Artificial protein cavities as specific ligand-binding templates: characterization of an engineered heterocyclic cation-binding site that preserves the evolved specificity of the parent protein.

Cavity complementation has been observed in many proteins, where an appropriate small molecule binds to a cavity-forming mutant. Here, the binding of compounds to the W191G cavity mutant of cytochrome c peroxidase is characterized by X-ray crystallography and binding thermodynamics. Unlike cavities created by removal of hydrophobic side-chains, the W191G cavity does not bind neutral or hydrophobic compounds, but displays a strong specificity for heterocyclic cations, consistent with the role of the protein to stabilize a tryptophan radical at this site. Ligand dissociation constants for the protonated cationic state ranged from 6 microM for 2-amino-5-methylthiazole to 1 mM for neutral ligands, and binding was associated with a large enthalpy-entropy compensation. X-ray structures show that each of 18 compounds with binding behavior bind specifically within the artificial cavity and not elsewhere in the protein. The compounds make multiple hydrogen bonds to the cavity walls using a subset of the interactions seen between the protein and solvent in the absence of ligand. For all ligands, every atom that is capable of making a hydrogen bond does so with either protein or solvent. The most often seen interaction is to Asp235, and most compounds bind with a specific orientation that is defined by their ability to interact with this residue. Four of the ligands do not have conventional hydrogen bonding atoms, but were nevertheless observed to orient their most polar CH bond towards Asp235. Two of the larger ligands induce disorder in a surface loop between Pro190 and Asn195 that has been identified as a mobile gate to cavity access. Despite the predominance of hydrogen bonding and electrostatic interactions, the small variation in observed binding free energies were not correlated readily with the strength, type or number of hydrogen bonds or with calculated electrostatic energies alone. Thus, as with naturally occurring binding sites, affinities to W191G are likely to be due to a subtle balance of polar, non-polar, and solvation terms. These studies demonstrate how cavity complementation and judicious choice of site can be used to produce a protein template with an unusual ligand-binding specificity.     

Streptococcus panodentis sp. nov. from the oral cavities of chimpanzees

Three strains TKU9, TKU49 and TKU50^T, were isolated from the oral cavities of chimpanzees (Pan troglodytes). The isolates were all gram‐positive, facultative anaerobic cocci that lacked catalase activity. Analysis of partial 16S rRNA gene sequences showed that the most closely related species was Streptococcus infantis (96.7%). The next most closely related species to the isolates were S. rubneri, S. mitis, S. peroris and S. australis (96.6 to 96.4%). Based on the rpoB and gyrB gene sequences, TKU50^T was clustered with other member of the mitis group. Enzyme activity and sugar fermentation patterns differentiated this novel bacterium from other members of the mitis group streptococci. The DNA G + C content of strain TKU50^T was 46.7 mol%, which is the highest reported value for members of the mitis group (40–46 mol%). On the basis of the phenotypic characterization, partial 16S rRNA gene and sequences data for two housekeeping gene (gyrB and rpoB), we propose a novel taxa, S. panodentis for TKU 50^T (type strain = CM 30579^T = DSM 29921^T), for these newly described isolates.     

Studies on the Structure and Development of Secretory Cavities in Poncirus Trifoliata

Light microscopical observation of thin sections revealed that the initials of secretory cavities in Poncirus trifoliata (L.) Raf. originated from parenchyma cells below the epidermis in early stages of development. The cavity lumen appeared in the center of the initials and gradually enlarged during subsequent development. Concurrently the ceils surrounding the central space differentiated into secretory cells and sheath cells. The developed cavities of fruit ,stem and leaf consisted of 2–5 layers of sheath cells and 2–3 layers of secretory cells surrounding a spherical space. The secretory cells lining the space were observed to remain intact throughout the plantt s life. On the basis of comparative studies with the aid of different kinds of fixatives, embedding media and sectionings,it was suggested that the ,manner of formation of the lacunao of secretory cavities in fruit peels of P. trifoliata, Citrus reticulata and C. sinensis were different. However,as seen in thin sections the secretory cavities of all the 3 species developed schizogenously. Our result with reference to views of other authers concluded the existance of a common schizogenous cavity formation in Rutaceae.     

The fluid mechanics of bolus ejection from the oral cavity

The squeezing action of the tongue against the palate provides driving forces to propel swallowed material out of the mouth and through the pharynx. Transport in respose to these driving forces, however, is dependent on the material properties of the swallowed bolus. Given the complex geometry of the oral cavity and the unsteady nature of this process, the mechanics governing the oral phase of swallowing are not well understood. In the current work, the squeezing flow between two approaching parallel plates is used as a simplified mathematical model to study the fluid mechanics of bolus ejection from the oral cavity. Driving forces generated by the contraction of intrinsic and extrinsic lingual muscles are modeled as a spatially uniform pressure applied to the tongue. Approximating the tongue as a rigid body, the motion of tongue and fluid are then computed simultaneously as a function of time. Bolus ejection is parameterized by the time taken to clear half the bolus from the oral cavity, t_1/2. We find that t_1/2 increases with increased viscosity and density and decreases with increased applied pressure. In addition, for low viscosity boluses (μapproximately 1000 cP), viscosity dominates. A transition region between these two regimes is found in which both properties affect the solution characteristics. The relationship of these results to the assessment and treatment of swallowing disorders is discussed.     

Gibbsiella dentisursi sp. nov., isolated from the bear oral cavity

A Gram-negative, rod-shaped, non-spore forming and non-motile bacterium, designated strain NUM 1720(T) , was isolated from the oral cavity of bears. Based on 16S rRNA gene sequence similarity, strain NUM 1720(T) was shown to be related to Gibbsiella quercinecans (99.4%). The gyrB and rpoB gene sequences of strain NUM 1720T showed 98.0% and 98.2% similarity with those of G. quercinecans. The DNA-DNA hybridization value of strain NUM 1720(T) with G. quercinecans was 63.8%. The G + C content of the genomic DNA of the isolates was 55.0 mol%. Fatty acid analysis data supported the affiliation of strain NUM 1720(T) to the genus Gibbsiella. The major menaquinone and ubiquinone were MK-8 and Q-8, respectively. Strain NUM 1720(T) can be differed from G. quercinecans by the reactions to acetoin, inositol and D-arabinose. Strain NUM 1720(T) therefore represents a novel species, for which the name Gibbsiella dentisursi sp. nov. is proposed, with type strain NUM 1720(T) (= JCM 17201(T) = DSM 23818(T)).     

Nest box contentions: Are nest boxes used by the species they target?

Nest boxes have grown in popularity as a habitat management tool in Australia during the last decade. This management use remains contentious because some studies suggest nest boxes are ineffective. There are three recent contentions: (i) nest boxes mostly benefit common species, (ii) exotic species may be dominant users of nest boxes, and (iii) species of conservation concern use nest boxes infrequently. We address these contentions using data from 1865 nest boxes involving eight nest box designs. These nest boxes were installed predominantly <200 m from a road in association with highway duplication and re‐alignment across 16 projects in New South Wales. The Common Brushtail Possum (Trichosurus vulpecula) is the species of most relevance to contention 1. It used 9% of boxes overall including 26% of ‘possum’ designated boxes. The most frequent nest box users were small petaurid gliders (mostly Sugar Gliders, Petaurus breviceps) which used 63% of ‘small glider’ designated boxes. This nest box and another suited to the Sugar Glider comprised 40% of all boxes installed, so it is not surprising that this species might be a common user. Exotic species were uncommon users of the nest boxes enabling contention 2 to be rejected. Active hives of Feral Honeybees (Apis mellifera) occupied just 1% of boxes, and another 1% of boxes were used by introduced rodents and birds. The Squirrel Glider (Petaurus norfolcensis) is the species most relevant to contention 3. It was seen in 80 boxes across 11 projects, representing 7% of the three types most frequently used. These observations are not consistent with the third contention. Nest boxes can provide many important insights about the requirements and interactions of hollow‐dependent fauna. However, they are not intended as an alternative to retaining hollow‐bearing trees.     

口腔微生态失衡导致口腔异味的研究

目的介绍口腔微生态失调与口腔疾病的关系,口腔疾病出现口腔气味异常的机制。综合分析口腔微生态与口腔健康的研究动态及意义。展望口腔微生态调整在口腔疾病治疗中的作用研究,尤其在消除口腔异昧的积极作用。方法由第一、二作者应用计算机通过pubmed检索NCBI数据库1992年至2007年相关文献,检索词为“Micro ecology”,限定语言种类为“English”;同时检索CNKI全文数据库、维普全文数据库1995年至2007年相关文献,检索词为“微生态”,限定语言种类为中文。纳入标准：文章内容与口腔微生态相关的研究、以及在口腔疾病研究领域有关。排除标准：较陈旧的文献和重复研究。结果共收集到106篇相关文献,21篇文献纳入本文,其中,19篇为综述和述评类文献,19篇为中文杂志,2篇为外文杂志。结论致病菌大量生长繁殖,口腔微生态失调,菌斑内微生物之间以及机体与菌斑之间相互作用分解蛋白产生硫化物,这些代谢产物包括H2S、CH3SH、CH3SCH3、吲哚、甲基吲哚、挥发脂肪酸和聚胺等发出刺激性气味,产生口腔异味。治疗口腔异味应该考虑平衡口腔微生态,调整口腔菌群。口腔异味的治疗又有利于口腔菌群平衡。提示我们治疗口腔疾病应该考虑口腔微生态平衡。     

猕猴腹部及盆腔结构的CT影像学观察

目的应用CT技术对成年猕猴进行断层扫描,建立猕猴腹部及盆腔CT断层扫描图谱。方法选择普通级实验猕猴6只,雌雄各半,年龄5～8岁,取头前尾后仰卧位,采用增强扫描CT技术,对其腹部及盆腔进行断层扫描,采集容积数据及对原始数据重建。通过观察、确认,精选具有解剖意义的扫描图像:腹部7张、盆腔10张(雌雄各5张),对其每个层面的主要脏器进行标注。结果 CT影像能分辨出大部分组织器官的细微变化,较大器官、大血管界面清晰,但较小器官和细小血管、神经、肌肉组织等界面尚不清晰。结论获得了健康成年猕猴腹部及盆腔的影像学图谱,为CT技术在猕猴影像学研究、疾病的临床诊断及科学实验方面的应用,提供影像学的基础资料。     

影响正常口腔念珠菌检出率的方法学研究

目的:研究不同检测方法对正常口腔念珠菌检出率的影响,寻找一种比较简便可靠的检测方法.方法:以健康的平均年龄7.4岁的儿童为检测人群,比较不同的取样部位,取样方法,检测方法,被检人群口腔中白色念珠菌以及其他念珠菌的检出率.结果:取样和检测方法对检出率有不同程度的影响,PCR检测方法的检出率显著高于培养法.结论:黏膜拭子加离心,和CHROMagar CandidaTM鉴定培养基相结合的方法是一种简便理想的分离培养方法,PCR方法则敏感度更高.     

Nest box revealed habitat preferences of arboreal mammals in box‐ironbark forest

Habitat preferences need to be understood if species are to be adequately managed or conserved. Habitat preferences are presumed to reflect requirements for food, shelter and breeding, as well as interactions with predators and competitors. However, one or more of these requirements may dominate. Tree‐cavity‐dependent wildlife species are one example where shelter or breeding site requirements may dominate. We installed 120 nest boxes across 40 sites to target the vulnerable Brush‐tailed Phascogale (Phascogale tapoatafa) and the non‐threatened Sugar Glider (Petaurus breviceps). The provision of shelter sites where few of quality are available may enable better resolution of habitat preferences. Over three years, we observed the Brush‐tailed Phascogale at 17 sites, whereas the Sugar Glider was observed at 39 sites. We tested four broad hypotheses (H1–H4) relating to habitat that may influence occupancy by these species. There was no influence of hollow (cavity) abundance (H1) on either species suggesting our nest boxes had satisfied their shelter requirements. There was no influence of habitat structure (canopy and tree proximity) (H2) immediately around the nest box trees. We found no influence of distance to the forest edge (H3). Variables at and away from the nest box site that appear to reflect foraging substrates (H4) were influential on the Brush‐tailed Phascogale. Sugar Glider occupancy was only influenced by a single variable at the nest box site. The lack of influence of any other variables is consistent with the very high occupancy observed, suggesting most of the forest habitat is suitable when shelter sites are available. We found no evidence that the Sugar Glider reduced site use by the Brush‐tailed Phascogale.     

Development of a computational fluid dynamics model for mucociliary clearance in the nasal cavity

Intranasal drug delivery has attracted significant attention because of the opportunity to deliver systemic drugs directly to the blood stream. However, the mucociliary clearance poses a challenge in gaining high efficacy of intranasal drug delivery because cilia continuously carry the mucus blanket towards the laryngeal region. To better understand mucus flow behaviour on the human nasal cavity wall, we present computational model development, and evaluation of mucus motion on a realistic nasal cavity model reconstructed from CT-scans. The model development involved two approaches based on the actual nasal cavity geometry namely: (i) unwrapped-surface model in 2D domain and (ii) 3D-shell model. Conservation equations of fluid motion were applied to the domains, where a mucus production source term was used to initiate the mucus motion. The analysis included mucus flow patterns, virtual saccharin tests and quantitative velocity magnitude analysis, which demonstrated that the 3D-shell model results provided better agreement with experimental data. The unwrapped-surface model also suffered from mesh-deformations during the unwrapping stage and this led to higher mucus velocity compared to experimental data. Therefore, the 3D-shell model was recommended for future mucus flow simulations. As a first step towards mucus motion modelling this study provides important information that accurately simulates a mucus velocity field on a human nasal cavity wall, for assessment of toxicology and efficacy of intranasal drug delivery.     

鼻腔结构影响人体嗅觉反应的数值模拟

采用一个符合实际解剖学的鼻腔结构,建立了鼻腔仿生模型和气味分子传输过程的控制方程,应用ANSYS软件,对鼻腔流场进行了数值模拟。结果显示吸气速度越大,流过嗅觉区的气味分子越多,越容易产生嗅觉;鼻腔入口处到嗅觉区的距离越短,流过嗅觉区的气味流量越大,越容易产生嗅觉。从而,丰富了嗅觉理论,使人们进一步认识嗅觉,为人工嗅觉提供了仿生理论依据。     

Growth, incidence and activities of dissimilatory sulfate-reducing bacteria in the human oral cavity

Abstract Viable counts and activities of sulfate-reducing bacteria were determined in the oral cavities of 12 healthy volunteers. Of these, 10 harboured viable sulfate-reducing bacteria populations. Six separate sites were sampled: the posterior tongue, anterior tongue, mid buccal mucosa, vestibular mucosa, supragingival plaque and subgingival plaque. Sulfate-reducing bacteria occurred in all areas, with the highest incidence in supragingival plaque. Viable counts and sulfate-reducing activities in each of the regions varied from 0 to 10⁸ cfu (g wet weight)⁻¹ and from 0 to 50 nmol (g wet weight) ⁻¹ h⁻¹, respectively. As sulfate-reducing bacteria can be detected in the oral cavity, they may potentially be involved in terminal oxidative processes carried out by the microflora of the mouth.     

Numerical modelling of nanoparticle deposition in the nasal cavity and the tracheobronchial airway

Recent advances in nanotechnology have seen the manufacture of engineered nanoparticles for many commercial and medical applications such as targeted drug delivery and gene therapy. Transport of nanoparticles is mainly attributed to the Brownian force which increases as the nanoparticle decreases to 1 nm. This paper first verifies a Lagrangian Brownian model found in the commercial computational fluid dynamics software Fluent before applying the model to the nasal cavity and the tracheobronchial (TB) airway tree with a focus on drug delivery. The average radial dispersion of the nanoparticles was 9x greater for the user-defined function model over the Fluent in-built model. Deposition in the nasal cavity was high for very small nanoparticles. The particle diameter range in which the deposition drops from 80 to 18% is between 1 and 10 nm. From 10 to 150 nm, however, there is only a small change in the deposition curve from 18 to 15%. A similar deposition curve profile was found for the TB airway.     

A preliminary 3D computed tomography study of the human maxillary sinus and nasal cavity

Despite centuries of investigation, the function of the maxillary sinus (MS) and underlying patterns governing its form remain elusive. In this study, we articulate a methodology for collecting volumetric data for the MS and nasal cavity (NC) from computed tomography (CT) scans and report details for a small sample of 39 dried human crania of known ecogeographic provenience useful for assessing variation in MS size and shape. We use scaling analyses to preliminarily test the hypothesis that volumes of the nasal cavity (NCV) and maxillary sinus (MSV) are inversely correlated such that the NC covaries with size of the face, whereas the MS "fills in" the leftover space [proposed by Shea: Am J Phys Anthropol 47 (1977):289-300]. Against expectation, MSV is not significantly correlated with NCV or any cranial size variable. NCV, on the other hand, scales isometrically with facial size. The results of this pilot study suggest that NCV covaries with facial size, but that the MS does not simply fill in the leftover space in the face. The role, if any, of the MSs in midfacial function and architecture remains unclear. Larger sample sizes, additional environmental variables, and assessment of MS and NC shape are necessary to resolve this issue.     

人类口腔小生境微生物的多样性

本文论述了人类口腔中微生物的物种多样性,口腔小生境的复杂性与微生物多样性的关系,以及口腔中微生物变化与人类疾病和健康的关系。