Rapid calculation of the solution scattering profile from a macromolecule of known structure

If one expands the structure factor equation in spherical coordinates, rotational averaging of the molecular Fourier transform, which leads directly to the solution scattering profile, is greatly simplified. It becomes a projection in the polar and azimuthal angular variables. The profile is given by I(R) = 1/2 infinity sigma n = 0 n sigma m = 0 epsilon mNm,n magnitude of Gm,n(R) 2 where Gm,n(R) = sigma jfjYm,n(theta j, phi j)jn(2 pi rjR) The index j runs over all atoms; r, theta, phi are atomic coordinates and epsilon and N are constants; the Ym,n are complex spherical harmonics, and jn are spherical Bessel functions; R = 2 sin theta/lambda. The effects of solvent have been modeled by subtracting from each protein atom a properly weighted water. Hydrogens have been included by using scattering curves fj derived from the spherical averaging of protein atoms with their attached hydrogens. This approach may also be satisfactory for neutron scattering. Published scattering profiles for lysozyme and BPTI have been accurately matched in less than one-tenth the time required by other methods. Separate, adjustable temperature factors for the protein, solvent waters, and bound waters are used, and appear to be needed. In the case of BPTI, as suggested by NMR observations, the observed diffraction pattern was much better accounted for by including only 4 tightly bound waters rather than the roughly 60 seen by crystallography.     

Spherical body formation in the spirochaete Brachyspira hyodysenteriae

When cultures of Brachyspira hyodysenteriae were grown under a wide range of in vitro conditions, at least 1% of the cells formed spherical bodies different to the normal helical form. This percentage increased considerably in aging cultures or following their incubation in caramelized media. Spherical body formation was initiated from a terminal localized swelling of the outer sheath followed by a retraction of the protoplasmic cylinder into the resulting swollen vesicle. As this occurred, the periplasmic flagella seemed to unwind from the protoplasmic cylinder. Once retracted, the protoplasmic cylinder was found to be wrapped in an organized manner around the inner surface of the membrane of the swollen vesicle. Although most were 2-3 microm in diameter, some much larger spherical bodies (6-12 microm diameter) were occasionally seen, with a corresponding increase in the visible number of peripheral protoplasmic cylinder cross-sections. Spherical bodies from older cultures did not contain protoplasmic cylinders arranged around the periphery, but instead were characterized by the presence of a centrally located, electron-dense body c. 0.5-0.8 mum in diameter. Brachyspira hyodysenteriae spherical bodies differ in both their structural organization and probable method of formation from similar structures described in other spirochaete genera.     

球面设计优化金线莲黄酮类物质提取工艺及糖耐受性的研究(英文)

以金线莲为材料,利用统计学实验设计方法对黄酮类物质的提取工艺进行了优化。选定液料比、乙醇浓度和时间三个因素的五个水平进行球面设计实验,建立黄酮提取率的二次回归方程,通过回归分析及岭脊分析得到优化提取组合条件。研究结果表明,当提取工艺条件为:液料比24,乙醇浓度63%,提取时间48 h时,黄酮提取率的最大预测值为1.107%,验证值为1.05%。葡萄糖耐受性试验结果表明:金线莲黄酮类萃取物能够提高正常小鼠对糖的耐受性。     

miRNA-182 and the regulation of the glioblastoma phenotype - toward miRNA-based precision therapeutics

Glioblastoma (GBM) is an incurable cancer, with survival rates of just 14-16 months after diagnosis.¹ Functional genomics have identified numerous genetic events involved in GBM development. One of these, the deregulation of microRNAs (miRNAs), has been attracting increasing attention due to the multiple biologic processes that individual miRNAs influence. Our group has been studying the role of miR-182 in GBM progression, therapy resistance, and its potential as GBM therapeutic. Oncogenomic analyses revealed that miR-182 is the only miRNA, out of 470 miRNAs profiled by The Cancer Genome Atlas (TCGA) program, which is associated with favorable patient prognosis, neuro-developmental context, temozolomide (TMZ) susceptibility, and most significantly expressed in the least aggressive oligoneural subclass of GBM. miR-182 sensitized glioma cells to TMZ-induced apoptosis, promoted glioma initiating cell (GIC) differentiation, and reduced tumor cell proliferation via knockdown of Bcl2L12, c-Met and HIF2A.² To deliver miR-182 to intracranial gliomas, we have characterized Spherical Nucleic Acids covalently functionalized with miR-182 sequences (182-SNAs). Upon systemic administration, 182-SNAs crossed the blood-brain/blood-tumor barrier (BBB/BTB), reduced tumor burden, and increased animal subject survival.^2-4 Thus, miR-182-based SNAs represent a tool for systemic delivery of miRNAs and a novel approach for the precision treatment of malignant brain cancers.     

Preparation of Spherical Crystal Agglomerates of Naproxen Containing Disintegrant for Direct Tablet Making by Spherical Crystallization Technique

The purpose of this research was to obtain directly compressible agglomerates of naproxen containing disintegrant by spherical crystallization technique. Acetone–water containing hydroxypropyl celloluse (HPC) and disintegrant was used as the crystallization system. In this study croscarmellose sodium (Ac–Di–Sol) was employed as disintegrant. The agglomerates were characterized by differential scanning calorimetry (DSC), powder X-ray diffraction (XRPD), and scanning electron microscopy and were evaluated for flow, packing and tableting properties and drug release. The growth of particle size and the spherical form of the agglomerates resulted in formation of products with good flow and packing properties. The improved compaction properties of the agglomerated crystals were due to their fragmentation occurred during compression. DSC and XRPD studies showed that naproxen particles, crystallized in the presence of HPC and Ac–Di–Sol did not undergo structural modifications. The dissolution rate of naproxen from tablets made of naproxen–(Ac–Di–Sol) agglomerates was enhanced significantly because of including the disintegrant in to the particles. This was attributed to an increase in the surface area of the practically water insoluble drug is exposed to the dissolution medium. In conclusion the spherical crystallization technique developed in this study is suitable for obtaining agglomerates of drug with disintegrant.     

Self‐assembly of short peptides composed of only aliphatic amino acids and a combination of aromatic and aliphatic amino acids

The morphology of structures formed by the self‐assembly of short N‐terminal t‐butyloxycarbonyl (Boc) and C‐terminal methyl ester (OMe) protected and Boc‐deprotected hydrophobic peptide esters was investigated. We have observed that Boc‐protected peptide esters composed of either only aliphatic hydrophobic amino acids or aliphatic hydrophobic amino acids in combination with aromatic amino acids, formed highly organized structures, when dried from methanol solutions. Transmission and scanning electron microscopic images of the peptides Boc‐Ile‐Ile‐OMe, Boc‐Phe‐Phe‐Phe‐Ile‐Ile‐OMe and Boc‐Trp‐Ile‐Ile‐OMe showed nanotubular structures. Removal of the Boc group resulted in disruption of the ability to form tubular structures though spherical aggregates were formed. Both Boc‐Leu‐Ile‐Ile‐OMe and H‐Leu‐Ile‐Ile‐OMe formed only spherical nanostructures. Dynamic light scattering studies showed that aggregates of varying dimensions were present in solution suggesting that self‐assembly into ordered structures is facilitated by aggregation in solution. Fourier transform infrared spectroscopy and circular dichroism spectroscopy data show that although all four of the protected peptides adopt well‐defined tertiary structures, upon removal of the Boc group, only H‐Phe‐Phe‐Phe‐Ile‐Ile‐OMe had the ability to adopt β‐structure. Our results indicate that hydrophobic interaction is a very important determinant for self‐assembly and presence of charged and aromatic amino acids in a peptide is not necessary for self‐assembly. Copyright © 2012 European Peptide Society and John Wiley & Sons, Ltd.     

Determination of bacterial rod shape by a novel cytoskeletal membrane protein

Cell shape is critical for growth, and some genes are involved in bacterial cell morphogenesis. Here, we report a novel gene, rodZ, required for the determination of rod shape in Escherichia coli. Cells lacking rodZ no longer had rod shape but rather were round or oval. These round cells were smaller than known round mutant cells, including mreB and pbpA mutants; both are known to lose rod shape. Morphogenesis from rod cells to round cells and vice versa, caused by depletion and overproduction of RodZ, respectively, revealed that RodZ could regulate the length of the long axis of the cell. RodZ is a membrane protein with bitopic topology such that the N‐terminal region including a helix‐turn‐helix motif is in the cytoplasm, whereas the C‐terminal region is exposed in the periplasm. GFP–RodZ forms spirals along the lateral axis of the cell beneath the cell membrane, similar to the MreB bacterial actin. Thus, RodZ may mediate spatial information from cytoskeletal proteins in the cytoplasm to a peptidoglycan synthesis machinery in the periplasm.     

A Convenient Method for Rapid Determination of Cereal Proteins: A Device to Eliminate the Effect of Color Substances on the Biuret Procedure

At least, four kinds of amylase inhibitors are found in culture of Streptomyces sp. No.280.¹⁾ A large amount of amylase inhibitors were produced by Streptomyces sp. No. 280 when cultivated on 3% oatmeal medium and it was found that the molecular weight of the inhibitors were transformed to smaller molecules during the cultivation time. The transformation of the amylase inhibitor was found to result from degradation of its carbohydrate moiety by α-amylase in the culture broth. The amylase inhibitor was hydrolyzed partially by the action of taka-amylase A or hog pancreatic α-amylase. With hydrolyzation of amylase inhibitor by α-amylase, neutral sugars (mainly maltose) were liberated from the amylase inhibitor and a modified inhibitor was newly formed, but amylase inhibitory activity against glucoamylase was not changed. The inhibitory activity against muscle Phosphorylase a, however, was almost completely lost.     

Complexes assembled from TMV-derived spherical particles and entire virions of heterogeneous nature

Previously, we described some structural features of spherical particles (SPs) generated by thermal remodelling of the tobacco mosaic virus. The SPs represent a universal platform that could bind various proteins. Here, we report that entire isometric virions of heterogeneous nature bind non-specifically to the SPs. Formaldehyde (FA) was used for covalent binding of a virus to the SPs surface for stabilizing the SP—virus complexes. Transmission and high resolution scanning electron microscopy showed that the SPs surface was covered with virus particles. The architecture of SP–virion complexes was examined by immunologic methods. Mean diameters of SPs and SP–human enterovirus C and SP–cauliflower mosaic virus (CaMV) compositions were determined by nanoparticle tracking analysis (NTA) in liquid. Significantly, neither free SPs nor individual virions were detected by NTA in either FA-crosslinked or FA-untreated compositions. Entirely, all virions were bound to the SPs surface and the SP sites within the SP–CaMV complexes were inaccessible for anti-SP antibodies. Likewise, the SPs immunogenicity within the FA-treated SPs–CaMV compositions was negligible. Apparently, the SP antigenic sites were hidden and masked by virions within the compositions. Previously, we reported that the SPs exhibited adjuvant activity when foreign proteins/epitopes were mixed with or crosslinked to SPs. We found that immunogenicity of entire CaMV crosslinked to SP was rather low which could be due to the above-mentioned masking of the SPs booster. Contrastingly, immunogenicity of the FA-untreated compositions increased significantly, presumably, due to partial release of virions and unmasking of some SPs-buster sites after animals immunization.     

Isolation and characterization of a novel mycovirus,PeSV, in <Emphasis Type="Italic">Pleurotus eryngii</Emphasis> and the development of a diagnostic system for it

A novel mycovirus was isolated from a cultivated edible mushroom, Pleurotus eryngii, with severe epidemic symptoms. Purification of the virus was carried out by a sequential procedure of polyethylene glycol precipitation, differential centrifugation, and equilibrium centrifugation in a CsCl gradient. Nuclease digestion assay and protein analysis revealed that the virus consisted of a single-stranded RNA (ssRNA) genome of 7.8 kbp which was encapsulated by a coat protein of 22 kDa. Transmission electron microscope showed that it was spherical with a diameter of 31 nm. Since there was neither a previous report on discovery of a virus in P. eryngii, nor known mushroom viruses with similar characteristics, we concluded that this is a novel virus and thus have named it as P. e ryngii Spherical Virus (PeSV). Because of a diagnostic test would be helpful in preventing the PeSV-related disease outbreaks, we developed a triple antibody sandwich-ELISA (TAS–ELISA) system using anti-PeSV mouse monoclonal and anti-PeSV rabbit polyclonal antibodies. The TAS–ELISA system successfully detected less than 0.5 μg of the virus particles in 1 g diseased mushroom tissue collected from various commercial farms.     

Light and Electron Microscopic Observations of Gametogenesis in Hastigerina pelagica (Foraminifera)*

SYNOPSIS. During gametogenesis mother individuals of Hastigerina pelagica (d'Orbigny) undergo significant morphological changes. Thirty h before gamete release, the cytoplasm changes from pale orange to bright red, possibly due to transport of stored lipids from the inner region to more peripheral parts of the cytoplasm. During the next 10 to 15 h the bubble capsule which surounds the calcareous shell is discarded. After all bubbles have disappeared, the individual sheds its spines by resorbing the spine bases close to the shell surface. A single mother nucleus divides into some hundreds of thousands of gamete nuclei within a span of ～ 20 h. A bulge of cytoplasm is extruded from the aperture and increases in size during the next 5 to 10 h. This bulge consists of cytoplasmic strands in which gametes and spherical bodies are embedded. The gametes and spherical bodies mature and are released during the afternoon and early evening. The gametes have 2 unequal acronematic flagella. A previously undescribed structure in foraminiferal reproduction is the spherical body which consists of a large vacuole surrounded by a thin cytoplasmic layer in which several nuclei, various typical cell organelles and multiple flagella are present. The spherical bodies are believed to play a role as receptacles of waste material, possibly including residual digestive enzymes, thereby protecting the gametes from lysis during the reproductive process. Fusion of gametes and further development into the next generation have not been observed.     

The pattern of pleiomorphism in stressed Salmonella Virchow populations is nutrient and growth phase dependent

AIMS: To describe the interactions of imposed osmotic and nutritional stress on the morphology of stationary and exponential phase S. Virchow cells. METHODS AND RESULTS: This study examined the morphology and viability of osmotically stressed exponential and stationary phase cultures of Salmonella Virchow under nutritionally deficient and competent conditions. In addition to normal morphology, salt-stressed cultures exhibited filamentous and spherical morphotypes, which were capable of reversion to normal morphology on stress removal. Proportions of atypical morphotypes were influenced by the phase of growth when the stress was applied. Salt-stressed exponential phase populations contained 54% filamentous, 30% spherical forms, salt-stressed stationary phase populations contained 16% filamentous, 79% spherical forms. Proportions of morphotypes were also influenced by the nutrient status of the medium, but not by metabolic by-products. CONCLUSIONS: Development of a range of morphotypes in response to stress (osmotic/nutritional), may offer population level advantages, increasing the survival potential of the population. SIGNIFICANCE AND IMPACT OF STUDY: The application of sublethal concentrations of salt may stimulate S. Virchow morphotype diversity, improving survival and rates of poststress recovery.     

Spherical bodies present within the germinal vesicle of Podarcis sicula previtellogenic oocyte derive from the temporaneous inactivation of ribosomal genes

In the present paper we have investigated the origin of the spherical bodies (SBs) present within the germinal vesicle of about 400 microm previtellogenic oocytes in the lizard Podarcis sicula. In particular, we have attempted to clarify whether they derive from the single, large nucleolus present in early diplotenic oocyte as a consequence of ribosomal gene inactivation. We have, therefore, experimentally induced a decrease in rRNA synthesis by injecting animals with D-galactosamine or by exposing them to low temperatures. The investigations carried out have demonstrated that both treatments induce significant ultrastructural changes in the nucleolar apparatus and in particular fragmentation and the formation of SBs comparable to those observed in germinal vesicle under physiological conditions. These results indicate that the germinal vesicle of Podarcis sicula has a nucleolar apparatus that significantly changes its aspect according to its functional status and reveal that in this species, the time course of rRNA synthesis is peculiar with respect to any other vertebrate oocyte studies so far.     

Head‐turning morphologies: Evolution of shape diversity in the mammalian atlas–axis complex

Mammals flex, extend, and rotate their spines as they perform behaviors critical for survival, such as foraging, consuming prey, locomoting, and interacting with conspecifics or predators. The atlas–axis complex is a mammalian innovation that allows precise head movements during these behaviors. Although morphological variation in other vertebral regions has been linked to ecological differences in mammals, less is known about morphological specialization in the cervical vertebrae, which are developmentally constrained in number but highly variable in size and shape. Here, we present the first phylogenetic comparative study of the atlas–axis complex across mammals. We used spherical harmonics to quantify 3D shape variation of the atlas and axis across a diverse sample of species, and performed phylogenetic analyses to investigate if vertebral shape is associated with body size, locomotion, and diet. We found that differences in atlas and axis shape are partly explained by phylogeny, and that mammalian subclades differ in morphological disparity. Atlas and axis shape diversity is associated with differences in body size and locomotion; large terrestrial mammals have craniocaudally elongated vertebrae, whereas smaller mammals and aquatic mammals have more compressed vertebrae. These results provide a foundation for investigating functional hypotheses underlying the evolution of neck morphologies across mammals.     

The correlated evolution of three-dimensional reproductive structures between male and female damselflies

For many taxa, species are defined by the morphologies of reproductive structures. In many odonates, these structures are the cerci of males (used to hold females during mating) and the thoracic plates of females where the male cerci contact the females' bodies. A previous study showed that the shapes of cerci of Enallagma males (Zygoptera: Coenagrionidae) are best explained by an evolutionary model of punctuated change at the time of speciation, with a homogeneous rate of change across the entire phylogeny of the genus. In the present study, we examine the evolution of shape change in the corresponding female plates. We found that, like male cerci, the shapes of Enallagma female thoracic plates could best be explained by an evolutionary model of punctuated change at the time of speciation, with a homogeneous rate of change across the clade. Moreover, the evolutionary contrasts quantifying the rates of change in male cerci and female thoracic plates were positively related across the history of the clade, demonstrating that these male and female structures evolve in a correlated fashion. This pattern of evolution suggests that these structures are primary signals of species identity during mating.     

Nucleic acid and prion protein interaction produces spherical amyloids which can function in vivo as coats of spongiform encephalopathy agent

The infectious agent of transmissible spongiform encephalopathies (TSE) has been considered to be PrP(SC), a structural isoform of cellular prion protein PrP(C). PrP(SC) can exist as oligomers and/or as amyloid polymers. Nucleic acids induce structural conversion of recombinant prion protein PrP and PrP(C) to PrP(SC) form in solution and in vitro. Here, we report that nucleic acids, by interacting with PrP in solution, produce amyloid fibril and fibres of different morphologies, similar to those identified in the diseased brains. In addition, the same interaction produces polymer lattices and spherical amyloids of different dimensions (15-150 nm in diameters). The polymer lattices show apparent morphological similarity to the two-dimensional amyloid crystals obtained from linear amyloids isolated in vivo. The spherical amyloids structurally resemble "spherical particles" observed in natural spongiform encephalopathy (SE) and in scrapie-infected brains (TSE). We suggest that spherical amyloids, PrP(SC)-amylospheroids, are probable constituents of the coat of the spherical particles found in vivo and the latter can act as protective coats of the SE and TSE agents in vivo.