Computational Modeling of DNA 3D Structures: From Dynamics and Mechanics to Folding

DNA carries the genetic information required for the synthesis of RNA and proteins and plays an important role in many processes of biological development. Understanding the three-dimensional (3D) structures and dynamics of DNA is crucial for understanding their biological functions and guiding the development of novel materials. In this review, we discuss the recent advancements in computer methods for studying DNA 3D structures. This includes molecular dynamics simulations to analyze DNA dynamics, flexibility, and ion binding. We also explore various coarse-grained models used for DNA structure prediction or folding, along with fragment assembly methods for constructing DNA 3D structures. Furthermore, we also discuss the advantages and disadvantages of these methods and highlight their differences.

Predicting 3D structures and stabilities for complex RNA pseudoknots in ion solutions

RNA pseudoknots are a kind of important tertiary motif, and the structures and stabilities of pseudoknots are generally critical to the biological functions of RNAs with the motifs. In this work, we have carefully refined our previously developed coarse-grained model with salt effect through involving a new coarse-grained force field and a replica-exchange Monte Carlo algorithm, and employed the model to predict structures and stabilities of complex RNA pseudoknots in ion solutions beyond minimal H-type pseudoknots. Compared with available experimental data, the newly refined model can successfully predict 3D structures from sequences for the complex RNA pseudoknots including SARS-CoV-2 programming-1 ribosomal frameshifting element and Zika virus xrRNA, and can reliably predict the thermal stabilities of RNA pseudoknots with various sequences and lengths over broad ranges of monovalent/divalent salts. In addition, for complex pseudoknots including SARS-CoV-2 frameshifting element, our analyses show that their thermally unfolding pathways are mainly dependent on the relative stabilities of unfolded intermediate states, in analogy to those of minimal H-type pseudoknots.

[Identification and functional analysis of combined oxidative phosphorylation deficiency 28 gene mutation]

Objective: To report a case of combined oxidative phosphorylation deficiency 28 (COXPD28) in China, identified the pathogenic mutation and explored the pathogenic mechanism preliminarily. Methods: The clinical characteristics of a patient with COXPD28 were retrospectively analyzed and the pathogenic mutations were identified by mitochondrial gene sequencing and whole exome sequencing. The wild-type and mutant plasmids of pathogenic genes were constructed, and effect of mutation on protein expression by quantitative real-time PCR (qPCR) and Western blot were evaluated. Statistical methods mainly used one-way ANOVA and LSD test. Results: A 21 year old female patient presented with lactic acid poisoning due to repeated chest distress and wheezing since childhood. The sequencing of the whole exon group gene found that solute carrier family 25 member 26 (SLC25A26) gene had a compound heterozygous mutation (c.34G>C, p.A12P; c.197C>A, p.A66E), which was the first report in China. In vitro function test showed that the expression levels of SLC25A26 mRNA and S-adenosylmethionine carrier (SAMC) protein in cells transfected with SLC25A26 mutant plasmid were significantly lower than those transfected with wild type plasmid. The p.A66E mutant plasmid reduced the expression level of SLC25A26 mRNA and SAMC protein to 6% and 26% of wild type plasmids respectively (both P<0.001), while p.A12P mutant plasmid decreased to 62% and 82% of wild type plasmids respectively (P<0.001, P=0.044). When the double mutant (p.A66E+p.A12P) plasmids were co-transfected, the expression levels of SLC25A26 mRNA and SAMC protein decreased to 47% and 57% of the wild type plasmids, respectively (P<0.001, P=0.001). Conclusion: The pathogenic mutation gene of this patient with COXPD28 is SLC25A26 gene mutation (p.A66E, p.A12P), which causes the decrease of SLC25A26 expression level, mitochondrial oxidative phosphorylation dysfunction, and induces COXPD28.

[Imaging and cerebrospinal fluid features of two cases with lymphomatosis cerebri]

This article reported the clinical experience of diagnosis and treatment for two patients with lymphomatosis cerebri. Case 1 was female and aged 53 years old, while case 2 was male and aged 69 years old. Progressive cognitive impairment was the main clinical manifestation in both patients. Brain magnetic resonance imaging (MRI) suggested leukoencephalopathy with patchy or mass enhancement. Cerebral blood flow was reduced on perfusion imaging in one patient. Brain biopsy confirmed diffuse large B-cell lymphoma in both cases. The concentration of interleukin-10 in cerebrospinal fluid (CSF) of two patients was significantly increased, however, the result of CSF flow cytology was negative. The current study suggests that interleukin-10 in CSF is an important biological indicator for the diagnosis of lymphomatosis cerebri, but CSF flow cytometry may not be helpful. Moreover, cerebral hypoperfusion can be present in patients with lymphomatosis cerebri.

Ab initio predictions for 3D structure and stability of single- and double-stranded DNAs in ion solutions

The three-dimensional (3D) structure and stability of DNA are essential to understand/control their biological functions and aid the development of novel materials. In this work, we present a coarse-grained (CG) model for DNA based on the RNA CG model proposed by us, to predict 3D structures and stability for both dsDNA and ssDNA from the sequence. Combined with a Monte Carlo simulated annealing algorithm and CG force fields involving the sequence-dependent base-pairing/stacking interactions and an implicit electrostatic potential, the present model successfully folds 20 dsDNAs (≤52nt) and 20 ssDNAs (≤74nt) into the corresponding native-like structures just from their sequences, with an overall mean RMSD of 3.4Å from the experimental structures. For DNAs with various lengths and sequences, the present model can make reliable predictions on stability, e.g., for 27 dsDNAs with/without bulge/internal loops and 24 ssDNAs including pseudoknot, the mean deviation of predicted melting temperatures from the corresponding experimental data is only ~2.0°C. Furthermore, the model also quantificationally predicts the effects of monovalent or divalent ions on the structure stability of ssDNAs/dsDNAs.

To determine 3D structures and quantify stability of single- (ss) and double-stranded (ds) DNAs is essential to unveil the mechanisms of their functions and to further guide the production and development of novel materials. Although many DNA models have been proposed to reproduce the basic structural, mechanical, or thermodynamic properties of dsDNAs based on the secondary structure information or preset constraints, there are very few models can be used to investigate the ssDNA folding or dsDNA assembly from the sequence. Furthermore, due to the polyanionic nature of DNAs, metal ions (e.g., Na⁺ and Mg²⁺) in solutions can play an essential role in DNA folding and dynamics. Nevertheless, ab initio predictions for DNA folding in ion solutions are still an unresolved problem. In this work, we developed a novel coarse-grained model to predict 3D structures and thermodynamic stabilities for both ssDNAs and dsDNAs in monovalent/divalent ion solutions from their sequences. As compared with the extensive experimental data and available existing models, we showed that the present model can successfully fold simple DNAs into their native-like structures, and can also accurately reproduce the effects of sequence and monovalent/divalent ions on structure stability for ssDNAs including pseudoknot and dsDNAs with/without bulge/internal loops.

[Analysis of China's influenza vaccine application policy based on the macro model of the health system]

This article uses the analysis framework of the macro model of the health system to analyze the influenza vaccine policy documents issued by the state and governments at all levels from three perspectives: structure, process and results, and provides a scientific basis for improving the application strategy of influenza vaccine. It is suggested that on the basis of continuing to strengthen publicity, mobilization and organizational guarantee, measures to promote the application of influenza vaccine in China by exploring multi-channel financing mechanisms, combining the experience of new crown vaccination to improve the convenience of influenza vaccination, and scientifically setting vaccination rate targets, improve preparedness for an influenza pandemic.

RNAStat: An Integrated Tool for Statistical Analysis of RNA 3D Structures

The 3D architectures of RNAs are essential for understanding their cellular functions. While an accurate scoring function based on the statistics of known RNA structures is a key component for successful RNA structure prediction or evaluation, there are few tools or web servers that can be directly used to make comprehensive statistical analysis for RNA 3D structures. In this work, we developed RNAStat, an integrated tool for making statistics on RNA 3D structures. For given RNA structures, RNAStat automatically calculates RNA structural properties such as size and shape, and shows their distributions. Based on the RNA structure annotation from DSSR, RNAStat provides statistical information of RNA secondary structure motifs including canonical/non-canonical base pairs, stems, and various loops. In particular, the geometry of base-pairing/stacking can be calculated in RNAStat by constructing a local coordinate system for each base. In addition, RNAStat also supplies the distribution of distance between any atoms to the users to help build distance-based RNA statistical potentials. To test the usability of the tool, we established a non-redundant RNA 3D structure dataset, and based on the dataset, we made a comprehensive statistical analysis on RNA structures, which could have the guiding significance for RNA structure modeling. The python code of RNAStat, the dataset used in this work, and corresponding statistical data files are freely available at GitHub (https://github.com/RNA-folding-lab/RNAStat).

SS-RNN: A Strengthened Skip Algorithm for Data Classification Based on Recurrent Neural Networks

Recurrent neural networks are widely used in time series prediction and classification. However, they have problems such as insufficient memory ability and difficulty in gradient back propagation. To solve these problems, this paper proposes a new algorithm called SS-RNN, which directly uses multiple historical information to predict the current time information. It can enhance the long-term memory ability. At the same time, for the time direction, it can improve the correlation of states at different moments. To include the historical information, we design two different processing methods for the SS-RNN in continuous and discontinuous ways, respectively. For each method, there are two ways for historical information addition: 1) direct addition and 2) adding weight weighting and function mapping to activation function. It provides six pathways so as to fully and deeply explore the effect and influence of historical information on the RNNs. By comparing the average accuracy of real datasets with long short-term memory, Bi-LSTM, gated recurrent units, and MCNN and calculating the main indexes (Accuracy, Precision, Recall, and F1-score), it can be observed that our method can improve the average accuracy and optimize the structure of the recurrent neural network and effectively solve the problems of exploding and vanishing gradients.

Salt-Dependent RNA Pseudoknot Stability: Effect of Spatial Confinement

Macromolecules, such as RNAs, reside in crowded cell environments, which could strongly affect the folded structures and stability of RNAs. The emergence of RNA-driven phase separation in biology further stresses the potential functional roles of molecular crowding. In this work, we employed the coarse-grained model that was previously developed by us to predict 3D structures and stability of the mouse mammary tumor virus (MMTV) pseudoknot under different spatial confinements over a wide range of salt concentrations. The results show that spatial confinements can not only enhance the compactness and stability of MMTV pseudoknot structures but also weaken the dependence of the RNA structure compactness and stability on salt concentration. Based on our microscopic analyses, we found that the effect of spatial confinement on the salt-dependent RNA pseudoknot stability mainly comes through the spatial suppression of extended conformations, which are prevalent in the partially/fully unfolded states, especially at low ion concentrations. Furthermore, our comprehensive analyses revealed that the thermally unfolding pathway of the pseudoknot can be significantly modulated by spatial confinements, since the intermediate states with more extended conformations would loss favor when spatial confinements are introduced.

An optical neural chip for implementing complex-valued neural network

Complex-valued neural networks have many advantages over their real-valued counterparts. Conventional digital electronic computing platforms are incapable of executing truly complex-valued representations and operations. In contrast, optical computing platforms that encode information in both phase and magnitude can execute complex arithmetic by optical interference, offering significantly enhanced computational speed and energy efficiency. However, to date, most demonstrations of optical neural networks still only utilize conventional real-valued frameworks that are designed for digital computers, forfeiting many of the advantages of optical computing such as efficient complex-valued operations. In this article, we highlight an optical neural chip (ONC) that implements truly complex-valued neural networks. We benchmark the performance of our complex-valued ONC in four settings: simple Boolean tasks, species classification of an Iris dataset, classifying nonlinear datasets (Circle and Spiral), and handwriting recognition. Strong learning capabilities (i.e., high accuracy, fast convergence and the capability to construct nonlinear decision boundaries) are achieved by our complex-valued ONC compared to its real-valued counterpart.

Effects of varying dietary intoxication with lead on the performance and ovaries of laying hens

In this study, we explored the effect of dietary lead nitrate on zootechnical performance, egg quality, accumulation of ovarian plumbum (Pb), follicular atresia rate, and ovarian oxidative stress in laying hens. Furthermore, the nuclear factor erythroid 2-related factor 2 (Nrf2) signaling molecule was studied to reveal the molecular mechanism of the stress. A total of 512 Hy-Line Brown laying hens aged 40 wk were randomly allocated to 4 groups (with 8 pens per group and 16 hens per pen). The Pb concentrations used to treat the 4 groups were 3.20, 33.20, 63.20, and 93.20 mg/kg. The results revealed that dietary Pb exposure significantly linearly reduced the zootechnical performance (P < 0.01) but significantly linearly increased the feed conversion ratio (P < 0.01). The dietary Pb exposure significantly linearly reduced the Haugh units (P < 0.01), albumen height (P < 0.01), eggshell thickness (P < 0.01), and eggshell strength (P < 0.01). In addition, the dietary Pb exposure significantly enhanced the follicular atresia rate (P < 0.01). After dietary Pb exposure, superoxide dismutase (P < 0.01) and glutathione peroxidase (GSH-Px) (P < 0.01) activities and glutathione (P < 0.01) contents were significant decreased quadratically, and there were significant linear decreases in the activities of catalase (CAT) (P < 0.01) and glutathione reductase (GR) (P < 0.01), whereas malondialdehyde content was significantly linearly increased (P < 0.01). In addition, except for manganese superoxide dismutase, the gene expressions of copper-zinc superoxide dismutase (P < 0.01), CAT (P < 0.01), and GR (P < 0.01) were significant decreased linearly. In addition, there were significantly quadratic decreases in the mRNA expressions of GSH-Px (P < 0.01) and Nrf2 (P < 0.01). By way of contrast, the Kelch-like ECH-associated protein 1 (Keap1) gene expression was significantly linearly increased (P < 0.01). In conclusion, dietary Pb exposure could induce oxidative stress by impairing the Nrf2-Keap1 signal pathway in the ovaries of laying hens.

Structure folding of RNA kissing complexes in salt solutions: predicting 3D structure, stability, and folding pathway

RNA kissing complexes are essential for genomic RNA dimerization and regulation of gene expression, and their structures and stability are critical to their biological functions. In this work, we used our previously developed coarse-grained model with an implicit structure-based electrostatic potential to predict three-dimensional (3D) structures and stability of RNA kissing complexes in salt solutions. For extensive RNA kissing complexes, our model shows great reliability in predicting 3D structures from their sequences, and our additional predictions indicate that the model can capture the dependence of 3D structures of RNA kissing complexes on monovalent/divalent ion concentrations. Moreover, the comparisons with extensive experimental data show that the model can make reliable predictions on the stability for various RNA kissing complexes over wide ranges of monovalent/divalent ion concentrations. Notably, for RNA kissing complexes, our further analyses show the important contribution of coaxial stacking to the 3D structures and stronger stability than the corresponding kissing-interface duplexes at high salts. Furthermore, our comprehensive analyses for RNA kissing complexes reveal that the thermally folding pathway for a complex sequence is mainly determined by the relative stability of two possible folded states of kissing complex and extended duplex, which can be significantly modulated by its sequence.

3D structure stability of the HIV-1 TAR RNA in ion solutions: A coarse-grained model study

As an extremely common structural motif, RNA hairpins with bulge loops [e.g., the human immunodeficiency virus type 1 (HIV-1) transactivation response (TAR) RNA] can play essential roles in normal cellular processes by binding to proteins and small ligands, which could be very dependent on their three-dimensional (3D) structures and stability. Although the structures and conformational dynamics of the HIV-1 TAR RNA have been extensively studied, there are few investigations on the thermodynamic stability of the TAR RNA, especially in ion solutions, and the existing studies also have some divergence on the unfolding process of the RNA. Here, we employed our previously developed coarse-grained model with implicit salt to predict the 3D structure, stability, and unfolding pathway for the HIV-1 TAR RNA over a wide range of ion concentrations. As compared with the extensive experimental/theoretical results, the present model can give reliable predictions on the 3D structure stability of the TAR RNA from the sequence. Based on the predictions, our further comprehensive analyses on the stability of the TAR RNA as well as its variants revealed that the unfolding pathway of an RNA hairpin with a bulge loop is mainly determined by the relative stability between different states (folded state, intermediate state, and unfolded state) and the strength of the coaxial stacking between two stems in folded structures, both of which can be apparently modulated by the ion concentrations as well as the sequences.

What is the best reference state for building statistical potentials in RNA 3D structure evaluation?

Knowledge-based statistical potentials have been shown to be efficient in protein structure evaluation/prediction, and the core difference between various statistical potentials is attributed to the choice of reference states. However, for RNA 3D structure evaluation, a comprehensive examination on reference states is still lacking. In this work, we built six statistical potentials based on six reference states widely used in protein structure evaluation, including averaging, quasi-chemical approximation, atom-shuffled, finite-ideal-gas, spherical-noninteracting, and random-walk-chain reference states, and we examined the six reference states against three RNA test sets including six subsets. Our extensive examinations show that, overall, for identifying native structures and ranking decoy structures, the finite-ideal-gas and random-walk-chain reference states are slightly superior to others, while for identifying near-native structures, there is only a slight difference between these reference states. Our further analyses show that the performance of a statistical potential is apparently dependent on the quality of the training set. Furthermore, we found that the performance of a statistical potential is closely related to the origin of test sets, and for the three realistic test subsets, the six statistical potentials have overall unsatisfactory performance. This work presents a comprehensive examination on the existing reference states and statistical potentials for RNA 3D structure evaluation.

Modeling Structure, Stability, and Flexibility of Double-Stranded RNAs in Salt Solutions

Double-stranded (ds) RNAs play essential roles in many processes of cell metabolism. The knowledge of three-dimensional (3D) structure, stability, and flexibility of dsRNAs in salt solutions is important for understanding their biological functions. In this work, we further developed our previously proposed coarse-grained model to predict 3D structure, stability, and flexibility for dsRNAs in monovalent and divalent ion solutions through involving an implicit structure-based electrostatic potential. The model can make reliable predictions for 3D structures of extensive dsRNAs with/without bulge/internal loops from their sequences, and the involvement of the structure-based electrostatic potential and corresponding ion condition can improve the predictions for 3D structures of dsRNAs in ion solutions. Furthermore, the model can make good predictions for thermal stability for extensive dsRNAs over the wide range of monovalent/divalent ion concentrations, and our analyses show that the thermally unfolding pathway of dsRNA is generally dependent on its length as well as its sequence. In addition, the model was employed to examine the salt-dependent flexibility of a dsRNA helix, and the calculated salt-dependent persistence lengths are in good accordance with experiments.

Predicting 3D structure and stability of RNA pseudoknots in monovalent and divalent ion solutions

RNA pseudoknots are a kind of minimal RNA tertiary structural motifs, and their three-dimensional (3D) structures and stability play essential roles in a variety of biological functions. Therefore, to predict 3D structures and stability of RNA pseudoknots is essential for understanding their functions. In the work, we employed our previously developed coarse-grained model with implicit salt to make extensive predictions and comprehensive analyses on the 3D structures and stability for RNA pseudoknots in monovalent/divalent ion solutions. The comparisons with available experimental data show that our model can successfully predict the 3D structures of RNA pseudoknots from their sequences, and can also make reliable predictions for the stability of RNA pseudoknots with different lengths and sequences over a wide range of monovalent/divalent ion concentrations. Furthermore, we made comprehensive analyses on the unfolding pathway for various RNA pseudoknots in ion solutions. Our analyses for extensive pseudokonts and the wide range of monovalent/divalent ion concentrations verify that the unfolding pathway of RNA pseudoknots is mainly dependent on the relative stability of unfolded intermediate states, and show that the unfolding pathway of RNA pseudoknots can be significantly modulated by their sequences and solution ion conditions.

Sculpting nanoparticle dynamics for single-bacteria-level screening and direct binding-efficiency measurement

Particle trapping and binding in optical potential wells provide a versatile platform for various biomedical applications. However, implementation systems to study multi-particle contact interactions in an optical lattice remain rare. By configuring an optofluidic lattice, we demonstrate the precise control of particle interactions and functions such as controlling aggregation and multi-hopping. The mean residence time of a single particle is found considerably reduced from 7 s, as predicted by Kramer’s theory, to 0.6 s, owing to the mechanical interactions among aggregated particles. The optofluidic lattice also enables single-bacteria-level screening of biological binding agents such as antibodies through particle-enabled bacteria hopping. The binding efficiency of antibodies could be determined directly, selectively, quantitatively and efficiently. This work enriches the fundamental mechanisms of particle kinetics and offers new possibilities for probing and utilising unprecedented biomolecule interactions at single-bacteria level.

Optical trapping is a versatile tool for biomedical applications. Here, the authors use an optofluidic lattice to achieve controllable multi-particle hopping and demonstrate single-bacteria-level screening and measurement of binding efficiency of biological binding agents through particle-enabled bacteria hopping.

High-resolution and multi-range particle separation by microscopic vibration in an optofluidic chip

An optofluidic chip is demonstrated in experiments for high-resolution and multi-range particle separation through the optically-induced microscopic vibration effect, where nanoparticles are trapped in loosely overdamped optical potential wells created with combined optical and fluidic constraints. It is the first demonstration of separating single nanoparticles with diameters ranging from 60 to 100 nm with a resolution of 10 nm. Nanoparticles vibrate with an amplitude of 3-7 μm in the loosely overdamped potential wells in the microchannel. The proposed optofluidic device is capable of high-resolution particle separation at both nanoscale and microscale without reconfiguring the device. The separation of bacteria from other larger cells is accomplished using the same chip and operation conditions. The unique trapping mechanism and the superb performance in high-resolution and multi-range particle separation of the proposed optofluidic chip promise great potential for a diverse range of biomedical applications.

Understanding the Relative Flexibility of RNA and DNA Duplexes: Stretching and Twist-Stretch Coupling

The flexibility of double-stranded (ds) RNA and dsDNA is crucial for their biological functions. Recent experiments have shown that the flexibility of dsRNA and dsDNA can be distinctively different in the aspects of stretching and twist-stretch coupling. Although various studies have been performed to understand the flexibility of dsRNA and dsDNA, there is still a lack of deep understanding of the distinctive differences in the flexibility of dsRNA and dsDNA helices as pertains to their stretching and twist-stretch coupling. In this work, we have explored the relative flexibility in stretching and twist-stretch coupling between dsRNA and dsDNA by all-atom molecular dynamics simulations. The calculated stretch modulus and twist-stretch coupling are in good accordance with the existing experiments. Our analyses show that the differences in stretching and twist-stretch coupling between dsRNA and dsDNA helices are mainly attributed to their different (A- and B-form) helical structures. Stronger basepair inclination and slide in dsRNA is responsible for the apparently weaker stretching rigidity versus that of dsDNA, and the opposite twist-stretch coupling for dsRNA and dsDNA is also attributed to the stronger basepair inclination in dsRNA than in dsDNA. Our calculated macroscopic elastic parameters and microscopic analyses are tested and validated by different force fields for both dsRNA and dsDNA.

Predicting 3D Structure, Flexibility, and Stability of RNA Hairpins in Monovalent and Divalent Ion Solutions

A full understanding of RNA-mediated biology would require the knowledge of three-dimensional (3D) structures, structural flexibility, and stability of RNAs. To predict RNA 3D structures and stability, we have previously proposed a three-bead coarse-grained predictive model with implicit salt/solvent potentials. In this study, we further develop the model by improving the implicit-salt electrostatic potential and including a sequence-dependent coaxial stacking potential to enable the model to simulate RNA 3D structure folding in divalent/monovalent ion solutions. The model presented here can predict 3D structures of RNA hairpins with bulges/internal loops (<77 nucleotides) from their sequences at the corresponding experimental ion conditions with an overall improved accuracy compared to the experimental data; the model also makes reliable predictions for the flexibility of RNA hairpins with bulge loops of different lengths at several divalent/monovalent ion conditions. In addition, the model successfully predicts the stability of RNA hairpins with various loops/stems in divalent/monovalent ion solutions.

Potential of mean force between like-charged nanoparticles: Many-body effect

Ion-mediated interaction is important for the properties of polyelectrolytes such as colloids and nucleic acids. The effective pair interactions between two polyelectrolytes have been investigated extensively, but the many-body effect for multiple polyelectrolytes still remains elusive. In this work, the many-body effect in potential of mean force (PMF) between like-charged nanoparticles in various salt solutions has been comprehensively examined by Monte Carlo simulation and the nonlinear Poisson-Boltzmann theory. Our calculations show that, at high 1:1 salt, the PMF is weakly repulsive and appears additive, while at low 1:1 salt, the additive assumption overestimates the repulsive many-body PMF. At low 2:2 salt, the pair PMF appears weakly repulsive while the many-body PMF can become attractive. In contrast, at high 2:2 salt, the pair PMF is apparently attractive while the many-body effect can cause a weaker attractive PMF than that from the additive assumption. Our microscopic analyses suggest that the elusive many-body effect is attributed to ion-binding which is sensitive to ion concentration, ion valence, number of nanoparticles and charges on nanoparticles.

First Report of Paulownia Witches'-Broom Phytoplasma in China

Paulownia witches'-broom (PaWB) is one of the most important diseases affecting Paulownia tomentosa trees in China. According to 2006 statistics, the disease has affected 880,000 ha of trees for timber production causing billions of dollars in economic losses. During the spring and summer of 2006, a survey was done in Shaanxi Province to confirm phytoplasma infection of paulownia trees exhibiting symptoms of witches'-broom, stunting, yellowing, and proliferating secondary shoots. Foliage samples were collected from 24 symptomatic and 8 symptomless paulownia plants in eight different production fields. Total DNA was extracted from 0.5 g of leaf midrib and stem phloem tissue with a modified cetyltrimethylammoniumbromide (CTAB) method (3). Resulting DNA extracts were analyzed by a nested PCR assay using phytoplasma 16S rRNA gene primer pairs R16mF2/R16mR1 followed by R16F2n/ R16R2 (1), which amplified a 1.4-kb and a 1.2-kb product, respectively, from symptomatic plants. Restriction fragment length polymorphism (RFLP) analysis of the nested 1.2-kb 16S rDNA products with AluI, MseI, HhaI, HpaI, RsaI, BfaI, HinfI, and TaqI endonuclease (2) indicated that all symptomatic plants were infected by a phytoplasma belonging to aster yellows group (16SrI) subgroup D (16SrI-D) phytoplasma strains. A 1.2-kb 16S rDNA sequence (GenBank Accession No. DQ851169) derived from representative strain PaWB-Shaanxi was identical (100%) to that of PaWB phytoplasma (L27033), a known subgroup 16SrI-D strain from Taiwan (2). The agreement between the RFLP analysis and sequence data confirms that PaWB from Shaanxi is a member of subgroup 16SrI-D. To our knowledge, this is the first report of PaWB disease being present in China and of its association with the 16SrI-D subgroup. References: (1) D. E. Gundersen and I.-M. Lee. Phytopathol. Mediterr. 35:144, 1996. (2) I.-M. Lee et al. Inst. J. Syst. Bacteriol. 48:1153, 1998. (3) Y. Qi et al. Biotechnol. Bull. 4:44, 2004.

Disruption of pRb-p16INK4 pathway: a common event in ampullary carcinogenesis

BACKGROUND/AIMS

Aberrations of the pRb (Retinoblastoma gene protein)-p16INK4 pathway play a critical role in carcinogenesis. Our objective is to evaluate its role in tumorigenesis and the development of ampullary cancer.

METHODOLOGY

We examined expression status of p16INK4 protein and pRb immunohistochemically and assessed their possible prognostic relevance in 36 ampullary cancers.

RESULTS

Thirty-four specimens (94.4%) exhibited alteration of p16INK4 and/or pRb expression, with 63.9% (23/36) of cancers showing p16INK4 negative expression and 94.4% (34/36) pRb abnormal expression. p16INK4 protein negative expression correlated significantly with tumor progression features such as advanced tumor stages (p=0.0291), lymph node metastasis (p=0.005), pancreas invasion (p=0.0002) and duodenum invasion (p=0.0101). Cases with both p16RNK4 protein negative expression and pRb overexpression showed poorer differentiation, more invasive growth (p=0.0425), higher level tumor stages (p=0.0079) and more frequent pancreas invasion (p=0.0024), compared with the others. p16INK4 protein expression showed no relationship with pRb expression (p=0.2199). No association was found in pRb expression status compared with any clinicopathological parameters analyzed.

CONCLUSIONS

The disruption of the pRb-p16NK4 pathway plays an important role in ampullary carcinogenesis, the absence of p16INK4 protein expression might be involved in ampullary tumor progression.

Telomerase expression and p53 status in hepatocellular carcinoma

OBJECTIVES

[corrected] Genomic instability is a driving force for tumorigenesis. Telomerase and p53 play central roles in maintaining genomic integrity. The purpose of this study was to assess the role of telomerase expression and p53 protein overexpression in hepatocellular carcinoma (HCC).

METHODS

Telomerase activity and p53 overexpression were investigated in 63 patients undergoing hepatectomy for HCC by a telomeric repeat amplification protocol and immunohistochemistry, respectively. The associations among telomerase expression, p53 overexpression, and clinicopathological features were analyzed, and independent prognostic factors in the recurrence of HCC after hepatectomy were determined.

RESULTS

Telomerase expression did not correlate with clinicopathological features except hepatitis virus status (p = 0.04) and was identified as a significant prognostic variable for HCC recurrence (p = 0.027) along with portal venous invasion (p = 0.001). In contrast, p53 overexpression strongly correlated with tumor differentiation (p < 0.0001) but did not reflect time to recurrence (p = 0.26). Telomerase expression did not correlate with p53 overexpression (p = 0.35).

CONCLUSIONS

The reactivation of telomerase was of significant value in predicting the recurrence of HCC after hepatectomy. However, p53 overexpression did not correlate with telomerase expression in HCC, nor did it reflect the time to recurrence.

Deregulation of G1/S transition is a common event in carcinoma of the ampulla of vater

BACKGROUND/AIMS

Aberrant expression of cell cycle regulators and subsequent deregulation of G1/S transition is one of the most important characteristics of human cancer. The aim of this study was to determine the overall pattern of deranged expression of the cell cycle regulators involved in the G1/S transition in ampullary carcinoma.

METHODOLOGY

Using immunohistochemistry, we investigated the expression of p21WAF1/CIP1, p27Kip1, p16INK4, cyclin D1, cyclin E, pRb and p53 in 14 resected specimens of ampullary carcinoma and defined the proliferative activity of each tumor by quantifying Ki-67 antigen.

RESULTS

Decreased expression of p21WAF1/CIP1, p27Kip1, and p16INK4 was detected in 6 (43%), 11 (79%), and 4 (29%) tumors, respectively. Four tumors (29%) overexpressed cyclin D1 and 8 (57%) overexpressed cyclin E. Eight tumors (57%) overexpressed pRb. Aberrant accumulation of p53 was observed in 10 (71%) of the tumors. Overall, the expression of two or more of these cell cycle regulators was altered in all of the 14 tumors. Decreased p21WAF1/CIP1 expression was related to higher TMN stage (P = 0.04) and lymphatic invasion (P = 0.04). The proliferative index was higher in tumors with decreased p27Kip expression (P = 0.005), and in tumors with cyclin E overexpression (P = 0.06).

CONCLUSIONS

Our observations suggest that deregulation of G1/S transition is a very common event in ampullary carcinoma, and that altered expression of cell cycle regulators is associated with the aggressive behavior of this tumor. Correcting the G1/S transition regulatory machinery may provide a novel therapy for this malignancy.

Proliferative marker Ki-67 in gallbladder carcinomas: high expression level predicts early recurrence after surgical resection

To evaluate the prognostic value of proliferative maker Ki-67, its expression was determined immunohistochemically in 37 gallbladder carcinomas (GBCs). A high Ki-67 index was significantly correlated with tumor lymphatic invasion (P=0.007) and vascular invasion (P=0.04). High Ki-67 index group and low Ki-67 index group showed different clinical courses. Five patients who experienced recurrences in high Ki-67 index group developed their recurrent diseases within one year after surgery and died soon after recurrence, while the recurrences (five cases) in low Ki-67 index group were distributed all stages after surgery. In conclusion, high Ki-67 index predicts early recurrence after surgery for GBCs.

[Treatment effects of electroacupuncture on gentamycin ototoxicity and its mechanism in guinea pigs]

AIM

To investigate the effects of electroacupuncture on gentamycin (GE) ototoxicity in guinea pigs.

METHODS

Brainstem auditory evoked potential (BAEP) and histochemistry were used in our study.

RESULTS

Electroacupuncture reduced the elevated BAEP thresholds and shortened the prolongated BAEP wave latencies and interpeak latencies. It protected the activity of mitochondrial enzyme in the cochlear hair cells and cochlear stria vascularis.

CONCLUSION

Electroacupuncture therapy can reduce GE ototoxicity. The mechanism of electroacupuncture therapy may be associated with its protected activity of mitochondrial enzyme and maintenance of energy metabolism of the cochlear hair cells and cochlear stria vascularis.

Reduced p21(WAF1/CIP1) expression is an early event in gallbladder carcinogenesis and is of prognostic significance for patients with carcinomas of the gallbladder

The molecular basis underlying the development and progression of gallbladder carcinoma (GBC) remains poorly understood. To evaluate the roles of p21(WAF1/CIP1) and p53 in gallbladder carcinogenesis and to assess their prognostic significance for patients with GBC, we used immunohistochemistry to examine the expression of p21(WAF1/CIP1) and p53 protein in a series of surgically resected specimens, including normal epithelia, precancerous lesions adenoma, and dysplasia, and carcinomas of the gallbladder. Reduced p21(WAF1/CIP1) expression was frequently observed in carcinomas (18 of 37 lesions; 49%), and even in precancerous lesions adenomas (3 of 7; 43%) and dysplasias (5 of 5; 100%). p53 overexpression was detected in 43% of the adenomas, 60% of the dysplasias and 57% of the carcinomas. There was an inverse relationship between p21(WAF1/CIP1) and p53 expression in GBCs (P =.01). Survival analysis indicated that reduced p21(WAF1/CIP1) expression was significantly associated with shortened disease-free and overall survival (P =.04 and.03, respectively) for patients with stages II to IV GBCs. These observations suggest that reduced p21(WAF1/CIP1) expression and p53 overexpression contribute to GBC from an early stage and that determination of p21(WAF1/CIP1) expression in surgically resected specimens would add prognostic information to conventional pathologic examinations for patients with advanced-stage GBC.

Cyclin D1 overexpression is a critical event in gallbladder carcinogenesis and independently predicts decreased survival for patients with gallbladder carcinoma

This study was designed to test the hypothesis that cyclin D1 overexpression is involved in the multistep process of gallbladder carcinogenesis and can be used to predict poor prognosis for patients with gallbladder carcinoma (GBC). Cyclin D1 expression was examined immunohistochemically in a series of specimens, including 8 normal epithelia, 8 benign adenomyoma lesions, 6 precancerous adenomas, and 37 carcinomas of the gallbladder. Four of the 6 (67%) adenomas and 15 of the 37 (41%) adenocarcinomas demonstrated cyclin D1 overexpression (>5% nuclear staining), whereas all normal epithelia and adenomyoma lesions were negative for cyclin D1. Kaplan-Meier curves showed that cyclin D1 overexpression was significantly related to decreased overall survival (P < 0.05) in patients with GBCs. The Cox proportional hazards model identified cyclin D1 overexpression as an independent prognostic marker for death (P = 0.024; risk ratio, 4.2; 95% confidence interval, 1.2-14.7). To test whether cyclin D1 overexpression is a critical event in gallbladder neoplasms, cyclin-dependent kinase inhibitor p27Kip1 was introduced to ascertain how cyclin D1 affects clinical outcomes. Subsequently, neoplasms were divided into three groups on the basis of the combination of cyclin D1 expression and p27Kip1 status, which had been determined previously. Group 1 showed no abnormality in either cyclin D1 or p27Kip1 expression. Group 2 showed aberrant expression of one of the two proteins, whereas group 3 showed concurrent abnormalities in both proteins. Results indicated that overall survival was greatest in group 1, followed by a significant decrease in group 2 and a more precipitous decrease in group 3. In conclusion, cyclin D1 overexpression is an early event in gallbladder carcinogenesis and independently predicts decreased survival for patients with GBC.

Overexpression of retinoblastoma protein predicts decreased survival and correlates with loss of p16INK4 protein in gallbladder carcinomas

This study was designed to determine whether the level of retinoblastoma protein (pRb) expression predicts tumor progression and prognosis in gallbladder carcinomas (GBCs) and the relationship between pRb and pl6INK4 protein expression. The expression of these two proteins was evaluated immunohistochemically in 37 tumors from 36 patients with GBC. pRb loss and overexpression were observed in 5 (13.5%) and 18 (48.6%) of the 37 tumors, respectively. Both pRb loss and overexpression were significantly correlated with advanced TNM stage, lymph node metastasis, and tumor perineural invasion. Moreover, pRb overexpression was significantly associated with decreased overall survival (P = 0.001; log-rank test). Further analysis indicated that the influence of pRb overexpression on survival was independent of TNM stage and lymph node metastasis. Loss of p16INK4 protein was observed in 28 of the 37 GBCs (75.7%), but was not significantly associated with any clinicopathological factors or survival. pRb overexpression was significantly associated with the loss of p161NK4 protein (P < 0.0001). These results suggest that pRb overexpression significantly predicts decreased survival in GBCs.

Alterations of retinoblastoma protein and p16INK4 protein expression in extrahepatic bile duct carcinomas

BACKGROUND/AIMS

Human cancer development results from dysfunction of G1-phase regulators of the cell cycle. Retinoblastoma protein and p16INK4 are the most essential links between cell cycle control and cancer. We examined the expression of p16INK4 and pRb and their possible prognostic relevance in 34 extrahepatic bile duct carcinomas.

METHODOLOGY

Expression of pRb and p16INK4 was determined using immunohistochemical techniques. Associations between expression of pRb and p16INK4 and the clinicopathological features were analyzed by using the chi 2 test and survival analysis was performed by Log-rank test.

RESULTS

Two (6%) extrahepatic bile duct carcinomas were pRb negative, 26 (76%) showed pRb overexpression, and 6 (18%) demonstrated moderate expression. Twenty-two (65%) tumors were p16INK4 negative and 12 (35%) were p16INK4-positive. Cases with pRb-negative or pRb overexpression were significantly correlated with tumor progression (P = 0.004) and TNM stage (P = 0.009). Alterations in pRb and p16INK4 expression did not correlate with patient outcome.

CONCLUSIONS

Alterations of pRb and p16INK4 expression are frequently involved in extrahepatic bile duct carcinomas, and that aberrant pRb expression significantly associates with tumor progression.

Reduced p21(WAF1/CIP1) protein expression is predominantly related to altered p53 in hepatocellular carcinomas

To investigate the relationship between the expression of p21(WAF1/CIP1) protein and p53 status and the possible role of the two proteins in hepatocellular carcinomas (HCCs), we examined the expression of p21(WAF1/CIP1) and p53 immunohistochemically in 81 tumours from 65 patients with hepatocellular carcinoma. p21(WAF1/CIP1) protein was absent from 59 of 81 tumours (72.8%), and altered p53 expression was found in 43 (53.1%). p21(WAF1/CIP1) expression was significantly associated with p53 status (P = 0.0008); 38 of 59 tumours lacking p21(WAF1/CIP1) protein were accompanied by altered p53 expression. Further analyses showed that p21(WAF1/CIP1) expression was inversely correlated with p53 expression in hepatitis C virus (HCV)-related HCCs, but not in HBV-related hepatocellular carcinomas and hepatocellular carcinomas without viral infection. All 11 tumours with intrahepatic metastasis showed altered p21(WAF1/CIP1) or p53 expression. In contrast, no intrahepatic metastasis was found in any of the 17 tumours without abnormal expression of either of the two proteins. These results suggest that: (1) different modes of p21(WAF1/CIP1) regulation are involved in HCCs differing in their hepatitis viral infection status, and p21(WAF1/CIP1) expression appears to be predominantly related to altered p53 in HCV-related HCCs; (2) disruption of the p53-p21(WAF1/CIP1) cell-cycle-regulating pathway may contribute to malignant progression of HCC.

Loss of p16(INK4) protein, alone and together with loss of retinoblastoma protein, correlate with hepatocellular carcinoma progression

To investigate the role of p16(INK4) protein absence in hepatocellular carcinoma progression, we examined p16(INK4) expression immunohistochemically in 81 primary and 23 metastatic lesions of hepatocellular carcinoma, in which retinoblastoma protein status had been determined. p16(INK4) protein was absent from 44% of the total of 104 tumors. The rate of p16(INK4) absence was twice as high in metastatic lesions (74%) compared with primary lesions (36%) (P=0.001). Loss of p16(INK4) and/or retinoblastoma protein was significantly associated with decreased tumor differentiation, vascular invasion and metastasis. In conclusion, p16(INK4) protein absence, alone and together with loss of retinoblastoma protein, contributes to hepatocellular carcinoma progression.

p27(Kip1) expression in normal epithelia, precancerous lesions, and carcinomas of the gallbladder: association with cancer progression and prognosis

p27(Kip1) is a cyclin-dependent kinase inhibitor that negatively regulates cell proliferation. This study was designed to evaluate the roles of p27(Kip1) in gallbladder carcinogenesis and the prognostic value of p27(Kip1) in patients with gallbladder carcinoma. p27(Kip1) expression was examined immunohistochemically in surgically resected specimens of 8 normal epithelia, 8 adenomyomatosis lesions, 6 precancerous adenomas, and 37 carcinomas of the gallbladder. Decreased p27(Kip1) expression (<50% nuclear staining) was observed in 16 of the 37 (43%) gallbladder carcinomas, but not in any specimen of normal epithelium, adenomyomatosis, or adenoma. The fact that all of the adenomas showed normal p27(Kip1) expression suggests that decreased p27(Kip1) expression is probably not an early event in gallbladder carcinogenesis. Decreased p27(Kip1) expression was significantly associated with less marked tumor cell differentiation (P =.017), lymphatic invasion (P =.046), lymph node metastasis (P =.007), and advanced TNM stage (stage IV vs. stage I, P =.026; stage IV vs. stage II, P =.005). This suggests that down-regulation of p27(Kip1) expression is a late event in gallbladder carcinogenesis, possibly promoting tumor progression and metastasis. Kaplan-Meier curves showed that decreased p27(Kip1) expression was significantly associated with shorter overall survival (P =.001) in patients with gallbladder carcinomas who had undergone radical surgery. Cox's proportional hazards model revealed decreased p27(Kip1) expression to be an independent predictor for death (P =.034; risk ratio, 3.9; 95% confidence interval, 1.1-13.7). In conclusion, decreased p27(Kip1) expression significantly correlates with tumor progression and predicts poor prognosis in gallbladder carcinomas.

[Genetic analysis of leaf-parent-type plants regenerated from somatic hybridization in Citrus]

The leaf indexes and stoma characteristics of leaf-parent-type regenerants were the same as those of the leaf parent Rough lemon, but quite different from the somatic hybrids. Leaf-parent-type plants were diploid (2n = 2x = 18). Patterns of POX, PPO, GOT isozymes were identical to those of Rough lemon. The plants were analyzed by using 54 arbitrary primers with polymorphisms. Most of the primers (52) showed that leaf-parent-type plants were in concordance with Rough lemon. However, with primer OPW-12, the plants contained a unique band of Hamlin sweet orange. Amplification products with primer OPV-04 showed slight differences among the accessions. The research suggested that most genetic constitutions of the leaf-parent-type plants were from leaf parent Rough lemon and a little from embryogenic suspension parent Hamlin sweet orange.

Decreased p27(Kip1) expression and cyclin D1 overexpression, alone and in combination, influence recurrence and survival of patients with resectable extrahepatic bile duct carcinoma

This study was undertaken to identify potential abnormalities of p27(Kip1) and cyclin D1 expression in extrahepatic bile duct carcinomas and to assess the prognostic significance of p27(Kip1) and cyclin D1 levels for patients with this disease. Decreased p27(Kip1) expression (<50% nuclei staining) and cyclin D1 overexpression (>5% nuclei staining) was observed immunohistochemically in 19 (56%) and 23 (68%) of the 34 tumors examined, respectively. Both decreased p27(Kip1) and cyclin D1 overexpression were associated with relapse (P =.0005 for p27(Kip1) and P =.0004 for cyclin D1). Kaplan-Meier curves showed that both decreased p27(Kip1) and cyclin D1 overexpression correlate significantly with shortened survival rates (for p27(Kip1), P =.0419 and P =.002 for overall and disease-free survival; for cyclin D1, P =.0392 and P =.0021 for overall and disease-free survival). Cox regression model analyses identified decreased p27(Kip1) and cyclin D1 overexpression as independent markers predicting death from relapse (P =.0371, risk ratio: 3.891 for p27(Kip1); P =.0429, risk ratio: 8.31 for cyclin D1). Decreased p27(Kip1) was associated with cyclin D1 overexpression (P =.0202), and coincident abnormalities of the 2 proteins occurred in 16 of the 34 (47%) tumors, indicating that extrahepatic bile duct carcinoma progression may require synchronous dysfunction of p27(Kip1) and cyclin D1 in about half of patients. Patients with tumors showing coincident abnormalities of p27(Kip1) and cyclin D1 showed even more frequent recurrence than patients with an alteration in only 1 of the 2 proteins. In conclusion, decreased p27(Kip1) expression and cyclin D1 overexpression, alone and in combination, predict poor prognosis in patients with resectable extrahepatic bile duct carcinoma.

Clinical evaluation of a rapid immunochromatographic assay based on the 38 kDa antigen of Mycobacterium tuberculosis on patients with pulmonary tuberculosis in China

SETTING

A rapid membrane-based antibody assay capable of diagnosing pulmonary tuberculosis within 15 min has been developed using the 38 kDa antigen from Mycobacterium tuberculosis.

OBJECTIVE

To determine the specificity and sensitivity of this assay and evaluate its usefulness in a clinical setting.

DESIGN

Sera from patients with active pulmonary tuberculosis were obtained from three hospitals in China. The control groups consisted of patients who were diagnosed with lung diseases other than tuberculosis and healthy subjects.

RESULTS

Antibody was detected in 54 of 61 (89%) sputum positive patients and 67 of 91 (74%) sputum negative patients who had been clinically diagnosed as having active pulmonary tuberculosis. Five out of 56 (9%) patients with respiratory diseases other than tuberculosis and 1 out of 30 (3%) healthy controls had a positive antibody response. The overall specificity of the assay was 93% and the positive predictive value was 95%. We conclude that this assay is rapid, sensitive and specific and will be a valuable aid in the clinical diagnosis of pulmonary tuberculosis.