Identifying cadmium and lead co-accumulation from living rice blade spectrum.

Neither cadmium (Cd) nor lead (Pb) is necessary for crop growth, but they both can accumulate in soil and crop tissues, resulting in land degradation and crop reduction. Few researchers have explored how to detect Cd-Pb co-accumulation in leaves using proximal sensing techniques, especially by low-cost, easy-to-use leaf clips that capture hyperspectral reflections at suitable foliar positions. In this study, a hyperspectral imager was employed to collect images of the rice canopy from a designed greenhouse experiment that included 16 pretreatments of Cd-Pb co-accumulation, followed by spectral extractions from 3 foliar positions: the blade root, the middle of the leaf, and the leaf apex. A support vector machine with leave-one-out cross-validation was performed to diagnose the contaminative levels based on the feature wavelengths selected by an improved successive projection algorithm. Partial least squares regression was used to predict Cd-Pb concentrations in rice blades. The results indicated that diagnostic accuracies were varied using spectra of different foliar positions. The blade root and leaf apex of rice blades were the optimal foliar position for detecting Cd and Pb contamination, respectively. At the optimal foliar positions, diagnostic accuracies exceeded 0.80 for distinguishing whether the rice is subject to Cd-Pb contamination. The Cd prediction performed 'very good' with a residual prediction deviation (RPD) of 2.21, a R2 of 0.79, and a root mean square error (RMSE)of 6.14, while that of Pb was 1.62, 0.61, and 186.54. Important wavelengths were identified at 659-694 nm and 667-694 nm to detect Cd and Pb contamination. In summary, our results verified the feasibility and clarified the optimal foliar positions of rice blades to detect Cd-Pb contamination. The wavelengths selecting have the great potential in the design of future leaf clips, and the optimal foliar position can provide suggestions to improve diagnostic performances in field applications.

Programmable allosteric DNA regulations for molecular networks and nanomachines.

Structure-based molecular regulations have been widely adopted to modulate protein networks in cells and recently developed to control allosteric DNA operations in vitro. However, current examples of programmable allosteric signal transmission through integrated DNA networks are stringently constrained by specific design requirements. Developing a new, more general, and programmable scheme for establishing allosteric DNA networks remains challenging. Here, we developed a general strategy for programmable allosteric DNA regulations that can be finely tuned by varying the dimensions, positions, and number of conformational signals. By programming the allosteric signals, we realized fan-out/fan-in DNA gates and multiple-layer DNA cascading networks, as well as expanding the approach to long-range allosteric signal transmission through tunable DNA origami nanomachines ~100 nm in size. This strategy will enable programmable and complex allosteric DNA networks and nanodevices for nanoengineering, chemical, and biomedical applications displaying sense-compute-actuate molecular functionalities.

Constructing DNA logic circuits based on the toehold preemption mechanism.

Strand displacement technology and ribozyme digestion technology have enriched the intelligent toolbox of molecular computing and provided more methods for the construction of DNA logic circuits. In recent years, DNA logic circuits have developed rapidly, and their scalability and accuracy in molecular computing and information processing have been fully demonstrated. However, existing DNA logic circuits still have some problems such as high complexity of DNA strands (number of DNA strands) hindering the expansion of practical computing tasks. In view of the above problems, we presented a toehold preemption mechanism and applied it to construct DNA logic circuits using E6-type DNAzymes, such as half adder circuit, half subtractor circuit, and 4-bit square root logic circuit. Different from the dual-track logic expressions, all the signals in the circuits of this study were monorail which substantially reduced the number of DNA strands in the DNA logic circuits. The presented preemption mechanism provides a way to simplify the implementation of large and complex DNA integrated circuits.

DNA circuits driven by conformational changes in DNAzyme recognition arms.

DNA computing plays an important role in nanotechnology due to the unique programmability and parallelism of DNA molecules. As an important tool to realize DNA computation, various logic computing devices have great application potential. The application of DNAzyme makes the achievements in the field of logical computing more diverse. In order to improve the efficiency of the logical units run by DNAzyme, we proposed a strategy to regulate the DNA circuit by the conformational change of the E6-type DNAzyme recognition arms driven by Mg2+. This strategy changes the single mode of DNAzyme signal transmission, extends the functions of E6-type DNAzyme, and saves the time of signal transmission in the molecular scale. To verify the feasibility of this strategy, first, we constructed DNA logic gates (YES, OR, and AND). Second, we cascade different logic gates (YES-YES, YES-AND) to prove the scalability. Finally, a self-catalytic DNA circuit is established. Through the experimental results, we verified that this DNAzyme regulation strategy relatively reduces the cost of logic circuits to some extent and significantly increases the reaction rate, and can also be used to indicate the range of Mg2+ concentrations. This research strategy provides new thinking for logical computing and explores new directions for detection and biosensors.

Allosteric DNAzyme-based DNA logic circuit: operations and dynamic analysis.

Recently, due to the dual roles of DNA and enzyme, DNAzyme has been widely used in the field of DNA circuit, which has a wide range of applications in bio-engineered system, information processing and biocomputing. In fact, the activity of DNAzymes was regulated by subunits assembly, pH control and metal ions triggers. However, those regulations required to change the sequences of whole DNAzyme, as separating parts and inserting extra DNA sequence. Inspired by the allosteric regulation of proteins in nature, a new allosteric strategy is proposed to regulate the activity of DNAzyme without DNA sequences changes. In this strategy, DNA strand displacement was used to regulate the DNAzyme structure, through which the activity of DNAzyme was well controlled. The strategy was applied to E6-type DNAzymes, and the operations of DNA logic circuit (YES, OR, AND, cascading and feedback) were established and simulated with the dynamic analyses. The allosteric regulation has potential to construct more complicated molecular systems, which can be applied to bio-sensing and detection.

Immune Response and Mechanisms of IFN-γ in Administration for Keratomycosis.

Purpose: To investigate the immune response and mechanisms of interferon-γ (IFN-γ) in the fungal keratitis in mice. Methods: Mice were divided into two groups: group A, topical PBS four times daily post-infection; group B: topical IFN-γ four times daily post-infection. At1, 3, 5, and 7 days, the corneal lesions and inflammatory responses were observed by slit lamp, and immunofluorescence staining was performed to evaluate F4/80+ and CD4+ cells. Using ELISA, and RT-PCR to detect the expression levels of macrophage migration inhibitory factor (MIF), macrophage inflammatory protein-2 (MIP-2), IL-4, IL-10, IL-12, and IFN-γ. Results: The treatment with IFN-γ decreased clinical scores and expression levels of IL-4, increased expression of F4/80+ and CD4+ cells, whereas IL-12, MIF, and MIP-2 were expressed highly, and the peaks of IL-10 and IFN-γ move forward. Conclusion: This experiment showed that IFN-γ eye drops increase the accumulation of macrophages and shorten the duration of fungal keratitis.

A study of retinopathy analysis in type 2 diabetes patients in Chinese population.

In this investigation, the risk factor that arises from diabetic retinopathy was assessed in type 2 diabetes patients. The study is based on a 5-year community-based program, which comprises of 750 participants of the Chinese population. The study comprises general eye examinations, retinopathy assessment, anthropometric and laboratory measurements. The data thus obtained was statistically analyzed and the factors related to Diabetic retinopathy (DR) were deduced. Statistical analysis observed that retinopathy is prone to diabetes patients with high blood pressure and hyperglycemia in Chinese patients with type 2 diabetes. To conclude, the occurrence of DR was associated in patients with baseline hyperglycemia and high blood pressure. In addition, the DR regression was mostly related to lower baseline glucose and lower serum triglyceride levels among the type 2 diabetes patients in the studied Chinese population.

Correcting Errors in Image Encryption Based on DNA Coding.

As a primary method, image encryption is widely used to protect the security of image information. In recent years, image encryption pays attention to the combination with DNA computing. In this work, we propose a novel method to correct errors in image encryption, which results from the uncertainty of DNA computing. DNA coding is the key step for DNA computing that could decrease the similarity of DNA sequences in DNA computing as well as correct errors from the process of image encryption and decryption. The experimental results show our method could be used to correct errors in image encryption based on DNA coding.

Constructing DNA Barcode Sets Based on Particle Swarm Optimization.

Following the completion of the human genome project, a large amount of high-throughput bio-data was generated. To analyze these data, massively parallel sequencing, namely next-generation sequencing, was rapidly developed. DNA barcodes are used to identify the ownership between sequences and samples when they are attached at the beginning or end of sequencing reads. Constructing DNA barcode sets provides the candidate DNA barcodes for this application. To increase the accuracy of DNA barcode sets, a particle swarm optimization (PSO) algorithm has been modified and used to construct the DNA barcode sets in this paper. Compared with the extant results, some lower bounds of DNA barcode sets are improved. The results show that the proposed algorithm is effective in constructing DNA barcode sets.

Identification of a novel GJA3 mutation in a large Chinese family with congenital cataract using targeted exome sequencing.

Autosomal dominant congenital cataract (ADCC) is a clinically and genetically heterogeneous ocular disease in children that results in serious visual impairments or even blindness. Targeted exome sequencing (TES) is an efficient method used for genetic diagnoses of inherited diseases. In the present study, we used a custom-made TES panel to identify the genetic defect of a four-generation Chinese family with bilateral pulverulent nuclear cataracts. A novel heterozygous missense mutation c.443C>T (p. T148I) in GJA3 was identified. The results of the bioinformatic analysis showed that the mutation was deleterious to the structure and hemichannel function of Cx46 encoded by GJA3. Plasmids expressing wild-type and mutant human Cx46 were constructed and ectopically expressed in human lens epithelial cells (HLECs) or human embryonic kidney (HEK-293) cells. Fluorescent images indicated aggregated signals of mutant protein in the cytoplasm, and a higher protein level was also detected in T148I stable cell lines. In summary, we identified a novel mutation in GJA3 for ADCC, which provided molecular insights into the pathogenic mechanism of ADCC.

Reversible Data Hiding Based on DNA Computing.

Biocomputing, especially DNA, computing has got great development. It is widely used in information security. In this paper, a novel algorithm of reversible data hiding based on DNA computing is proposed. Inspired by the algorithm of histogram modification, which is a classical algorithm for reversible data hiding, we combine it with DNA computing to realize this algorithm based on biological technology. Compared with previous results, our experimental results have significantly improved the ER (Embedding Rate). Furthermore, some PSNR (peak signal-to-noise ratios) of test images are also improved. Experimental results show that it is suitable for protecting the copyright of cover image in DNA-based information security.

IWO Algorithm Based on Niche Crowding for DNA Sequence Design.

The design of DNA sequences is essential for the implementation of DNA computing, where the quantity and quality can directly affect the accuracy and efficiency of calculations. Many studies have focused on the design of good DNA sequences to make DNA computing more reliable. However, DNA sequence design needs to satisfy various constraints at the same time, which is an NP-hard problem. In this study, we specify appropriate constraints that should be satisfied in the design of DNA sequences and we propose evaluation formulae. We employ the Invasive Weed Optimization (IWO) algorithm and the niche crowding in the algorithm to solve the DNA sequence design problem. We also improve the spatial dispersal in the traditional IWO algorithm. Finally, we compared the sequences obtained with existing sequences based on the results obtained using a comprehensive fitness function, which demonstrated the efficiency of the proposed method.

Parallel DNA Arithmetic Operation With One Error Detection Based on 3-Moduli Set.

The redundant residue number system is introduced into DNA computing in order to overcome the negative effect caused by the instability of the biochemical reactions and the error hybridizations. Based on the Adleman-Lipton model and a special 3-moduli set, the DNA encoding scheme for redundant residue numbers is presented and the DNA algorithm of one-digit error detection is proposed. The parallel DNA arithmetic operation can be realized in redundant residue number system with error detection, and which can improve the reliability of DNA computing and simplify the DNA encoding scheme.

Zinc phthalocyanine tetrasulfonate (ZnPcS4): a new photosensitizer for photodynamic therapy in choroidal neovascularization.

PURPOSE: The aim of this sutdy was to demonstrate the selective localization of a new photosensitizer, zinc phthalocyanine tetrasulfonate (ZnPcS(4)), in rat eyes and investigate the ability of ZnPcS(4) to produce a photochemical closure of experimental choroidal neovascularization (CNV) upon irradiation with a 670-nm laser light. METHODS: To determine the biodistribution of ZnPcS(4) and the optimal timing of laser irradiation after photosensitizer administration, fluorescence microscopy with ZnPcS(4) was performed. CNV was created in the fundi of Brown-Norway rats using the argon laser model and documented by fluorescein angiography (FFA) and optical coherence tomography (OCT). Photodynamic therapy (PDT) was performed at the dose of 2.0 mg/m(2) and laser fluences of 600 mW/cm(2) on the CNV and on normal retina and choroid. Treatment outcomes were assessed by FFA and OCT and confirmed by light and electron microscopy. RESULTS: Fluorescence microscopy demonstrated intense ZnPcS(4) fluorescence from the CNV, choriocapillaris, and retinal pigment epithelial cells. Peak ZnPcS(4) intensities in the choriocapillaris and CNV were detected at 10-20 min after an intravenous injection. FFA and OCT indicated that irradiation with 670 nm of laser light 20 min after a ZnPcS(4) injection produced a complete closure of CNV with minimal damage to the overlying retina. Histologic studies, using light and electron microscopy, demonstrated CNV endothelial cell necrosis with minimal damage to the surrounding tissues. CONCLUSIONS: ZnPcS(4) selectively localizes to the choriocapillaris and CNV in rats, resulting in the occlusion of laser-induced CNV with minimal damage to the retina tissues. ZnPcS(4) -PDT is a potential new strategy for the treatment of macular degeneration and other human diseases manifesting as CNV.