De novo diploid genome assembly using long noisy reads

The high sequencing error rate has impeded the application of long noisy reads for diploid genome assembly. Most existing assemblers failed to generate high-quality phased assemblies using long noisy reads. Here, we present PECAT, a Phased Error Correction and Assembly Tool, for reconstructing diploid genomes from long noisy reads. We design a haplotype-aware error correction method that can retain heterozygote alleles while correcting sequencing errors. We combine a corrected read SNP caller and a raw read SNP caller to further improve the identification of inconsistent overlaps in the string graph. We use a grouping method to assign reads to different haplotype groups. PECAT efficiently assembles diploid genomes using Nanopore R9, PacBio CLR or Nanopore R10 reads only. PECAT generates more contiguous haplotype-specific contigs compared to other assemblers. Especially, PECAT achieves nearly haplotype-resolved assembly on B. taurus (Bison×Simmental) using Nanopore R9 reads and phase block NG50 with 59.4/58.0 Mb for HG002 using Nanopore R10 reads.

Quantitative structure-activity relationship model development for estimating the predicted No-effect concentration of petroleum hydrocarbon and derivatives in the ecological risk assessment

Quantitative structure-activity relationship (QSAR) is a cost-effective solution to directly and accurately estimating the environmental safety thresholds (ESTs) of pollutants in the ecological risk assessment due to the lack of toxicity data. In this study, QSAR models were developed for estimating the Predicted No-Effect Concentrations (PNECs) of petroleum hydrocarbons and their derivatives (PHDs) under dietary exposure, based on the quantified molecular descriptors and the obtained PNECs of 51 PHDs with given acute or chronic toxicity concentrations. Three high-reliable QSAR models were respectively developed for PHDs, aromatic hydrocarbons and their derivatives (AHDs), and alkanes, alkenes and their derivatives (ALKDs), with excellent fitting performance evidenced by high correlation coefficient (0.89-0.95) and low root mean square error (0.13-0.2 mg/kg), and high stability and predictive performance reflected by high internal and external verification coefficient (Q2LOO, 0.66-0.89; Q2F1, 0.62-0.78; Q2F2, 0.60-0.73). The investigated quantitative relationships between molecular structure and PNECs indicated that 18 autocorrelation descriptors, 3 information index descriptors, 4 barysz matrix descriptors, 6 burden modified eigenvalues descriptors, and 1 BCUT descriptor were important molecular descriptors affecting the PNECs of PHDs. The obtained results supported that PNECs of PHDs can be accurately estimated by the influencing molecular descriptors and the quantitative relationship from the developed QSAR models, that provided a new feasible solution for ESTs derivation in the ecological risk assessment.

Construction of quercetin-fucoidan nanoparticles and their application in cancer chemo-immunotherapy treatment

Fucoidan (FU), a natural marine polysaccharide, is an immunomodulator with great potential in tumor immunotherapy. In this work, a FU encapsulated nanoparticle named QU@FU-TS was developed, which contained the anticancer phytochemical quercetin (QU) and had the potential for cancer chemo-immunotherapy. QU@FU-TS were constructed through molecular self-assembly using green material tea saponin (TS) as the linking molecule. The molecular dynamics (MD) simulation showed that QU was bound to the hydrophobic tail of TS. At the same time, FU spontaneously assembled with the hydrophilic head of TS to form the outer layer of the QU@FU-TS. The molecular interactions between QU and TS were mainly π-stacking and hydrogen bonds. The bonding of FU and TS was maintained through the formation of multiple hydrogen bonds between the sulfate ester group and the hydroxy group. The inhibitory effects of QU@FU-TS on A549 cell proliferation were more potent than that by free QU. The antitumor activity of QU@FU-TS was mediated through various mechanisms, including the induction of oxidative stress, blocking cell cycle progression, and promoting cell apoptosis. Moreover, QU@FU-TS has been demonstrated to impede the proliferation and migration of cancer cells in vivo. The expression levels of macrophage surface markers increased under the treatment of QU@FU-TS, suggesting the potential of QU@FU-TS to serve as an immunotherapeutic agent by promoting macrophage activation.

DNA 5-methylcytosine detection and methylation phasing using PacBio circular consensus sequencing

Long single-molecular sequencing technologies, such as PacBio circular consensus sequencing (CCS) and nanopore sequencing, are advantageous in detecting DNA 5-methylcytosine in CpGs (5mCpGs), especially in repetitive genomic regions. However, existing methods for detecting 5mCpGs using PacBio CCS are less accurate and robust. Here, we present ccsmeth, a deep-learning method to detect DNA 5mCpGs using CCS reads. We sequence polymerase-chain-reaction treated and M.SssI-methyltransferase treated DNA of one human sample using PacBio CCS for training ccsmeth. Using long (≥10 Kb) CCS reads, ccsmeth achieves 0.90 accuracy and 0.97 Area Under the Curve on 5mCpG detection at single-molecule resolution. At the genome-wide site level, ccsmeth achieves >0.90 correlations with bisulfite sequencing and nanopore sequencing using only 10× reads. Furthermore, we develop a Nextflow pipeline, ccsmethphase, to detect haplotype-aware methylation using CCS reads, and then sequence a Chinese family trio to validate it. ccsmeth and ccsmethphase can be robust and accurate tools for detecting DNA 5-methylcytosines.

Iridoids from Patrinia heterophylla and their anti-inflammatory activity

A phytochemical investigation led to the isolation of five undescribed compounds (1-5) from the methanol extract of the rhizomes and roots of Patrinia heterophylla. The structures and configurations of these compounds were characterized by HRESIMS, ECD, and NMR data analyses. These compounds were assayed for their anti-inflammatory potential using LPS-stimulated BV-2 cells, of which compound 4 showed strong nitric oxide (NO) inhibitory effects with an IC₅₀ of 6.48 μM. The potential anti-inflammatory mechanism was examined utilizing Western blotting and molecular docking. Further in vivo anti-inflammatory experiments revealed that compound 4 inhibited the production of NO and reactive oxygen species in the zebrafish model.

A Quantitative Structure-Activity Relationship Approach to Determine Biotoxicity of Amide Herbicides for Ecotoxicological Risk Assessment

Amide herbicides have been widely applied in agriculture and found to be widespread and affect nontarget organisms in the environment. To better understand the biotoxicity mechanisms and determine the toxicity to the nontarget organisms for the hazard and risk assessment, five QSAR models were developed for the biotoxicity prediction of amide herbicides toward five aquatic and terrestrial organisms (including algae, daphnia, fish, earthworm and avian species), based on toxicity concentration and quantitative molecular descriptors. The results showed that the developed models complied with OECD principles for QSAR validation and presented excellent performances in predictive ability. In combination, the investigated QSAR relationship led to the toxicity mechanisms that eleven electrical descriptors (E_HOMO, E_LUMO, α_xx, α_yy, α_zz, μ, qN^-, Q_xx, Q_yy, qH⁺, and q^-), four thermodynamic descriptors (Cv, S^θ, H^θ, and ZPVE), and one steric descriptor (V_m) were strongly associated with the biotoxicity of amide herbicides. Electrical descriptors showed the greatest impacts on the toxicity of amide herbicides, followed by thermodynamic and steric descriptors.

The role of MnO2 crystal morphological scale and crystal structure in selective catalytic degradation of azo dye

MnO₂, as a representative manganese-based catalyst with many kinds of crystal forms, has been widely used to activate PMS. However, the role of morphological scale and crystal structures on the catalytic capability of MnO₂ still lacks further study. In this study, four different crystal forms of MnO₂ (α-MnO₂, β-MnO₂, γ-MnO₂, and δ-MnO₂) are succeeded in being fabricated via hydrothermal processes and evaluated by activating PMS for the removal of Reactive Yellow X-RG, typical azo dye. Experiment results indicate that α-MnO₂ with a one-dimensional structure exhibits the best catalytic performance among the four as-prepared MnO₂, which can be attributed to its broadest crystal interplanar distance (0.692), the highest portion of Mn (III)/Mn (IV) (4.194), and lowest value of average oxidation state AOS (2.696). Correlation analysis confirms that interplanar distance is the most relative factor with the catalytic activity of MnO₂ among the three studied factors (R² = 0.99715). Meanwhile, the morphological scale structure of α-MnO₂ can also account for its highest catalytic ability among the four as-prepared MnO₂, including its large specific area and advantageous one-dimensional nanostructure. Furthermore, according to the response surface methodology, when the dosage of PMS is 2.369 g/L, the dosage of α-MnO₂ is 0.991 g/L, and the initial dye concentration is 1025 mg/L, the maximum removal rate of Reactive Yellow X-RG is up to 97.38%.

NanoSNP: a progressive and haplotype-aware SNP caller on low-coverage nanopore sequencing data

MOTIVATION

Oxford Nanopore sequencing has great potential and advantages in population-scale studies. Due to the cost of sequencing, the depth of whole-genome sequencing for per individual sample must be small. However, the existing single nucleotide polymorphism (SNP) callers are aimed at high-coverage Nanopore sequencing reads. Detecting the SNP variants on low-coverage Nanopore sequencing data is still a challenging problem.

RESULTS

We developed a novel deep learning-based SNP calling method, NanoSNP, to identify the SNP sites (excluding short indels) based on low-coverage Nanopore sequencing reads. In this method, we design a multi-step, multi-scale and haplotype-aware SNP detection pipeline. First, the pileup model in NanoSNP utilizes the naive pileup feature to predict a subset of SNP sites with a Bi-long short-term memory (LSTM) network. These SNP sites are phased and used to divide the low-coverage Nanopore reads into different haplotypes. Finally, the long-range haplotype feature and short-range pileup feature are extracted from each haplotype. The haplotype model combines two features and predicts the genotype for the candidate site using a Bi-LSTM network. To evaluate the performance of NanoSNP, we compared NanoSNP with Clair, Clair3, Pepper-DeepVariant and NanoCaller on the low-coverage (∼16×) Nanopore sequencing reads. We also performed cross-genome testing on six human genomes HG002-HG007, respectively. Comprehensive experiments demonstrate that NanoSNP outperforms Clair, Pepper-DeepVariant and NanoCaller in identifying SNPs on low-coverage Nanopore sequencing data, including the difficult-to-map regions and major histocompatibility complex regions in the human genome. NanoSNP is comparable to Clair3 when the coverage exceeds 16×.

AVAILABILITY AND IMPLEMENTATION

https://github.com/huangnengCSU/NanoSNP.git.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Semi-automated assembly of high-quality diploid human reference genomes

The current human reference genome, GRCh38, represents over 20 years of effort to generate a high-quality assembly, which has benefitted society1,2. However, it still has many gaps and errors, and does not represent a biological genome as it is a blend of multiple individuals3,4. Recently, a high-quality telomere-to-telomere reference, CHM13, was generated with the latest long-read technologies, but it was derived from a hydatidiform mole cell line with a nearly homozygous genome5. To address these limitations, the Human Pangenome Reference Consortium formed with the goal of creating high-quality, cost-effective, diploid genome assemblies for a pangenome reference that represents human genetic diversity6. Here, in our first scientific report, we determined which combination of current genome sequencing and assembly approaches yield the most complete and accurate diploid genome assembly with minimal manual curation. Approaches that used highly accurate long reads and parent-child data with graph-based haplotype phasing during assembly outperformed those that did not. Developing a combination of the top-performing methods, we generated our first high-quality diploid reference assembly, containing only approximately four gaps per chromosome on average, with most chromosomes within ±1% of the length of CHM13. Nearly 48% of protein-coding genes have non-synonymous amino acid changes between haplotypes, and centromeric regions showed the highest diversity. Our findings serve as a foundation for assembling near-complete diploid human genomes at scale for a pangenome reference to capture global genetic variation from single nucleotides to structural rearrangements.

[Advances on optic disc morphological features and peripapillary structure changes in high myopia]

High myopia is an important cause of low vision and blindness in the world, most of which are characterized by the prolongation of the axial length, accompanied by various degenerative changes of fundus posterior pole, especially in the optic disc area and peripapillary structures, such as optic disc tilt, optic cup and rim changes, chorioretinal atrophy, posterior staphyloma and intrachoroidal cavitation, and so on. This article reviews the optic disc morphological features and peripapillary structure changes of high myopia, in order to reveal the pathogenesis of high myopia and provide new ideas for finding more effective prevention and treatment methods.

Fec: a fast error correction method based on two-rounds overlapping and caching

The third-generation sequencing technology has advanced genome analysis with long-read length, but the reads need error correction due to the high error rate. Error correction is a time-consuming process especially when the sequencing coverage is high. Generally, for a pair of overlapping reads A and B, the existing error correction methods perform a base-level alignment from B to A when correcting the read A. And another base-level alignment from A to B is performed when correcting the read B. However, based on our observation, the base-level alignment information can be reused. In this article, we present a fast error correction tool Fec, using two-rounds overlapping and caching. Fec can be used independently or as an error correction step in an assembly pipeline. In the first round, Fec uses a large window size (20) to quickly find enough overlaps to correct most of the reads. In the second round, a small window size (5) is used to find more overlaps for the reads with insufficient overlaps in the first round. When performing base-level alignment, Fec searches the cache first. If the alignment exists in the cache, Fec takes this alignment out and deduces the second alignment from it. Otherwise, Fec performs base-level alignment and stores the alignment in the cache. We test Fec on nine datasets, and the results show that Fec has 1.24-38.56 times speed-up compared to MECAT, CANU and MINICNS on five PacBio datasets and 1.16-27.8 times speed-up compared to NECAT and CANU on four nanopore datasets.

AVAILABILITY AND IMPLEMENTATION

Fec is available at https://github.com/zhangjuncsu/Fec.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Lipid accumulation product is a reliable indicator for identifying metabolic syndrome: the China Multi-Ethnic Cohort (CMEC) Study

BACKGROUND

Previous studies have shown that lipid accumulation product (LAP) was associated with the risk of cardiometabolic disease. It is not clear whether LAP could be used as a marker to identify metabolic syndrome (MetS) among Chinese ethnic groups.

AIM

To assess the reliability of LAP as a maker to identify MetS among Dong adults.

DESIGN

Population-based cross-sectional study.

METHOD

We included 6494 Dong individuals (1403 patients) aged 30-79 years from southwest China. MetS was established by Chinese Diabetes Society. Logistic regression model was utilized to calculate odds ratios (ORs) and 95% confidence intervals (CIs). Receiver operating characteristic (ROC) curve was utilized to calculate area under the ROC curve (AUC) and 95% CIs to obtain the identification ability for MetS.

RESULTS

The risk of MetS was increased with per 5 units increase of LAP (OR 1.37 [95% CI, 1.34-1.39]). Similar results were found in subgroup analyses and sensitivity analyses. Clustered metabolic risk associated with per 5 units increase of LAP was observed for people with 1 (OR 1.59 [95% CI, 1.53-1.65]), 2 (2.15 [2.06-2.24]), 3 (2.59 [2.48-2.71]), 4 (2.81 [2.69-2.95]) and 5 (3.03 [2.87-3.21]) MetS components. LAP presented higher AUC (0.915 [95% CI, 0.907-0.923]) than other included obesity indices (P < 0.05).

CONCLUSION

These data support evidence that LAP was related to the risk of MetS, had a high AUC and could be a reliable index for identifying MetS patients among Dong adults in Chinese.

Genome-wide identification and expression analyses of C2H2 zinc finger transcription factors in Pleurotus ostreatus

The C2H2-type zinc finger proteins (C2H2-ZFPs) regulate various developmental processes and abiotic stress responses in eukaryotes. Yet, a comprehensive analysis of these transcription factors which could be used to find candidate genes related to the control the development and abiotic stress tolerance has not been performed in Pleurotus ostreatus. To fill this knowledge gap, 18 C2H2-ZFs were identified in the P. ostreatus genome. Phylogenetic analysis indicated that these proteins have dissimilar amino acid sequences. In addition, these proteins had variable protein characteristics, gene intron-exon structures, and motif compositions. The expression patterns of PoC2H2-ZFs in mycelia, primordia, and young and mature fruiting bodies were investigated using qRT-PCR. The expression of some PoC2H2-ZFs is regulated by auxin and cytokinin. Moreover, members of PoC2H2-ZFs expression levels are changed dramatically under heat and cold stress, suggesting that these genes may participate in abiotic stress responses. These findings could be used to study the role of P. ostreatus-derived C2H2-ZFs in development and stress tolerance.

Comprehensive chemical characterization of dissolved organic matter in typical point-source refinery wastewaters

In petroleum refineries, the electric desalting, distillation, and stripping processes could generate large amounts of wastewaters that contain toxic substances. In this study, eight wastewater samples were collected from the three typical refining processes for comprehensive chemical characterization of the dissolved organic matter (DOM) using excitation emission matrix fluorescence spectroscopy, gas chromatography-mass spectrometry, and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Results showed that protein-like components and benzene were ubiquitous in all these wastewaters. Oxygen-containing volatile organic compounds had higher contents in crude distillation and stripping wastewater than those in electric desalting wastewater. Among the three refinery processes, molecular composition of DOM in the stripping wastewater had the highest complexity. The O_x and O_xS_y class species assigned from the negative-ion electrospray ionization FT-ICR MS were dominant in all wastewaters. The O_xS₂ class species which were effectively removed during stripping treatment had highest relative abundance in stripping influent. These results are instructive to guide the development of "divide and conquer" and would improve the treatment and management of refinery wastewater streams.

SACall: A Neural Network Basecaller for Oxford Nanopore Sequencing Data Based on Self-Attention Mechanism

Highly portable Oxford Nanopore sequencer producing long reads in real-time at low cost has made many breakthroughs in genomics studies. However, a major limitation of nanopore sequencing is its high errors when deciphering DNA sequences from noisy and complex raw data. In this paper, we developed an end-to-end basecaller, SACall, based on convolution layers, transformer self-attention layers and a CTC decoder. In SACall, the convolution layers are used to downsample the signals and capture the local patterns. To achieve the contextual relevance of signals, self-attention layers are adopted to calculate the similarity of the signals at any two positions in the raw signal sequence. Finally, the CTC decoder generates the DNA sequence by a beam search algorithm. We use a benchmark consisting of nine isolated genomes to test the quality of different basecallers including SACall, Albacore, and Guppy. The performances of basecallers are evaluated from the perspective of read accuracy, assembly quality, and consensus accuracy. Among most of the genomes in the test benchmark, the reads basecalled by SACall have fewer errors than the reads basecalled by other basecallers. When assembling the basecalled reads of each genome, the assembly from SACall basecalled reads achieves a higher assembly identity. In addition, there are fewer errors in the polished assembly from reads basecalled by SACall compared to those basecalled by Albacore and Guppy. In general, SACall outperforms the Nanopore official basecallers Albacore and Guppy in the benchmark. Moreover, SACall is an open-source and freely available basecaller, which gives a chance for researchers to train their own basecalling models on specific data and basecall Nanopore reads.

Genome-wide detection of cytosine methylations in plant from Nanopore data using deep learning

In plants, cytosine DNA methylations (5mCs) can happen in three sequence contexts as CpG, CHG, and CHH (where H = A, C, or T), which play different roles in the regulation of biological processes. Although long Nanopore reads are advantageous in the detection of 5mCs comparing to short-read bisulfite sequencing, existing methods can only detect 5mCs in the CpG context, which limits their application in plants. Here, we develop DeepSignal-plant, a deep learning tool to detect genome-wide 5mCs of all three contexts in plants from Nanopore reads. We sequence Arabidopsis thaliana and Oryza sativa using both Nanopore and bisulfite sequencing. We develop a denoising process for training models, which enables DeepSignal-plant to achieve high correlations with bisulfite sequencing for 5mC detection in all three contexts. Furthermore, DeepSignal-plant can profile more 5mC sites, which will help to provide a more complete understanding of epigenetic mechanisms of different biological processes.

BlockPolish: accurate polishing of long-read assembly via block divide-and-conquer

Long-read sequencing technology enables significant progress in de novo genome assembly. However, the high error rate and the wide error distribution of raw reads result in a large number of errors in the assembly. Polishing is a procedure to fix errors in the draft assembly and improve the reliability of genomic analysis. However, existing methods treat all the regions of the assembly equally while there are fundamental differences between the error distributions of these regions. How to achieve very high accuracy in genome assembly is still a challenging problem. Motivated by the uneven errors in different regions of the assembly, we propose a novel polishing workflow named BlockPolish. In this method, we divide contigs into blocks with low complexity and high complexity according to statistics of aligned nucleotide bases. Multiple sequence alignment is applied to realign raw reads in complex blocks and optimize the alignment result. Due to the different distributions of error rates in trivial and complex blocks, two multitask bidirectional Long short-term memory (LSTM) networks are proposed to predict the consensus sequences. In the whole-genome assemblies of NA12878 assembled by Wtdbg2 and Flye using Nanopore data, BlockPolish has a higher polishing accuracy than other state-of-the-arts including Racon, Medaka and MarginPolish & HELEN. In all assemblies, errors are predominantly indels and BlockPolish has a good performance in correcting them. In addition to the Nanopore assemblies, we further demonstrate that BlockPolish can also reduce the errors in the PacBio assemblies. The source code of BlockPolish is freely available on Github (https://github.com/huangnengCSU/BlockPolish).

Endogenous asymmetric dimethylarginine accumulation precipitates the cardiac and mitochondrial dysfunctions in type 1 diabetic rats

Myocardial mitochondrial function and biogenesis are suppressed in diabetes, but the mechanisms are unclear. Increasing evidence suggests that asymmetric dimethylarginine (ADMA) is associated with diabetic cardiovascular complications. This study was to determine whether endogenous ADMA accumulation contributes to cardiac and mitochondrial dysfunctions of diabetic rats and elucidate the potential mechanisms. Diabetic rat was induced by single intraperitoneal injection of streptozotocin (50 mg/kg). N-acetylcysteine was given (250 mg/kg/d) by gavage for 12w. Cardiac function was detected by echocardiography. Left ventricle papillary muscles were isolated to examine myocardial contractility. Myocardial ATP and mitochondrial DNA contents were measured to evaluate mitochondrial function and biogenesis. Endogenous ADMA accumulation was augmented resulting in decreased nitric oxide (NO) production and increased oxidative stress, suggesting NO synthase (NOS) uncoupling in the myocardium of T1DM rats compared with control rats. ADMA augmentation was associated with cardiac and mitochondrial dysfunctions along with myocardial uncoupling protein-2 (UCP2) upregulation and peroxisome proliferator-activated receptor-γ coactivator-1α (PGC-1α) downregulation in T1DM rats. Exogenous ADMA could directly inhibit myocardial contractility, mitochondrial function and biogenesis in parallel with decreasing NO content and PGC-1α expression while increasing oxidative stress and UCP2 expression in papillary muscles and cardiomyocytes. Treatment with antioxidant N-acetylcysteine, also an inhibitor of NOS uncoupling, either ameliorated ADMA-associated cardiac and mitochondrial dysfunctions or reversed ADMA-induced NO reduction and oxidative stress enhance in vivo and in vitro. These results indicate that myocardial ADMA accumulation precipitates cardiac and mitochondrial dysfunctions in T1DM rats. The underlying mechanism may be related to NOS uncoupling, resulting in NO reduction and oxidative stress increment, ultimate PGC-1α down-regulation and UCP2 up-regulation.

NeuralPolish: a novel Nanopore polishing method based on alignment matrix construction and orthogonal Bi-GRU Networks

MOTIVATION

Oxford Nanopore sequencing producing long reads at low cost has made many breakthroughs in genomics studies. However, the large number of errors in Nanopore genome assembly affect the accuracy of genome analysis. Polishing is a procedure to correct the errors in genome assembly and can improve the reliability of the downstream analysis. However, the performances of the existing polishing methods are still not satisfactory.

RESULTS

We developed a novel polishing method, NeuralPolish, to correct the errors in assemblies based on alignment matrix construction and orthogonal Bi-GRU networks. In this method, we designed an alignment feature matrix for representing read-to-assembly alignment. Each row of the matrix represents a read, and each column represents the aligned bases at each position of the contig. In the network architecture, a bi-directional GRU network is used to extract the sequence information inside each read by processing the alignment matrix row by row. After that, the feature matrix is processed by another bi-directional GRU network column by column to calculate the probability distribution. Finally, a CTC decoder generates a polished sequence with a greedy algorithm. We used five real data sets and three assembly tools including Wtdbg2, Flye and Canu for testing, and compared the results of different polishing methods including NeuralPolish, Racon, MarginPolish, HELEN and Medaka. Comprehensive experiments demonstrate that NeuralPolish achieves more accurate assembly with fewer errors than other polishing methods and can improve the accuracy of assembly obtained by different assemblers.

AVAILABILITY

https://github.com/huangnengCSU/NeuralPolish.git.

[Application of dual-channel contrast-enhanced ultrasound in classification of hilar cholangiocarcinoma and diagnosis of etiology of low biliary obstruction]

Objective: To investigate the clinical value of dual-channel contrast-enhanced ultrasound (DCUS) in the classification of hilar cholangiocarcinoma and the diagnosis of the etiology of low obstructive jaundice. Methods: The data of 114 patients with obstructive jaundice examined by the Department of Ultrasound of Lanzhou University Second Hospital from October 2018 to February 2020 were retrospectively collected. There were 60 males and 54 females, aged 37~84 (63±10) years. All patients underwent preoperative transvenous contrast-enhanced ultrasound (CEUS), intraoperative puncture needles, postoperative ultrasound-guided percutaneous transhepatic cholangiocarcinography (UG-PTC) and three-dimensional ultrasound cholangiography (3D-USC) through an external drainage tube, known as DCUS. The classification of hilar cholangiocarcinoma and the nature of low biliary tract obstruction were determined according to the characteristics of DCUS images. All patients who have received DCUS underwent magnetic resonance cholangiopancreatography (MRCP) and X-ray cholangiography. X-ray cholangiography was used as the gold standard for classification of hilar cholangiocarcinoma, and the accuracy of US, CEUS and DCUs was analyzed. Low obstructive jaundice was characterized by surgical pathology as the gold standard, and the diagnostic efficacy of conventional ultrasound (US), CEUS and DCUs was analyzed. At the same time, the receiver operating characteristic (ROC) curve was used to compare the efficacy of MRI+MRCP and DCUS in determination of the nature of low biliary obstruction. Results: The coincidence rates of US, CEUS, and DCUS in the classification of hilar cholangiocarcinoma and X-ray cholangiography were: 75.6% (34/45), 82.2% (37/45), and 93.3% (42/45), respectively. The coincidence rates of US, CEUS, and DCUS in the determination of the nature of low biliary obstruction and surgical pathology were 56.5% (39/69), 82.6% (57/69), and 85.5% (59/69), respectively. Compared with conventional ultrasound, CEUS had no statistically significant difference in the diagnosis of hilar cholangiocarcinoma (P=0.438), and DCUS had statistically significant difference in the diagnosis of hilar cholangiocarcinoma (P=0.039).ROC curve analysis suggested that the cut-off value of MRI+MRCP grade and DCUS grade for diagnosing benign and malignant low biliary obstruction were both 2.5; the area under the curve (AUC) were 0.897 and 0.906, respectively (both P<0.01); sensitivity were 77.5% and 93.1%, respectively; and the specificity were 87.5% and 82.8%, respectively. Conclusion: The value of DCUS in the classification of hilar cholangiocarcinoma and the qualitative diagnosis of low biliary tract obstruction was comparable to that of X-ray cholangiography and MRCP. DCUS had important clinical application value in the classification of hilar cholangiocarcinoma and the etiological diagnosis of low obstructive jaundice.

Efficient assembly of nanopore reads via highly accurate and intact error correction

Long nanopore reads are advantageous in de novo genome assembly. However, nanopore reads usually have broad error distribution and high-error-rate subsequences. Existing error correction tools cannot correct nanopore reads efficiently and effectively. Most methods trim high-error-rate subsequences during error correction, which reduces both the length of the reads and contiguity of the final assembly. Here, we develop an error correction, and de novo assembly tool designed to overcome complex errors in nanopore reads. We propose an adaptive read selection and two-step progressive method to quickly correct nanopore reads to high accuracy. We introduce a two-stage assembler to utilize the full length of nanopore reads. Our tool achieves superior performance in both error correction and de novo assembling nanopore reads. It requires only 8122 hours to assemble a 35X coverage human genome and achieves a 2.47-fold improvement in NG50. Furthermore, our assembly of the human WERI cell line shows an NG50 of 22 Mbp. The high-quality assembly of nanopore reads can significantly reduce false positives in structure variation detection.

Molecular characterization and overexpression of mnp6 and vp3 from Pleurotus ostreatus revealed their involvement in biodegradation of cotton stalk lignin

Fungal secretory heme peroxidase (Class II POD) plays a significant role in biomass conversion due to its lignin-degrading activity. In this study, genome-wide identification and bioinformatics were performed to analyze P leurotus ostreatus peroxidases (PoPODs). A total of six manganese peroxidases (MnPs) and three versatile peroxidases (VPs) were obtained. Bioinformatics analysis and qRT-PCR showed that P. ostreatus mnp6 (Pomnp6) and P. ostreatus vp3 (Povp3) could be involved in lignin degradation. Both Pomnp6 and Povp3 transgenetic fungi showed significantly increased lignin degradation of cotton stalks. ¹H-NMR revealed that Pomnp6 and Povp3 may preferentially degrade S-lignin in cotton stalks and mainly break β-O-4' bond linkages and hydroxyl. These results support the possible utility of Pomnp6 and Povp3 in natural straw resources and development of sustainable energy.

The Comparative Study on Two Models of Syndrome Differentiation of the Hand, Foot and Mouth Disease: An Investigation Analysis of the Signs and Symptoms on 2 325 Cases

Objective To realize the characteristics of “zheng” differentiation-treatment for hand, foot and mouth disease (HFMD), a new methodology of syndrome differentiation for different stages of HFMD has been explored.

Methods Total of 2 325 cases with HFMD were recorded by distributing them into exterior syndrome stage, interior syndrome stage, severe syndrome stage and recovered syndrome stage, respectively, and the main symptoms and subsidiary symptoms of different stages of HFMD have been observed. The major and minor pathogenesis of HFMD in different stages were obtained, and compared with the “2010 Guideline for the Diagnosis and Treatment of HFMD”.

Results It was found that the major pathogenesis of exterior stage was defined as “the invation of the wenevil to the defender of the body with the collaterals got involved”, and the minor as “qi deficiency”; in interior stage, “the fury of Gan-Yang” was the main pathogenesis, and “qi in chaos and qi deficiency” was the minor; in severe syndrome stage, “the damage of heart, liver and lung” was the main pathogenesis, and “qi in chaos” was the minor; and the pathogenesis of recovered stage was “qi-yin deficiency”. Compared with the “2010 Guideline for the Diagnosis and Treatment of HFMD”, it showed that “the obstruction of the fei-pi qi by the mixture of shi-re evil” and “the mixture of shi-re” in vivo was quite difficult to be explained in completely different context in the general situation; in the severe stage, the TCM clinical characteristics of syndrome differentiation might lose; in the early acute severe cases, the phenomenon that xin-yang and fei-qi almost ran out was difficult to be observed, then, the line between the severe and the acute severe became vague.

Conclusions The theory of syndrome differentiation by stages of HFMD was reasonable in the actual situation of clinical description on HFMD which was expected to be further tested and widely applied in the “zheng” differentiation-treatment of HFMD in the future.

MicroRNA expression profiling identifies miR-328 regulates cancer stem cell-like SP cells in colorectal cancer

Background:

Side population (SP) cells and their relationship to stem cell-like properties have been insufficiently studied in colorectal cancer (CRC). MicroRNAs (miRNAs) have attracted much attention but their roles in the maintenance of SP phenotype remain unclear.

Methods:

The SPs from CRC cell lines and primary cell cultures were analysed for stem cell-like properties. MiRNA microarray analysis identified miR-328 as a potential stemness miRNA of SP phenotype. The level of miR-328 expression in clinical samples and its correlation with SP fraction were determined. Gain-of-function and loss-of-function studies were performed to examine its roles in cancer stem-like SP cells. Furthermore, bioinformatics prediction and experimental validation were used to identify miR-328 target genes.

Results:

The SP cells sorted from CRC possess cancer stem cell (CSC)-like properties, including self-renewal, differentiation, resistance to chemotherapy, invasive and strong tumour formation ability. MiR-328 expression was significantly reduced in SP cells compared with Non-SP cells (P<0.05). Moreover, miR-328 expression was downregulated in CRC (n=33, P<0.05) and low miR-328 expression tend to correlate with high SP fraction (n=15, r=0.6559, P<0.05, Pearson's correlation). Functional studies indicated that miR-328 expression affects the number of SP cells. In addition, miR-328 overexpression reversed drug resistance and inhibited cell invasion of SP cells. Furthermore, luciferase reporter assay demonstrated that miR-328 directly targets ABCG2 and MMP16 and affects the levels of mRNA and protein expression in SP cells.

Conclusion:

These findings indicate that CRC contain cancer stem-like SP cells. MiR-328 has an important role in maintaining cancer stem-like SP phenotype that may be a potential target for effective CRC therapy.

Effects of Rapamycin on Breast Cancer Cell Migration through the Cross-Talk of MAPK Pathway

Phase I/II clinical studies with rapamycin analogs in breast and other cancers have demonstrated favorable responses. However, little is known on the effects of the mTOR inhibitor on breast cancer cell metastasis, which is a major cause of morbidity and death. We developed a highly sensitive 3-dimensional (3D) proliferation/invasion assay using quantitative bioluminescence (BL) imaging and applied this assay to evaluate the effects of rapamycin on the triple negative breast cancer cell line MDA-MB231. Without cytotoxicity of rapamycin on this cell line, rapamycin at 10nM inhibited the cell migration/invasion, but not at 1nM and 100nM, which was confirmed by the time-lapse single cell tracking analysis. The quantification of cytoskeleton changes showed most potent effects of 10nM rapamycin on the MDA-MB231 cells, with the formation and rearrangement of specialized cell membrane structures and actin fiber implicated in cell motility. Then, the Panorama Cell Signaling Antibody Microarray, enabling the global comparative analysis of cell signal proteins simultaneously, was exploited to analyze the effects of rapamycin on the cellular signaling network of the MDA-MB231 breast cancer cell line. 100nM rapamycin activated the MAPK pathway obviously, through the attenuated negative feedback of activated S6K1 to PI3K-Raf, which increased the expressions of activated Jun N-terminus kinase (JNK), Erk1/2, MEK-1, Raf-pS621, and MAPK-activated protein kinase 2 (MAPKAPK2) in the cells exposed to 100nM rapamycin. MEK inhibitor U0126 or PD98059 could restore the anti-migration effects of 100nM rapamycin on the MDA-MB231 cells. Furthermore, the combination of MEK inhibitors and rapamycin performed synergism on inhibiting the cell proliferation and migration/invasion. Accordingly, rapamycin at a certain dose suppresses MDA-MB231 cell migration/invasion, and the co-targeting of mTOR and MAPK pathways enhances the inhibition on cell proliferation and migration/invasion, underscoring the potential therapeutic utility of rapamycin, and rapamycin combining with MAPK inhibitors in triple negative breast cancer progression, and the results highlight the cross-talk homeostasis of mTOR and MAPK pathways in cancer treatment.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 5080.

[Morphological and microscopic identification of herba artemisiae scopariae and its adulterants]

Pharmacognostical studies of Herba Artemisiae Scopariae and its adulterants were compared on morphological and microscopic characteristics. The detailed characteristics of powder microscopic identification were described.

Human nuclear respiratory factor 2 alpha subunit cDNA: isolation, subcloning, sequencing, and in situ hybridization of transcripts in normal and monocularly deprived macaque visual system

Nuclear respiratory factor 2 (NRF-2) has been shown to contribute to the transcriptional regulation of a number of subunits of respiratory chain enzymes, including cytochrome c oxidase (CO). Our recent study demonstrated a parallel distribution of the alpha subunit proteins of NRF-2 (NRF-2 alpha) with CO in the monkey striate cortex, and that it can be regulated by neuronal activity. To determine whether this regulation is at the transcriptional level, the present study examined the expression of NRF-2 alpha mRNA in normal and monocularly deprived adult monkeys. A partial NRF-2 alpha cDNA was isolated from a human brain cDNA library. Sequence analysis revealed that it shared 99% identity with the published sequence from human HeLa cells. Riboprobes of NRF-2 alpha was generated and labeled with digoxigenin-11-UTP for in situ hybridization. The expression pattern of NRF-2 alpha mRNA in the normal striate cortex paralleled that of CO activity. It was highly expressed in layers IVC and VI, which contained high levels of CO, and more densely expressed in puffs of layers II and III than in interpuffs. In monkeys monocularly treated with tetrodotoxin for 1 day to 2 weeks, both NRF-2 alpha expression and CO activity were reduced in deprived ocular dominance columns of the visual cortex and in deprived layers of the lateral geniculate nucleus. These data indicate that, in the normal and visually deprived adult monkeys, NRF-2 alpha is regulated by neuronal activity at the transcriptional level.

Nuclear respiratory factor-2 subunit protein: correlation with cytochrome oxydase and regulation by functional activity in the monkey primary visual cortex

Previous studies have shown that a transcription factor of the Ets family, nuclear respiratory factor 2 (NRF-2), can activate in vitro the gene expression of cytochrome oxidase (CO), a mitochondrial enzyme of oxidative metabolism. The goals of our present study were to determine whether the distribution of NRF-2 alpha subunit proteins correlated with that of CO activity in the macaque monkey visual cortex and whether the level could be perturbed by visual deprivation. We generated polyclonal antibodies specifically against human NRF-2 alpha subunit. In normal monkeys, patterns of NRF-2 alpha distribution resembled closely that of CO activity: 1) NRF-2 alpha immunoreactivity was localized in both nuclei and cytoplasm of neurons, but the levels differed among various laminae; 2) layers IVA, IVC, and VI, which had high CO activity, were labeled more densely by NRF-2 alpha than layers I, IVB, and V, which contained lower levels of both NRF-2 alpha and CO activity; and 3) CO-rich puffs in layers II and III contained a higher level of NRF-2 alpha than CO-poor interpuffs. From 1 day to 7 days after monocular impulse blockade with tetrodotoxin, there was a progressive reduction of NRF-2 alpha in deprived ocular dominance columns, in parallel with decreases in CO activity. These results suggest that local levels of NRF-2 in the monkey visual cortex closely reflect neuronal physiological and metabolic levels revealed by CO activity and that the expression of NRF-2 alpha, like that of CO, is regulated tightly by neural functional activity.

Neurochemical organization of the macaque retina: effect of TTX on levels and gene expression of cytochrome oxidase and nitric oxide synthase and on the immunoreactivity of Na+ K+ ATPase and NMDA receptor subunit I

The present study examined the relationship between an important energy-generating enzyme (cytochrome oxidase; CO), a key energy-consuming enzyme (Na+ K+ ATPase) and neurochemicals associated with excitatory glutamatergic synapses (NMDAR1 and neuronal nitric oxide synthase, nNOS) in the adult macaque retina. Polyclonal antibodies against neuronal nitric oxide synthase and N-methyl-D-aspartate receptor subunit I were generated for immunohistochemical examination and labeled sites not previously reported were found. We have also isolated cDNAs for cytochrome oxidase subunits III (mitochondrial-encoded) and IV (nuclear-encoded), as well as for a fragment of neuronal nitric oxide synthase, from a human cDNA library. The distributions of mRNAs of these genes were analyzed by in situ hybridization. We found that three or more of the markers examined coexisted in a number of sites: (a) In the inner segments of photoreceptors, high energy demand for maintaining the dark current was placed by Na+ K+ ATPase. This was partially met by ATP-generating enzymes such as CO. Neuronal NOS was also present there for the synthesis of NO and the cascading event leading to the generation of cGMP and the gating of channels for visual transduction. (b) Both the outer and inner plexiform layers had detectable amounts of all four markers, although the levels varied among them. This was most likely due to the presence of depolarizing glutamatergic synapses arising from photoreceptors and bipolar cells and such synaptic events were energy-demanding. The involvement of NMDA receptors and nNOS in these synaptic layers is strongly implicated in the present study. (c) All four markers were present in the majority of retinal ganglion cells, with some inherent heterogeneity related to intensity and size. Retinal ganglion cells are known to receive excitatory synapses from glutamatergic bipolar cells and are themselves highly active. The presence of both NMDAR1 and nNOS in these cells were verified in the present study and the energy demands related to these synaptic activities were necessarily high. Thus, active ion transporting functions related to synaptic or non-synaptically induced repolarization from the basis for an interrelationship between the neurochemicals/enzymes studied. Finally, (d) all four markers and the gene expression of CO and nNOS in the macaque retina were regulated by neuronal activity.

Mitochondrial- and nuclear-encoded subunits of cytochrome oxidase in neurons: differences in compartmental distribution, correlation with enzyme activity, and regulation by neuronal activity

Cytochrome oxidase (CO), a mitochondrial energy-generating enzyme, contains both mitochondrial- and nuclear-encoded subunits. In neurons, local levels of CO activity vary among different neuronal compartments, reflecting local demands for energy. The goals of the present study were to determine if compartmental distribution of CO subunit proteins from the two genomes was correlated with local CO activity, and if their expression was regulated proportionately in neurons. The subcellular distributions of mitochondrial-encoded CO III and nuclear-encoded CO Vb proteins were quantitatively analyzed in mouse cerebellar sections subjected to postembedding immunocytochemistry. Local levels of subunit proteins were also compared to local CO activity, as revealed by CO cytochemistry. In order to study the regulation of subunit protein expression, we assessed changes in immunoreactivity of the two CO subunits as well as changes in CO activity in mouse superior colliculus after 1 to 7 days of monocular enucleation. We found that immunoreaction product for both CO III and CO Vb existed almost exclusively in mitochondria, but their compartmental distributions were different. CO III was nonhomogeneously distributed among different neuronal compartments, where its local level was positively correlated with that of CO activity. In contrast, the subcellular distribution of CO Vb was relatively uniform and did not bear a direct relationship with that of CO activity. Moreover, the two subunit proteins were disproportionately regulated by neuronal activity. CO III and CO activity exhibited parallel decreases after the deprivation of afferent input, and their changes were earlier and to a greater degree than that of CO Vb proteins. Thus, the present findings indicate that the local expression and/or distribution of CO subunit proteins from the two genomes may involve different regulatory mechanisms in neurons. Our data also suggest that the activity-dependent regulation of mitochondrial-encoded CO subunits is likely to play a major role in controlling the local levels of CO content and its activity.

Metabolic and neurochemical plasticity of gamma-aminobutyric acid-immunoreactive neurons in the adult macaque striate cortex following monocular impulse blockade: quantitative electron microscopic analysis

The purpose of the present study was to examine the effects of retinal impulse blockade on gamma-aminobutyric acid (GABA)-immunoreactive (GABA-IR) neurons in cytochrome oxidase (CO)-rich puffs of the adult monkey striate cortex. Specifically, we wished to know if changes occurred in their CO activity, GABA immunoreactivity, and synaptic organization. A double-labeling technique, which combined CO histochemistry and postembedding GABA immunocytochemistry on the same ultrathin sections, was used to reveal simultaneously the distribution of the two markers. We quantitatively compared changes in GABA-IR neurons of deprived puffs (DPs) with respect to non-deprived puffs (NPs) 2 weeks after monocular tetrodotoxin treatment. We found that the proportion of darkly CO reactive mitochondria in GABA-IR neurons of DPs drastically decreased to about half of those in NPs. There was a greater reduction of CO levels in GABA-IR axon terminals than in their cell bodies and dendrites. In contrast, most non-GABA-IR neurons displayed no significant change in their CO levels. Morphologically, GABA-IR neurons and axon terminals in DPs showed a significant shrinkage in their mean size. GABA immunoreactivity, as indicated by the density of immunogold particles in GABA-IR neurons, declined in DPs, and a greater decrease was also found in axon terminals than in cell bodies or dendrites. Moreover, the numerical density of GABA-IR axon terminals and synapses in DPs was significantly reduced without changes in that of asymmetric and symmetric synapses. Thus, the present results support the following conclusions: 1) Oxidative metabolism and neurotransmitter expression in GABA-IR neurons are tightly regulated by neuronal activity in adult monkey striate cortex; 2) GABA-IR neurons are much more vulnerable to functional deprivation than non-GABA-IR ones, suggesting that these inhibitory neurons have stringent requirement for sustained excitatory input to maintain their heightened oxidative capacity; and 3) intracortical inhibition mediated by GABA transmission following afferent deprivation may be decreased in deprived puffs, because the oxidative capacity and transmitter level in GABAergic neurons, especially in their axon terminals, are dramatically reduced.

Differential glutamatergic innervation in cytochrome oxidase-rich and -poor regions of the macaque striate cortex: quantitative EM analysis of neurons and neuropil

One of the hallmarks of the primate striate cortex is the presence of cytochrome oxidase (CO)-rich puffs and CO-poor interpuffs in its supragranular layers. However, the neurochemical basis for their differences in metabolic activity and physiological properties is not well understood. The goals of the present study were to determine whether CO levels in postsynaptic neuronal compartments were correlated with the proportion of excitatory glutamate-immunoreactive (Glu-IR) synapses they received and if Glu-IR terminals and synapses in puffs differed from those in interpuffs. By combining CO histochemistry and postembedding Glu immunocytochemistry on the same ultrathin sections, the simultaneous distribution of the two markers in individual neuronal profiles was quantitatively analyzed. As a comparison, adjacent sections were identically processed for the double labeling of CO and GABA, an inhibitory neurotransmitter. In both puffs and interpuffs, most axon terminals forming asymmetric synapses (84%)--but not symmetric ones, which were GABA-IR--were intensely immunoreactive for Glu. GABA-IR neurons received mainly Glu-IR synapses on their cell bodies, and they had three times as many mitochondria darkly reactive for CO than Glu-rich neurons, which received only GABA-IR axosomatic synapses. In puffs, GABA-IR neurons received a significantly higher ratio of Glu-IR to GABA-IR axosomatic synapses and contained about twice as many darkly CO-reactive mitochondria than those in interpuffs. There were significantly more Glu-IR synapses and a higher ratio of Glu- to GABA-IR synapses in the neuropil of puffs than of interpuffs. Moreover, Glu-IR axon terminals in puffs contained approximately three times more darkly CO-reactive mitochondria than those in interpuffs, suggesting that the former may be synaptically more active. Thus, the present results are consistent with our hypothesis that the levels of oxidative metabolism in postsynaptic neurons and neuropil are positively correlated with the proportion of excitatory synapses they receive. Our findings also suggest that excitatory synaptic activity may be more prominent in puffs than in interpuffs, and that the neurochemical and synaptic differences may constitute one of the bases for physiological and functional diversities between the two regions.

Double labeling of GABA and cytochrome oxidase in the macaque visual cortex: quantitative EM analysis

In the primate striate cortex, cytochrome oxidase (CO)-rich puffs differ from CO-poor interpuffs in their metabolic levels and physiological properties. The neurochemical basis for their metabolic and physiological differences is not well understood. The goal of the present study was to examine the relationship between the distribution of gamma aminobutyric acid (GABA)/non-GABA synapses and CO levels in postsynaptic neuronal profiles and to determine whether or not a difference existed between puffs and interpuffs. By combining CO histochemistry and postembedding GABA immunocytochemistry on the same ultrathin sections, the simultaneous distribution of the two markers in individual neuronal profiles was quantitatively analyzed. In both puffs and interpuffs, GABA-immunoreactive (GABA-IR) neurons were the only cell type that received both non-GABA-IR (presumed excitatory) and GABA-IR (presumed inhibitory) axosomatic synapses, and they had three times as many mitochondria darkly reactive for CO than non-GABA-IR neurons, which received only GABA-IR axosomatic synapses. GABA-IR neurons and terminals in puffs had a larger mean size, about twice as many darkly reactive mitochondria, and a higher ratio of non-GABA-IR to GABA-IR axosomatic synapses than those in interpuffs (2.3:1 vs. 1.6:1; P < 0.01). There were significantly more synapses of both non-GABA-IR and GABA-IR types in the neuropil of puffs than of interpuffs; however, the ratio of non-GABA-IR to GABA-IR synapses was significantly higher in puffs (2.86:1) than in interpuffs (2.08:1; P < 0.01). Our results are consistent with the hypothesis that the level of oxidative metabolism in postsynaptic neurons and neuronal processes is tightly governed by the strength and proportion of excitatory over inhibitory synapses. Thus, the present results suggest that (1) GABA-IR neurons in the macaque striate cortex have a higher level of oxidative metabolism than non-GABA ones because their somata receive direct excitatory synapses and their terminals are more tonically active; (2) the higher proportion of presumed excitatory synapses in puffs imposes a greater energy demand there than in interpuffs; and (3) excitatory synaptic activity may be more prominent in puffs than in interpuffs because puffs receive a greater proportion of excitatory synapses from multiple sources including the lateral geniculate nucleus, which is not known to project to the interpuffs.