De novo assembly is a difficult issue for heterozygous diploid genomes. The advent of high-throughput short-read and long-read sequencing technologies provides both new challenges and potential ...solutions to the issue. Here, we present HaploMerger2 (HM2), an automated pipeline for rebuilding both haploid sub-assemblies from the polymorphic diploid genome assembly. It is designed to work on pre-existing diploid assemblies, which are typically created by using de novo assemblers. HM2 can process any diploid assemblies, but it is especially suitable for diploid assemblies with high heterozygosity (≥3%), which can be difficult for other tools. This pipeline also implements flexible and sensitive assembly error detection, a hierarchical scaffolding procedure and a reliable gap-closing method for haploid sub-assemblies. Using HM2, we demonstrate that two haploid sub-assemblies reconstructed from a real, highly-polymorphic diploid assembly show greatly improved continuity.
Source code, executables and the testing dataset are freely available at https://github.com/mapleforest/HaploMerger2/releases/.
hshengf2@mail.sysu.edu.cn.
Supplementary data are available at Bioinformatics online.
Unspecific peroxygenases (UPO) (EC 1.11.2.1) represent an intriguing oxidoreductase sub-subclass of heme proteins with peroxygenase and peroxidase activity. With over 300 identified substrates, UPOs ...catalyze numerous oxidations including 1- or 2- electron oxygenation, selective oxyfunctionalizations, which make them most significant in organic syntheses and potentially attractive as industrial biocatalysts. There are very few UPOs available with distinct properties, notably, MroUPO which shows behavior ranging between UPO and another heme-thiolate peroxidase, called Chloroperoxidase (CPO). It prompted us to search for more UPOs in fungal kingdom which led us to studying their relationship with CPO.
In this study, we searched for novel UPOs in more than 800 fungal genomes and found 113 putative UPO-encoding sequences distributed in 35 different fungal species (or strains), amongst which single sequence per species were subjected to phylogeny study along with CPOs. Our phylogenetic study show that the UPOs are distributed in Basidiomycota and Ascomycota phyla of fungi. The sequence analysis helped to classify the UPOs into five distinct subfamilies: classic AaeUPO and four new subfamilies with potential new traits. We have also shown that each of these five subfamilies (supported by) have their own signature motifs. Surprisingly, some of the CPOs appeared to be a type of UPOs indicating that they were previously identified incorrectly. Selection pressure was observed on important motifs in UPOs which could have driven their functional divergence. Furthermore, the sites having different evolutionary rates caused by the functional divergence were also identified on some motifs along with the other relevant amino acid residues. Finally, we predicted critical amino acids responsible for the functional divergence in the UPOs and identified some sequence differences among UPOs, CPOs, and MroUPO to predict it's ranging behavior.
This study discovers new UPOs, provides a glimpse of their evolution from CPOs, and presents new insight on their functional divergence. We present a new classification of UPOs and shed new light on its phylogenetics. These different UPOs may exhibit a wide range of characteristics and specificities which may help in various fields of synthetic chemistry and industrial biocatalysts, and may as well lead to an advancement towards the understanding of physiological role of UPOs in fungi.
•A new tunnel model which considers the dislocation and rotational deformation is adopted.•The variational method is used to analyze the responses of existing tunnel due to upper excavation.•Tunnel ...deformation and reaction force can be presented in finite series, and no discretization process is required.•The validity of the proposed method is verified through comparison with filed data and other theoretical methods.
This paper aims to provide an analytical solution for evaluating the deformation of a segmental tunnel induced by upper basement excavation. To this end, a model considering shear dislocation and rotation of a segmental tunnel is proposed and the interaction between tunnel and ground is modeled using a two-parameter Pasternak foundation model. The vertical displacement of the tunnel is then approximated by the finite Fourier series. Energy balance equations for the tunnel and soil are obtained via energy method and then the governing equation is derived based on the principle of minimum potential energy. With the variational approach, expressions for the tunnel heave, relative vertical deformation, rotational angle and shear force between two tunnel rings are derived. The feasibility of the proposed model is validated against the field data and the results obtained using Euler-Bernoulli beam and Winkler beam, indicating that the proposed method can be used to effectively estimate the responses of a segmental tunnel to upper excavation. Finally, a parametric analysis is performed to examine the effects of different factors on the responses of existing shield tunnel to upper deep excavation.
Co-option of RAG1 and RAG2 for antigen receptor gene assembly by V(D)J recombination was a crucial event in the evolution of jawed vertebrate adaptive immunity. RAG1/2 are proposed to have arisen ...from a transposable element, but definitive evidence for this is lacking. Here, we report the discovery of ProtoRAG, a DNA transposon family from lancelets, the most basal extant chordates. A typical ProtoRAG is flanked by 5-bp target site duplications and a pair of terminal inverted repeats (TIRs) resembling V(D)J recombination signal sequences. Between the TIRs reside tail-to-tail-oriented, intron-containing RAG1-like and RAG2-like genes. We demonstrate that ProtoRAG was recently active in the lancelet germline and that the lancelet RAG1/2-like proteins can mediate TIR-dependent transposon excision, host DNA recombination, transposition, and low-efficiency TIR rejoining using reaction mechanisms similar to those used by vertebrate RAGs. We propose that ProtoRAG represents a molecular “living fossil” of the long-sought RAG transposon.
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•A new cut-and-paste DNA transposon called ProtoRAG has been discovered in lancelets•It has the structural features expected for the hypothetical RAG transposon•It is capable of TIR-dependent DNA cleavage, transposition, and self-resealing•It hence represents a molecular “living fossil” of the long-sought RAG transposon
A family of DNA transposons discovered in fish-like marine chordates may hold the key for the evolution of adaptive immunity in higher organisms.
Water management in the catalyst layers (CLs) of proton-exchange membrane fuel cells is crucial for its commercialization and popularization. However, the high experimental or computational cost in ...obtaining water distribution and diffusion remains a bottleneck in the existing experimental methods and simulation algorithms, and further mechanistic exploration at the nanoscale is necessary. Herein, we integrate, for the first time, molecular dynamics simulation with our customized analysis framework based on a multiattribute point cloud dataset and an advanced deep learning network. This was achieved through our workflow that generates simulated transport data of water molecules in the CLs as the training and test dataset. Deep learning framework models the multibody solid–liquid system of CLs on a molecular scale and completes the mapping from the Pt/C substrate structure and Nafion aggregates to the density distribution and diffusion coefficient of water molecules. The prediction results are comprehensively analyzed and error evaluated, which reveals the highly anisotropic interaction landscape between 50,000 pairs of interacting nanoparticles and explains the structure and water transport property relationship in the hydrated Nafion film on the molecular scale. Compared to the conventional methods, the proposed deep learning framework shows computational cost efficiency, accuracy, and good visual display. Further, it has a generality potential to model macro- and microscopic mass transport in different components of fuel cells. Our framework is expected to make real-time predictions of the distribution and diffusion of water molecules in CLs as well as establish statistical significance in the structural optimization and design of CLs and other components of fuel cells.
Whole-genome shotgun assembly has been a long-standing issue for highly polymorphic genomes, and the advent of next-generation sequencing technologies has made the issue more challenging than ever. ...Here we present an automated pipeline, HaploMerger, for reconstructing allelic relationships in a diploid assembly. HaploMerger combines a LASTZ-ChainNet alignment approach with a novel graph-based structure, which helps to untangle allelic relationships between two haplotypes and guides the subsequent creation of reference haploid assemblies. The pipeline provides flexible parameters and schemes to improve the contiguity, continuity, and completeness of the reference assemblies. We show that HaploMerger produces efficient and accurate results in simulations and has advantages over manual curation when applied to real polymorphic assemblies (e.g., 4%-5% heterozygosity). We also used HaploMerger to analyze the diploid assembly of a single Chinese amphioxus (Branchiostoma belcheri) and compared the resulting haploid assemblies with EST sequences, which revealed that the two haplotypes are not only divergent but also highly complementary to each other. Taken together, we have demonstrated that HaploMerger is an effective tool for analyzing and exploiting polymorphic genome assemblies.
Vertebrates diverged from other chordates ~500 Myr ago and experienced successful innovations and adaptations, but the genomic basis underlying vertebrate origins are not fully understood. Here we ...suggest, through comparison with multiple lancelet (amphioxus) genomes, that ancient vertebrates experienced high rates of protein evolution, genome rearrangement and domain shuffling and that these rates greatly slowed down after the divergence of jawed and jawless vertebrates. Compared with lancelets, modern vertebrates retain, at least relatively, less protein diversity, fewer nucleotide polymorphisms, domain combinations and conserved non-coding elements (CNE). Modern vertebrates also lost substantial transposable element (TE) diversity, whereas lancelets preserve high TE diversity that includes even the long-sought RAG transposon. Lancelets also exhibit rapid gene turnover, pervasive transcription, fastest exon shuffling in metazoans and substantial TE methylation not observed in other invertebrates. These new lancelet genome sequences provide new insights into the chordate ancestral state and the vertebrate evolution.
It has been speculated that before vertebrates evolved somatic diversity-based adaptive immunity, the germline-encoded diversity of innate immunity may have been more developed. Amphioxus occupies ...the basal position of the chordate phylum and hence is an important reference to the evolution of vertebrate immunity. Here we report the first comprehensive genomic survey of the immune gene repertoire of the amphioxus Branchiostoma floridae. It has been reported that the purple sea urchin has a vastly expanded innate receptor repertoire not previously seen in other species, which includes 222 toll-like receptors (TLRs), 203 NOD/NALP-like receptors (NLRs), and 218 scavenger receptors (SRs). We discovered that the amphioxus genome contains comparable expansion with 71 TLR gene models, 118 NLR models, and 270 SR models. Amphioxus also expands other receptor-like families, including 1215 C-type lectin models, 240 LRR and IGcam-containing models, 1363 other LRR-containing models, 75 C1q-like models, 98 ficolin-like models, and hundreds of models containing complement-related domains. The expansion is not restricted to receptors but is likely to extend to intermediate signal transducers because there are 58 TIR adapter-like models, 36 TRAF models, 44 initiator caspase models, and 541 death-fold domain-containing models in the genome. Amphioxus also has a sophisticated TNF system and a complicated complement system not previously seen in other invertebrates. Besides the increase of gene number, domain combinations of immune proteins are also increased. Altogether, this survey suggests that the amphioxus, a species without vertebrate-type adaptive immunity, holds extraordinary innate complexity and diversity.
Background:
Ligustrazine injection has been widely used as adjunctive therapy in the treatment of acute cerebral infarction (ACI) during the past decades in China, but its clinical efficacy is not ...yet well confirmed. This study aims to evaluate the efficacy of ligustrazine injection as adjunctive therapy for ACI.
Methods:
Databases including China National Knowledge Infrastructure (CNKI), China Science and Technology Journal Database (VIP), PubMed, Medline, Google Scholar, Chinese Biomedical Literature Database, Cochrane Library, Embase, Sino-Med, Wanfang Database, and Chinese Science Citation Database were systematically searched for the published randomized controlled trials (RCTs) on ligustrazine injection in the treatment of ACI until November 2020. Meta-analysis was performed on the primary outcome measure (i.e., clinical effective rate) and the secondary outcome measure i.e., neurological deficit score (NDS), fibrinogen, low shear blood viscosity (LBV), and high shear blood viscosity (HBV). The quality of the included RCTs was assessed according to the M scoring system (the refined Jadad scale). Sensitivity analysis and subgroup analysis were conducted according to the methodological quality, years of publication, and sample size.
Results:
Nineteen RCTs, containing 2022 patients, were included in this study. Meta-analysis indicated that ligustrazine injection combined with Western medicine could achieve a better effect in the treatment of ACI than using Western medicine alone in terms of clinical effective rate (RR = 1.24; 95% CI, 1.19–1.29), NDS (MD = −3.88; 95%CI, −4.51 to −3.61), fibrinogen (MD = −0.59; 95% CI, −0.76 to −0.42), LBV (MD = −2.11; 95% CI, −3.16 to −1.06), and HBV (MD = −0.88; 95% CI, −1.20 to −0.55).
Conclusions:
This research indicated that ligustrazine injection as adjunctive therapy seemed to be more effective than using western medicine alone in treating ACI. However, more evidence is required to confirm the efficacy of ligustrazine injection due to the low methodological quality of the included RCTs.
As adjunctive therapy, puerarin injection has been widely applied for the treatment of unstable angina pectoris (UAP) in China during the past decades. However, the efficacy of puerarin injection as ...adjunctive therapy for UAP has not been well confirmed. The purpose of this meta-analysis was to summarize the available evidence to estimate the efficacy of puerarin injection in treating UAP.
A systematic review and meta-analysis with subgroup analysis and sensitivity analysis according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) principle were carried out to evaluate the efficacy of puerarin injection as adjunctive therapy in treating UAP.
To obtain the published randomized controlled trials (RCTs) on puerarin injection, databases, namely, China National Knowledge Infrastructure (CNKI), Wanfang Database, Chinese Biomedical Literature Database, Sino-Med, PubMed, China Science and Technology Journal Database (VIP), Medline, Google Scholar, Cochrane Library, Chinese Science Citation Database, and Embase were systematically searched until June 2021. In this meta-analysis, Review Manager version 5.3 software and Stata version 12.0 software were employed to analyze the collected data. Based on the methodological quality, years of publications, sample size and dosages, sensitivity analysis, and subgroup analysis were performed. The GRADE assessment was conducted by the software GRADEpro version 3.6 software.
A total of 17 RCTs involving 1,459 patients were included in this meta-analysis. Results indicated that puerarin injection as adjunctive therapy was more superior than conventional Western medicine alone in reducing angina symptoms risk ratio (RR) = 1.22, 95% CI 1.16 to 1.28,
= 8.11,
< 0.00001 and improving ECG (RR = 1.32, 95% CI 1.20 to 1.44,
= 6.00,
< 0.00001), meanwhile reducing the frequency of angina attack mean difference (MD) = -2.22, 95% CI -2.53 to -1.90,
= 13.97,
< 0.00001 and the duration of angina attack (MD = -2.00, 95% CI -2.39 to -1.61,
= 9.99,
< 0.00001) for the treatment of UAP. Results from the GRADE assessment suggested that the comprehensive quality of this evidence was low.
This meta-analysis indicated that puerarin injection was more effective than using conventional Western medicine alone in the treatment of UAP. However, because of the low methodological quality of the included RCTs, more evidence was still needed to verify the efficacy of puerarin injection.
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