Despite numerous challenges in their theoretical description and practical implementation, amorphous drugs are of growing importance to the pharmaceutical industry. One such challenge is to gain molecular level understanding of the propensity of a molecule to form and remain as a glassy solid. In this study, a series of structurally similar diarylamine compounds was examined to elucidate the role of supramolecular aggregation on crystallization kinetics from supercooled liquid state. The structural similarity of the compounds makes it easier to isolate the molecular features that affect crystallization kinetics and glass forming ability of these compounds. To examine the role of hydrogen-bonded aggregation and motifs on crystallization kinetics, a combination of thermal and spectroscopic techniques was employed. Using variable temperature FTIR, Raman, and solid-state NMR spectroscopies, the presence of hydrogen bonding in the melt and glassy state was examined and correlated with observed phase transition behaviors. Spectroscopic results revealed that the formation of hydrogen-bonded aggregates involving carboxylic acid and pyridine nitrogen (acid-pyridine aggregates) between neighboring molecules in the melt state impedes crystallization, while the presence of carboxylic acid dimers (acid-acid dimers) in the melt favors crystallization. This study suggests that glass formation of small molecules is influenced by the type of intermolecular interactions present in the melt state and the kinetics associated with the molecules to assemble into a crystalline lattice. For the compounds that form acid-pyridine aggregates, the formation of energy degenerate chains, produced due to conformational flexibility of the molecules, presents a kinetic barrier to crystallization. The poor crystallization tendency of these aggregates stems from the highly directional hydrogen-bonding interactions needed to form the acid-pyridine chains. Conversely, for the compounds that form acid-acid dimers, the nondirectional van der Waals forces needed to construct a nucleus promote rapid assembly and crystallization.

The roles of carbohydrates, proteins and lipids in the process of aggregation of natural marine organic matter investigated by means of 2D correlation spectroscopy applied to infrared spectra.

PubMed

Mecozzi, Mauro; Pietrantonio, Eva; Pietroletti, Marco

2009-01-01

In this paper the marine organic matter soluble in an alkaline medium called extractable humic substance (EHS), was extracted from three sediment samples of Tyrrhenian Sea and separated by precipitation at pH 2 in the two fractions of fulvic acids (FAs) and humic acids (HAs). FAs were further fractionated in seven sub-samples of different molecular weight (mw) by means of seven different ultrafiltration membranes operating in the range between mw<1 kDa and mw>100 kDa. Then the qualitative composition of each sample of fractionated FAs and HAs was studied by means of one-dimensional Fourier transform infrared spectroscopy in reflectance mode (FTIR-DRIFT) and by two-dimensional (2D) correlation spectroscopy both in wavelength-wavelength (WW) and in sample-sample (SS) mode. The application of 2D correlation WW spectroscopy allows to elucidate the different roles played by carbohydrates and proteins with respect to some lipid compounds such as fatty acids and ester fatty acids during the process of aggregate formations from mw approximately 1 kDa to higher size aggregates. In addition, 2D correlation WW spectroscopy allows to observe some peculiar interactions between carbohydrates and proteins in the formation of EHS aggregates, interactions which vary from a sample to another sample. The results of 2D correlation SS spectroscopy confirm the general evidences obtained by 2D WW spectroscopy and moreover, they also describe the formation of EHS aggregates as a complex process where evolutionary links and connectivity between aggregates of neighbour molecular size ranges are not evident. Two-dimensional correlation spectroscopy applied to FTIR spectroscopy shows to be a powerful tool for the investigation of the mechanisms involved in EHS aggregation because it supports the acquisition of structural information which sometimes can be hardly obtained by one-dimensional FTIR spectroscopy.

Lysosomal membrane permeability stimulates protein aggregate formation in neurons of a lysosomal disease.

PubMed

Micsenyi, Matthew C; Sikora, Jakub; Stephney, Gloria; Dobrenis, Kostantin; Walkley, Steven U

2013-06-26

Protein aggregates are a common pathological feature of neurodegenerative diseases and several lysosomal diseases, but it is currently unclear what aggregates represent for pathogenesis. Here we report the accumulation of intraneuronal aggregates containing the macroautophagy adapter proteins p62 and NBR1 in the neurodegenerative lysosomal disease late-infantile neuronal ceroid lipofuscinosis (CLN2 disease). CLN2 disease is caused by a deficiency in the lysosomal enzyme tripeptidyl peptidase I, which results in aberrant lysosomal storage of catabolites, including the subunit c of mitochondrial ATP synthase (SCMAS). In an effort to define the role of aggregates in CLN2, we evaluated p62 and NBR1 accumulation in the CNS of Cln2(-/-) mice. Although increases in p62 and NBR1 often suggest compromised degradative mechanisms, we found normal ubiquitin-proteasome system function and only modest inefficiency in macroautophagy late in disease. Importantly, we identified that SCMAS colocalizes with p62 in extra-lysosomal aggregates in Cln2(-/-) neurons in vivo. This finding is consistent with SCMAS being released from lysosomes, an event known as lysosomal membrane permeability (LMP). We predicted that LMP and storage release from lysosomes results in the sequestration of this material as cytosolic aggregates by p62 and NBR1. Notably, LMP induction in primary neuronal cultures generates p62-positive aggregates and promotes p62 localization to lysosomal membranes, supporting our in vivo findings. We conclude that LMP is a previously unrecognized pathogenic event in CLN2 disease that stimulates cytosolic aggregate formation. Furthermore, we offer a novel role for p62 in response to LMP that may be relevant for other diseases exhibiting p62 accumulation.

Molecules of the quinoline family block tau self-aggregation: implications toward a therapeutic approach for Alzheimer's disease.

PubMed

Navarrete, Leonardo P; Guzmán, Leonardo; San Martín, Aurelio; Astudillo-Saavedra, Luis; Maccioni, Ricardo B

2012-01-01

The neurofibrillary tangles (NFTs) generated by self-aggregation of anomalous forms of tau represent a neuropathological hallmark of Alzheimer's disease (AD). These lesions begin to form long before the clinical manifestation of AD, and its severity is correlated with cognitive impairment in patients. We focused on the search for molecules that interact with aggregated tau of the Alzheimer's type and that may block its aggregation before the formation of NFTs. We show that molecules from a family of quinolines interact specifically with oligomeric forms of tau, inhibiting their assembly into AD filaments. The quinolines 2-(4-methylphenyl)-6-methyl quinoline (THQ-4S) and 2-(4-aminophenyl)-6-methylquinoline (THQ-55) inhibited in vitro aggregation of heparin-induced polymers of purified brain tau and aggregates of human recombinant tau. They also interact with paired helical filaments (PHFs) purified from AD postmortem brains. In vitro studies indicated a significantly lower inhibitory effect of amyloid-β42 on the aggregation, suggesting that tau aggregates are specific targets for quinoline interactions. These compounds showed highly lipophilic properties as corroborated with the analysis of total polar surface areas, and evaluation of their molecular properties. Moreover, these quinolines exhibit physical chemical properties similar to drugs able to penetrate the human brain blood barrier. Docking studies based on tau modeling, as a structural approach to the analysis of the interaction of tau-binding ligands, indicated that a C-terminal tau moiety, involved in the formation of PHFs, seems to be a site for binding of quinolines. Studies suggest the potential clinical use of these quinolines and of their derivatives to inhibit tau aggregation and possible therapeutic routes for AD.

A discrete three-layer stack aggregate of a linear porphyrin tetramer: solution-phase structure elucidation by NMR and X-ray scattering.

PubMed

Hutin, Marie; Sprafke, Johannes K; Odell, Barbara; Anderson, Harry L; Claridge, Tim D W

2013-08-28

Formation of stacked aggregates can dramatically alter the properties of aromatic π-systems, yet the solution-phase structure elucidation of these aggregates is often impossible because broad distributions of species are formed, giving uninformative spectroscopic data. Here, we show that a butadiyne-linked zinc porphyrin tetramer forms a remarkably well-defined aggregate, consisting of exactly three molecules, in a parallel stacked arrangement (in chloroform at room temperature; concentration 1 mM-0.1 μM). The aggregate has a mass of 14.7 kDa. Unlike most previously reported aggregates, it gives sharp NMR resonances and aggregation is in slow exchange on the NMR time scale. The structure was elucidated using a range of NMR techniques, including diffusion-editing, (1)H-(29)Si HMBC, (1)H-(1)H COSY, TOCSY and NOESY, and (1)H-(13)C edited HSQC spectroscopy. Surprisingly, the (1)H-(1)H COSY spectrum revealed many long-range residual dipolar couplings (RDCs), and detailed analysis of magnetic field-induced (1)H-(13)C RDCs provided further evidence for the structural model. The size and shape of the aggregate is supported by small-angle X-ray scattering (SAXS) data. It adopts a geometry that maximizes van der Waals contact between the porphyrins, while avoiding clashes between side chains. The need for interdigitation of the side chains prevents formation of stacks consisting of more than three layers. Although a detailed analysis has only been carried out for one compound (the tetramer), comparison with the NMR spectra of other oligomers indicates that they form similar three-layer stacks. In all cases, aggregation can be prevented by addition of pyridine, although at low pyridine concentrations, disaggregation takes many hours to reach equilibrium.

Lysosomal Membrane Permeability Stimulates Protein Aggregate Formation in Neurons of a Lysosomal Disease

PubMed Central

Micsenyi, Matthew C.; Sikora, Jakub; Stephney, Gloria; Dobrenis, Kostantin

2013-01-01

Protein aggregates are a common pathological feature of neurodegenerative diseases and several lysosomal diseases, but it is currently unclear what aggregates represent for pathogenesis. Here we report the accumulation of intraneuronal aggregates containing the macroautophagy adapter proteins p62 and NBR1 in the neurodegenerative lysosomal disease late-infantile neuronal ceroid lipofuscinosis (CLN2 disease). CLN2 disease is caused by a deficiency in the lysosomal enzyme tripeptidyl peptidase I, which results in aberrant lysosomal storage of catabolites, including the subunit c of mitochondrial ATP synthase (SCMAS). In an effort to define the role of aggregates in CLN2, we evaluated p62 and NBR1 accumulation in the CNS of Cln2−/− mice. Although increases in p62 and NBR1 often suggest compromised degradative mechanisms, we found normal ubiquitin–proteasome system function and only modest inefficiency in macroautophagy late in disease. Importantly, we identified that SCMAS colocalizes with p62 in extra-lysosomal aggregates in Cln2−/− neurons in vivo. This finding is consistent with SCMAS being released from lysosomes, an event known as lysosomal membrane permeability (LMP). We predicted that LMP and storage release from lysosomes results in the sequestration of this material as cytosolic aggregates by p62 and NBR1. Notably, LMP induction in primary neuronal cultures generates p62-positive aggregates and promotes p62 localization to lysosomal membranes, supporting our in vivo findings. We conclude that LMP is a previously unrecognized pathogenic event in CLN2 disease that stimulates cytosolic aggregate formation. Furthermore, we offer a novel role for p62 in response to LMP that may be relevant for other diseases exhibiting p62 accumulation. PMID:23804102

Oil-suspended particulate material aggregates as a tool in preventing potential ecotoxicological impacts in the São Paulo river, Todos os Santos Bay, Bahia, Brazil: Influence of salinity and suspended particulate material.

PubMed

Miranda, Lorena S; Moreira, Ícaro T A; Oliveira, Olívia M C; Santos, Carlito P; Pinheiro, Samires M M; Oliveira, Lua M L; Martins, Adriele B O; Filho, Milton S C

2016-11-15

Recent studies have revealed the occurrence of a natural process of interaction between oil droplets and suspended particulate material, resulting in the formation of aggregates which are dispersed in the water column, known as oil-suspended particulate material aggregates (OSAs). The experiments aimed to investigate the contribution of OSAS in indicating where most likely is the oil sedimentation in the São Paulo river, Todos os Santos Bay, Brazil, in order to predict possible ecotoxicological risks caused by oil spills. The results showed that salinity and MPS concentration interfere on the formation of aggregates. In addition, the point 3 was nominated as the most vulnerable area to the potential ecotoxicological impacts of oil spills and should be treated as a priority area for the application of preventive and mitigating techniques. Copyright © 2016 Elsevier Ltd. All rights reserved.

Inhibition of cyclooxygenase-independent platelet aggregation by sodium salicylate.

PubMed

Violi, F; Alessandri, C; Praticò, D; Guzzo, A; Ghiselli, A; Balsano, F

1989-06-15

The effect of acetylsalicylic acid (ASA) on platelet aggregation (PA) and thromboxane A2 (TxA2) formation was investigated in vitro and ex vivo after 1 g or 300 mg ASA administration to healthy subjects. 50-100 microM ASA inhibited PA by single aggregating agent such as platelet aggregating factor (PAF) or epinephrine and reduced to less than or equal to 5% of control platelet TxB2 formation, but did not influence PA by epinephrine plus PAF. The latter was inhibited by increasing ASA concentration. In samples incubated with 100 microM ASA and stimulated with epinephrine plus PAF, PA could be inhibited by the addition of 100-300 microM sodium salicylate. After 300 mg-1 g ASA administration to healthy subjects, the inhibition of PA by epinephrine plus PAF was more marked by highest doses of ASA. This study suggests that aspirin inhibits PA with a cyclooxygenase-independent mechanism; this effect is mediated, at least in vitro, by salicylic acid.

Feedbacks Between Soil Structure and Microbial Activities in Soil

NASA Astrophysics Data System (ADS)

Bailey, V. L.; Smith, A. P.; Fansler, S.; Varga, T.; Kemner, K. M.; McCue, L. A.

2017-12-01

Soil structure provides the physical framework for soil microbial habitats. The connectivity and size distribution of soil pores controls the microbial access to nutrient resources for growth and metabolism. Thus, a crucial component of soil research is how a soil's three-dimensional structure and organization influences its biological potential on a multitude of spatial and temporal scales. In an effort to understand microbial processes at scale more consistent with a microbial community, we have used soil aggregates as discrete units of soil microbial habitats. Our research has shown that mean pore diameter (x-ray computed tomography) of soil aggregates varies with the aggregate diameter itself. Analyzing both the bacterial composition (16S) and enzyme activities of individual aggregates showed significant differences in the relative abundances of key members the microbial communities associated with high enzyme activities compared to those with low activities, even though we observed no differences in the size of the biomass, nor in the overall richness or diversity of these communities. We hypothesize that resources and substrates have stimulated key populations in the aggregates identified as highly active, and as such, we conducted further research that explored how such key populations (i.e. fungal or bacterial dominated populations) alter pathways of C accumulation in aggregate size domains and microbial C utilization. Fungi support and stabilize soil structure through both physical and chemical effects of their hyphal networks. In contrast, bacterial-dominated communities are purported to facilitate micro- and fine aggregate stabilization. Here we quantify the direct effects fungal versus bacterial dominated communities on aggregate formation (both the rate of aggregation and the quality, quantity and distribution of SOC contained within aggregates). A quantitative understanding of the different mechanisms through which fungi or bacteria shape aggregate formation could alter how we currently treat our predictions of soil biogeochemistry. Current predictions are largely site- or biome-specific; quantitative mechanisms could underpin "rules" that operate at the pore-scale leading to more robust, mechanistic models.

Latitudinal variation in sensitivity of flower bud formation to high temperature in Japanese Taraxacum officinale.

PubMed

Yoshie, Fumio

2014-05-01

Control of flowering time plays a key role in the successful range expansion of plants. Taraxacum officinale has expanded throughout Japan during the 110 years after it was introduced into a cool temperate region. The present study tested a hypothesis that there is a genetic difference in the bud formation time in relation to temperature along latitudinal gradient of T. officinale populations. In Experiment 1, plants from three populations at different latitudes (26, 36, and 43°N) were grown at three temperatures. Time to flower bud appearance did not significantly differ among the three populations when plants were grown at 14 °C, whereas it increased with increasing latitude when grown at 19 and 24 °C. Rosette diameter was not different among the populations, indicating that the variation in bud formation time reflected a difference in genetic control rather than size variation. The latitudinal variation in bud appearance time was confirmed by Experiment 2 in which plants from 17 population were used. In Experiment 3, the size of plants that exhibited late-flowering was studied to test a hypothesis that the variation in flowering time reflects dormancy of vegetative growth, but the late-flowering plants were found to continue growth, indicating that vegetative dormancy was not the cause of the variation. The results clearly indicate that the degree of suppression of flower bud formation at high temperature decreases with latitude from north to south, which is under genetic control.

Study of the aggregation mechanism of polyglutamine peptides using replica exchange molecular dynamics simulations.

PubMed

Nakano, Miki; Ebina, Kuniyoshi; Tanaka, Shigenori

2013-04-01

Polyglutamine (polyQ, a peptide) with an abnormal repeat length is the causative agent of polyQ diseases, such as Huntington's disease. Although glutamine is a polar residue, polyQ peptides form insoluble aggregates in water, and the mechanism for this aggregation is still unclear. To elucidate the detailed mechanism for the nucleation and aggregation of polyQ peptides, replica exchange molecular dynamics simulations were performed for monomers and dimers of polyQ peptides with several chain lengths. Furthermore, to determine how the aggregation mechanism of polyQ differs from those of other peptides, we compared the results for polyQ with those of polyasparagine and polyleucine. The energy barrier between the monomeric and dimeric states of polyQ was found to be relatively low, and it was observed that polyQ dimers strongly favor the formation of antiparallel β-sheet structures. We also found a characteristic behavior of the monomeric polyQ peptide: a turn at the eighth residue is always present, even when the chain length is varied. We previously showed that a structure including more than two sets of β-turns is stable, so a long monomeric polyQ chain can act as an aggregation nucleus by forming several pairs of antiparallel β-sheet structures within a single chain. Since the aggregation of polyQ peptides has some features in common with an amyloid fibril, our results shed light on the mechanism for the aggregation of polyQ peptides as well as the mechanism for the formation of general amyloid fibrils, which cause the onset of amyloid diseases.

Hydroxychavicol, a novel betel leaf component, inhibits platelet aggregation by suppression of cyclooxygenase, thromboxane production and calcium mobilization.

PubMed

Chang, M C; Uang, B J; Tsai, C Y; Wu, H L; Lin, B R; Lee, C S; Chen, Y J; Chang, C H; Tsai, Y L; Kao, C J; Jeng, J H

2007-09-01

Platelet hyperactivity is important in the pathogenesis of cardiovascular diseases. Betel leaf (PBL) is consumed by 200-600 million betel quid chewers in the world. Hydroxychavicol (HC), a betel leaf component, was tested for its antiplatelet effect. We tested the effect of HC on platelet aggregation, thromboxane B(2) (TXB(2)) and reactive oxygen species (ROS) production, cyclooxygenase (COX) activity, ex vivo platelet aggregation and mouse bleeding time and platelet plug formation in vivo. The pharmacokinetics of HC in rats was also assessed. HC inhibited arachidonic acid (AA) and collagen-induced platelet aggregation and TXB(2) production. HC inhibited the thrombin-induced TXB(2) production, but not platelet aggregation. SQ29548, suppressed collagen- and thrombin-induced TXB(2) production, but not thrombin-induced platelet aggregation. HC also suppressed COX-1/COX-2 enzyme activity and the AA-induced ROS production and Ca(2+) mobilization. HC further inhibited the ex vivo platelet aggregation of platelet-rich plasma (>100 nmole/mouse) and prolonged platelet plug formation (>300 nmole/mouse) in mesenteric microvessels, but showed little effect on bleeding time in mouse tail. Moreover, pharmacokinetics analysis found that more than 99% of HC was metabolized within 3 min of administration in Sprague-Dawley rats in vivo. HC is a potent COX-1/COX-2 inhibitor, ROS scavenger and inhibits platelet calcium signaling, TXB(2) production and aggregation. HC could be a potential therapeutic agent for prevention and treatment of atherosclerosis and other cardiovascular diseases through its anti-inflammatory and antiplatelet effects, without effects on haemostatic functions.

Rigid aggregates: theory and applications

NASA Astrophysics Data System (ADS)

Richardson, D. C.

2005-08-01

Numerical models employing ``perfect'' self-gravitating rubble piles that consist of monodisperse rigid spheres with configurable contact dissipation have been used to explore collisional and rotational disruption of gravitational aggregates. Applications of these simple models include numerical simulations of planetesimal evolution, asteroid family formation, tidal disruption, and binary asteroid formation. These studies may be limited by the idealized nature of the rubble pile model, since perfect identical spheres stack and shear in a very specific, possibly over-idealized way. To investigate how constituent properties affect the overall characteristics of a gravitational aggregate, particularly its failure modes, we have generalized our numerical code to model colliding, self-gravitating, rigid aggregates made up of variable-size spheres. Euler's equation of rigid-body motion in the presence of external torques are implemented, along with a self-consistent prescription for handling non-central impacts. Simple rules for sticking and breaking are also included. Preliminary results will be presented showing the failure modes of gravitational aggregates made up of smaller, rigid, non-idealized components. Applications of this new capability include more realistic aggregate models, convenient modeling of arbitrary rigid shapes for studies of the stability of orbiting companions (replacing one or both bodies with rigid aggregates eliminates expensive interparticle collisions while preserving the shape, spin, and gravity field of the bodies), and sticky particle aggregation in dense planetary rings. This material is based upon work supported by the National Aeronautics and Space Administration under Grant No. NAG511722 issued through the Office of Space Science and by the National Science Foundation under Grant No. AST0307549.

Determination of critical nucleation number for a single nucleation amyloid-β aggregation model.

PubMed

Ghosh, Preetam; Vaidya, Ashwin; Kumar, Amit; Rangachari, Vijayaraghavan

2016-03-01

Aggregates of amyloid-β (Aβ) peptide are known to be the key pathological agents in Alzheimer disease (AD). Aβ aggregates to form large, insoluble fibrils that deposit as senile plaques in AD brains. The process of aggregation is nucleation-dependent in which the formation of a nucleus is the rate-limiting step, and controls the physiochemical fate of the aggregates formed. Therefore, understanding the properties of nucleus and pre-nucleation events will be significant in reducing the existing knowledge-gap in AD pathogenesis. In this report, we have determined the plausible range of critical nucleation number (n(*)), the number of monomers associated within the nucleus for a homogenous aggregation model with single unique nucleation event, by two independent methods: A reduced-order stability analysis and ordinary differential equation based numerical analysis, supported by experimental biophysics. The results establish that the most likely range of n(*) is between 7 and 14 and within, this range, n(*) = 12 closely supports the experimental data. These numbers are in agreement with those previously reported, and importantly, the report establishes a new modeling framework using two independent approaches towards a convergent solution in modeling complex aggregation reactions. Our model also suggests that the formation of large protofibrils is dependent on the nature of n(*), further supporting the idea that pre-nucleation events are significant in controlling the fate of larger aggregates formed. This report has re-opened an old problem with a new perspective and holds promise towards revealing the molecular events in amyloid pathologies in the future. Copyright © 2015 Elsevier Inc. All rights reserved.

Life cycle of Arabidopsis thaliana under microgravity condition in the International Space Station Kibo module

NASA Astrophysics Data System (ADS)

Karahara, Ichirou; Soga, Kouichi; Hoson, Takayuki; Kamisaka, Seiichiro; Yano, Sachiko; Shimazu, Toru; Tamaoki, Daisuke; Tanigaki, Fumiaki; Kasahara, Haruo; Yashiro, Umi; Suto, Takamichi; Yamaguchi, Takashi; Kasahara, Hirokazu

2012-07-01

Gravity is an important environmental factors for growth and development of plants throughout their life cycle. We have designed an experiment, which is called Space Seed, to examine the effects of microgravity on the seed to seed life cycle of plants. We have carried out this experiment using a newly developed apparatus, which is called the Plant Experiment Unit (PEU) and installed in the Cell Biology Experiment Facility (CBEF) onboard International Space Station (ISS). The CBEF is equipped with a turntable generating artificial gravity to perform 1-G control experiment as well as micro-G experiment on board. Arabidopsis thaliana seeds sown on dry rockwool in PEUs were transported from Kennedy Space Center to the ISS Kibo module by Space Shuttle Discovery in STS-128 mission. This experiment was started on Sep. 10, 2009 and terminated on Nov. 11, 2009. Arabidopsis seeds successfully germinated, and the plants passed through both vegetative and reproductive processes, such as formation of rosette leaves, bolting of inflorescence stems, flowering, formation of siliques and seeds. Vegetative and reproductive growth were compared among micro-G plants, 1-G control, and the ground control.

Demonstration of specific binding of heparin to Plasmodium falciparum-infected vs. non-infected red blood cells by single-molecule force spectroscopy

NASA Astrophysics Data System (ADS)

Valle-Delgado, Juan José; Urbán, Patricia; Fernàndez-Busquets, Xavier

2013-04-01

Glycosaminoglycans (GAGs) play an important role in the sequestration of Plasmodium falciparum-infected red blood cells (pRBCs) in the microvascular endothelium of different tissues, as well as in the formation of small clusters (rosettes) between infected and non-infected red blood cells (RBCs). Both sequestration and rosetting have been recognized as characteristic events in severe malaria. Here we have used heparin and pRBCs infected by the 3D7 strain of P. falciparum as a model to study GAG-pRBC interactions. Fluorescence microscopy and fluorescence-assisted cell sorting assays have shown that exogenously added heparin has binding specificity for pRBCs (preferentially for those infected with late forms of the parasite) vs. RBCs. Heparin-pRBC adhesion has been probed by single-molecule force spectroscopy, obtaining an average binding force ranging between 28 and 46 pN depending on the loading rate. No significant binding of heparin to non-infected RBCs has been observed in control experiments. This work represents the first approach to quantitatively evaluate GAG-pRBC molecular interactions at the individual molecule level.Glycosaminoglycans (GAGs) play an important role in the sequestration of Plasmodium falciparum-infected red blood cells (pRBCs) in the microvascular endothelium of different tissues, as well as in the formation of small clusters (rosettes) between infected and non-infected red blood cells (RBCs). Both sequestration and rosetting have been recognized as characteristic events in severe malaria. Here we have used heparin and pRBCs infected by the 3D7 strain of P. falciparum as a model to study GAG-pRBC interactions. Fluorescence microscopy and fluorescence-assisted cell sorting assays have shown that exogenously added heparin has binding specificity for pRBCs (preferentially for those infected with late forms of the parasite) vs. RBCs. Heparin-pRBC adhesion has been probed by single-molecule force spectroscopy, obtaining an average binding force ranging between 28 and 46 pN depending on the loading rate. No significant binding of heparin to non-infected RBCs has been observed in control experiments. This work represents the first approach to quantitatively evaluate GAG-pRBC molecular interactions at the individual molecule level. Electronic supplementary information (ESI) available. See DOI: 10.1039/c2nr32821f

Glycation induces formation of amyloid cross-beta structure in albumin.

PubMed

Bouma, Barend; Kroon-Batenburg, Loes M J; Wu, Ya-Ping; Brünjes, Bettina; Posthuma, George; Kranenburg, Onno; de Groot, Philip G; Voest, Emile E; Gebbink, Martijn F B G

2003-10-24

Amyloid fibrils are components of proteinaceous plaques that are associated with conformational diseases such as Alzheimer's disease, transmissible spongiform encephalopathies, and familial amyloidosis. Amyloid polypeptides share a specific quarternary structure element known as cross-beta structure. Commonly, fibrillar aggregates are modified by advanced glycation end products (AGE). In addition, AGE formation itself induces protein aggregation. Both amyloid proteins and protein-AGE adducts bind multiligand receptors, such as receptor for AGE, CD36, and scavenger receptors A and B type I, and the serine protease tissue-type plasminogen activator (tPA). Based on these observations, we hypothesized that glycation induces refolding of globular proteins, accompanied by formation of cross-beta structure. Using transmission electron microscopy, we demonstrate here that glycated albumin condensates into fibrous or amorphous aggregates. These aggregates bind to amyloid-specific dyes Congo red and thioflavin T and to tPA. In contrast to globular albumin, glycated albumin contains amino acid residues in beta-sheet conformation, as measured with circular dichroism spectropolarimetry. Moreover, it displays cross-beta structure, as determined with x-ray fiber diffraction. We conclude that glycation induces refolding of initially globular albumin into amyloid fibrils comprising cross-beta structure. This would explain how glycated ligands and amyloid ligands can bind to the same multiligand "cross-beta structure" receptors and to tPA.

Impact of Microcystis aeruginosa Exudate on the Formation and Reactivity of Iron Oxide Particles Following Fe(II) and Fe(III) Addition.

PubMed

Garg, Shikha; Wang, Kai; Waite, T David

2017-05-16

Impact of the organic exudate secreted by a toxic strain of Microcystis aeruginosa on the formation, aggregation, and reactivity of iron oxides that are formed on addition of Fe(II) and Fe(III) salts to a solution of the exudate is investigated in this study. The exudate has a stabilizing effect on the particles formed with decreased aggregation rate and increased critical coagulant concentration required for diffusion-limited aggregation to occur. These results suggest that the presence of algal exudates from Microcystis aeruginosa may significantly influence particle aggregation both in natural water bodies where Fe(II) oxidation results in oxide formation and in water treatment where Fe(III) salts are commonly added to aid particle growth and contaminant capture. The exudate also affects the reactivity of iron oxide particles formed with exudate coated particles undergoing faster dissolution than bare iron oxide particles. This has implications to iron availability, especially where algae procure iron via dissolution of iron oxide particles as a result of either reaction with reducing moieties, light-mediated ligand to metal charge transfer and/or reaction with siderophores. The increased reactivity of exudate coated particles is attributed, for the most part, to the smaller size of these particles, higher surface area and increased accessibility of surface sites.

A conserved tad pilus promotes Vibrio vulnificus oyster colonization.

PubMed

Pu, Meng; Duriez, Patrick; Arazi, Mattan; Rowe-Magnus, Dean A

2018-02-01

Vibrio vulnificus has the highest death rate (>35%) and per-case economic burden ($3.3 million) of any foodborne pathogen in the United States. Infections occur via open wounds or following ingestion of contaminated seafood, most infamously oysters. We isolated a 1000th generation descendant, designated NT that exhibited increased biofilm and aggregate formation relative to its parent. We identified two significant causal changes underlying these phenotypes. First, the entire 24-kb capsular polysaccharide biosynthesis locus, which is essential for virulence but inhibits biofilm formation, had been purged from the genome. However, NT formed more extensive biofilms and aggregates than a defined cps mutant, suggesting that additional factor(s) contributed to its phenotypes. Second, the expression of a tight adherence (tad) pilus locus was elevated in NT. Deletion of the associated pilin (flp) decreased NT biofilm and aggregate formation. Furthermore, NTΔflp strains were deficient relative to NT in an oyster colonization model, demonstrating a positive correlation between the biofilm and aggregation phenotypes associated with Tad pilus production and efficient bacterial retention by feeding oysters. Despite being widely distributed in the Vibrionaceae, this is the first demonstration of a bona fide physiological role for a Tad pilus in this bacterial family. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Amyloid fibrils: formation, replication, and physics behind them

NASA Astrophysics Data System (ADS)

Saric, Andela

The assembly of normally soluble proteins into long fibrils, known as amyloids, is associated with a range of pathologies, including Alzheimer's and Parkinson's diseases. A large number of structurally unrelated proteins form this type of fibrils, and we are in a pursuit of physical principles that underlie the amyloid formation and propagation. We show that small disorders oligomers, which are increasingly believed to be the prime cause for cellular toxicity, serve as nucleation centers for the fibril formation. We then relate experimentally measurable kinetic descriptors of amyloid aggregation to the microscopic mechanisms of the process. Once formed, amyloid fibrils can catalyse the formation of new oligomers and fibrils in a process that resembles self-replication. By combining simulations with biosensing and kinetic measurements of the aggregation of Alzheimer's A β peptide, we propose a mechanistic explanation for the self-replication of protein fibrils, and discuss its thermodynamic signature. Finally, we consider the design of possible inhibitors of the fibril self-replication process. Mechanistic understandings provided here not only have implications for future efforts to control pathological protein aggregation, but are also of interest for the rational assembly of bionanomaterials, where achieving and controlling self-replication is one of the unfulfilled goals.

A-type dimeric epigallocatechin-3-gallate (EGCG) is a more potent inhibitor against the formation of insulin amyloid fibril than EGCG monomer.

PubMed

Nie, Rong-Zu; Zhu, Wei; Peng, Jin-Ming; Ge, Zhen-Zhen; Li, Chun-Mei

2016-06-01

Because fibrillary protein aggregates is regarded to be closely associated with many diseases such as Alzheimer's disease, diabetes, and Parkinson's disease, growing interest and researches have been focused on finding potential fibrillation inhibitors. In the present study, the inhibitory effects of epigallocatechin-3-gallate (EGCG) and A-type dimeric epigallocatechin-3-gallate (A-type EGCG dimer) on the formation of insulin fibrillation were compared by multi-dimensional approaches including thioflavin-T (ThT) fluorescence assay, 1-anilinonaphthalene-8-sulfonic (ANS) fluorescence assay, dynamic light scattering (DLS), transmission electron microscopy (TEM), Fourier transform infrared (FTIR) spectroscopy and circular dichroism (CD) spectroscopy. Our results confirmed that A-type EGCG dimer is a more potent inhibitor against the formation of bovine insulin amyloid fibril than EGCG. In addition, A-type EGCG dimer could not only inhibit insulin amyloid fibril formation, but also change the aggregation pathway and induce bovine insulin into amorphous aggregates. The results of the present study may provide a new guide on finding novel anti-amyloidogenic agents. Copyright © 2016 Elsevier B.V. and Société française de biochimie et biologie Moléculaire (SFBBM). All rights reserved.

Live and heat-killed Lactobacillus spp. interfere with Streptococcus mutans and Streptococcus oralis during biofilm development on titanium surface.

PubMed

Ciandrini, E; Campana, R; Baffone, W

2017-06-01

This research investigates the ability of live and heat-killed (HK) Lactic Acid Bacteria (LAB) to interfere with Streptococcus mutans ATCC 25175 and Streptococcus oralis ATCC 9811 during biofilm formation. Eight Lactobacillus spp. and two oral colonizers, pathogenic Streptococcus mutans and resident Streptococcus oralis, were characterized for their aggregation abilities, cell surface properties and biofilm formation ability on titanium surface. Then, the interference activity of selected live and HK Lactobacillus spp. during S. mutans and S. oralis biofilm development were performed. The cell-free culture supernatants (CFCS) anti-biofilm activity was also determined. LAB possess good abilities of auto-aggregation (from 14.19 to 28.97%) and of co-aggregation with S. oralis. The cell-surfaces characteristics were most pronounced in S. mutans and S. oralis, while the highest affinities to xylene and chloroform were observed in Lactobacillus rhamnosus ATCC 53103 (56.37%) and Lactobacillus paracasei B21060 (43.83%). S. mutans and S. oralis developed a biofilm on titanium surface, while LAB showed a limited or no ability to create biofilm. Live and HK L. rhamnosus ATCC 53103 and L. paracasei B21060 inhibited streptococci biofilm formation by competition and displacement mechanisms with no substantial differences. The CFCSs of both LAB strains, particularly the undiluted one of L. paracasei B21060, decreased S. mutans and S. oralis biofilm formation. This study evidenced the association of LAB aggregation abilities and cell-surface properties with the LAB-mediated inhibition of S. mutans and S. oralis biofilm formation. Lactobacilli showed different mechanisms of action and peculiar strain-specific characteristics, maintained also in the heat-killed LAB. Copyright © 2017 Elsevier Ltd. All rights reserved.

A model for thin layer formation by delayed particle settling at sharp density gradients

NASA Astrophysics Data System (ADS)

Prairie, Jennifer C.; White, Brian L.

2017-02-01

Thin layers - regions where plankton or particles accumulate vertically on scales of a few meters or less - are common in coastal waters, and have important implications for both trophic dynamics and carbon cycling. These features can form by a variety of biological and physical mechanisms, including localized growth, shear-thinning, and directed swimming. An additional mechanism may result in the formation of thin layers of marine aggregates, which have been shown to decrease their settling velocity when passing through sharp density gradients, a behavior termed delayed settling. Here, we apply a simple vertical advection-diffusion model to predict the properties of aggregate thin layers formed by this process. We assume a constant vertical flux of particles from the surface, which is parameterized by observations from laboratory experiments with marine aggregates. The formation, maintenance, and shape of the layers are described in relation to non-dimensional numbers that depend on environmental conditions and particle settling properties. In particular, model results demonstrate layer intensity and sharpness both increase with higher Péclet number (Pe), that is, under conditions with weaker mixing relative to layer formation. Similarly, more intense and sharper layers are found when the delayed settling behavior of aggregates is characterized by a lower velocity minimum. The model also predicts layers that are vertically asymmetric and highly "peaky" when compared with a Gaussian distribution, features often seen in thin layers in natural environments. Lastly, by comparing model predictions with observations of thin layers in the field, we are able to gain some insight into the applicability of delayed settling as a thin layer formation mechanism in different environmental conditions.

Study of tissue engineered bone nodules by Fourier transform infrared spectroscopy.

PubMed

Aydin, Halil Murat; Hu, Bin; Suso, Josep Sulé; El Haj, Alicia; Yang, Ying

2011-02-21

The key criteria for assessing the success of bone tissue engineering are the quality and quantity of the produced minerals within the cultured constructs. The accumulation of calcium ions and inorganic phosphates in culture medium serves as nucleating agents for the formation of hydroxyapatite, which is the main inorganic component of bone. Bone nodule formation is one of the hallmarks of mineralization in such cell cultures. In this study, we developed a new two-step procedure to accelerate bone formation in which mouse bone cell aggregates were produced first on various chemically treated non-adhesive substrates. After this step, the bone cells' growth and mineralization were followed in conventional culture plates. The number and size of cell aggregates were studied with light microscopy. The minerals' formation in the form of nodules produced by the cell aggregates and the bone crystal quality were studied with Fourier Transform Infrared (FTIR) spectroscopy. The FTIR spectra of the ash specimens (mineral phase only) from thermal gravimetric analysis (TGA) provided valuable information of the quality of the minerals. The υ(4) PO(4) region (550-650 cm(-1)), which reveals apatitic and non-apatitic HPO(4) or PO(4) environments, and phosphate region (910-1180 cm(-1)) were examined for the minerals produced in the form of nodules. The peak position and intensity of the spectra demonstrate that the quality of the bone produced by cell aggregates, especially from the bigger ones, which were formed on Plunoric treated substrates, exhibit a composition more similar to that of native bone. This work establishes a new protocol for high quality bone formation and characterization, with the potential to be applied to bone tissue engineering.

Effect of homogenisation in formation of thermally induced aggregates in a non- and low- fat milk model system with microparticulated whey proteins.

PubMed

Torres, Isabel Celigueta; Nieto, Gema; Nylander, Tommy; Simonsen, Adam Cohen; Tolkach, Alexander; Ipsen, Richard

2017-05-01

The objective of the research presented in this paper was to investigate how different characteristics of whey protein microparticles (MWP) added to milk as fat replacers influence intermolecular interactions occurring with other milk proteins during homogenisation and heating. These interactions are responsible for the formation of heat-induced aggregates that influence the texture and sensory characteristics of the final product. The formation of heat-induced complexes was studied in non- and low-fat milk model systems, where microparticulated whey protein (MWP) was used as fat replacer. Five MWP types with different particle characteristics were utilised and three heat treatments used: 85 °C for 15 min, 90 °C for 5 min and 95 °C for 2 min. Surface characteristics of the protein aggregates were expressed as the number of available thiol groups and the surface net charge. Intermolecular interactions involved in the formation of protein aggregates were studied by polyacrylamide gel electrophoresis and the final complexes visualised by darkfield microscopy. Homogenisation of non-fat milk systems led to partial adsorption of caseins onto microparticles, independently of the type of microparticle. On the contrary, homogenisation of low-fat milk resulted in preferential adsorption of caseins onto fat globules, rather than onto microparticles. Further heating of the milk, led to the formation of heat induced complexes with different sizes and characteristics depending on the type of MWP and the presence or not of fat. The results highlight the importance of controlling homogenisation and heat processing in yoghurt manufacture in order to induce desired changes in the surface reactivity of the microparticles and thereby promote effective protein interactions.

F-aggregate centers formation in BaLiF3 crystals

NASA Astrophysics Data System (ADS)

Prado, L.; Gomes, L.; Baldochi, S. L.; Morato, S. P.; Vieira, N. D.

The kinetics of F-aggregate centers formation is investigated in the inverted fluoroperovskite of BaLiF3 submitted to electron-irradiation. By studies of the changes in the absorption spectra during storage of samples in the dark, at room temperature, it was possible to verify a surprising and interesting dependence on defect formation with the crystal growth direction. In spite of its cubic structure, crystals grown in the <100> and <111> directions and submitted to the same conditions of irradiation, showed in particular, to enhance the production of a defect absorbing at 630 nm in <100> crystals which we believe to correspond to F+2-centers in BaLiF3

Enhanced DNA Sensing via Catalytic Aggregation of Gold Nanoparticles

PubMed Central

Huttanus, Herbert M.; Graugnard, Elton; Yurke, Bernard; Knowlton, William B.; Kuang, Wan; Hughes, William L.; Lee, Jeunghoon

2014-01-01

A catalytic colorimetric detection scheme that incorporates a DNA-based hybridization chain reaction into gold nanoparticles was designed and tested. While direct aggregation forms an inter-particle linkage from only ones target DNA strand, the catalytic aggregation forms multiple linkages from a single target DNA strand. Gold nanoparticles were functionalized with thiol-modified DNA strands capable of undergoing hybridization chain reactions. The changes in their absorption spectra were measured at different times and target concentrations and compared against direct aggregation. Catalytic aggregation showed a multifold increase in sensitivity at low target concentrations when compared to direct aggregation. Gel electrophoresis was performed to compare DNA hybridization reactions in catalytic and direct aggregation schemes, and the product formation was confirmed in the catalytic aggregation scheme at low levels of target concentrations. The catalytic aggregation scheme also showed high target specificity. This application of a DNA reaction network to gold nanoparticle-based colorimetric detection enables highly-sensitive, field-deployable, colorimetric readout systems capable of detecting a variety of biomolecules. PMID:23891867

Using Human iPSC-Derived Neurons to Model TAU Aggregation

PubMed Central

Verheyen, An; Diels, Annick; Dijkmans, Joyce; Oyelami, Tutu; Meneghello, Giulia; Mertens, Liesbeth; Versweyveld, Sofie; Borgers, Marianne; Buist, Arjan; Peeters, Pieter; Cik, Miroslav

2015-01-01

Alzheimer’s disease and frontotemporal dementia are amongst the most common forms of dementia characterized by the formation and deposition of abnormal TAU in the brain. In order to develop a translational human TAU aggregation model suitable for screening, we transduced TAU harboring the pro-aggregating P301L mutation into control hiPSC-derived neural progenitor cells followed by differentiation into cortical neurons. TAU aggregation and phosphorylation was quantified using AlphaLISA technology. Although no spontaneous aggregation was observed upon expressing TAU-P301L in neurons, seeding with preformed aggregates consisting of the TAU-microtubule binding repeat domain triggered robust TAU aggregation and hyperphosphorylation already after 2 weeks, without affecting general cell health. To validate our model, activity of two autophagy inducers was tested. Both rapamycin and trehalose significantly reduced TAU aggregation levels suggesting that iPSC-derived neurons allow for the generation of a biologically relevant human Tauopathy model, highly suitable to screen for compounds that modulate TAU aggregation. PMID:26720731

Small static electric field strength promotes aggregation-prone structures in amyloid-β(29-42)

NASA Astrophysics Data System (ADS)

Lu, Yan; Shi, Xiao-Feng; Salsbury, Freddie R.; Derreumaux, Philippe

2017-04-01

The formation of senile plaques in central neural system resulting from the aggregation of the amyloid β (Aβ) of 40 and 42 residues is one of the two hallmarks of Alzheimer's disease. Numerous experiments and computational studies have shown that the aggregation of Aβ peptides in vitro is very complex and depends on many factors such as pH, agitation, temperature, and peptide concentration. The impact of a static electric field (EF) on amyloid peptide aggregation has been much less studied, although EFs may have some applications to treat Parkinson's disease symptoms. Here, we study the influence of an EF strength of 20 mV/nm, present in the human brains, on the conformation of the Aβ29-42 dimer. Our 7 μs non-equilibrium atomistic simulations in aqueous solution show that this field-strength promotes substantially the formation of β-hairpins, believed to be a very important intermediate state during aggregation. This work also suggests that structural biology experiments conducted under appropriate EF strengths may help reduce the conformational heterogeneity of Aβ1-40/Aβ1-42 dimers and provide significant insights into their structures that may be disease-causing.

Theoretical insights into aggregation-induced helicity modulation of a perylene bisimide derivative.

PubMed

Liang, Lijun; Li, Xin

2018-02-12

Formation of helical chiroptical self-assemblies via noncovalent interaction is a widely observed phenomenon in nature, the mechanism of which remains insufficiently understood. Employing an amphiphilic perylene-sugar dyad molecule (PBI-HAG) as an example, we report that the modulatable supramolecular helicity may emerge from an aggregating process that is dominated by competition between two types of noncovalent interaction: hydrogen bonding and π-π stacking. The interplay between these two driving forces, which is greatly affected by the solvent environment, determines the morphology the supramolecular assembly of PBI-HAGs. In particular, a non-layered supramolecular structure was formed in octane owing to stabilization effects of intermolecular hydrogen bonds, whereas a layered supramolecular structure was formed in water because of energetically favorable π-π stacking of aromatic rings. The formation of distinct supramolecular architectures in different solvents was reinforced by simulated circular dichroism spectra, which show opposite signals consistent with experimental observations. The results of this study could help us understand aggregation-induced supramolecular chirality of noncovalent self-assemblies. Graphical abstract Left Typical structures of amphiphilic perylene-sugar dyad (PBI-HAG) aggregates in different octane and water. Right Simulated CD and UV-Vis spectra of core PBIs aggregates in octane and water.