The transcriptional landscape of Populus pattern/effector-triggered immunity and how PagWRKY18 involved in it.

Plants trigger a robust immune response by activating massive transcriptome reprogramming through crosstalk between PTI and ETI. However, how PTI and ETI contribute to the quantitative or/and qualitative output of immunity and how they work together when both are being activated were unclear. In this study, we performed a comprehensive overview of pathogen-triggered transcriptomic reprogramming by analyzing temporal changes in the transcriptome up to 144 h after Colletotrichum gloeosporioides inoculated in Populus. Moreover, we constructed a hierarchical gene regulatory network of PagWRKY18 and its potential target genes to explore the underlying regulatory mechanisms of PagWRKY18 that are not yet clear. Interestingly, we confirmed that PagWRKY18 protein can directly bind the W-box elements in the promoter of a transmembrane leucine-rich repeat receptor-like kinase, PagSOBIR1 gene, to trigger PTI. At the same time, PagWRKY18 functions in disease tolerance by modulation of ROS homeostasis and induction of cell death via directly targeting PagGSTU7 and PagPR4 respectively. Furthermore, PagPR4 can interact with PagWRKY18 to inhibit the expression of PagPR4 genes, forming a negative feedback loop. Taken together, these results suggest that PagWRKY18 may be involved in regulating crosstalk between PTI and ETI to activate a robust immune response and maintain intracellular homeostasis.

1.7†µm sub-200 fs vortex beams generation from a thulium-doped all-fiber laser.

The pulsed 1.7 µm vortex beams (VBs) has significant research prospects in the fields of imaging and material processing. We experimentally demonstrate the generation of sub-200 fs pulsed VBs at 1.7 µm based on a home-made mode-selective coupler (MSC). Through dispersion management technology in a thulium-doped fiber laser, the stable linearly polarized VBs pulse directly emitting from the cavity is measured to be 186 fs with central wavelength of 1721.2 nm. By controlling the linear superposition of LP11 modes, cylindrical vector beams (CVBs) can also be obtained. In addition, a variety of bound states pulsed VBs at 1.7 µm can also be observed. Our finding provides an effective way to generate ultrashort pulsed VBs and CVBs at 1.7 µm waveband.

Hyperuricemia and coronary heart disease: The mediating role of blood pressure and thrombospondin 3.

BACKGROUND & AIMS: Although hyperuricemia is a known risk factor for coronary heart disease (CHD), little is known about the role of blood pressure in mediating this association. The purpose of this study is to investigate the role of blood pressure-related indicators and Thrombospondin 3 (THBS3) in the association between hyperuricemia and CHD. METHODS AND RESULTS: Our observational epidemiology study included 593 CHD cases and 760 controls from a residential stable sample. We also chose 43 new CHD patients and 43 controls to test the expression levels of THBS3 using ELISA kits. We used logistic regression models and mediating effect analysis to investigate the relationships between hyperuricemia and CHD, as well as the mediating role of blood pressure-related indicators and THBS3. In the general population (OR: 2.001 [95% CI: 1.528-2.622]), male population (OR: 1.591 [95% CI: 1.119-2.262]), and female population (OR: 2.813 [95% CI: 1.836-4.310]), hyperuricemia is an independent risk factor for CHD. In general, average systolic blood pressure (SBP) and average pulse pressure difference (PPD) mediated 3.35% and 4.59%, respectively, of the association between hyperuricemia and CHD, and 6.60% and 6.60% in women. However, in the male population, we have not yet found that blood pressure-related indicators had a significant mediating effect. Meanwhile, we found that THBS3 mediated 19.23% of the association between hyperuricemia and CHD. CONCLUSIONS: Average SBP, PPD, and THBS3 all play a role in the association of hyperuricemia and CHD. In the female population, similar mediating results in blood pressure-related indicators were observed.

Multifeature analysis of age-related microbiome structures reveals defense mechanisms of Populus tomentosa trees.

Root microbiota composition shifts during the development of most annual plants. Although some perennial plants can live for centuries, the host-microbiome partnerships and interaction mechanisms underlying their longevity remain unclear. To address this gap, we investigated age-related changes in the root metabolites, transcriptomes, and microbiome compositions of 1- to 35-yr-old Populus tomentosa trees. Ten co-response clusters were obtained according to their accumulation patterns, and members of each cluster displayed a uniform and clear pattern of abundance. Multi-omics network analysis demonstrated that the increased abundance of Actinobacteria with tree age was strongly associated with the flavonoid biosynthesis. Using genetic approaches, we demonstrate that the flavonoid biosynthesis regulator gene Transparent Testa 8 is associated with the recruitment of flavonoid-associated Actinobacteria. Further inoculation experiments of Actinobacteria isolates indicated that their colonization could significantly improve the host's phenotype. Site-directed mutagenesis revealed that the hyBl gene cluster, involved in biosynthesis of an aminocyclitol hygromycin B analog in Streptomyces isolate bj1, is associated with disease suppression. We hypothesize that interactions between perennial plants and soil microorganisms lead to gradual enrichment of a subset of microorganisms that may harbor a wealth of currently unknown functional traits.

Changes in Mobile Health Apps Usage Before and After the COVID-19 Outbreak in China: Semilongitudinal Survey.

BACKGROUND: Mobile health (mHealth) apps are rapidly emerging technologies in China due to strictly controlled medical needs during the COVID-19 pandemic while continuing essential services for chronic diseases. However, there have been no large-scale, systematic efforts to evaluate relevant apps. OBJECTIVE: We aim to provide a landscape of mHealth apps in China by describing and comparing digital health concerns before and after the COVID-19 outbreak, including mHealth app data flow and user experience, and analyze the impact of COVID-19 on mHealth apps. METHODS: We conducted a semilongitudinal survey of 1593 mHealth apps to study the app data flow and clarify usage changes and influencing factors. We selected mHealth apps in app markets, web pages from the Baidu search engine, the 2018 top 100 hospitals with internet hospitals, and online shopping sites with apps that connect to smart devices. For user experience, we recruited residents from a community in southeastern China from October 2019 to November 2019 (before the outbreak) and from June 2020 to August 2020 (after the outbreak) comparing the attention of the population to apps. We also examined associations between app characteristics, functions, and outcomes at specific quantiles of distribution in download changes using quantile regression models. RESULTS: Rehabilitation medical support was the top-ranked functionality, with a median 1.44 million downloads per app prepandemic and a median 2.74 million downloads per app postpandemic. Among the top 10 functions postpandemic, 4 were related to maternal and child health: pregnancy preparation (ranked second; fold change 4.13), women's health (ranked fifth; fold change 5.16), pregnancy (ranked sixth; fold change 5.78), and parenting (ranked tenth; fold change 4.03). Quantile regression models showed that rehabilitation (P75, P90), pregnancy preparation (P90), bodybuilding (P50, P90), and vaccination (P75) were positively associated with an increase in downloads after the outbreak. In the user experience survey, the attention given to health information (prepandemic: 249/375, 66.4%; postpandemic: 146/178, 82.0%; P=.006) steadily increased after the outbreak. CONCLUSIONS: mHealth apps are an effective health care approach gaining in popularity among the Chinese population following the COVID-19 outbreak. This research provides direction for subsequent mHealth app development and promotion in the postepidemic era, supporting medical model reformation in China as a reference, which may provide new avenues for designing and evaluating indirect public health interventions such as health education and health promotion.

Capacity-enhanced and kinetic-expedited zinc-ion storage ability in a Zn3V3O8/VO2 cathode enabled by heterostructural design.

Heterostructured double-phase composites are promising electrode candidates for high-performance secondary metal batteries due to their superior capacity and ion transfer kinetics compared with the pristine phase. Herein, a Zn3V3O8/VO2 (ZVO/VO) heterostructure with abundant phase boundaries was designed as the cathode for aqueous zinc-ion batteries (ZIBs). The preparation method is based on a solid pre-intercalation approach, and the Zn content in the ZVO/VO heterostructure can be precisely controlled. The electrochemical performance of ZVO/VO containing different amounts of Zn, pristine ZVO, and VO phases was compared. ZVO/VO showed superior capacity and cycling stability compared to pristine ZVO and VO. The ZVO/VO heterostructure showed a capacity of 328.4 mA h g-1 at 0.3 A g-1 after 200 cycles. The long-term cycling performance of ZVO/VO was evaluated at 3 A g-1, and it delivered a capacity retention of 90.5% after 1000 cycles. The ion storage mechanism of the ZVO/VO electrode was analyzed by ex situ X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS) and scanning electron microscopy (SEM). This work provides a simple strategy for designing vanadium-based heterostructure composites as advanced cathodes for ZIBs.

Soil Layers Impact Lithocarpus Soil Microbial Composition in the Ailao Mountains Subtropical Forest, Yunnan, China.

Plant litter decomposition is a complex, long-term process. The decomposition of litterfall is a major process influencing nutrient balance in forest soil. The soil microbiome is exceptionally diverse and is an essential regulator of litter decomposition. However, the microbiome composition and the interaction with litterfall and soil remain poorly understood. In this study, we examined the bacterial and fungal community composition of Lithocarpus across soil samples from different sampling seasons. Our results displayed that the microbiome assembly along the soil layer is influenced predominantly by the soil layer rather than by the sampling season. We identified that the soil layer strongly affected network complexity and that bacterial and fungal microbiomes displayed different patterns in different soil layers. Furthermore, source tracking and community composition analysis indicated that there are significantly different between soil and litter. Moreover, our results demonstrate that few dominant taxa (2% and 4% of bacterial and fungal phylotypes) dominated in the different soil layers. Hydnodontaceae was identified as the most important biomarker taxa for humic fragmented litter fungal microbiome and Nigrospora and Archaeorhizomycetaceae for organic soil and the organic mineral soil layer, and the phylum of Acidobacteria for the bacteria microbiome. Our work provides comprehensive evidence of significant microbiome differences between soil layers and has important implications for further studying soil microbiome ecosystem functions.

Association between fine particulate matter and coronary heart disease: A miRNA microarray analysis.

Several studies have reported an association between residential surrounding particulate matter with an aerodynamic diameter ≤2.5 µm (PM2.5) and coronary heart disease (CHD). However, the underlying biological mechanism remains unclear. To fill this research gap, this study enrolled a residentially stable sample of 942 patients with CHD and 1723 controls. PM2.5 concentration was obtained from satellite-based annual global PM2.5 estimates for the period 1998-2019. MicroRNA microarray and pathway analysis of target genes was performed to elucidate the potential biological mechanism by which PM2.5 increases CHD risk. The results showed that individuals exposed to high PM2.5 concentrations had higher risks of CHD than those exposed to low PM2.5 concentrations (odds ratio = 1.22, 95% confidence interval: 1.00, 1.47 per 10 µg/m3 increase in PM2.5). Systolic blood pressure mediated 6.6% of the association between PM2.5 and CHD. PM2.5 and miR-4726-5p had an interaction effect on CHD development. Bioinformatic analysis demonstrated that miR-4726-5p may affect the occurrence of CHD by regulating the function of RhoA. Therefore, individuals in areas with high PM2.5 exposure and relative miR-4726-5p expression have a higher risk of CHD than their counterparts because of the interaction effect of PM2.5 and miR-4726-5p on blood pressure.

Transposable Elements: Distribution, Polymorphism, and Climate Adaptation in Populus.

Transposable elements (TEs) are a class of mobile genetic elements that make effects on shaping rapid phenotypic traits of adaptive significance. TE insertions are usually related to transcription changes of nearby genes, and thus may be subjected to purifying selection. Based on the available genome resources of Populus, we found that the composition of Helitron DNA family were highly variable and could directly influence the transcription of nearby gene expression, which are involving in stress-responsive, programmed cell death, and apoptosis pathway. Next, we indicated TEs are highly enriched in Populus trichocarpa compared with three other congeneric poplar species, especially located at untranslated regions (3'UTRs and 5'UTRs) and Helitron transposons, particularly 24-nt siRNA-targeted, are significantly associated with reduced gene expression. Additionally, we scanned a representative resequenced Populus tomentosa population, and identified 9,680 polymorphic TEs loci. More importantly, we identified a Helitron transposon located at the 3'UTR, which could reduce WRKY18 expression level. Our results highlight the importance of TE insertion events, which could regulate gene expression and drive adaptive phenotypic variation in Populus.

Drought Stress Triggers Shifts in the Root Microbial Community and Alters Functional Categories in the Microbial Gene Pool.

Drought is a major threat to crop productivity and causes decreased plant growth, poor yields, and crop failure. Nevertheless, the frequency of droughts is expected to increase in the coming decades. The microbial communities associated with crop plants can influence how plants respond to various stresses; hence, microbiome manipulation is fast becoming an effective strategy for improving the stress tolerance of plants. The effect of drought stress on the root microbiome of perennial woody plants is currently poorly understood. Using Populus trees as a model ecosystem, we found that the diversity of the root microbial community decreased during drought treatment and that compositional shifts in microbes during drought stress were driven by the relative abundances of a large number of dominant phyla, including Actinobacteria, Firmicutes, and Proteobacteria. A subset of microbes, including Streptomyces rochei, Bacillus arbutinivorans, B. endophyticus, B. megaterium, Aspergillus terreus, Penicillium raperi, Trichoderma ghanense, Gongronella butleri, and Rhizopus stolonifer, was isolated from the drought-treated poplar rhizosphere soils, which have potentially beneficial to plant fitness. Further controlled inoculation experiments showed that the isolated bacterial and fungal isolates positively impacted plant growth and drought tolerance. Collectively, our results demonstrate the impact of drought on root microbiome structure and provide a novel example of manipulating root microbiomes to improve plant tolerance.

High energy switchable pulsed High-order Mode beams in a mode-locking Raman all-fiber laser with high efficiency.

High energy pulsed High-order Mode (HOM) beams has great potential in materials processing and particle acceleration. We experimentally demonstrate a high energy mode-locking Raman all-fiber laser with switchable HOM state. A home-made fiber mode-selective coupler (MSC) is used as the mode converter with a wide bandwidth of 60 nm. By combining advantages of MSC and stimulated Raman scattering, 1.1 µJ pulsed HOM beams directly emitting from the all-fiber cavity can be achieved. After controlling the category and phase delay of vector modal superposition, different pulsed HOM beams including cylindrical vector beams (CVBs) (radial and angular) and optical vortex beams (OVBs) are reasonably obtained with high purity (all over 95%), as well as arbitrary switching. Furtherly, the slope efficiency of HOM beams in the mode-locking and continuous wave operations are as much as 20.3% and 31.8%, respectively. It may provide an effective way to achieve high energy pulsed HOM beams.

Genome-Wide Analysis of Coding and Non-coding RNA Reveals a Conserved miR164-NAC-mRNA Regulatory Pathway for Disease Defense in Populus.

MicroRNAs (miRNAs) contribute to plant defense responses by increasing the overall genetic diversity; however, their origins and functional importance in plant defense remain unclear. Here, we employed Illumina sequencing technology to assess how miRNA and messenger RNA (mRNA) populations vary in the Chinese white poplar (Populus tomentosa) during a leaf black spot fungus (Marssonina brunnea) infection. We sampled RNAs from infective leaves at conidia germinated stage [12 h post-inoculation (hpi)], infective vesicles stage (24 hpi), and intercellular infective hyphae stage (48 hpi), three essential stages associated with plant colonization and biotrophic growth in M. brunnea fungi. In total, 8,938 conserved miRNA-target gene pairs and 3,901 Populus-specific miRNA-target gene pairs were detected. The result showed that Populus-specific miRNAs (66%) were more involved in the regulation of the disease resistance genes. By contrast, conserved miRNAs (>80%) target more whole-genome duplication (WGD)-derived transcription factors (TFs). Among the 1,023 WGD-derived TF pairs, 44.9% TF pairs had only one paralog being targeted by a miRNA that could be due to either gain or loss of a miRNA binding site after the WGD. A conserved hierarchical regulatory network combining promoter analyses and hierarchical clustering approach uncovered a miR164-NAM, ATAF, and CUC (NAC) transcription factor-mRNA regulatory module that has potential in Marssonina defense responses. Furthermore, analyses of the locations of miRNA precursor sequences reveal that pseudogenes and transposon contributed a certain proportion (∼30%) of the miRNA origin. Together, these observations provide evolutionary insights into the origin and potential roles of miRNAs in plant defense and functional innovation.

Watt-level superfluorescent fiber source near 3 µm.

We report a watt-level mid-infrared (mid-IR) superfluorescent fiber source from ${{\rm Er}^{3 +}}$-doped ZBLAN fiber near 3 µm spectral range. With the power amplifier configuration, the mid-IR superfluorescent fiber source with power up to 1.85 W has been delivered successfully with slope efficiency about 18.6%. The experimental results may pave an avenue toward a high-power, high-temporal-stability superfluorescent source for versatile mid-IR applications.

Hepcidin deficiency causes bone loss through interfering with the canonical Wnt/ß-catenin pathway via Forkhead box O3a.

OBJECTIVE: Hepcidin deficiency is known to cause body iron accumulation and bone microarchitecture defects, but the exact underlying mechanisms of hepcidin deficiency-induced bone loss remain unclear. Our objective was to understand the molecular mechanism of hepcidin deficiency-induced bone loss. METHODS: The bone phenotypes of wild type (WT) and hepcidin knockout (Hepcidin-KO) mice were measured by microcomputed tomography. The osteoclastic marker of the bone was measured by tartrate-resistant acid phosphatase staining. The osteoblastic marker of the bone was measured by immunostaining of osteocalcin. Primary osteoblastic and osteoclastic differentiation was performed using bone marrow cells. The mature osteoclast was determined by tartrate-resistant acid phosphatase staining, pit formation assay and relative gene expression. The mature osteoblast was determined by alkaline phosphatase activity, alkaline phosphatase staining, Alizarin Red staining and relative gene expression. The protein expression of ß-catenin, TCF4/TCF7L2 and Forkhead box O3a (FOXO3a) was measured by Western blot and their combination by co-immunoprecipitation. In vivo study was performed by tail vein administration of FOXO3a-RNAi using an adeno-associated virus in Hepcidin-KO mice. RESULTS: We found that Hepcidin-KO mice exhibited iron accumulation and bone loss compared with WT mice. The osteoclastic differentiation of bone marrow-derived macrophages from Hepcidin-KO mice was not significantly different from that of bone marrow-derived macrophages from WT mice. However, the osteoblastic differentiation of bone marrow-derived mesenchymal stem cells from Hepcidin-KO mice was obviously decreased compared with that of bone marrow-derived mesenchymal stem cells from WT mice. Furthermore, it was confirmed in this study that upon hepcidin deficiency, ß-catenin, TCF4/TCF7L2 and FOXO3a expression in bone tissues was not altered, but ß-catenin combination with TCF4/TCF7L2 was strongly inhibited by ß-catenin combination with FOXO3a, indicating that the canonical Wnt/ß-catenin pathway was affected. Tail vein administration of FOXO3a-RNAi using an adeno-associated virus in Hepcidin-KO mice resulted in bone mass recovery. CONCLUSION: These findings suggested that hepcidin deficiency might cause bone loss by interfering with the canonical Wnt/ß-catenin pathway via FOXO3a, and FOXO3a inhibition would be a possible approach to treat hepcidin deficiency-induced bone loss. THE TRANSLATIONAL POTENTIAL OF THIS ARTICLE: Hepcidin deficiency, as well as iron accumulation, has been considered as a risk factor for osteoporosis. For this kind of osteoporosis, inhibition of FOXO3a either by neutralized antibody or AAV-mediated RNAi, represents an effective and promising method.

An Efficient Cobalt Phosphide Electrocatalyst Derived from Cobalt Phosphonate Complex for All-pH Hydrogen Evolution Reaction and Overall Water Splitting in Alkaline Solution.

The development of low-cost and highly efficient electrocatalysts via an eco-friendly synthetic method is of great significance for future renewable energy storage and conversion systems. Herein, cobalt phosphides confined in porous P-doped carbon materials (Co-P@PC) are fabricated by calcinating the cobalt-phosphonate complex formed between 1-hydroxyethylidenediphosphonic acid and Co(NO3 )2 in alkaline solution. The P-containing ligand in the complex acts as the carbon source as well as in situ phosphorizing agent for the formation of cobalt phosphides and doping P element into carbon material upon calcination. The Co-P@PC exhibits high activity for all-pH hydrogen evolution reaction (overpotentials of 72, 85, and 76 mV in acidic, neutral, and alkaline solutions at the current density of 10 mA cm-2 ) and oxygen evolution reaction in alkaline solution (an overpotential of 280 mV at the current density of 10 mA cm-2 ). The alkaline electrolyzer assembled from the Co-P@PC electrodes delivers the current density of 10 mA cm-2 at the voltage of 1.60 V with a durability of 60 h. The excellent activity and long-term stability of the Co-P@PC derives from the synergistic effect between the active cobalt phosphides and the porous P-doped carbon matrix.

Rapamycin improves bone mass in high-turnover osteoporosis with iron accumulation through positive effects on osteogenesis and angiogenesis.

Iron accumulation is an independent risk factor for type I osteoporosis, but the molecular mechanisms of the phenomenon are not well defined, and effective therapy has not been reported. Here, we found that the level of mTOR was increased both in wild-type mouse models with iron accumulation and transgenic mouse models (Hepc-/-) of high-turnover osteoporosis with iron accumulation. We show that an increased level of mTOR can depress osteogenesis and angiogenesis by Cxcl9 both in bone and in vitro. Suppression of mTOR in mouse models by rapamycin and in vitro by siRNA transfection recovered both osteogenesis and angiogenesis. These findings revealed the role of mTOR in osteogenesis and angiogenesis in high-turnover osteoporosis with iron accumulation and showed that rapamycin targeting of mTOR ameliorates osteogenesis and angiogenesis to improve bone mass.

Applied anatomical study of the modified anconeus flap approach.

PURPOSE: Conventional surgical therapy for an intercondylar humerus fracture might result in multiple potential complications. Our study was conducted to evaluate the modified anconeus flap approach by adequately exposing the distal humeral articular surface, avoiding osteotomy of the olecranon and transection of the main part of the triceps brachial tendon from the olecranon. METHODS: Preparations of 20 upper limb specimens from adult cadavers were used in this study. We investigated the anatomical features of the distal tendon of the triceps brachii. Then, we designed a modified anconeus flap approach in cadaver specimens combined with the medial paratricipital approach, and we compared the extent of exposure of the distal humeral articular surface between the triceps-reflecting anconeus pedicle approach and this modified approach. RESULTS: The downward neurovascular bundles supplying the anconeus were located far from the intramuscular tendon of the triceps brachii. In addition, the medial head of the triceps was continuous with the anconeus near the lateral epicondyle of the humerus. These anatomical properties could assist in reducing adverse events in surgery. The percentage of the exposed humerus distal articular surface was 42.7% by applying the modified anconeus flap approach combined with the medial paratricipital approach. The modified anconeus flap approach can overcome the shortcomings of osteotomy or triceps transverse and fulfill reduction and internal fixation of most distal humerus intercondylar fractures. CONCLUSIONS: The present study has demonstrated a new approach for adequately exposing the distal humeral articular surface during surgery for an intercondylar humerus fracture. With this modified approach, osteotomy of the olecranon and the separation or transection of the main part of the triceps brachial tendon from the olecranon are not necessarily required. Therefore, we suggest that this novel approach could be applied as the primary surgical approach in intercondylar humerus fracture surgeries if the surgeons are familiar with the regional features of distal tendon of the triceps brachii and anconeus.

High performance transcription factor-DNA docking with GPU computing.

BACKGROUND: Protein-DNA docking is a very challenging problem in structural bioinformatics and has important implications in a number of applications, such as structure-based prediction of transcription factor binding sites and rational drug design. Protein-DNA docking is very computational demanding due to the high cost of energy calculation and the statistical nature of conformational sampling algorithms. More importantly, experiments show that the docking quality depends on the coverage of the conformational sampling space. It is therefore desirable to accelerate the computation of the docking algorithm, not only to reduce computing time, but also to improve docking quality. METHODS: In an attempt to accelerate the sampling process and to improve the docking performance, we developed a graphics processing unit (GPU)-based protein-DNA docking algorithm. The algorithm employs a potential-based energy function to describe the binding affinity of a protein-DNA pair, and integrates Monte-Carlo simulation and a simulated annealing method to search through the conformational space. Algorithmic techniques were developed to improve the computation efficiency and scalability on GPU-based high performance computing systems. RESULTS: The effectiveness of our approach is tested on a non-redundant set of 75 TF-DNA complexes and a newly developed TF-DNA docking benchmark. We demonstrated that the GPU-based docking algorithm can significantly accelerate the simulation process and thereby improving the chance of finding near-native TF-DNA complex structures. This study also suggests that further improvement in protein-DNA docking research would require efforts from two integral aspects: improvement in computation efficiency and energy function design. CONCLUSIONS: We present a high performance computing approach for improving the prediction accuracy of protein-DNA docking. The GPU-based docking algorithm accelerates the search of the conformational space and thus increases the chance of finding more near-native structures. To the best of our knowledge, this is the first ad hoc effort of applying GPU or GPU clusters to the protein-DNA docking problem.