Showing papers by "Hong Zhang published in 2012"

Guidelines for the use and interpretation of assays for monitoring autophagy

Abstract: In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.

Receptor protein complexes are in control of autophagy.

Abstract: In autophagic processes a variety of cargos is delivered to the degradative compartment of cells. Recent progress in autophagy research has provided support for the notion that when autophagic processes are operating in selective mode, a receptor protein complex will process the cargo. Here we present a concept of receptor protein complexes as comprising a functional tetrad of components: a ligand, a receptor, a scaffold and an Atg8 family protein. Our current understanding of each of the four components and their interaction in the context of cargo selection are considered in turn.

The C. elegans ATG101 homolog EPG-9 directly interacts with EPG-1/Atg13 and is essential for autophagy.

Abstract: Autophagy is an evolutionarily conserved catabolic process that involves the engulfment of cytoplasmic contents in a closed double-membrane structure, called the autophagosome, and their subsequent delivery to the vacuole/lysosomes for degradation. Genetic screens in Saccharomyces cerevisiae have identified more than 30 autophagy-related (Atg) genes that are essential for autophagosome formation. Here we isolated a novel autophagy gene, epg-9, whose loss of function causes defective autophagic degradation of a variety of protein aggregates during C. elegans embryogenesis. Mutations in epg-9 also reduce survival of animals under food depletion conditions. epg-9 mutants exhibit autophagy phenotypes characteristic of those associated with loss of function of unc-51/Atg1 and epg-1/Atg13. epg-9 encodes a protein with significant homology to mammalian ATG101. EPG-9 directly interacts with EPG-1/Atg13. Our study indicates that EPG-9 forms a complex with EPG-1 in the aggrephagy pathway in C. elegans.

Searching drug-like anti-cancer compound(s) based on G-quadruplex ligands.

Abstract: G-quadruplex structure is a four-stranded form of DNA, which is associated with cancer cell proliferation. G-quadruplexstabilized ligands have the potential to interfere with telomere replication by blocking the elongation procedure catalyzed by telomerase, and therefore have the potential to be anti-cancer drugs. A considerable number of novel compounds capable of targeting G-quadruplex at high affinity and specificity have been reported. Among them, several G-quadruplex ligands have shown promising anti-cancer activity in tumor xenograft models, and entered phase II clinical trials on cancer patients. This review summarized recent developments of Gquadruplex ligands as anti-cancer drugs and several powerful strategies to discover novel G-quadruplex ligands as anti-cancer drug candidates by screening natural product extracts and structural optimization of previously identified typical compounds.

Residual body removal during spermatogenesis in C. elegans requires genes that mediate cell corpse clearance

Abstract: Generation of spermatozoa involves segregation of most of the cytoplasm into residual bodies, which are detached from spermatids and eliminated in mammals. However, the molecular and cellular mechanism underlying the removal of residual bodies remains largely unknown. Here, we demonstrate that during C. elegans spermatogenesis residual bodies are engulfed and degraded by gonadal sheath cells, a process that uses the same set of genes underlying apoptotic cell removal. The two partially redundant engulfment pathways that clear cell corpses also mediate phagocytosis of residual bodies, possibly by recognizing the ‘eat me’ signal phosphatidylserine exposed on the surface. The residual body-containing phagosome undergoes a maturation process involving sequential steps including dynamic coating with PtdIns(3)P and association of RAB small GTPases. The genetic hierarchy of residual body removal in hermaphrodites is similar to that of cell corpse clearance, but male residual body removal involves a distinct hierarchy, with differential use of the engulfment genes. Efficient removal of residual bodies regulates the number of spermatids and effective transfer of spermatids during male matings. Our results indicate that a similar molecular mechanism is employed for the removal of residual bodies and apoptotic cell corpses in C. elegans.

Improved Four-Component Model-Based Target Decomposition for Polarimetric SAR Data

Abstract: An improved four-component model-based target decomposition scheme for polarimetric synthetic aperture radar data is proposed in this letter. The reason for the emergence of the negative powers in the Yamaguchi decomposition has been analyzed, and three corresponding additional steps are added in the proposed scheme. First, the orientation angle compensation is applied to the coherency matrix. Second, the coherency matrix with the maximum entropy, i.e., the identity matrix is used as the volume scattering model instead of the traditional ones. Third, corresponding power constraints are appended to the scheme. Moreover, the densely vegetated areas and the residual areas are processed separately via the H/α/A classification in the proposed scheme. Finally, the polarimetric-scattering-characteristic-preserving classification is utilized to verify the improvements of the proposed scheme. To demonstrate the effectiveness of the decomposition, an Advanced Land Observing Satellite Phased-Array-type L-band Synthetic Aperture Radar polarimetric image acquired over Beijing, China, is analyzed, and the results are presented in this letter. With negative powers eliminated by the proposed scheme, improvements can be observed in the experimental results, particularly for the urban areas.

Four-Component Model-Based Decomposition of Polarimetric SAR Data for Special Ground Objects

Abstract: A four-component model-based decomposition for polarimetric synthetic aperture radar (SAR) images is proposed to deal with the ground objects with orientation angles around 45°. In the previous decompositions, these special targets are mixed with the vegetated areas. With the deficiency of the previous decompositions analyzed, the ambiguity between two scattering mechanisms is clarified. A rotated Fresnel dihedral reflection model is introduced in the proposed algorithm, to model the scattering characteristics of these special targets. The nonnegative eigenvalue decomposition is applied to the remainder coherency matrix to prevent negative powers of the decomposed scattering mechanisms. Another advantage of the proposed decomposition is that it makes use of all the information provided by the coherency matrix, which remains unachieved in the previous model-based decompositions. Experimental Synthetic Aperture Radar (E-SAR) L-band polarimetric SAR data acquired over Oberpfaffenhofen, Germany, are analyzed in this letter. Experimental results indicate that the special ground objects have acquired correct scattering mechanisms, which verifies the effectiveness of the proposed method.

Ship detection based on feature confidence for high resolution SAR images

Abstract: Ship detection is an important application of global monitoring of ocean environment and maritime traffic. Synthetic aperture radar (SAR) systems are active sensors offering unique good spatial resolution regardless of weather or other conditions. It has been widely used for ship detection. An improved ship detection for high resolution SAR images based on the ship feature confidence is proposed in this paper. The features include kernel density estimation, length-width ratio and the number of target pixels. Targets with high feature confidence will be interpreted as ships. The COSMO-SkyMed SAR image is adopted for investigating the proposed algorithm. Experiment results illustrate that the method can achieve good performances.

Residual body removal during spermatogenesis in C. elegans requires genes that mediate cell corpse clearance

Abstract: Generation of spermatozoa involves segregation of most of the cytoplasm into residual bodies, which are detached from spermatids and eliminated in mammals. However, the molecular and cellular mechanism underlying the removal of residual bodies remains largely unknown. Here, we demonstrate that during C. elegans spermatogenesis residual bodies are engulfed and degraded by gonadal sheath cells, a process that uses the same set of genes underlying apoptotic cell removal. The two partially redundant engulfment pathways that clear cell corpses also mediate phagocytosis of residual bodies, possibly by recognizing the ‘eat me’ signal phosphatidylserine exposed on the surface. The residual body-containing phagosome undergoes a maturation process involving sequential steps including dynamic coating with PtdIns(3)P and association of RAB small GTPases. The genetic hierarchy of residual body removal in hermaphrodites is similar to that of cell corpse clearance, but male residual body removal involves a distinct hierarchy, with differential use of the engulfment genes. Efficient removal of residual bodies regulates the number of spermatids and effective transfer of spermatids during male matings. Our results indicate that a similar molecular mechanism is employed for the removal of residual bodies and apoptotic cell corpses in C. elegans.

A unified three-component scattering model for polarimetric coherent target decomposition

Abstract: In this article, first, the properties of the symmetric scattering space are examined based on the representation of the maximum symmetric scattering component proposed by Touzi. The symmetric scattering unit disc in the complex plane is mapped to a more intuitive unit sphere representation, and a new simpler classification method for symmetric scatterers is proposed based on a simplified symmetric scatterer scattering matrix metric distance. Then, a unified three-component scattering model for polarimetric coherent target decomposition (CTD) is proposed. Pauli decomposition, sphere, dihedral, helix (SDH) decomposition and Cameron decomposition can be expressed as a simplified form of the unified model with some certain restrictions, respectively. In addition, SDH decomposition and Cameron decomposition are proved to be equivalent by verification of restrictions’ consistency. Finally, by the combination of SDH decomposition and symmetric scatterer classification, a scattering matrix classification scheme ...

Urban change detection for high-resolution fully polarimetric SAR using a modified heterogeneous clutter model

Abstract: Based on the clutter statistical characteristics of fully polarimetric SAR (PolSAR) image, this paper presents a novel change detection method using a modified heterogeneous clutter model. Firstly, a multilook product model is introduced to describe the heterogeneous clutter in PolSAR data, and a new generalized likelihood ratio test (GLRT) distance is presented to measure the degree of evolution between the statistical characteristics of multi temporal full SAR images. Compared with spherically invariant random vectors (SIRV) distance, the stochastic texture description is considered in proposed GLRT distance. Afterwards, Kittler and Illingworth (K&I) minimum error threshold segmentation method is applied to extract the changed area.

Improvement of Pol SAR calibration based on the Ainsworth algorithm

Abstract: Fully polarimetric synthetic aperture radar (SAR) data analysis has found wide application for terrain classification, land-use, soil moisture, and ground cover classification. Critical to all analyses and applications is accurate calibration of the relative amplitudes of and phases between the various polarimetric channels. In this paper, we propose an improved algorithm to estimate the parameters stable and accurately based on the Ainsworth and the Quegan algorithms. The processing of this new algorithm is: 1) Initial the crosstalk parameters with the estimations of the Quegan algorithm; 2) Calculate the correction values of these four estimations and update the crosstalk parameters with Newton iteration method. Since there is none approximate in the process of the parameters estimation, this algorithm can accurately solve all parameters, even if the crosstalk is high. To verify the effect of proposed calibration algorithm, this paper analyse the accuracy of proposed algorithm with simulated distort PolSAR data. Then the simulated and Chinese airborne X-band PolSAR data before and after calibrated are decomposed respectively with Cloude's algorithm. The results confirm the proposed algorithm can solve all parameters more stable and accurately.

Change detection of polarimetric SAR images applied to specific land cover type

Abstract: In this paper, we will propose a novel PolSAR change detection method applied to specific land cover type, i.e., from class ω i to class ω j . Firstly, a new distance measure is derived to extract the difference map belonging to the specified change. Then, Kittler and Illingworth (KI) minimum error threshold segmentation method is applied to obtain the binary change mask. Two Radarsat-2 fully polarimetric images in Suzhou city, China, acquired on April 9, 2009 and June 15, 2010 separately, are used for our experiment. It is shown that the proposed change detection method will give a good performance to achieve the specified change areas of PoSAR images.

Analysis of polarimetric ship signatures with Radarsat-2 quad-pol imagery

Abstract: Polarimetric information can be used to characterize the target and benefit for ship classification in SAR image. In this paper, three types of features from fine quad-polarization Radarsat-2 SAR image, such as target to clutter ratio, distribution of scatter point, coherent decomposition component, are analyzed of three types of ships such as bulk carrier, container ship and oil tanker. Preliminary results show that target to clutter ratio is not suitable to discriminate the three types of ships. HH polarization is optimal for ship detection to HV,VH and VV polarization under the condition of the incidence angle of about 48 degrees. Distribution of strong backscattering can reflect the geometry structure of ship in SAR image, and it can be a good feature for ship classification. Furthermore, the feature will be more reliable in higher resolution SAR image. Polarimetric coherent decomposition benefits for understanding scatter mechanism of scatters of different ship. However it has some limitations for ship type recognition. More features and more ship chips should be investigated for the further conclusion.

Change detection based on polarization decomposition using RADARSAT-2 Quad-pol data

Abstract: Thanks to the capability to operate in almost all weather conditions and during both day and night time, change detection (CD) based on SAR data is developed rapidly in recent years, especially with the successful operation of full polarization space-borne SAR system. Most of the CD methods based on Quad-pol SAR data are through the analysis of statistical characteristics of the polarimetric covariance matrix or coherency matrix. In this study, we proposed a new CD method by comparing the difference between the scatter components, obtained by polarimetric target decomposition, to extract the difference map and then an adaptive KI algorithm is carried out to find an appreciate threshold for segmenting to get the change. Two RADARSAT-2 quad polarimetric images acquired over the Suzhou City in China are analyzed for validation in the experiment and the effectiveness of the proposed method is presented in the result.

Civilian ship classification based on structure features in high resolution SAR images

Abstract: With the globalization there is an increasing degree of concern on the ship traffic monitoring. Civilian ship classification is an important research area, as it can help to improve sea traffic surveillance and control activities. By making use of the new generation SAR satellites like COSMO-SkyMed, civilian ship classification in high resolution SAR images is a hotspot and preceding problem in SAR applications. This paper presents a ship classification method that uses single-pol COSMO-SkyMed images to categorize civilian ships into three types, including bulk carriers, container ships and oil tankers. The experimental results based on ship structure features show that the whole classification accuracy is above 80%.

Improved scattering-model-based speckle filter of polarimetric SAR data

Abstract: An improved speckle filter that preserves scattering characteristics for polarimetric SAR images is proposed. Lee proposed a scattering model based filter for polarimetric images in 2006. It is derived from the Freeman Decomposition to ensure that only the pixels belonging to the same scattering characteristics are included for filtering. However, some urban areas will mix up with the vegetated areas in the model-based decomposition, which confronts with the basic concept of the filter and decline the filtering effect. An improved four-component polarimetric decomposition is applied to overcome this problem. The proposed filter include the orientation angle compensation of the scattering matrix, a new volume scattering model, and two power constraints to deal with the previous problems. Experimental results indicate that the proposed algorithm have acquired an improved filtering effect for polarimetric SAR images.

A novel normalized scanning algorithm for wake detection in SAR images

Abstract: This paper presents a novel normalized scanning algorithm for detecting ship wakes in SAR (Synthetic Aperture Radar) images. Unlike most of wake detection algorithm is based on Radon transform, the proposed algorithm is based on normalized scanning. The technique takes advantage of the displacement between the ship and perspective wake in azimuth direction. The proposed algorithm can determine the offset in azimuth direction and the movement direction of ship. Then we can get the velocity vector of the ship. Although the computational complexity is very small, the normalized scan algorithm is robust in high noise environment. Experiment work outs are carried over in real SAR images. Results show that the ship wake detection based on normalized scan is better than traditional technique.

Ship detection based on improved S-NMF method for fully polarimetric Radarsat-2 data

Abstract: It's worth to investigate that the false alarm is reduced with polarimetic information while keeping the detection ratio when the fully polarimetic SAR images used for ship detection. An improved S-NMF (Sparseness-Nonnegative Matrix Factorization) for ship detection according to the nonnegative and sparseness characteristics of eigenvalues is proposed in this paper. The first two eigenvalues are used for NMF decomposition since they take most of the energy of the targets, and then we combine the advantage of the third eigenvalue which could get rid of the false alarms for ship detection with the OS-CFAR method. The proposed method is validated using Radarsat-2 fully polarimetric images with the corresponding AIS data. Results show that it cannot only detect most of the ships, but also reduce the false alarms effectively, and has good ability when the detection conditions change.

Development of a Portable Phosphate Detection System Using Cobalt Based Microelectrodes

Abstract: This paper presents a portable phosphate detection system based on electrochemical reaction mechanism using cobalt modified microelectrodes. The microelectrodes were fabricated by MEMS (Micro-electromechanical Systems) technology and modified by electrodeposition of cobalt. The performances of the microsensors were characterized by testing a series of standard phosphate solution. MSP430F4793 microcontroller was applied to control the detection process at low power consumption. Comparing with the test results achieved by using traditional electrochemical workstation method, this portable detection system has similar characteristics with the concentration range from 10-6 to 10-4 mol/L.