A Bayesian method for classification of images from electron micrographs

Particle classification is an important component of multivariate statistical analysis methods that has been used extensively to extract information from electron micrographs of single particles. Here we describe a new Bayesian Gibbs sampling algorithm for the classification of such images. This algorithm, which is applied after dimension reduction by correspondence analysis or by principal components analysis, dynamically learns the parameters of the multivariate Gaussian distributions that characterize each class. These distributions describe tilted ellipsoidal clusters that adaptively adjust shape to capture differences in the variances of factors and the correlations of factors within classes. A novel Bayesian procedure to objectively select factors for inclusion in the classification models is a component of this procedure. A comparison of this algorithm with hierarchical ascendant classification of simulated data sets shows improved classification over a broad range of signal-to-noise ratios.     

Image processing of electron micrographs of human alpha 2-macroglobulin half-molecules induced by Cd2+

Human alpha 2-macroglobulin is a tetrameric plasma inhibitor of proteinases. Its dissociation by Cd2+ gives functional dimers. Electron microscopy of negatively stained dimers shows their round-ended cylindrical shape with furrows delimiting 3 main stain-excluding domains. Image processing of electron micrographs shows the existence of 2 main orientations of the dimers on the carbon support film. The dimer is composed of 2 curved monomers linked in a central domain, and related by a 90 degree rotation. Taking into account the known primary structure of alpha 2-macroglobulin and the linkage of the 2 constitutive monomers by 2 disulfide bonds, the molecular organization of the dimer is discussed, extended to the tetrameric molecule and compared to the published models of human alpha 2-macroglobulin.     

The kinetics of nucleation and growth of sickle cell hemoglobin fibers

Polymerization of sickle cell hemoglobin (HbS) in deoxy state is one of the basic events in the pathophysiology of sickle cell anemia. For insight into the polymerization process, we monitor the kinetics of nucleation and growth of the HbS polymer fibers. We define a technique for the determination of the rates J and delay times theta of nucleation and the fiber growth rates R of deoxy-HbS fibers, based on photolysis of CO-HbS by laser illumination. We solve numerically time-dependent equations of heat conductance and CO transport, coupled with respective photo-chemical processes, during kinetics experiments under continuous illumination. After calibration with experimentally determined values, we define a regime of illumination ensuring uniform temperature and deoxy-HbS concentration, and fast (within <1 s) egress to steady conditions. With these procedures, data on the nucleation and growth kinetics have relative errors of <5% and are reproducible within 10% in independent experiments. The nucleation rates and delay times have steep, exponential dependencies on temperature. In contrast, the average fiber growth rates only weakly depend on temperature. The individual growth rates vary by up to 40% under identical conditions. These variations are attributed to instability of the coupled kinetics and diffusion towards the growing end of a fiber. The activation energy for incorporation of HbS molecules into a polymer is E(A)=50 kJ mol(-1), a low value indicating the significance of the hydrophobic contacts in the HbS polymer. More importantly, the contrast between the strong theta(T) and weak R(T) dependencies suggests that the homogenous nucleation of HbS polymers occurs within clusters of a precursor phase. This conclusion may have significant consequences for the understanding of the pathophysiology of sickle cell anemia and should be tested in further work.     

Molecular Determination of Vascular Endothelial Growth Factor,miRNA-423 Gene Abnormalities by Utilizing ARMS-PCR and Their Association with Fetal Hemoglobin Expression in the Patients with Sickle Cell Disease

Recent studies have indicated that microRNA and VEGF are considered to be genetic modifiers and are associated with elevated levels of fetal haemoglobin HbF, and thus they reduce the clinical impact of sickle haemoglobin (HbS) patients. This cross-sectional study was performed on clinical confirmed subjects of SCD cases. miR-423-rs6505162 C>T and VEGF-2578 C>A genotyping was conducted by ARMS-PCR in SCD and healthy controls. A strong clinical significance was reported while comparing the association of miR-423 C>T genotypes between SCD patients and controls (p = 0.031). The microRNA-423 AA genotype was associated with an increased severity of SCD in codominant model with odd ratio (OR = 2.36, 95% CI, (1.15–4.84), p = 0.018) and similarly a significant association was observed in recessive inheritance model for microRNA-423 AA vs (CC+CA) genotypes (OR = 2.19, 95% CI, (1.32–3.62), p < 0.002). The A allele was associated with SCD severity (OR = 1.57, 95% CI, (1.13–2.19), p < 0.007). The distribution of VEGF-2578 C>A genotypes between SCD patients and healthy controls was significant (p < 0.013). Our results indicated that in the codominant model, the VEGF-2578-CA genotype was strongly associated with increased SCD severity with OR = 2.56, 95% CI, (1.36–4.82), p < 0.003. The higher expression of HbA1 (65.9%), HbA2 (4.40%), was reported in SCD patients carrying miR-423-AA genotype than miR-423 CA genotype in SCD patients carrying miR-423 CA genotype HbA1 (59.98%), HbA2 (3.74%) whereas SCD patients carrying miR-423 CA genotype has higher expression of HbF (0.98%) and HbS (38.1%) than in the patients carrying AA genotype HbF (0.60%), HbS (36.1%). ARMS-PCR has been proven to be rapid, inexpensive and is highly applicable to gene mutation screening in laboratories and clinical practices. This research highlights the significance of elucidating genetic determinants that play roles in the amelioration of the HbF levels that is used as an indicator of severity of clinical complications of the monogenic disease. Further well-designed studies with larger sample sizes are necessary to confirm our findings.     

The effects of soil horizons and faunal excrement on bacterial distribution in an upland grassland soil

The density and spatial location of bacteria were investigated within different horizons of an upland grassland soil before and after a liming treatment to increase the numbers of large soil fauna. Bacterial cells were located by image analysis of stained thin sections and densities calculated from these data. Excrement from macro- and meso-fauna was identified using micromorphology and the densities of bacteria on specific areas of excrement measured by image analysis. There were significant differences among horizons in the density of bacterial cells, with the minimum density found in the horizon with least evidence of earthworm activity, but no difference in density between the organic H and organo-mineral Ah horizons. Soil improvement by liming significantly increased bacterial densities in all three horizons, with the greatest increase found in the horizon with the smallest density before liming. There were no differences in bacterial density between areas dominated by excrement from earthworms and excrement from enchytraeids, although densities in both areas were significantly increased by liming. Variability in bacterial density at spatial scales of less than 1 mm was linked to the occurrence of excrement. Bacterial densities within areas of both types of excrement were significantly greater than those in the surrounding soil. However, the frequency distribution of the ratios of density in excrement to that in the soil was bimodal, with a majority of occurrences having a ratio near 1 and only some 20-30% having a much larger ratio. These variations can probably be explained by variations in the age of the excrement and its suitability as a substrate.     

Structure of the rotor of the bacterial flagellar motor revealed by electron cryomicroscopy and single-particle image analysis

The FliF ring is the base for self-assembly of the bacterial flagellum and the FliF/FliG ring complex is the core of the rotor of the flagellar motor. We report the structures of these two ring complexes obtained by electron cryomicroscopy and single-particle image analysis at 22A and 25A resolution, respectively. Direct comparison of these structures with the flagellar basal body made by superimposing the density maps on the central section reveals many interesting features, such as how the mechanically stable connection between the ring and the rod is formed, how directly FliF domains are involved in the near axial density of the basal body forming the proximal end of the central channel for a potential gating mechanism, some indication of flexibility in the connection of FliF and FliG, and structural and functional similarities to the head-to-tail connectors of bacteriophages.     

Study of the microbial aggregation in Mycobacterium using image analysis and electron microscopy

Cellular aggregation, which occurs in both prokaryotes and eukaryotes, is controlled by the hydrophobicity as well as the electrokinetic potential of the cell surface and substratum. It is known that the Mycobacterium genus form aggregates, but the influence of sugar on the cellular aggregation has not been reported for this genus. The mutant strain Mycobacterium sp. MB-3683 that transforms sterol to androstenedione (AD), a steroidal precursor used by the pharmaceutical industries, was employed in this study. This strain was cultivated in a synthetic medium on three sugars (glycerol, glucose and fructose) at different concentrations, and at 144 h microbial growth, cellular aggregation, hydrophobicity, lipid content, fatty acid composition, and width of cellular walls were measured. It was observed that at different sugar concentrations, similar growth and pH were obtained. However, in fructose, the aggregation level was significantly high, followed by glycerol and glucose (fructose < glycerol < glucose). These results were confirmed using electron microscopy and the aggregate area quantified by image analysis. Hydrophobicity was the highest in fructose and the lowest in glucose. The total lipids, in contrast to cellular hydrophobicity, were higher in glucose than glycerol. Although, the hydrophilic-lipophilic balance (HLB) of principal fatty acids isolated was similar regardless of sugar used. In glycerol and fructose, the paraffins were observed, which are responsible for the high cellular hydrophobicity detected above. The width of cell wall of the organisms grown on glucose and fructose was similar, but in glycerol the walls were very thin. There is a correspondence between cell wall width and lipid content.     

An approach to the architecture of Scutigera coleoptrata hemocyanin by electron microscopy and image processing

Summary— The 6 × 6meric hemocyanin of the centipede Scutigera coleoptrata, prepared by the single layer negative staining technique with uranyl acetate, has been investigated under the electron microscope. Isolated molecules were windowed from selected digitized micrographs. After alignment, they were submitted to correspondence analysis and hierarchical ascendant classification. Two main clusters of molecules were differentiated, and their average images were obtained. A 3D-model constructed from these images is proposed.     

The use of spatially patterned methods for vegetation restoration and management across systems

Widespread degradation of natural lands has created an urgent need for restoration. However, the high cost of conventional techniques limits the extent and success of restoration efforts. As a result, practitioners have developed new cost‐effective techniques. Spatially patterned restoration methods, where established clusters of plant species serve as propagule sources across a broad target area, have been proposed as practical restoration techniques. The spatial patterning is expected to reduce initial costs and provide ecological benefits such as increasing habitat heterogeneity. Over the past three decades, multiple spatially patterned restoration methods have emerged around the globe; however, it is unclear whether applications and theoretical foundations have been connected across methods. We conducted a literature review and bibliometric network analyses to (1) examine patterns in focal study systems, cost‐effectiveness, and ecological outcomes for spatially patterned restoration methods and (2) analyze connectivity among the bodies of literature associated with common spatially patterned restoration methods to identify knowledge gaps and synergies. We found the three most commonly studied methods are applied nucleation, slot seeding, and strip seeding. Applied nucleation studies mainly occurred in tropical forests and emphasized plant diversity and seed‐dispersing animal visitation. Slot‐seeding and strip‐seeding studies both primarily occurred in temperate grasslands and emphasized plant establishment and production. Applied nucleation and slot‐seeding approaches had distinct theoretical bases, as evidenced by patterns in reference citation, while strip‐seeding approaches did not draw from a unified body of literature. We discuss the need for full economic analyses and theoretical links between the different methods.     

Variation in stomatal aperture in leaves of Avena fatua L. observed by low-temperature scanning electron microscopy

Abstract. A novel technique to record the variability of stomatal aperture over the leaf surface is described. This combines observations of leaf surfaces using low-temperature scanning electron microscopy (LTSEM), with digital image analysis to produce the most accurate aperture measurements obtained to date. Leaf samples are rapidly immobilized by cryo-fixation in liquid nitrogen and stored in a purpose-built cryo-storage system. Specimens can be collected in the field, remote from the cryopreparation system, and stored for up to several weeks before being examined on the LTSEM. The advantages of this method are that the time frame of the measurements is accurately known, and is identical for all stomatal apertures in a sample, and the precision of the measurements is not limited by the resolving power of the microscope. Measurements of stomatal aperture were obtained from leaves of field grown Avena fatua using the above procedure. Leaf surface conductance (g_sur) was determined by porometry immediately before cryo-fixation of the same region of the leaf. Measurements of aperture size showed a high degree of variability within each specimen, with coefficients of variation similar to those found in previous studies. Stomatal conductance (g_s) was calculated from stomatal dimensions using formulae derived elsewhere. A linear regression between the computed values of g_s and porometric estimates of g_sur showed good agreement with the regression line passing through the origin with a slope of 1.0 (R²=0.96). Applications of the experimental system are discussed.     

对地贫红细胞的显微激光散射和图象分析

应用显微准弹性激光散射(MQLS)技术与显微生物医学图象分析技术对地中海贫血红细胞及胞内血红蛋白动态特性进行了研究.在实验中,比较了正常人及地贫患者红细胞胞内血红蛋白聚集体的平均流体力学半径、平均平动扩散系数及红细胞膜的搏动频率等动态特性参数,以及细胞的截面积、规化形状因子、长径、短径、灰度等图象分析数据,发现地贫红细胞的血红蛋白聚合物平均流体力学半径远远大于正常人红细胞的,其大小变异亦较正常人大,且其膜搏动频率也较为缓慢,细胞的截面积也变小.这反映了地贫红细胞内有较大的蛋白质聚合物存在和红细胞变形能力差的特性.研究还表明,显微准弹性激光散射技术结合图象分析技术,可使测量的可比性和准确性大大提高,预期可广泛适用于各种活细胞动态特性的研究.     

The viability assessment of ethanol-producing yeast by computer-aided fluorescence microscopy

A vital staining of the ethanol-producing yeast Saccharomyces cerevisiae with ethidium bromide and DAPI allows intact and damaged cells to be differentiated by fluorescence microscopy. A computer image analysis procedure is developed for the automatic determination of the relative number of damaged cells using ImageJ software (National Institute of Health, United States; http://rsb.info.nih.gov./ij/). A good correlation has been found between the viability rates determined by the plate count method and the relative numbers of intact cells assessed by the developed procedure in the dry-yeast preparations rehydrated under various conditions.     

The motility of human spermatozoa as influenced by prostasomes at various pH levels.

Human semen contains several components among which spermatozoa, membranous vesicles called 'prostasomes', secreted by the prostate gland and unorganized material. Prostasomes possess an unusual lipid composition, contain a number of proteins and small molecules and have been claimed to take a part in the immune response, in seminal fluid liquefaction and in sperm motility. Since sperm may come in contact with an acidic environment in the vagina, it may be of some interest to know whether prostasomes may affect spermatozoon motility or may protect spermatozoa upon the exposure to an acidic milieu. Human semen was supplied by donors. From whole semen we collected spermatozoa by centrifugation and used the supernatant to prepare prostasomes (centrifugation at 105,000 g for 120 min, followed by purification step on Sephadex G 200); spermatozoa were then collected by a swim-up procedure and exposed to an acidic pH medium (from 5 to 7) in the presence or absence of prostasomes. Spermatozoa motility was subsequently assessed with a superimposed image analysis system (SIAS). Results indicate that the motility of spermatozoa was affected by the pH value of the medium. Acidic media reduced the percentage of motile cells and decreased the straight line velocity of spermatozoa (VLS). Prostasomes had a protective effect and increased the percentage of motile cells. However, they did not change the characteristics of motility (curvilinear and straight). Prostasomes may be considered as a system for counteracting the negative effects of acidic pH values that may be present in the vagina after coitus.     

Structure and dynamics of the force-generating domain of myosin probed by multifrequency electron paramagnetic resonance

Spin-labeling and multifrequency EPR spectroscopy were used to probe the dynamic local structure of skeletal myosin in the region of force generation. Subfragment 1 (S1) of rabbit skeletal myosin was labeled with an iodoacetamide spin label at C707 (SH1). X-and W-band EPR spectra were recorded for the apo state and in the presence of ADP and nucleotide analogs. EPR spectra were analyzed in terms of spin-label rotational motion within myosin by fitting them with simulated spectra. Two models were considered: rapid-limit oscillation (spectrum-dependent on the orientational distribution only) and slow restricted motion (spectrum-dependent on the rotational correlation time and the orientational distribution). The global analysis of spectra obtained at two microwave frequencies (9.4 GHz and 94 GHz) produced clear support for the second model and enabled detailed determination of rates and amplitudes of rotational motion and resolution of multiple conformational states. The apo biochemical state is well-described by a single structural state of myosin (M) with very restricted slow motion of the spin label. The ADP-bound biochemical state of myosin also reveals a single structural state (M*, shown previously to be the same as the post-powerstroke ATP-bound state), with less restricted slow motion of the spin label. In contrast, the extra resolution available at 94 GHz reveals that the EPR spectrum of the S1.ADP.V_i-bound biochemical state of myosin, which presumably mimics the S1.ADP.P_i state, is resolved clearly into three spectral components (structural states). One state is indistinguishable from that of the ADP-bound state (M*) and is characterized by moderate restriction and slow motion, with a mole fraction of 16%. The remaining 84% (M**) contains two additional components and is characterized by fast rotation about the x axis of the spin label. After analyzing EPR spectra, myosin ATPase activity, and available structural information for myosin II, we conclude that post-powerstroke and pre-powerstroke structural states (M* and M**) coexist in the S1.ADP.V_i biochemical state. We propose that the pre-powerstroke state M** is characterized by two structural states that could reflect flexibility between the converter and N-terminal domains of myosin.     

Dynamical differences of hemoglobin and the ionotropic glutamate receptor in different states revealed by a new dynamics alignment method

A new algorithm for comparison of protein dynamics is presented. Compared protein structures are superposed and their modes of motions are calculated using the anisotropic network model. The obtained modes are aligned using the dynamic programming algorithm of Needleman and Wunsch, commonly used for sequence alignment. Dynamical comparison of hemoglobin in the T and R2 states reveals that the dynamics of the allosteric effector 2,3‐bisphosphoglycerate binding site is different in the two states. These differences can contribute to the selectivity of the effector to the T state. Similar comparison of the ionotropic glutamate receptor in the kainate+(R,R)‐2b and ZK bound states reveals that the kainate+(R,R)‐2b bound states slow modes describe upward motions of ligand binding domain and the transmembrane domain regions. Such motions may lead to the opening of the receptor. The upper lobes of the LBDs of the ZK bound state have a smaller interface with the amino terminal domains above them and have a better ability to move together. The present study exemplifies the use of dynamics comparison as a tool to study protein function. Proteins 2017; 85:1507–1517. © 2014 Wiley Periodicals, Inc.     

The power of data synthesis to shape the future of the restoration community and capacity

Restoration efforts will be taking place over the next decade(s) in the largest scope and capacity ever seen. Immense commitments, goals, and budgets are set, with impactful wide‐reaching potential benefits for people and the environment. These are ambitious aims for a relatively new branch of science and practice. It is time for restoration action to scale up, the legacy of which could impact over 350 million hectares targeted for the U.N. Decade on Ecosystem Restoration. However, restoration still proceeds on a case‐by‐case, trial by error basis and restoration outcomes can be variable even under similar conditions. The ability to put each case into context—what about it worked, what did not, and why—is something that the synthesis of data across studies can facilitate. The link between data synthesis and predictive capacity is strong. There are examples of extremely ambitious and successful efforts to compile data in structured, standardized databases which have led to valuable insights across regional and global scales in other branches of science. There is opportunity and challenge in compiling, standardizing, and synthesizing restoration monitoring data to inform the future of restoration practice and science. Through global collation of restoration data, knowledge gaps can be addressed and data synthesized to advance toward a more predictive science to inform more consistent success. The interdisciplinary potential of restoration ecology sits just over the horizon of this decade. Through truly collaborative synthesis across foci within the restoration community, we have the opportunity to rapidly reach that potential and achieve extraordinary outcomes together.     

The impact of site conditions and seed dispersal on restoration success in alluvial meadows

Abstract. We studied the restoration success of flood plain meadows in the northern Upper Rhine valley, where between 1988 and 1992, 35 ha of arable land was converted into grassland and subsequently managed for nature conservation. Remnant populations of typical alluvial meadow species were found in old meadows and along drainage ditches that dissect the whole area. We analysed the site conditions and phytosociological relevés in old and new meadows. Small differences in site parameters between old and new meadows contrasted with a clear floristic differentiation between the two meadow types. The vegetation of old meadows was much more differentiated along prevailing environmental gradients than the vegetation of new meadows. Despite the favourable site conditions for the re‐establishment of species‐rich meadows on the former arable land, restoration success was limited to the vicinity of remnant stands. In contrast to old meadows, indicator species of new grassland were still typical species of regularly disturbed ruderal and arable habitats, often capable of building up a persistent seed bank. The precise mapping of 23 target species revealed that even wind dispersal predominantly leads to re‐establishment in the close circumference of parent plants. We found no indication that regular flooding, hay‐making and autumnal grazing had an impact on recolonization of newly created grassland. Even under favourable conditions for the re‐establishment of target species, restoration success in alluvial meadows proved to be strongly dispersal limited. We discuss the implications of our findings for future restoration management in grasslands.     

Characterization of Penicillium chrysogenum physiology in submerged cultures by color and monochrome image analysis

Although filamentous microorganisms are widely used in industrial fermentation processes, their growth and differentation are not yet fully understood, because their biomass is structured, and therefore difficult to descrbie and to quantify. This lack of appropriate tools can hinder the optimization and control of the fermentation. A quantitative image analysis method was therefore developed for characterizing the physiology of the penicillin-producing mold Penicillium chrysogenum. This method is based on a differntial staining procedure showing six physiological states: growing material, three differentiated states characterzied by an increasing granulation, a highly vacuolized state, and dead segments having lost their cytoplasm. The image analysis software, with versions written for monochrome and color images, consisted of a semiautomatic binary mask computation step and a fully automatic segmentation step based on a fuzzy classification. (c) 1995 John Wiley & Sons, Inc.     

Classification and measurement of fungal pellets by automated image analysis

An automated image analysis method for classifying and measuring pellets of filamentous fungi growing in submerged fermentations has been developed. The method discriminates between pelleted mycelial growth and loose aggregates of dispersed hyphae. Pellets are classified into smooth and hairy types. In both cases, the core of the pellet is identified and its shape and size characterized. For hairy pellets the annular region is also characterized. The method was tested on pellets of Aspergillus niger ATCC 11414 grown in a defined medium in shake flasks. This rapid method makes practical extensive studies on the morphology of pellets in submerged fermentations and the influence of fermentation conditions on that morphology.