Coarse-Grained Simulation of Amyloid Nucleation under Cooperative Effects of Peptides / 医用生物力学

Objective To explore the cooperative effect from β-propensity of amyloidogenic peptides on amyloid nucleation and its related products. Methods Based on a coarse-grained model for amyloidogenic peptides containing two states ( a soluble state and a β-sheet-forming state), with the consideration of two kinds of cooperative effects on β-propensity of peptides ( inhibiting and promoting the conformational conversion of peptides), the regulation of cooperative effects from amyloidogenic peptides on amyloid nucleation was analyzed through Monte Carlo simulations. Results In the case of the cooperative effect inhibiting the conformational conversion of peptides, amyloid nucleation occurred only within a certain interval of the peptide concentration, as well as inside the oligomers with certain sizes. Besides, the coexistence of on-pathway and off-pathway oligomers was observed. In the case of the cooperative effect promoting the conformational conversion of peptides, the β-sheet protofibril could be observed at physiological concentration as low as 4 μmol / L. Conclusions In this study, a more realistic coarse-grained model for amyloidogenic peptides was developed by introducing the cooperative effects of local concentration on β-propensity of amyloidogenic peptides, with observation of some intriguing phenomena not reported in previous simulations. The research findings not only improve current understandings about the mechanism of amyloid formation, but also provide theoretic references for the therapeutic strategies for curing neurodegenerative diseases

Anti urolithiatic activity of Cyperus rotundus tubers: In silico, In vitro and In vivo approaches

Abstract The present research evaluated the anti urolithic potential of Cyperus rotundus tubers extract using in silico, in vitro and in vivo techniques. In silicostudy was performed of Cyperus rotundus constituents and pathological protein oxalate oxidase (PDB Id: 2ETE). In vitrostudy, nucleation and aggregation assay involved for assessment of ethanol extract of Cyperus rotundus tuber (50-3000 µg/ml).In vivo studies involved that the Cyperus rotundusethanolic extract (100, 200 and 400 mg/kg B.wt.) wastreatedonsodium oxalate induced urolithiatic rats for seven days,evaluated kidney function by urine and serum biochemical analysis and statistical analysis performed usingGraphPad prism5 software.In silico results showedthat Cyperus rotundus constituents,Humulene epoxide, 4-Oxo-alpha-ylangene, Cubebol were exhibited better binding energyonoxalate oxidase.Ethanolic extract of Cyperus rotundustuber was exhibited nucleation, aggregation of calcium oxalate monohydrate crystals inhibition in dosedependent manner. Sodium oxalate treatment was triggered biochemical changesin the urine that have been substantially prevented by the ethanolic extract of Cyperus rotundus tuber. The current findings Cyperus rotundus anti urolithic activity due to antioxidant essential oils. The molecular docking results could be used to optimize lead and develop the appropriate urolithiasis treatment.

Evaluation of the growth medium of a new ice-nucleating-active Pseudomonas: A response surface methodology approach

Aims@#Attention to ice nucleation proteins has increased for more than two decades. Ice nucleation proteins have been utilized for artificial snow-making known as Snowmax™, cryopreservation of tissues and cells, and cloud condensation nuclei. There is a direct relationship between bacterial growth and ice nucleation activity. Therefore, the optimization of the culture medium seems necessary.@*Methodology and results@#The effect of different carbon and nitrogen sources on the growth of a new native Pseudomonas sp. IRL.INP1 was evaluated by using fractional factorial design, the path of the steepest ascent experiment and central composite design. Ice nucleation activity, biomass and whole-cell protein were identified afterward. The model predicted by response surface methodology indicated that the maximum bacterial growth was observed when sucrose, ammonium sulfate [(NH4)2SO4] and manganese (II) (Mn2+) were utilized at 12.46 g/L, 321.97 mg/L and 938.09 µM, respectively. Also, 1.10 g/L biomass and 0.85 µg/µL whole-cell proteins were gained, and the isolate showed ice nucleation activity 31 sec sooner after optimization.@*Conclusion, significance and impact of study@#Ice nucleation proteins are growth-dependent and the growth condition optimization leads to higher bacterial cells growth. Therefore, best bacterial growth was obtained when proper carbon and nitrogen sources were used, and ice nucleation activity was observed in shorter time. This is the first study concerning ice nucleation activity optimization using different carbon and nitrogen sources.

Vegetation and seed bank of an open-scrub bush restinga formation in the Southeastern coast of Brazil

Introduction: Restingas are coastal plain ecosystems located along Eastern Brazil, corresponding to about 5 000 km.The restinga vegetation is associated with the Atlantic rainforest biome and comprises four distinct main formation zones: coastal grasslands, shrublands, open-forests and marsh zones. Especially due to coastal urbanization, this is a threatened ecosystem that, through its different shrub formations, exhibits a unique mosaic as a result of the vegetation distribution in nuclei of different covering, physiognomy and floristic composition. Objective: We aimed to characterize the above and belowground composition of a conserved, non-flooded, open-scrub, nuclei (patches of bushes) formation of restinga in Linhares, ES, southeastern Brazil. Methods: The vegetation survey was conducted using the line intercept method. Diameter and height of the first six nuclei were measured in five transects separated by 50 m, totaling 30 nuclei up to 350 m away from the shore line. The phytosociology and Shannon Index of the aboveground vegetation community were calculated. In the same 30 nuclei, leaf litter and topsoil layer (15 x 15 x 10 cm) samples were collected to survey the viable seed bank, which was later placed in a greenhouse for germination and seedling identification. The Sørensen Similarity index (SSi) was used to compare the floristic composition between the leaf litter and topsoil layer seed banks. Nuclei volume and number of species were calculated as well. Results: In the aboveground vegetation, 54 plant species belonging to 32 families were identified, totaling 1 098 individuals. The nuclei showed a diversity (H') of 3.08 nats, and an average diameter of 11.5 m (s = 9.1), area of 526.4 m2 (s = 1 081.7), and height of 2.9 m (s = 1.1). Davilla flexuosa, followed by Smilax rufescens, presented the highest IVI (Importance Value Index). A total of 1 839 seedlings from 32 species and 19 families were identified in the seed bank. Enydra sessilis (Asteraceae) had the highest seed density (544), while the family with highest species richness was Cyperaceae. A low similarity between the vegetation surveyed and the seed bank composition was found (only 5 species in common, SSi = 0.10). Conclusions: The results indicate that a post-disturbance early community, established from the seed bank, would have a substantially different species composition, but with other potential species to restore vegetation over the long-term succession.

Introducción: Las restingas son ecosistemas llanos costeros ubicados a lo largo del este de Brasil, que corresponden a unos 5 000 km de la costa atlántica brasileña. La vegetación de restinga está asociada con el bioma de la selva tropical atlántica y comprende cuatro zonas de formación principales: praderas costeras, matorrales, bosques abiertos y zonas pantanosas. Especialmente debido a la urbanización costera, este es un ecosistema amenazado, que, a través de sus formaciones arbustivas, exhibe un mosaico único, como resultado de la distribución de la vegetación en núcleos de diferentes coberturas, fisonomía y composición florística. Objetivo: Caracterizar la composición florística superficial y subterránea de una formación conservada, no inundada, de núcleos de matorral abierto de restinga en Linhares, ES, costa del sureste de Brasil. Métodos: La vegetación se muestreó utilizando el método de la línea de intercepción. El diámetro y la altura de los primeros seis núcleos se midieron en cinco transectos instalados cada 50 m, con un total de 30 núcleos distantes hasta 350 m de la línea de costa. Se muestreó la comunidad de vegetación y se calculó su fitosociología e índice de Shannon. En los mismos 30 núcleos, se recogió la hojarasca más la capa superior del suelo (15 x 15 x 10 cm) para examinar el banco de semillas viable, que luego se colocó en un invernadero para germinar e identificar las plántulas. El índice de similitud de Sørensen se usó para comparar la composición florística entre la hojarasca y el banco de semillas de la capa superficial del suelo y también se calculó la regresión entre el volumen del núcleo y el número de especies. Resultados: En la vegetación superficial se identificaron 54 especies de plantas pertenecientes a 32 familias, con un total de 1 098 plantas. Los núcleos registraron una diversidad (H') de 3.08 nats, y un diámetro promedio de 11.5 m (s = 9.1), área de 526.4 m² (s = 1 081.7) y altura de 2.9 m (s = 1.1). Davilla flexuosa, seguida de Smilax rufescens, presentó el VI (Valor de Importancia) más alto. Se identificaron un total de 1 839 plántulas de 32 especies y 19 familias en el banco de semillas. Enydra sessilis (Asteraceae) tuvo la mayor densidad de semillas viables (544), pero la familia con mayor riqueza de especies fue Cyperaceae. Se encontró una baja similitud entre la vegetación y la composición del banco de semillas (solo 5 especies en común, índice de Sørensen = 0.10). Conclusiones: Los resultados indican que una comunidad recién establecida después de una alteración podría tener una composición de especies sustancialmente diferente, pero con otras especies potenciales para restaurar la vegetación a largo plazo.

Nucleação na formação de estruvita: estado da arte / Nucleation in the formation of struvite: state of art

RESUMO Estimativas recentes indicam que a duração de toda a reserva de rochas fosfatadas do planeta não ultrapassa 400 anos e que a produção de fertilizantes nitrogenados é insustentável energeticamente. Atualmente, o tratamento de esgoto está sendo visto como uma unidade de recuperação de recursos (água, energia e nutrientes) em vez de uma de final de tubo. Portanto, as tecnologias de recuperação devem ser priorizadas em relação às de remoção. Estruvita (fosfato de amônio e magnésio) é um cristal que pode ser produzido a partir do esgoto doméstico e tem maior eficiência agrícola do que os fertilizantes convencionais. Apesar de a cristalização ser um tema bastante estudado em todo o mundo e extremamente desenvolvido tecnologicamente, sua utilização na engenharia sanitária ainda não é comum, especialmente no Brasil. Um dos assuntos menos pesquisados na formação da estruvita é a nucleação. Portanto, o presente artigo traz uma revisão bibliográfica crítica e atual e mostra as lacunas no conhecimento sobre esse assunto.

ABSTRACT Recent estimation for the duration of global phosphate reserves does not exceed 400 years and the production of nitrogen fertilizers is energetically unsustainable. Nowadays, wastewater treatment plants have been seen as resource recovery facilities (water, energy and nutrients) instead of "end-of-pipe" utilities. Thus, nutrient-recovery technologies should be prioritized over the removal ones. Struvite (phosphate of ammonium and magnesium) is a crystal, produced from sewage, with a higher agricultural efficiency when compared to conventional fertilizers. Despite the crystallization is a topic extensively studied worldwide and highly technologically developed, its use in sanitary engineering is still not common, especially in Brazil. As the aspects related to struvite nucleation have been insufficiently studied, this paper presents a critical and updated literature review, and shows the gaps in the current knowledge about this topic.

Development of carrier-free nanocrystals of poorly water-soluble drugs by exploring metastable zone of nucleation

There has been increasing interest in research and development of nanocrystals for the delivery of poorly water-soluble drugs that can be directly produced from solution. Compared with traditional carrier-based or encapsulation designs, drug nanocrystals circumvent possible side-effects due to carrier polymers and poor stability issues associated with encapsulation. The production of carrier-free nanocrystals requires careful control of nucleation and thus a thorough understanding of the relevant solution's metastable zone. A solution may stay supersaturated without forming any nuclei and become metastable. The maximal degree of supersaturation is known as the metastable zone width. When nucleation is triggered directly from the metastable zone, it helps to produce homogeneous nuclei leading to uniform nanocrystals. Herein, we report a study in which the solubility and metastable limit of paclitaxel (PTX) in ethanol aqueous solution were measured at 40 °C. A wide range of metastable compositions were studied to prepare carrier-free PTX nanocrystals with particle size smaller than 250 nm and PDI less than 0.25. Compared with the raw material, dissolution rate of PTX nanocrystals was significantly increased. The study enables production of high-quality drug nanocrystals for treating patients.

Review of the mechanism of biomimetic intrafibrillar mineralization / 口腔疾病防治

@#Bone is a hierarchically structured and highly mineralized hard tissue composed of an organic phase (type I collagen and noncollagenous proteins) and an inorganic phase (nanohydroxyapatite). Intrafibrillar mineralized collagen is the basic structural unit of bone tissue and is of high significance due to its superior mechanical and biological properties. Thus, to truly understand the unique properties of bone, it is necessary to review the most basic structural level of bone. In this article, we review the recent advances in understanding the development of intrafibrillar mineralization and the prevailing theories in the formation of such intrafibrillar minerals. Understanding the mechanisms of intrafibrillar mineralization may facilitate the development of engineered bone for clinical applications and provide deeper insight into the nature of biomineralization.

Conformation-locked nucleation strategies ofα-helical peptides / 国际药学研究杂志

Protein-protein interactions(PPI)with large and shallow interfaces are generally undruggable targets. Many PPI in-volved in vital biological processes are mediated by helixes,therefore PPI can be easily targeted by helical epitope mimics. However, the application of peptide was limited by its conformational flexibility and low stability until the significant work was done by Arora ,et al who applied nucleation and crosslinking strategies to lock peptides in helical conformation. The conformation-locked strategies helps to improve peptide stability,cell permeability,and afterwards target intracellular PPI. At present,the conformation-locked strategies of peptides have achieved great development,and have become a hot spot in peptide research field. In this paper,the recent develop-ment,centering nucleation strategies,applications and bright prospects of helical conformation-locked peptides,are reviewed in order to provide theoretical basis for drug design based on PPI.

Annual changes in a bird assembly on artificial perches: Implications for ecological restoration in a subtropical agroecosystem / Variação anual na assembleia de aves em poleiros artificiais: Implicações para a restauração ecológica em agroecossistema subtropical

Artificial perches are used in tropical forest restoration projects to increase the dispersal of seeds into restored areas. The ability of perches to enhance seed deposition depends on their ability to attract seed dispersing birds, as well as the correlation between the season of bird visits to perches and the phenology of fruit production in adjacent forests. Using data collected from a large-scale restoration project, we characterized the community of birds that utilize artificial perches over the course of one year. We hypothesized that the structure of a bird assemblage that uses artificial perches is affected by seasonal variation. We aimed to describe the richness, abundance and diversity of a bird assemblage on artificial perches in a subtropical Atlantic forest restoration experiment in Southern Brazil. Richness and abundance estimates of the avian fauna were obtained from eight artificial perches placed in four experimental plots (∼2 y-old). Parameters of richness and abundance were compared using ANOVA. The bird assemblage was described using SHE analysis [richness (S), diversity (H') and evenness (E)], with additional estimates of occurrence and dominance. In total, 451 records of 32 ± 3.16 SD species were obtained. Thraupidae was the most numerous family (nine species, 28.12% of the total). Richness and abundance varied seasonally and were highest during spring and summer. Five migratory species of flycatchers were recorded between spring and early autumn. Perches were ineffective in attracting specialized frugivorous birds, emphasizing that seed dispersal tends to be carried out primarily by generalist omnivores in the initial phase of forest regeneration.

Poleiros artificiais são usados em projetos de restauração de florestas tropicais para aumentar a dispersão de sementes em áreas restauradas. A capacidade de poleiros para melhorar a deposição de sementes depende da sua capacidade de atrair aves dispersoras, bem como a correspondência entre a estação de visitas de aves nos poleiros e a fenologia da produção de frutos nas florestas adjacentes. Usando dados coletados a partir de um projeto de restauração de grande escala, que caracterizaram a comunidade de aves que utilizam poleiros artificiais ao longo de um ano, foi testada a hipótese que a estrutura da assembleia de aves em poleiros artificiais é afetada por variações sazonais. O objetivo foi descrever a riqueza, abundância e diversidade da assembleia de aves que visitam poleiros artificiais em um experimento de restauração florestal da mata Atlântica subtropical no sul do Brasil. Estimativas de riqueza e abundância da avifauna foram obtidas de oito poleiros artificiais colocados em quatro parcelas experimentais (∼2 anos de idade). Parâmetros de riqueza e abundância foram comparados usando ANOVA. A assembleia de aves foi descrita por meio de análise SHE [riqueza (S), diversidade (H') e equitabilidade (E)], com estimativas adicionais de ocorrência e dominância. No total, foram obtidos 451 registos de 32 ± 3,16 DP espécies. Thraupidae foi a família mais abundante (nove espécies, 28.12% do total). Riqueza e abundância variaram sazonalmente, sendo mais elevadas durante a primavera e verão. Foram registradas cinco espécies migratórias de tiranídeos entre a primavera e o início do outono. Poleiros foram ineficazes na atração de aves frugívoras especializados, enfatizando que a dispersão de sementes tende a ser realizada principalmente por onívoros generalistas na fase inicial de regeneração florestal.

Odontogenic Keratocyst- The Controversies in Nomenclature and Treatment Modalities.

Summary: Odontogenic keratocysts (OKC) now officially known as Keratocystic odontogenic tumor (KCOT) is a benign odontogenic intraosseous tumor which is potentially agrressive having distinguished clinical and histopathological features. Based on a literature review, more aggressive treatment — either resection or enucleation supplemented with Carnoy’s solution with or without peripheral ostectomy — results in a lower recurrence rate than enucleation alone or marsupialization. WHO’s reclassification of this lesion from cyst to tumour underscores its aggressive nature and should motivate clinicians to manage the disease in a correspondingly aggressive manner. The purpose of this paper is to review and discuss the redesignation of KCOT and the implications for treatment.

Optimization of the whole-cell catalytic activity of recombinant Escherichia coli cells with surface-immobilized organophosphorus hydrolase.

Previous studies have verified the feasibility of using Escherichia coli systems that display organophosphorous hydrolase (OPH) on the cell surface as whole-cell catalysts. However, the inefficient display of the enzyme on cell surfaces remains unaddressed. In the present study, multiple optimization experiments on full-length and truncated ice nucleation protein anchors, E. coli host cells, culture media, and culture conditions were performed to optimize whole-cell OPH enzymatic activity. The results show that apart from the dramatic effect of isopropyl-b-d-thiogalactoside concentration and culture temperature, the coordination between the anchor protein, culture media, and host cells is essential for highly efficient OPH display. Under optimal conditions, namely, culturing in M9 medium, 20 °C induction temperature, 0.1 mmol l-1 IPTG, and 100 μmol l-1 Co2+, the engineered E. coli strain MB109-406 that expresses the fusion enzyme InaK-N-OPH exhibited a whole-cell OPH activity of 0.62 U mg-1 ?cell d.wt. This result is much higher than that of several currently available OPH-displaying systems, which shows the potential of the current system for further large-scale industrial or environmental applications.

The role of osteopontin in nucleation in different bile systems / 中华肝胆外科杂志

Objective To investigate the role of osteopontin (OPN) in the pathogenesis ot cholesterol gallstone formation in bile.Methods The nucleation time of OPN in model bile and human gallbladder bile was studied by the nucleation time assay,the effect of OPN on cholesterol crystal growth in model bile was examined by the cholesterol crystal growth assay.The effect of OPN on vesicle was detected by the transmission electron microscopy in model bile and gallbladder bile; then the content of OPN and calcium were detected via the commercial kits in human bile.Results Osteopontin prolonged nucleation time in a dose dependent manner in model bile and human bile,and this effect was correlated with calcium.Compared with control group,the nucleation times were prolonged by 1.50and 1.93 times in lithogenic bile at the concentration of osteopontin 50 μg/ml and 100 μg/ml (P＜0.01),respectively. Nucleation time were prolonged by 1.17 and 1.33 times in normal bile (P＜0.01) and by 1.29 and 1.48 times in model bile (P＜0.01),respectively.The rate of cholesterol crystals growth was not influenced by calcium ions,but inhibited by osteopontin in a dose dependent manner in the model bile.Furthermore,the formation,aggregation and fusion of vesicles were delayed by osteopontin in bile samples as indicated by the transmission electron microscopy.The concentration of osteopontin [(0.53± 0.08) mg/ml vs. (0.65 ± 0.14) mg/ml,P＜0.05] and the calcium ions [ (0.71 ± 0.17) mmol/L vs. ( 0.84 ± 0.08 ) mmol/L,P ＜ 0.05 ] were lower in lithogenic bile than in control.Conclusions Osteopontin can inhibit the cholesterol gallstone formation in model and human gallbladder bile as the anti nucleating factor.

Cloning, protein expression and display of synthetic multi-epitope mycobacterial antigens on Salmonella typhi Ty21a cell surface.

Expressing proteins of interest as fusion to proteins of bacterial envelope is a powerful technique for biotechnological and medical applications. The synthetic gene (VacII) encoding for T-cell epitopes of selected genes of Mycobacterium tuberculosis namely, ESAT6, MTP40, 38 kDa, and MPT64 was fused with N- terminus of Pseudomonas syringae ice nucleation protein (INP) outer membrane protein. The fused genes were cloned into a bacterial expression vector pKK223-3. The recombinant protein was purified by Ni-NAT column. VacII gene was displayed on the cell surface of Salmonella typhi Ty21a using N-terminal region of ice nucleation proteins (INP) as an anchoring motif. Glycine method confirmed that VacII was anchored on the cell surface. Western blot analysis further identified the synthesis of INP derivatives containing the N-terminal domain INP- VacII fusion protein of the expected size (52 kDa).

Surface Display of Domain Ⅲ of Japanese Encephalitis Virus E Protein on Salmonella Typhimurium by Using an Ice Nucleation Protein / 中国病毒学·英文版

A bacterial cell surface display technique based on an ice nucleation protein has been employed for the development of live vaccine against viral infection.Due to its ubiquitous ability to invade host cells,Salmonella typhimurium might be a good candidate for displaying viral antigens.We demonstrated the surface display of domain III of Japanese encephalitis virus E protein and the enhanced green fluorescent protein on S.typhimurium BRD509 using the ice nucleation protein.The effects of the motif in the ice nucleation protein on the effective display of integral protein were also investigated.The results showed that display motifs in the protein can target integral foreign protein on the surface of S.typhimurium BRD509.Moreover,recombinant strains with surface displayed viral proteins retained their invasiveness,suggesting that the recombinant S.typhimurium can be used as live vaccine vector for eliciting complete immunogenicity.The data may yield better understanding of the mechanism by which ice nucleation protein displays foreign proteins in the Salmonella strain.

Analysis of biliary pro-nucleating vesicular protein with lectin coupled to a peroxidase / 中华消化杂志

Objective To explore the structure and type of sugar chain in 33 500 pro-nucleating protein, and its role in gallstone formation. Methods The 33 500 vesicular protein was examined by dot-immunobinding assay of lectin coupled to a peroxidase (HRP-DSA,HRP-ConA,HRP-WGA). The morphology of biliary vesicles was observed under transmission electron microscopy in process of massive vesicular aggregation, culmination and crystal formation. The protein and its enzymatic deglycosylation fractions nucleation promoting activity were detected by cholesterol crystal growth assay. Results 33 500 vesicular protein with multiantennary and complicated glycan displayed apparent potency of nucleation promotion, which clearly reflected by HRP-DSA immunobinding, and derived crystal growth curve indices. It, Ig, Ic were presented as 0.57, 1.52, 1.63 respectively, but after treated by N-glycanase enzyme, no promoting activity was found. Conclusions Our data suggest the sugar chain play an important role in pro-nucleating process, and may be involved in the gallstone formation.

THE EFFECT OF PRESERVATION ON ICE NUCLEATION ACTIVITY OF INA BACTERIA / 微生物学通报

The effect of 5 store methods at 3 different temperature on ice nucleation activity of INA bacteria were evaluated. The results showed that some store methods could decrease the ice nucleation activity. The effect increased as the temperature of increased. The effect on survival and on activity is different. Different strains had different susceptibility and adaptability. It was found that the freeze-drying method storing at -20℃ and freezing in sterile distilled water storing at -20℃ could be used for most INA bacteria. Freezing in 10% glycerin could not be used for the store of INA bacteria.

CLONIG AND CHARACTERIZATION OF A NEW ICE NUCLEATION ACTIVE GENE FROM ICE NUCLEATION ACTIVE BACTERIUM ERWINIA ANANAS 110 / 微生物学通报

Using the chromosomal DNA of an ice nucleation active bacterium Erwinia ananas 110 as template, an ice nucleation active (ina) gene was amplified by PCR with Taq plusI DNA polymerase. After sequencing and compared with reported ina genes, the cloned gene was identified as a new ina gene and was registered in GenBank at the accession number of AF387802. The new ina gene, named as iceA, has 3921 bp for its coding region, which encodes 1306 amino acids consisting of repetitive segment (R-domain, 1104aa), which is flanked by N-and C-terminal sequences, with 161 aa and 41aa, respectively.