Three-Dimensional Reconstruction with Contrast Transfer Function Correction from Energy-Filtered Cryoelectron Micrographs: Procedure and Application to the 70SEscherichia coliRibosome

Cryoelectron microscopy provides the means of studying macromolecules in their native state. However, the contrast transfer function (CTF) makes the images and the three-dimensional (3D) maps derived from them difficult to interpret. We developed methods to determine the CTF from experimental data and to obtain a CTF-corrected 3D reconstruction. The CTF correction and 3D reconstruction accomplished in one step make it easy to combine different defocus data sets and decrease the error accumulation in the computation. These methods were applied to energy-filtered images of the 70SEscherichia coliribosome, resulting in a distortion-free 3D map of the ribosome at 1/24.5 Å⁻¹resolution, as determined by the differential phase residual resolution criterion.     

双源CT三维重建前交叉韧带移植物新技术

目的:探讨双源CT(DSCT)三维重建前交叉韧带(anterior cruciate ligament,ACL)重建术后移植物的技术方法。方法:对30例ACL损伤后移植重建术后患者进行DSCT扫描,利用软件三维重建ACL移植物的三维图像,对图像效果进行分析。结果:采用设定的参数和方法,30例患者的ACL移植物均获得三维重现,其中24例获得清晰的移植物图像,6例移植物图像略模糊。结论:DSCT可以重建出移植术后ACL移植物的三维图像,对临床检验、评估重建技术、修正重建方法、实现解剖重建有重大价值。     

DCE-MRI of the Liver: Reconstruction of the Arterial Input Function Using a Low Dose Pre-Bolus Contrast Injection

Purpose

To assess the quality of the arterial input function (AIF) reconstructed using a dedicated pre-bolus low-dose contrast material injection imaged with a high temporal resolution and the resulting estimated liver perfusion parameters.

Materials and Methods

In this IRB–approved prospective study, 24 DCE-MRI examinations were performed in 21 patients with liver disease (M/F 17/4, mean age 56 y). The examination consisted of 1.3 mL and 0.05 mmol/kg of gadobenate dimeglumine for pre-bolus and main bolus acquisitions, respectively. The concentration-curve of the abdominal aorta in the pre-bolus acquisition was used to reconstruct the AIF. AIF quality and shape parameters obtained with pre-bolus and main bolus acquisitions and the resulting estimated hepatic perfusion parameters obtained with a dual-input single compartment model were compared between the 2 methods. Test–retest reproducibility of perfusion parameters were assessed in three patients.

Results

The quality of the pre-bolus AIF curve was significantly better than that of main bolus AIF. Shape parameters peak concentration, area under the time activity curve of gadolinium contrast at 60 s and upslope of pre-bolus AIF were all significantly higher, while full width at half maximum was significantly lower than shape parameters of main bolus AIF. Improved liver perfusion parameter reproducibility was observed using pre-bolus acquisition [coefficient of variation (CV) of 4.2%–38.7% for pre-bolus vs. 12.1–71.4% for main bolus] with the exception of distribution volume (CV of 23.6% for pre-bolus vs. 15.8% for main bolus). The CVs between pre-bolus and main bolus for the perfusion parameters were lower than 14%.

Conclusion

The AIF reconstructed with pre-bolus low dose contrast injection displays better quality and shape parameters and enables improved liver perfusion parameter reproducibility, although the resulting liver perfusion parameters demonstrated no clinically significant differences between pre-bolus and main bolus acquisitions.     

Three-Dimensional Reconstruction from Reduced Sets of Very Noisy Images Acquired Following a Single-Axis Tilt Schema: Application of a New Three-Dimensional Reconstruction Algorithm and Objective Comparison with Weighted Backprojection

In this work we propose a reconstruction algorithm (ART with blobs) that has not been previously used in electron Tomography and we compare it with the standard method in the field (weighted back projection, WBP). We assume that only a limited set of very noisy images, collected around a single axis tilt, is available; which is a typical situation in Electron Tomography. In general, the reconstruction problem is underdetermined (due to the limited number of projections) and the data are inconsistent (due to the high level of noise). The evaluation of the results is performed in a rigorous way by a task-oriented approach which makes use of numerical observers. ART with blobs outperforms WBP for a number of key tasks. Results are presented both for simplified line integral data and for realistic simulations of macromolecular structures embedded in amorphous ice.     

A Three-Dimensional Finite Element Analysis of Heat Transfer in the Forearm

Abstract

The finite element method was used to analyze heat transfer within a section of the forearm while exposed to different ambient conditions and with different metabolic states. The three-dimensional model accounts for the different material properties of bone, muscle and blood and incorporates a single artery-vein pair for counter-current heat exchange. The geometry of the model was developed from anatomical cross-sectional images of the forearm. The model was used to determine the effects or rest vs. exercise, free vs. forced surface convection and 0°C vs. — 20 °C external temperatures. The results of the model were compared to experimental data and the model exhibits qualitatively correct behaviour. This model can be used to study hyperthermia, burns and cryogenic freezing of tissue.     

A Three-Dimensional Finite Element Analysis of Heat Transfer in the Forearm

The finite element method was used to analyze heat transfer within a section of the forearm while exposed to different ambient conditions and with different metabolic states. The three-dimensional model accounts for the different material properties of bone, muscle and blood and incorporates a single artery-vein pair for counter-current heat exchange. The geometry of the model was developed from anatomical cross-sectional images of the forearm. The model was used to determine the effects or rest vs. exercise, free vs. forced surface convection and 0 degrees C vs. -20 degrees C external temperatures. The results of the model were compared to experimental data and the model exhibits qualitatively correct behaviour. This model can be used to study hyperthermia, burns and cryogenic freezing of tissue.     

三维重建在口腔解剖生理学教学中的应用*

口腔解剖生理学是口腔专业重要的基础课程,本学科理论知识内容复杂,实践操作技能要求高,给老师和初学者在教与学的过程中带来很大的压力。本学科自开课以来一直在探讨选择最佳的教学方法,随着计算机图像技术的不断完善,CT三维重建也随之问世,颌面部三维重建模型,逼真形象,便于操作和理解,大大降低了学习难度,显著提高了教学质量,取得相当客观的效果。     

Innate Functions of Immunoglobulin M Lessen Liver Gene Transfer with Helper-Dependent Adenovirus

The immune system poses obstacles to viral vectors, even in the first administration to preimmunized hosts. We have observed that the livers of B cell-deficient mice were more effectively transduced by a helper-dependent adenovirus serotype-5 (HDA) vector than those of WT mice. This effect was T-cell independent as shown in athymic mice. Passive transfer of the serum from adenovirus-naïve WT to Rag1KO mice resulted in a reduction in gene transfer that was traced to IgM purified from serum of adenovirus-naïve mice. To ascribe the gene transfer inhibition activity to either adenoviral antigen-specific or antigen-unspecific functions of IgM, we used a monoclonal IgM antibody of unrelated specificity. Both the polyclonal and the irrelevant monoclonal IgM inhibited gene transfer by the HDA vector to either cultured hepatocellular carcinoma cells or to the liver of mice in vivo. Adsorption of polyclonal or monoclonal IgMs to viral capsids was revealed by ELISAs on adenovirus-coated plates. These observations indicate the existence of an inborn IgM mechanism deployed against a prevalent virus to reduce early post-infection viremia. In conclusion, innate IgM binding to adenovirus serotype-5 capsids restrains gene-transfer and offers a mechanism to be targeted for optimization of vector dosage in gene therapy with HDA vectors.     

染色体三维结构重建方法研究

染色体三维结构重构问题是近年生物领域中基因组学的热点研究问题,是以二维交互频率数据为基础来预测其三维空间结构。最新相关实验表明染色质的三维空间结构对于基因表达、调控等方面都具有重要意义。而Hi-c数据能利用染色质交互信息形成二维接触矩阵重构出染色体三维结构。本综述以染色体三维结构重建方法为研究对象,通过对染色体三维结构重建方法进行比较分析,综述了目前基于Hi-c数据在染色体三维结构重建中的经典方法,系统介绍了染色体三维结构重建技术的发展脉络,以促进染色体三维结构重建的进一步研究。     

16层螺旋CT三维重建成像技术在骨盆骨折中的临床意义

目的:探讨16层螺旋CT三维重建成像技术在骨盆骨折中的临床意义.方法:选取2011年8月～2012年8月我院收治的骨盆外伤患者共60例,比较CT、DR片2种检查方法.结果:16层螺旋CT片检查出53处阳性,而DR片查出43处阳性及1例假阳性.2种检查方法比较:敏感度差异存在统计学意义(P＜0.05).结论:16层螺旋CT三维重建成像技术在骨盆外伤的诊断上有着显著的优势,综合使用VRT、SSD、CPR、MPR技术,能够检测出DR片不易发现的骨折,提高了诊断符合率,对骨盆骨折的诊断有着重要的临床意义.     

A Three-Dimensional Musculoskeletal Model of the Human Knee Joint. Part 2: Analysis of Ligament Function

A three-dimensional model of the knee is used to study ligament function during anterior-posterior (a-p) draw, axial rotation, and isometric contractions of the extensor and flexor muscles. The geometry of the model bones is based on cadaver data. The contacting surfaces of the femur and tibia are modeled as deformable; those of the femur and patella are assumed to be rigid. Twelve elastic elements are used to describe the geometry and mechanical properties of the cruciate ligaments, the collateral ligaments, and the posterior capsule. The model is actuated by thirteen musculotendinous units, each unit represented as a three-element muscle in series with tendon. The calculations show that the forces applied during a-p draw are substantially different from those applied by the muscles during activity. Principles of knee-ligament function based on the results of in vitro experiments may therefore be overstated. Knee-ligament forces during straight a-p draw are determined solely by the changing geometry of the ligaments relative to the bones: ACL force decreases with increasing flexion during anterior draw because the angle between the ACL and the tibial plateau decreases as knee flexion increases; PCL force increases with increasing flexion during posterior draw because the angle between the PCL and the tibial plateau increases. The pattern of ligament loading during activity is governed by the geometry of the muscles spanning the knee: the resultant force in the ACL during isometric knee extension is determined mainly by the changing orientation of the patellar tendon relative to the tibia in the sagittal plane; the resultant force in the PCL during isometric knee flexion is dominated by the angle at which the hamstrings meet the tibia in the sagittal plane.     

A Three-Dimensional Musculoskeletal Model of the Human Knee Joint. Part 2: Analysis of Ligament Function

A three-dimensional model of the knee is used to study ligament function during anterior-posterior (a-p) draw, axial rotation, and isometric contractions of the extensor and flexor muscles. The geometry of the model bones is based on cadaver data. The contacting surfaces of the femur and tibia are modeled as deformable; those of the femur and patella are assumed to be rigid. Twelve elastic elements are used to describe the geometry and mechanical properties of the cruciate ligaments, the collateral ligaments, and the posterior capsule. The model is actuated by thirteen musculotendinous units, each unit represented as a three-element muscle in series with tendon. The calculations show that the forces applied during a-p draw are substantially different from those applied by the muscles during activity. Principles of knee-ligament function based on the results of in vitro experiments may therefore be overstated. Knee-ligament forces during straight a-p draw are determined solely by the changing geometry of the ligaments relative to the bones: ACL force decreases with increasing flexion during anterior draw because the angle between the ACL and the tibial plateau decreases as knee flexion increases; PCL force increases with increasing flexion during posterior draw because the angle between the PCL and the tibial plateau increases. The pattern of ligament loading during activity is governed by the geometry of the muscles spanning the knee: the resultant force in the ACL during isometric knee extension is determined mainly by the changing orientation of the patellar tendon relative to the tibia in the sagittal plane; the resultant force in the PCL during isometric knee flexion is dominated by the angle at which the hamstrings meet the tibia in the sagittal plane.     

颅底孔在多层CT三维重建中的测量研究

探讨颅底MSCT三维重建图像效果及主要孔的正常值,采用多层螺旋CT(MSCT),对200名正常成人(男100名,女100名)进行颅脑扫描,利用电子计算机三维重建程序立体地显示颅底外面的卵圆孔、棘孔、颈动脉管外口、破裂孔、茎乳孔、枕骨大孔,并观察其形态和测出其内径及其性差。     

Three-Dimensional Reconstruction of Rabbit-Derived Pneumocystis carinii from Serial-Thin Sections I: Trophozoite

The highly complex ultrastructural morphology of the endomembrane system in Pneumocystis carinii led us to perform three-dimensional reconstruction from serial-thin sections using the CATIA (Conception Assistée Tridimensionnelle Inter Active) Dassault system program. The three-dimensional reconstruction of a small trophozoite made it possible to better understand the morphological relationship among organelles and to suggest cytophysiological hypotheses. By reconstructing other parasite stages, we gathered information about the evolution of organelles during the life cycle and about their physiology.     

A Chimeric Type 2 Adenovirus Vector with a Type 17 Fiber Enhances Gene Transfer to Human Airway Epithelia

In studies of the genetic disease cystic fibrosis, recombinant adenovirus type 2 (Ad2) and Ad5 are being investigated as vectors to transfer cystic fibrosis transmembrane conductance regulator cDNA to airway epithelia. However, earlier work has shown that human airway epithelia are resistant to infection by Ad2 and Ad5. Therefore, we examined the efficiency of other adenovirus serotypes at infecting airway epithelia. We found that several serotypes of adenoviruses, in particular, wild-type Ad17, infected a greater number of cells than wild-type Ad2. The increased efficiency of wild-type Ad17 could be explained by increased fiber-dependent binding to the epithelia. Therefore, we constructed a chimeric virus, Ad2(17f)/betaGal-2, which is identical to Ad2/betaGal-2 with the exception of having the fiber protein of Ad17 replace Ad2 fiber. This vector retained the increased binding and efficiency of gene transfer to well-differentiated human airway epithelia. These data suggest that inclusion of Ad17 fiber into adenovirus vectors may improve the outlook for gene delivery to human airway epithelia.     

Three-Dimensional Reconstruction of Rabbit-Derived Pneumocystis carinii from Serial-Thin Sections II: Intermediate Precyst

Three-dimensional reconstruction of a binucleate intermediate precyst of Pneumocystis carinii was performed from serial-thin sections using the CATIA (Conception Assistée Tridimensionnelle Inter Active) Dassault system program. The presence of a mitochondrion, complex well-developed endoplasmic structures, and numerous Golgi vesicles was established. A better understanding of the ultrastructure of rabbit-derived P. carinii stages made it possible to formulate hypotheses on the evolution and physiology of the endomembrane system. Thus, the presence of the well-developed endoplasmic saccular structure and more than 230 Golgi vesicles in its vicinity might be implicated in the differentiation of the parasite surface structures and might also be related to nuclear division and individualization of intracystic bodies.     

Factors Influencing Adeno-Associated Virus-Mediated Gene Transfer to Human Cystic Fibrosis Airway Epithelial Cells: Comparison with Adenovirus Vectors

Adeno-associated virus (AAV) vectors appear promising for use in gene therapy in cystic fibrosis (CF) patients, yet many features of AAV-mediated gene transfer to airway epithelial cells are not well understood. We compared the transduction efficiencies of AAV vectors and adenovirus (Ad) vectors in immortalized cell lines from CF patients and in nasal epithelial primary cultures from normal humans and CF patients. Similar dose-dependent relationships between the vector multiplicities of infection and the efficiencies of lacZ gene transfer were observed. However, levels of transduction for both Ad and recombinant AAV (rAAV) were significantly lower in the airway epithelial cell than in the control cell lines HeLa and HEK 293. Transduction efficiencies differed among cultured epithelial cell types, with poorly differentiated cells transducing more efficiently than well-differentiated cells. A time-dependent increase in gene expression was observed after infection for both vectors. For Ad, but not for AAV, this increase was dependent on prolonged incubation of cells with the vector. Furthermore, for rAAV (but not for rAd), the delay in maximal transduction could be abrogated by wild-type Ad helper infection. Thus, although helper virus is not required for maximal transduction, it increases the kinetics by which this is achieved. Expression of Ad E4 open reading frame 6 or addition of either hydroxyurea or camptothecin resulted in increased AAV transduction, as previously demonstrated for nonairway cells (albeit to lower final levels), suggesting that second-strand synthesis may not be the sole cause of inefficient transduction. Finally, the efficiency of AAV-mediated ex vivo gene transfer to lung cells was similar to that previously described for Ad vectors in that transduction was limited to regions of epithelial injury and preferentially targeted basal-like cells. These studies address the primary factors influencing rAAV infection of human airway cells and should impact successful gene delivery in CF patients.