PdmIRD: missense variants pathogenicity prediction for inherited retinal diseases in a disease-specific manner.

Accurate discrimination of pathogenic and nonpathogenic variation remains an enormous challenge in clinical genetic testing of inherited retinal diseases (IRDs) patients. Computational methods for predicting variant pathogenicity are the main solutions for this dilemma. The majority of the state-of-the-art variant pathogenicity prediction tools disregard the differences in characteristics among different genes and treat all types of mutations equally. Since missense variants are the most common type of variation in the coding region of the human genome, we developed a novel missense mutation pathogenicity prediction tool, named Prediction of Deleterious Missense Mutation for IRDs (PdmIRD) in this study. PdmIRD was tailored for IRDs-related genes and constructed with the conditional random forest model. Population frequencies and a newly available prediction tool were incorporated into PdmIRD to improve the performance of the model. The evaluation of PdmIRD demonstrated its superior performance over nonspecific tools (areas under the curves, 0.984 and 0.910) and an existing eye abnormalities-specific tool (areas under the curves, 0.975 and 0.891). We also demonstrated the submodel that used a smaller gene panel further slightly improved performance. Our study provides evidence that a disease-specific model can enhance the prediction of missense mutation pathogenicity, especially when new and important features are considered. Additionally, this study provides guidance for exploring the characteristics and functions of the mutated proteins in a greater number of Mendelian disorders.

Cobalt-based tripodal complexes as molecular catalysts for photocatalytic CO2 reduction.

Construction of artificial photosynthetic systems including CO2 reduction is a promising pathway to produce carbon-neutral fuels and mitigate the greenhouse effect concurrently. However, the exploitation of earth-abundant catalysts for photocatalytic CO2 reduction remains a fundamental challenge, which can be assisted by a systematic summary focusing on a specific catalyst family. Cobalt-based complexes featuring tripodal ligands should merit more insightful discussion and summarization, as they are one of the most examined catalyst families for CO2 photoreduction. In this feature article, the key developments of cobalt-based tripodal complexes as molecular catalysts for light-driven CO2 reduction are discussed to offer an upcoming perspective, analyzing the present progress in electronic/steric tuning through ligand modification and dinuclear design to achieve a synergistic effect, as well as the bottlenecks for further development.

Development of Gelatin-Silk Sericin Incorporated with Poly(vinyl alcohol) Hydrogel-Based Nanocomposite for Articular Cartilage Defects in Rat Knee Joint Repair.

Sericin, a silk protein, has a high potential for use as an extracellular matrix in tissue engineering applications. In this study, novel gelatin (GEL) and silk sericin (SS) were incorporated with a polyvinyl alcohol) PVA hydrogel nanocomposite (GEL-SS-PVA) scaffold that can be applied to repair cartilage. Glutaraldehyde was used as a cross-linking agent, with hydrochloric acid acting as an initiator. The microstructure characteristics of the obtained GEL-SS and GEL-SS-PVA scaffolds were also examined using FTIR and XRD spectra and their enhanced thermal stability was assessed by TGA. The blended GEL-SS and GEL-SS-PVA scaffolds were confirmed by SEM analysis to be highly porous with optimum pore sizes of 172 and 58 µm, respectively. Smaller pore sizes and improved uniformity were observed as the concentration of PVA in the GEL-SS-PVA scaffold increased. PVA decreased the tensile strength and elongation of the membranes but increased the modulus. Swelling studies showed high swellability and complete degradation in the presence of phosphate-buffered saline. Cytocompatibility of the GEL-SS-PVA scaffolds showed that these had the highest potential to promote cell proliferation as evaluated with standard microscopy using L929 fibroblasts. The prepared GEL-SS composite scaffold incorporated with the PVA hydrogel was implanted in full-thickness articular cartilage defects in rats. The repair effect of cartilage defects was observed and evaluated among the GEL-SS-PVA, GEL-SS, and control operation groups. The defects were almost completely repaired after 14 weeks in the GEL-SS-PVA group, thereby indicating that the GEL-SS-PVA composite had a favorable effect on articular cartilage defects in rat knee joint repair.

Mutual regulation of ROS accumulation and cell autophagy in wheat roots under hypoxia stress.

Here, we explored the mutual regulation of radical oxygen species (ROS) and autophagy in wheat (Triticum aestivum L.) roots under hypoxia stress. We also analyzed differences between the responses of the stele and the cortex in the two wheat cultivars Huamai 8 (waterlogging-tolerant) and Huamai 9 (waterlogging-sensitive) to hypoxia stress. In situ detection and ultracytochemical localization analysis in wheat roots showed that hypoxia stress caused greater increases in ROS levels and the expression levels of alternative oxidase (AOX) and antioxidant enzymes in the stele than in the cortex. The analysis of exogenous ROS addition and the inhibition of its production revealed the pivotal roles played by ROS in autophagy. Moreover, transmission electron microscopy and qRT-PCR analysis indicated that the stele had a higher level of autophagy than the cortex and that the two wheat cultivars primarily differed in the type and number of autophagosomes. Additional research revealed that autophagy could remove excess ROS, as pre-treatment with the autophagy inhibitor 3-methyladenine increased ROS levels in roots and the addition of the autophagy inducer rapamycin reduced root ROS levels. In conclusion, hypoxia stress induced ROS accumulation in wheat roots where ROS acted as an autophagy signal. Furthermore, higher levels of autophagy and antioxidant enzyme expression in the stele facilitated the elimination of oxidative damage caused by excessive ROS and thereby increased cell survival; in the cortex, a large number of cells died and formed aerenchyma.

Mutational Pattern in Multiple Pulmonary Nodules Are Associated With Early Stage Lung Adenocarcinoma.

The clinical significance of mutation in multiple pulmonary nodules is largely limited by single gene mutation-directed analysis and lack of validation of gene expression profiles. New analytic strategy is urgently needed for comprehensive understanding of genomic data in multiple pulmonary nodules. In this study, we performed whole exome sequencing in 16 multiple lung nodules and 5 adjacent normal tissues from 4 patients with multiple pulmonary nodules and decoded the mutation information from a perspective of cellular functions and signaling pathways. Mutated genes as well as mutation patterns shared in more than two lesions were identified and characterized. We found that the number of mutations or mutated genes and the extent of protein structural changes caused by different mutations is positively correlated with the degree of malignancy. Moreover, the mutated genes in the nodules are associated with the molecular functions or signaling pathways related to cell proliferation and survival. We showed a developing pattern of quantity (the number of mutations/mutated genes) and quality (the extent of protein structural changes) in multiple pulmonary nodules. The mutation and mutated genes in multiple pulmonary nodules are associated with cell proliferation and survival related signaling pathways. This study provides a new perspective for comprehension of genomic mutational data and might shed new light on deciphering molecular evolution of early stage lung adenocarcinoma.

Anchoring CoII Ions into a Thiol-Laced Metal-Organic Framework for Efficient Visible-Light-Driven Conversion of CO2 into CO.

Using solar energy to convert CO2 into valuable fuels or chemicals offers a powerful solution to urgent energy and environmental problems. However, the development of efficient and selective catalysts remains a considerable scientific challenge. To address this, catalytically active CoII centers can be anchored into the porous matrix of metal-organic frameworks (MOFs) by utilizing a robust Zr-based MOF (Zr-DMBD) functionalized with freestanding thiol groups to enable efficient post-synthetic metal insertion. The thus-prepared Zr-DMBD-Co MOF solids are modified by well-defined Co-thiolate units and have the capability of photocatalytically converting CO2 into CO with high efficiency and selectivity under visible-light irradiation in a water-containing system. The turnover number and CO selectivity reach as high as 97 941 and 98 %, respectively.

Highly efficient and selective visible-light driven CO2-to-CO conversion by a Co-based cryptate in H2O/CH3CN solution.

Herein, we report a mononuclear Co(ii) cryptate which exhibits highly efficient and selective photocatalytic CO2-to-CO conversion in H2O/CH3CN solution. The TON and selectivity reach as high as 51 392 and 98%, respectively.

The release of cytochrome c and the regulation of the programmed cell death progress in the endosperm of winter wheat (Triticum aestivum L.) under waterlogging.

It has been shown in mammalian systems that the mitochondria can play a key role in the regulation of apoptosis by releasing intermembrane proteins (such as cytochrome c) into the cytosol. Cytochrome c released from the mitochondria to the cytoplasm activates proteolytic enzyme cascades, leading to specific nuclear DNA degradation and cell death. This pathway is considered to be one of the important regulatory mechanisms of apoptosis. Previous studies have shown that endosperm cell development in wheat undergoes specialized programmed cell death (PCD) and that waterlogging stress accelerates the PCD process; however, little is known regarding the associated molecular mechanism. In this study, changes in mitochondrial structure, the release of cytochrome c, and gene expression were studied in the endosperm cells of the wheat (Triticum aestivum L.) cultivar "huamai 8" during PCD under different waterlogging durations. The results showed that waterlogging aggravated the degradation of mitochondrial structure, increased the mitochondrial permeability transition (MPT), and decreased mitochondrial transmembrane potential (ΔΨm), resulting in the advancement of the endosperm PCD process. In situ localization and western blotting of cytochrome c indicated that with the development of the endosperm cell, cytochrome c was gradually released from the mitochondria to the cytoplasm, and waterlogging stress led to an advancement and increase in the release of cytochrome c. In addition, waterlogging stress resulted in the increased expression of the voltage-dependent anion channel (VDAC) and adenine nucleotide translocator (ANT), suggesting that the mitochondrial permeability transition pore (MPTP) may be involved in endosperm PCD under waterlogging stress. The MPTP inhibitor cyclosporine A effectively suppressed cell death and cytochrome c release during wheat endosperm PCD. Our results indicate that the mitochondria play important roles in the PCD of endosperm cells and that the increase in mitochondrial damage and corresponding release of cytochrome c may be one of the major causes of endosperm PCD advancement under waterlogging.

Series of edge-sharing bi-triangle Ln4 clusters with a µ4-NO3- bridge: syntheses, structures, luminescence, and the SMM behavior of the Dy4 analogue.

A series of Ln4 clusters, [Ln4L2(µ3-OH)2(µ4-NO3)(NO3)4(OCH3)(H2O)]·xMeCN·yMeOH (Ln = Gd (1), Tb (2), Dy (3), Ho (4), Er (5), Yb (6), L = 2-{[2-(2-hydroxy-ethoxy)-ethylimino]-methyl}-6-methoxyphenol), have been synthesized by the reaction of Ln(NO)3 and a Schiff-base ligand formed in situ. The six complexes display similar structures, with an overall metal core comprising two edge-sharing triangular Ln3 units linked by a µ4-NO3(-) bridge. The luminescence spectrum of complex 2 shows the characteristic emission of the Tb(III) ions. The magnetic susceptibility studies reveal that the Ln(III) ions are very weakly interacting in all six compounds. Frequency dependence of the ac-susceptibility was found for 3, suggesting a typical single-molecule magnet (SMM) behavior with an anisotropic barrier of 28 K.

[2,2'-(1,1'-Binaphthyl-2,2'-diyldiimino)-diethanol-κN,N',O]dichloridocopper(II).

In the title complex, [CuCl(2)(C(24)H(24)N(2)O(2))], the Cu(II) cation is N,N',O-chelated by a 2,2'-(1,1'-binaphthyl-2,2'-diyldiimino)-diethanol ligand and coordinated by two chloride anions in a distorted square-pyramidal geometry. In the diethanol ligand, the two naphthalene ring systems are twisted with respect to each other at a dihedral angle of 68.30 (9)°. The uncoord-inated hy-droxy group links with a coordinated chloride anion via an intra-molecular O-H⋯Cl hydrogen bond. Inter-molecular N-H⋯O and N-H⋯Cl hydrogen bonds occur in the crystal structure.

Haplotype analysis of the genes encoding glutamine synthetase plastic isoforms and their association with nitrogen-use- and yield-related traits in bread wheat.

Glutamine synthetase (GS) plays a key role in the growth, nitrogen (N) use and yield potential of cereal crops. Investigating the haplotype variation of GS genes and its association with agronomic traits may provide useful information for improving wheat N-use efficiency and yield. We isolated the promoter and coding region sequences of the plastic glutamine synthetase isoform (GS2) genes located on chromosomes 2A, 2B and 2D in bread wheat. By analyzing nucleotide sequence variations of the coding region, two, six and two haplotypes were distinguished for TaGS2-A1 (a and b), TaGS2-B1 (a-f) and TaGS2-D1 (a and b), respectively. By analyzing the frequency data of different haplotypes and their association with N use and agronomic traits, four major and favorable TaGS2 haplotypes (A1b, B1a, B1b, D1a) were revealed. These favorable haplotypes may confer better seedling growth, better agronomic performance, and improved N uptake during vegetative growth or grain N concentration. Our data suggest that certain TaGS2 haplotypes may be valuable in breeding wheat varieties with improved agronomic performance and N-use efficiency.

Genomic distribution of quantitative trait loci for yield and yield-related traits in common wheat.

A major objective of quantitative trait locus (QTL) studies is to find genes/markers that can be used in breeding programs via marker assisted selection (MAS). We surveyed the QTLs for yield and yield-related traits and their genomic distributions in common wheat (Triticum aestivum L.) in the available published reports. We then carried out a meta-QTL (MQTL) analysis to identify the major and consistent QTLs for these traits. In total, 55 MQTLs were identified, of which 12 significant MQTLs were located on wheat chromosomes 1A, 1B, 2A, 2D, 3B, 4A, 4B, 4D and 5A. Our study showed that the genetic control of yield and its components in common wheat involved the important genes such as Rht and Vrn. Furthermore, several significant MQTLs were found in the chromosomal regions corresponding to several rice genomic locations containing important QTLs for yield related traits. Our results demonstrate that meta-QTL analysis is a powerful tool for confirming the major and stable QTLs and refining their chromosomal positions in common wheat, which may be useful for improving the MAS efficiency of yield related traits.

Science letters: Proteomic analysis of differentially expressed proteins in mice with concanavalin A-induced hepatitis.

OBJECTIVE: To find new protein biomarkers for the detection and evaluation of liver injury and to analyze the relationship between such proteins and disease progression in concanavalin A (Con A)-induced hepatitis. METHODS: Twenty-five mice were randomly divided into five groups: an untreated group, a control group injected with phosphate buffered saline (PBS), and groups with Con A-induced hepatitis evaluated at 1, 3 and 6 h. Two-dimensional gel electrophoresis (2-DE) and mass spectrometry (MS) were used to identify differences in protein expression among groups. Quantitative real-time polymerase chain reaction (qRT-PCR) was performed to verify the results. RESULTS: In mice with Con A-induced hepatitis, expression levels of four proteins were increased: RIKEN, fructose bisphosphatase 1 (fbp1), ketohexokinase (khk), and Chain A of class pi glutathione S-transferase. Changes in fbp1 and khk were confirmed by qRT-PCR. CONCLUSION: Levels of two proteins, fbp1 and khk, are clearly up-regulated in mice with Con A-induced hepatitis.

[A method of extraction and separation of wheat gluten].

After removing gliadin and other proteins with 7.5% 2-propanol and 0.3 mol/L NaI, the total glutenin subunits were extracted with two kinds of buffer, one containing 25% 2-propanol, 0.04 mol/L Tris-HCI (pH=8.0), 10% SDS and 2% DDT and the other containing 25% 2-propanol, 0.04 mol/L Tris-HCI (pH=8.0), 10% SDS and 1.4% VP. In SDS-PAGE electrophoresis (4% stacking gel and 13% resolving ge1) system HMW-GS and LMW-GS were clearly separated by the improved method with only a single step. The background of the SDS-PAGE gel was gliadin-free. It was more effective and applicable to separate and distinguish the complex LMW-GS. This method will be used in wheat protein separation, variety identification and improvement.

[Identification of genes related to resistance to Magnaporthe grisea using differential display technique in rice].

Rice blast caused by Magnaporthe grisea is one of the most serious constraints on high productivity. Understanding the mechanism of the infection of Magnaporthe grisea and the change of gene expression after infection is useful to control blast disease in rice. This work presents the isolation of differentially expressed cDNA fragments from rice leaf induced by the inoculum suspension of Magnaporthe grisea using mRNA differential display technique. Total 87 differential expressed cDNA fragments were recoveried and reamplified. The dot-blotting results showed that 6 fragments of 81 were confirmed to be the expression induced by Magnaporthe grisea inoculum. Those fragments were then cloned into vectors for sequencing. Sequence analysis through Internet Blast searching showed that 3 fragments were novel gene fragments. One was homologous with a putative malate synthase gene on rice chromosome 4 with 78% identities of amino acid; one was highly homologous (75% identity) with rice RPR1 gene on chromosome 11, which has a conservative structure of NBS-LRR domain and may be related to signal transduction of rice defense reaction;another one was homologous with a putative thioredoxin gene on rice chromosome 6 with the identity of 72%.

[Preliminary gene-mapping of photoperiod-temperature sensitive genic male sterility in wheat (Triticum aestivum L.)].

The photoperiod-temperature sensitive genic male sterile (PTSGMS) line in wheat is important for the utilization of heterosis. The wheat line, BAU3338, is an excellent PTSGMS material identified in the recent years. In this study, its PTSGMS genes were mapped using molecular markers, SSR and ISSR. The result of molecular analysis showed that the two PTSGMS loci were identified and designated as ptms1 and ptms2, respectively. In addition, the genetic effect analysis indicated that the locus effect of ptms1 was 2-3 times larger than that of ptms2.

[Differential expression of genes related to photoperiod-temperature sensitive genic male sterility in wheat, revealed by mRNA differential display using G-box family primer].

mRNA differential display with G-box family primer was used to analyze the differential expression of genes of the photoperiod-temperature sensitive genic male sterile(PTSGMS) line of wheat, BAU3338, between the sterile and fertile conditions. The result indicated that gene expression was significantly different between the two types of condition during the fertility transformation phase. The twelve qualitatively different DNA bands were identified with reverse Northern blot hybridization and five positive clones, HT1-G10, HT1-G3, HT2-G2, HT1-G4 and HT2-G5 were sequenced. The homology search indicated that HT1-G10 was highly homological (96%) to the partial sequences of Triticum aestivum chloroplast genes, rbcL and atpB, HT1-G3 was also homological (88%) to Triticum aestivum histone H2A gene and the other three gene fragments were new sequences in Gen-Bank. The analysis of the candidate gene fragments supplied some effective evidences to reveal the developmental mechanism of PTSGMS.

Mapping quantitative trait loci for plant height in wheat (Triticum aestivum L.) using a F2:3 population.

To detect quantitative trait loci (QTLs) controlling plant height, the plant height of 240 F2:3 lines derived from the cross of a dwarf wheat line ND3338 with a tall line F390, was assessed in field trials at two locations with three replications in 2000 and 2001. Microsatellite markers were used to construct a framework linkage map containing 215 loci with 21 linkage groups, and covering the whole genome about 3600cM. With the method of interval mapping, seven putative QTLs affecting plant height were detected on chromosomes 1B, 4B (two regions), 6A (two regions), 6D and 7A, respectively. Phenotypic variations explained by each QTL ranged from 5.2% to 50.1%, and in each environment the total putative QTLs explained about 64.8%-75% of the total phenotypic variation respectively. A major QTL located on chromosome arm 4BS near the locus Xgwm113, around the Rht-Blb locus, explained a large part of the phenotypic variation (27.8%-36.2% depending on the years or the locations). Except the QTL on chromosome 7A, all the other QTLs from ND3338 decreased the plant height, variously from 0.94 cm to 9.33 cm. Most of the identified QTLs were consistent in all the environments, and should be useful in future marker-assisted-selection programs for breeding dwarf and semi-dwarf wheat cultivars.