Genomic characterization of a novel ureolytic bacteria, Lysinibacillus capsici TSBLM, and its application to the remediation of acidic heavy metal-contaminated soil.

Soil heavy metal contamination is an essential challenge in ecological and environmental management, especially for acidic soils. Microbially induced carbonate precipitation (MICP) is an effective and environmentally friendly remediation technology for heavy metal contaminated sites, and one of the key factors for its realization lies in the microorganisms. In this study, Lysinibacillus capsici TSBLM was isolated from heavy metal contaminated soil around a gold mine, and inferred to be a novel ureolytic bacteria after phylogenomic inference and genome characterization. The urease of L. capsici TSBLM was analyzed by genetic analysis and molecular docking, and further applied this bacteria to the remediation of Cu and Pb in solution and acidic soils to investigate its biomineralization mechanism and practical application. The results revealed L. capsici TSBLM possessed a comprehensive urease gene cluster ureABCEFGD, and the encoded urease docked with urea at the lowest binding energy site (ΔG = -3.43 kcal/mol) connected to three amino acids threonine, aspartic, and alanine. The urease of L. capsici TSBLM is synthesized intracellularly but mainly functions extracellularly. L. capsici TSBLM removes Cu/Pb from the solution by generating heavy metal carbonates or co-precipitating with CaCO3 vaterite. For acidic heavy metal-contaminated soil, the carbonate-bound states of Cu and Pb increased significantly from 7 % to 16 % and from 23 % to 35 % after 30 days by L. capsici TSBLM. Soil pH improved additionally. L. capsici TSBLM maintained the dominant status in the remediated soil after 30 days, demonstrating good environmental adaptability and curing persistence. The results provided new strain resources and practical application references for the remediation of acidic heavy metal contaminated soil based on MICP.

Biomineralization of heavy metals based on urea transport and hydrolysis within a new bacterial isolate, B. intermedia TSBOI.

A newly isolated ureolytic bacteria, Brucella intermedia TSBOI, exhibited microbially induced calcite precipitation (MICP) which is a promising technique for the remediation of heavy metals in polluted environments. Brucella intermedia TSBOI achieved 90-100% removal of 1 mmol/L Cu2+/Pb2+/Zn2+ within 72 h. A distinctive feature lies in B. intermedia TSBOI's capacity for the transport and hydrolysis of urea, considered to be critical for its strong urease activity. This study explored the mechanisms of this capacity at the genetic, molecular and protein levels through complete genome sequencing, molecular docking and enzymatic reaction kinetics. The results revealed that, for urea hydrolysis, B. intermedia TSBOI exhibited a comprehensive urease gene cluster, with the key gene ureC demonstrating an absolute expression level approximating to 4 × 104 copies/RNA ng under optimal conditions. Results also confirmed the strong spontaneous, energy-independent binding ability of it's urease to urea, with the lowest Gibbs free energy binding site linking to the three amino acids, alanine, asparagine and serine. The urea transport gene yut presented and expressed, with the absolute expression enhanced in response to increasing urea concentrations. The significant positive correlation between ureC/yut expression levels and urease activity provided a theoretical basis for B. intermedia TSBOI's heavy metal bioremediation potential. ENVIRONMENTAL IMPLICATION: Heavy metals (Cu, Pb and Zn) were studied in this study. Heavy metals are hazardous due to their toxicity, persistence, and ability to bioaccumulate in living organisms. They can cause severe health issues, harm ecosystems, and contaminate air, water, and soil. A novel ureolytic bacteria, Brucella intermedia TSBOI, exhibited microbially induced carbonate precipitation capability was isolated which removed 90-100% of 1 mmol/L Cu2+/Pb2+/Zn2+ within 72 h. Its advantages in urea hydrolysis and transport facilitate the remediation of actual heavy metal contaminated environments.

Single-cell multi-omics sequencing of human spermatogenesis reveals a DNA demethylation event associated with male meiotic recombination.

Human spermatogenesis is a highly ordered process; however, the roles of DNA methylation and chromatin accessibility in this process remain largely unknown. Here by simultaneously investigating the chromatin accessibility, DNA methylome and transcriptome landscapes using the modified single-cell chromatin overall omic-scale landscape sequencing approach, we revealed that the transcriptional changes throughout human spermatogenesis were correlated with chromatin accessibility changes. In particular, we identified a set of transcription factors and cis elements with potential functions. A round of DNA demethylation was uncovered upon meiosis initiation in human spermatogenesis, which was associated with male meiotic recombination and conserved between human and mouse. Aberrant DNA hypermethylation could be detected in leptotene spermatocytes of certain nonobstructive azoospermia patients. Functionally, the intervention of DNA demethylation affected male meiotic recombination and fertility. Our work provides multi-omics landscapes of human spermatogenesis at single-cell resolution and offers insights into the association between DNA demethylation and male meiotic recombination.

IRF9 inhibits CyHV-3 replication by regulating the PI3K-AKT signalling pathway in common carp (Cyprinus carpio) epithelial cells.

Interferon regulatory factor 9 (IRF9) is an important transcriptional regulator involved in innate and adaptive immunity. Cyprinid herpesvirus-3 (CyHV-3) is a virus causing widespread death and great economic loss in farmed common carp (Cyprinus carpio). However, the effect of IRF9 on CyHV-3 infection in common carp has not been reported. In this study, during CyHV-3 infection, IRF9 overexpression in common carp fin epithelial (CCF) cells significantly reduced the expression of viral factor thymidine kinase (TK) and open reading frame 72 (ORF72), and knockdown of IRF9 produced the opposite results (p < 0.05). In CCF cells. The IRF9 protein was expression in the nucleus and was rapidly induced in CCF cells by CyHV-3 infection. In addition, several genes associated with virus infection, including type I interferon (IFNI), IFN-stimulated gene 15 (ISG15), myxovirus resistance 1 (Mx1) and Viperin were induced in CCF cells overexpressing IRF9 upon CyHV-3 infection. IRF9 overexpression induced by CyHV-3 infection significantly increased the gene expression of Mx1 and phosphoinositide 3-kinase (PI3K) and the protein expression of protein kinase B (AKT) (p < 0.01). Interestingly, IRF9 did not significantly affect Mx1 gene expression when AKT protein levels remained unchanged during CyHV-3 infection of CCF cells. Furthermore, a significant resistance-related locus was found in the IRF9 sequence in "Longke-11" mirror carp (M11) and Yellow River carp (p < 0.05). These results indicated that IRF9 inhibited viral replication by upregulating the expression of Mx1 via the PI3K-AKT signalling pathway during CyHV-3 infection in CCF cells and provide some basis for the study of the antiviral molecular mechanisms of common carp.

Effects of Different Dietary Protein Levels on the Growth Performance, Physicochemical Indexes, Quality, and Molecular Expression of Yellow River Carp (Cyprinus carpio haematopterus).

A 12-week rearing trial was carried out to estimate effects on the growth performance, physicochemical indexes, quality, and the molecular expression of Yellow River Carp (Cyprinus carpio haematopterus) using five practical diets, including dietary protein levels of 220, 250, 280, 310, and 340 g/kg. The results illustrated that the fish's weight gain (WG) and specific growth rate (SGR) were significantly influenced, with an ascending dietary protein level of up to 250 g/kg (p < 0.05). The carp muscle contents of total saturated fatty acids (∑SFA), monounsaturated fatty acids (∑MUFA), polyunsaturated fatty acids (∑PUFA), and fatty acids (∑FA) decreased significantly with the ascending dietary protein levels, except for the 250 g/kg protein diet (p < 0.05). Only the glutamic acid and total essential amino acid (∑EAA) contents were significantly influenced by the ascending dietary protein levels (p < 0.05). The relative GH expression of the carp muscle significantly decreased with the increase in the dietary protein level up to 310 g/kg, and then it significantly increased (p < 0.05). In the intestines, the peak relative TOR expression was observed on the 220 g/kg protein diet, while the relative 4EBP1 expression was significantly influenced by the dietary protein level up to 250 g/kg (p < 0.05). In the muscle, the peak relative TOR and 4EBP1 expression levels were observed on the 250 g/kg protein diet. In gills, the lowest relative Rhag, Rhbg, and Rhcg1 expression levels were observed on the 250 g/kg protein diet. Based on all of the aforementioned results, the optimal dietary protein level for Cyprinus carpio haematopterus (160.24 ± 15.56 g) is 250-280 g/kg.

The chemical reprogramming of unipotent adult germ cells towards authentic pluripotency and de novo establishment of imprinting.

Although somatic cells can be reprogrammed to pluripotent stem cells (PSCs) with pure chemicals, authentic pluripotency of chemically induced pluripotent stem cells (CiPSCs) has never been achieved through tetraploid complementation assay. Spontaneous reprogramming of spermatogonial stem cells (SSCs) was another non-transgenic way to obtain PSCs, but this process lacks mechanistic explanation. Here, we reconstructed the trajectory of mouse SSC reprogramming and developed a five-chemical combination, boosting the reprogramming efficiency by nearly 80- to 100-folds. More importantly, chemical induced germline-derived PSCs (5C-gPSCs), but not gPSCs and chemical induced pluripotent stem cells, had authentic pluripotency, as determined by tetraploid complementation. Mechanistically, SSCs traversed through an inverted pathway of in vivo germ cell development, exhibiting the expression signatures and DNA methylation dynamics from spermatogonia to primordial germ cells and further to epiblasts. Besides, SSC-specific imprinting control regions switched from biallelic methylated states to monoallelic methylated states by imprinting demethylation and then re-methylation on one of the two alleles in 5C-gPSCs, which was apparently distinct with the imprinting reprogramming in vivo as DNA methylation simultaneously occurred on both alleles. Our work sheds light on the unique regulatory network underpinning SSC reprogramming, providing insights to understand generic mechanisms for cell-fate decision and epigenetic-related disorders in regenerative medicine.

Alveolar Macrophages-Mediated Translocation of Intratracheally Delivered Perfluorocarbon Nanoparticles to Achieve Lung Cancer 19F-MR Imaging.

Recent advances in intratracheal delivery strategies have sparked considerable biomedical interest in developing this promising approach for lung cancer diagnosis and treatment. However, there are very few relevant studies on the behavior and mechanism of imaging nanoparticles (NPs) after intratracheal delivery. Here, we found that nanosized perfluoro-15-crown-5-ether (PFCE NPs, ∼200 nm) exhibite significant 19F-MRI signal-to-noise ratio (SNR) enhancement than perfluorooctyl bromide (PFOB NPs) up to day 7 after intratracheal delivery. Alveolar macrophages (AMs) engulf PFCE NPs, become PFCE NPs-laden AMs, and then migrate into the tumor margin, resulting in increased tumor PFCE concentration and 19F-MRI signals. AMs-mediated translocation of PFCE NPs to lung draning lymph nodes (dLNs) decreases the background PFCE concentration. Our results shed light on the dynamic AMs-mediated translocation of intratracheally delivered PFC NPs for effective lung tumor visualization and reveal a pathway to develop and promote the clinical translation of an intratracheal delivery-based imaging strategy.

Integrative Transcriptomic Analysis Reveals the Immune Mechanism for a CyHV-3-Resistant Common Carp Strain.

Anti-disease breeding is becoming the most promising solution to cyprinid herpesvirus-3 (CyHV-3) infection, the major threat to common carp aquaculture. Virus challenging studies suggested that a breeding strain of common carp developed resistance to CyHV-3 infection. This study illustrates the immune mechanisms involved in both sensitivity and anti-virus ability for CyHV3 infection in fish. An integrative analysis of the protein-coding genes and long non-coding RNAs (lncRNAs) using transcriptomic data was performed. Tissues from the head kidney of common carp were extracted at days 0 (the healthy control) and 7 after CyHV-3 infection (the survivors) and used to analyze the transcriptome through both Illumina and PacBio sequencing. Following analysis of the GO terms and KEGG pathways involved, the immune-related terms and pathways were merged. To dig out details on the immune aspect, the DEGs were filtered using the current common carp immune gene library. Immune gene categories and their corresponding genes in different comparison groups were revealed. Also, the immunological Gene Ontology terms for lncRNA modulation were retained. The weighted gene co-expression network analysis was used to reveal the regulation of immune genes by lncRNA. The results demonstrated that the breeding carp strain develops a marked resistance to CyHV-3 infection through a specific innate immune mechanism. The featured biological processes were autophagy, phagocytosis, cytotoxicity, and virus blockage by lectins and MUC3. Moreover, the immune-suppressive signals, such as suppression of IL21R on STAT3, PI3K mediated inhibition of inflammation by dopamine upon infection, as well as the inhibition of NLRC3 on STING during a steady state. Possible susceptible factors for CyHV-3, such as ITGB1, TLR18, and CCL4, were also revealed from the non-breeding strain. The results of this study also suggested that Nramp and PAI regulated by LncRNA could facilitate virus infection and proliferation for infected cells respectively, while T cell leukemia homeobox 3 (TLX3), as well as galectin 3 function by lncRNA, may play a role in the resistance mechanism. Therefore, immune factors that are immunogenetically insensitive or susceptible to CyHV-3 infection have been revealed.

CellCall: integrating paired ligand-receptor and transcription factor activities for cell-cell communication.

With the dramatic development of single-cell RNA sequencing (scRNA-seq) technologies, the systematic decoding of cell-cell communication has received great research interest. To date, several in-silico methods have been developed, but most of them lack the ability to predict the communication pathways connecting the insides and outsides of cells. Here, we developed CellCall, a toolkit to infer inter- and intracellular communication pathways by integrating paired ligand-receptor and transcription factor (TF) activity. Moreover, CellCall uses an embedded pathway activity analysis method to identify the significantly activated pathways involved in intercellular crosstalk between certain cell types. Additionally, CellCall offers a rich suite of visualization options (Circos plot, Sankey plot, bubble plot, ridge plot, etc.) to present the analysis results. Case studies on scRNA-seq datasets of human testicular cells and the tumor immune microenvironment demonstrated the reliable and unique functionality of CellCall in intercellular communication analysis and internal TF activity exploration, which were further validated experimentally. Comparative analysis of CellCall and other tools indicated that CellCall was more accurate and offered more functions. In summary, CellCall provides a sophisticated and practical tool allowing researchers to decipher intercellular communication and related internal regulatory signals based on scRNA-seq data. CellCall is freely available at https://github.com/ShellyCoder/cellcall.

Distribution of the microbial community and antibiotic resistance genes in farmland surrounding gold tailings: A metagenomics approach.

Metal mining has caused the accumulation of waste mine tailing dumps from abandoned mines. The pollution of farmlands surrounding metal tailings by heavy metals has been a long-recognized problem. However, the distribution of antibiotic resistance genes (ARGs) in tailings and the main factors influencing this distribution have rarely been reported. In this study, a metagenomics approach was used to investigate the microbial community and ARGs present in farmland surrounding gold tailings in northern China. The results showed that the main pollutants in the farmland were As, Pb, and Cd. Proteobacteria and Actinobacteria were the dominant phyla of microbes in farmlands surrounding gold tailings. A total of 75 ARGs with 327 ARG subtypes were detected in soil samples. Macrolide-, lincosaminide-, and streptogramin B resistant genes accounted for the majority of ARGs in this study, and Actinobacteria, Proteobacteria, and Acidobacteria were the hosts of most ARGs. Partial least squares path modeling revealed that the microbial community was the most influential driver moderating the distribution of soil ARGs near tailings, and heavy metals have direct and partially indirect effects on these ARGs. In contrast to previous analyses of ARGs, our study found that mobile gene elements had a minimal impact on ARGs. Overall, this study presents a complete ARG survey that sheds light on the distribution and fate of ARGs under heavy metal contamination in farmland around gold tailings.

Structure optimization of gasket based on orthogonal experiment and NSGA-II.

With the aim of enhancing both reliability and fatigue life of gasket, this study combines finite element analysis, orthogonal experimental design, dynamically-guided multi-objective optimization, and the non-dominated sorting genetic algorithm with elitist strategy to optimize the geometric parameters of the cylinder gasket. The finite element method was used to analyze the temperature field, thermal-mechanical coupling stress field, and deformation of cylinder gasket. The calculation results were experimentally validated by measured temperature data, and comparison results show that the maximum error between calculated value and experiment value is 7.1%, which is acceptable in engineering problems. Based on above results and orthogonal experiment design method, the effects of five factors, including diameter of combustion chamber circle, diameter of coolant flow hole, length of the insulation zone between third and fourth cylinders, thickness of gasket, and bolt preload, on three indexes: temperature, stress, and deformation of gasket, were examined in depth. Through the variance analysis of the results, three important factors were identified to proceed later calculation. The dynamically guided multi-objective optimization strategy and the non-dominated sorting genetic algorithm were effectively used and combined to determine the optimal geometric parameters of cylinder gasket. Furthermore, calculation results suggest that temperature, stress, and deformation of the optimized cylinder gasket have been improved by 27.88 K, 16.84 MPa, and 0.0542 mm, respectively when compared with the origin object, which shows the excellent performance of gasket optimization and effectiveness of the proposed optimization strategy.

Precise Cancer Anti-acid Therapy Monitoring Using pH-Sensitive MnO2@BSA Nanoparticles by Magnetic Resonance Imaging.

Microfluctuations in a pH gradient create a harsh microenvironment in tumors, leaving behind the most aggressive, invasive, and drug-resistant tumor cells. Directly visualizing the spatiotemporal distribution of pH variations and accurately quantifying the dynamic acid-base changes during cancer treatment are critical to estimate prognosis and to evaluate therapeutic efficacy. However, the quantification of subtle pH variations dynamically and noninvasively remains challenging. The purpose of this study is to determine and visualize dynamic acid-base changes in solid tumors during anti-acid treatments by magnetic resonance imaging (MRI) using pH-sensitive nanoparticles. We report the development of pH-sensitive nanoparticles, MnO2@BSA, that rapidly and strongly amplify the MR contrast signal in response to the extracellular acidic environment of solid tumors. The spatiotemporal distribution and dynamic fluctuations of pH heterogeneity in NCI-H460 lung tumors were observed with MnO2@BSA at different time points after an anti-acid treatment with esomeprazole, which directly interferes with the acidic microenvironment of the tumor. Imaging results were validated using a pH microsensor. MRI of pH-sensitive MnO2@BSA nanoparticles provided direct readouts of the kinetics of pH gradient fluctuations during esomeprazole treatment. A significant MR signal reduction was observed at the 48 h time point after treatment. The manipulated extracellular pH changes detected noninvasively by MRI coincided with the extracellular pH fluctuations measured with a pH microsensor (pH 6.12-6.63). Immunofluorescence and Western blot analyses confirmed the expression of V-ATPase in NCI-H460 lung cancer cells, which could be inhibited by esomeprazole, as detected by ELISA assay. Overall, these results demonstrate that MnO2@BSA MRI has great potential as a noninvasive tool to accurately monitor pH fluctuations, thereby paving the way for the dynamic detection of acidic microenvironments in vivo without the need for pH microsensors.

Creep-Fatigue Experiment and Life Prediction Study of Piston 2A80 Aluminum Alloy.

In order to improve the reliability and service life of vehicle and diesel engine, the fatigue life prediction of the piston in a heavy diesel engine was studied by finite element analysis of piston, experiment data of aluminum alloy, fatigue life model based on energy dissipation criteria, and machine learning algorithm. First, the finite element method was used to calculate and analyze the temperature field, thermal stress field, and thermal-mechanical coupling stress field of the piston, and determine the area of heavy thermal and mechanical load that will affect the fatigue life of the piston. Second, based on the results of finite element calculation, the creep-fatigue experiment of 2A80 aluminum alloy was carried out, and the cyclic response characteristics of the material under different loading conditions were obtained. Third, the fatigue life prediction models based on energy dissipation criterion and twin support vector regression are proposed. Then, the accuracy of the two models was verified using experiment data. The results show that the model based on the twin support vector regression is more accurate for predicting the material properties of aluminum alloy. Based on the established life prediction model, the fatigue life of pistons under actual service conditions is predicted. The calculation results show that the minimum fatigue life of the piston under plain condition is 2113.60 h, and the fatigue life under 5000 m altitude condition is 1425.70 h.

Study on the spatial distribution of ureolytic microorganisms in farmland soil around tailings with different heavy metal pollution.

Ureolytic microorganisms, a kind of microorganism which can secrete urease and decompose urea, have great potential in remediation of soil heavy metals based on microbial induced carbonate precipitation. However, the horizontal and vertical distribution of ureolytic microbial community in heavy metals contaminated soils is poorly understood. In this study, urease genes in agricultural soils surrounding tailings were first investigated using metagenomic in two dimensions: heavy metal pollution (Low-L, Middle-M, High-H) and soil depth (0-20 cm, 20-40 cm, 40-60 cm, 60-80 cm, 80-100 cm). Results showed that the effect of heavy metal concentration on ureolytic microorganisms was indeed significant, while the changes of ureolytic microorganisms with increasing soil depth varied in the vertical direction at the same level of heavy metal contamination. H site had the highest diversity of ureolytic microorganisms except for the topsoil. And at the same heavy metal contamination level, the ureolytic microbial diversity was lower in deeper soils. Proteobacteria, Actinobacteria and Thaumarchaeota (Archaea) were the dominant phyla of ureolytic microorganisms in all three sites, accounting for more than 80% of the total. However, the respond to the heavy metal concentrations of three phyla were different, which were increasing, decreasing and essentially unchanged, respectively. Besides, other environmental factors such as SOM and pH had different effects on ureolytic microorganisms, with Proteobacteria being positively correlated and Actinobacteria being the opposite. Another phenomenon was that Actinobacteria and Verrucomicrobia were biomarkers of group L, which could significantly explain the difference with the other two sites. These results provided valuable information for further research on the response mechanism and remediation of heavy metal pollution by ureolytic microbial system.

Efficacy of silver needle therapy for the treatment of chronic nonspecific low back pain: a prospective, single-center, randomized, parallel-controlled clinical trial.

BACKGROUND: Chronic nonspecific low back pain (CNSLBP) troubles approximately 30% of people worldwide. Silver needle therapy (SNT) is a treatment method to relieve soft tissue pain through heating. Therefore, this study aimed to observe the effects of SNT on CNSLBP. METHODS: In this study, 100 patients were randomly divided into 2 groups: silver needle (SN) group and control group (n = 50). In the SN group, patients received SNT and physiotherapy, while patients received physiotherapy alone in the control group. At the 6-month follow-up, the numerical rating scale (NRS), Oswestry Disability Index (ODI), Short-Form 12 of quality of life (SF-12), the natural logarithms of low-frequency measurement (InLF), and the natural logarithms of high-frequency measurement (InHF) of heart rate variability (HRV) were recorded. RESULTS: In both groups, NRS, ODI, SF-12 scores, and HRV at 2 weeks after treatment were improved and maintained for 6 months. Compared with the control group, more significant improvements were observed in the NRS and SF-12 scores at 1, 2, 3, and 6 months and in the ODI scores at 1 and 2 months in the SN group (P <  0.05). However, there was no significant difference between the groups in the ODI scores at 3 and 6 months. InLF and InHF in the SN group were higher than those in the control group at 3 and 6 months (P <  0.05). CONCLUSIONS: SNT relieved pain and improved quality of life and autonomic nerve activity, especially parasympathetic nerve, in patients with CNSLBP, without serious complications. TRIAL REGISTRATION: Chinese Clinical Trial Registry No. ChiCTR-OOC-17013237 . Registered on November 11, 2017.

Genome-based development of 15 microsatellite markers in fluorescent multiplexes for parentage testing in captive tigers.

As one of the most endangered species, tiger (Panthera tigris) inbreeding has become an urgent issue to address. Using a microsatellite (short tandem repeat, STR) identification system, paternity testing may be helpful to avoid inbreeding in captive breeding programs. In this study, we developed a genome-based identification system named tiger pedigree identification multiplex system (TPI-plex). By analyzing the entire tiger genome, 139,967 STR loci were identified and 12.76% of these displayed three to six alleles among three re-sequenced individual tiger genomes. A total of 204 candidate STRs were identified and screened with a reference population containing 31 unrelated captive tigers. Of these, 15 loci were chosen for inclusion in the multiplex panel. The mean allele number and mean expected heterozygosity (He) were 7.3333 and 0.7789, respectively. The cumulative probability of exclusion (CPE) and total probability of discrimination power (TDP) reached 0.999999472 and 0.999999999999995, respectively. The results showed that the TPI-plex system can be applied in routine pedigree identification for captive tigers. We also added a sex identification marker named TAMEL into the TPI-plex for sex determination.

Characterization of the mitochondrial genome of Megalobrama terminalis in the Heilong River and a clearer phylogeny of the genus Megalobrama.

Megalobrama terminalis distributed in Sino-Russian Heilong-Amur River basin has decreased dramatically in the last few decades. It has been listed in the Red Book of the Russian Federation as an endangered fish species. Here, the complete mitochondrial (mt) genome sequence of M. terminalis in the Heilong River (MTH) was first determined and characterized. Additionally, we identified a population-specific single nucleotide polymorphism (SNP) locus in MTH which could effectively separate MTH from the six other populations of the genus Megalobrama in the absence of hybridization. Moreover, phylogenetic analyses determined that the Xi River M. hoffmanni is located at the basal branch of the clade, and the rest of the group is divided into two assemblages, namely, one containing M. terminalis from Qiantang River and Jinsha River Reservoir/Longxi River M. Pellegrini/MTH and the other containing M. amblycephala from Liangzi Lake and Yi River. We clarify the intraspecies identity of MTH and construct a clearer phylogeny of the genus Megalobrama, which will contribute to the germplasm identification, protection and development of MTH in the future.

BS-virus-finder: virus integration calling using bisulfite sequencing data.

Background: DNA methylation plays a key role in the regulation of gene expression and carcinogenesis. Bisulfite sequencing studies mainly focus on calling single nucleotide polymorphism, different methylation region, and find allele-specific DNA methylation. Until now, only a few software tools have focused on virus integration using bisulfite sequencing data. Findings: We have developed a new and easy-to-use software tool, named BS-virus-finder (BSVF, RRID:SCR_015727), to detect viral integration breakpoints in whole human genomes. The tool is hosted at https://github.com/BGI-SZ/BSVF. Conclusions: BS-virus-finder demonstrates high sensitivity and specificity. It is useful in epigenetic studies and to reveal the relationship between viral integration and DNA methylation. BS-virus-finder is the first software tool to detect virus integration loci by using bisulfite sequencing data.

Origin of the Reflectin Gene and Hierarchical Assembly of Its Protein.

Cephalopods, the group of animals including octopus, squid, and cuttlefish, have remarkable ability to instantly modulate body coloration and patterns so as to blend into surrounding environments [1, 2] or send warning signals to other animals [3]. Reflectin is expressed exclusively in cephalopods, filling the lamellae of intracellular Bragg reflectors that exhibit dynamic iridescence and structural color change [4]. Here, we trace the possible origin of the reflectin gene back to a transposon from the symbiotic bioluminescent bacterium Vibrio fischeri and report the hierarchical structural architecture of reflectin protein. Intrinsic self-assembly, and higher-order assembly tightly modulated by aromatic compounds, provide insights into the formation of multilayer reflectors in iridophores and spherical microparticles in leucophores and may form the basis of structural color change in cephalopods. Self-assembly and higher-order assembly in reflectin originated from a core repeating octapeptide (here named protopeptide), which may be from the same symbiotic bacteria. The origin of the reflectin gene and assembly features of reflectin protein are of considerable biological interest. The hierarchical structural architecture of reflectin and its domain and protopeptide not only provide insights for bioinspired photonic materials but also serve as unique "assembly tags" and feasible molecular platforms in biotechnology.