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Lyssaviruses cause rabies, which is an acute neurological disease responsible for more than 59,000 human deaths annually and has no available effective treatments. The phosphoprotein (P) of lyssaviruses (lyssavirus-P) plays multiple roles in virus replication and immune evasion. Lyssavirus-P has been identified as the major type I interferon (IFN-I) antagonist, while the precise site and precise molecular mechanism remain unclear. Herein, we found that substitution of site 179 of lyssavirus-P from serine (Ser) to proline (Pro) impairs its antagonism function of IFN-I by sequence alignment and site mutations. Subsequent studies demonstrated that lyssavirus-P containing S179 specifically interacted with I-kappa B kinase ε (IKKε). Specifically, lyssavirus-P containing S179 interacted simultaneously with the kinase domain (KD) and scaffold dimerization domain (SDD) of IKKε, competing with TNF receptor-associated factor 3 (TRAF3) and IFN regulatory factor 3 (IRF3) for binding with IKKε, leading to the inhibition of IFN production. Furthermore, S179 was involved in the viral pathogenicity of the typical lyssavirus rabies virus in a mouse model. Interestingly, we found that S179 is conserved among most lyssavirus-P and functional for IFN antagonism. Collectively, we identified S179 of lyssavirus-P is essential for IFN-I inhibition, which provides deep insight into the immune evasion strategies of lyssaviruses. IMPORTANCE Interferon (IFN) and the IFN-induced cellular antiviral response constitute the first line of defense against viral invasion. Evading host innate immunity, especially IFN signaling, is the key step required for lyssaviruses to establish infection. In this study, S179 of lyssavirus phosphoprotein (lyssavirus-P) was identified as the key site for antagonizing IFN-I production. Mechanistically, lyssavirus-P containing S179 specifically targets the key kinase IKKε and disrupts its interaction with TRAF3 and IRF3. S179P mutation in the P protein of the typical lyssavirus rabies virus (RABV) attenuated its pathogenicity in a mouse model. Our findings provide deep insight into the immune evasion strategies of lyssaviruses, which is helpful for the development of effective antiviral therapeutics.

Taking into consideration the difficulties in predicting the properties of liquid production and evaluating the irreducible water saturation of low-porosity and ultra-low-permeability sandstone reservoirs, the relationships between the irreducible water saturation and logging reservoir evaluation parameters are explored based on a large number of core mercury injection experiment. When the permeability cumulative contribution value reaches 99.9%, the lower limit of pore throat radius is determined as 0.025 μm and the corresponding irreducible water saturation is more accurate. The experimental results of 77 samples in the research area showed that the irreducible water saturation has a good correlation with the median pore throat radius which has a good correlation with the porosity. The irreducible water saturation is consistent with the nuclear magnetic experiment results. Therefore, a new method to determine the irreducible water saturation based on logging data is established. The application results of this method in tight sandstone reservoirs in the Keshen area show that the fluid types identified by the relationship between the calculated irreducible water saturation and total water saturation are consistent with the actual test results, which confirms the accuracy and feasibility of this method. This method solves the problem of irreducible water saturation evaluation in low-porosity and ultra-low-permeability sandstone reservoirs. In the field or other situations where core testing is lacking, accurate irreducible water saturation can be obtained based on only porosity. It also lays a foundation for further improving the prediction accuracy of fluid properties, which has broad application prospects.

Rabies, caused by rabies virus (RABV), is a widespread zoonosis that is nearly 100% fatal. Alteration of the metabolic environment affects viral replication and the immune response during viral infection. In this study, glucose uptake was increased in mouse brains at the late stage of infection with different RABV strains (lab-attenuated CVS strain and wild-type DRV strain). To illustrate the mechanism underlying glucose metabolism alteration, comprehensive analysis of lysine acetylation and target analysis of energy metabolites in mouse brains infected with CVS and DRV strains were performed. A total of 156 acetylated sites and 115 acetylated proteins were identified as significantly different during RABV infection. Compared to CVS- and mock-infected mice, the lysine acetylation levels of glycolysis and tricarboxylic acid (TCA) cycle enzymes were decreased, and enzyme activity was upregulated in DRV-infected mouse brains. Metabolomic analysis revealed high levels of oxaloacetate (OAA) in RABV-infected mouse brains. Specifically, the OAA level in CVS-infected mouse brains was higher than that in DRV-infected mouse brains, which contributed to the enhancement of the metabolic rate at the substrate level. Finally, we confirmed that OAA could reduce excessive neuroinflammation in CVS-infected mouse brains by inhibiting JNK and P38 phosphorylation. Taken together, this study provides fresh insight into the different strategies the host adapts to regulate glucose metabolism for energy requirements after different RABV strain infections and suggests that OAA treatment is a strategy to prevent neural damage during RABV infection. IMPORTANCE Both viral replication and the host immune response are highly energy dependent. It is important to understand how the rabies virus affects energy metabolism in the brain. Glucose is the direct energy source for cell metabolism. Previous studies have revealed that there is some association between acetylation and metabolic processes. In this study, comprehensive protein acetylation and glucose metabolism analysis were conducted to compare glucose metabolism in mouse brains infected with different RABV strains. Our study demonstrates that the regulation of enzyme activity by acetylation and OAA accumulation at the substrate level are two strategies for the host to respond to energy requirements after RABV infection. Our study also indicates the role OAA could play in neuronal protection by suppressing excessive neuroinflammation.

Rabies, caused by rabies virus (RABV), is fatal to both humans and animals around the world. Effective clinical therapy for rabies has not been achieved, and vaccination is the most effective means of preventing and controlling rabies. Although different vaccines, such as live attenuated and inactivated vaccines, can induce different immune responses, different expressions of pattern recognition receptors (PRRs) also cause diverse immune responses. Toll-like receptor 4 (TLR4) is a pivotal PRR that induces cytokine production and bridges innate and adaptive immunity. Importantly, TLR4 recognizes various virus-derived pathogen-associated molecular patterns (PAMPs) and virus-induced damage-associated molecular patterns (DAMPs), usually leading to the activation of immune cells. However, the role of TLR4 in the humoral immune response induced by RABV has not yet been revealed. Based on TLR4-deficient (TLR4(−/−)) and wild-type (WT) mouse models, we report that TLR4-dependent recruitment of the conventional type 2 dendritic cells (CD8α(−) CD11b(+) cDC2) into secondary lymph organs (SLOs) is critical for antigen presentation. cDC2-initiated differentiation of follicular helper T (Tfh) cells promotes the proliferation of germinal center (GC) B cells, the formation of GCs, and the production of plasma cells (PCs), all of which contribute to the production of RABV-specific IgG and virus-neutralizing antibodies (VNAs). Collectively, our work demonstrates that TLR4 is necessary for the recruitment of cDC2 and for the induction of RABV-induced humoral immunity, which is regulated by the cDC2-Tfh-GC B axis. IMPORTANCE Vaccination is the most efficient method to prevent rabies. TLR4, a well-known immune sensor, plays a critical role in initiating innate immune response. Here, we found that TLR4-deficient (TLR4(−/−)) mice suppressed the induction of humoral immune response after immunization with rabies virus (RABV), including reduced production of VNAs and RABV-specific IgG compared to that occurred in wild-type (WT) mice. As a consequence, TLR4(−/−) mice exhibited higher mortality than that of WT mice after challenge with virulent RABV. Importantly, further investigation found that TLR4 signaling promoted the recruitment of cDC2 (CD8α(+) CD11b(−)), a subset of cDCs known to induce CD4(+) T-cell immunity through their MHC-II presentation machinery. Our results imply that TLR4 is indispensable for an efficient humoral response to rabies vaccine, which provides new insight into the development of novel rabies vaccines.

Rabies is a fatal zoonosis that causes encephalitis in mammals, and vaccination is the most effective method to control and eliminate rabies. Virus-like vesicles (VLVs), which are characterized as infectious, self-propagating membrane-enveloped particles composed of only Semliki Forest virus (SFV) replicase and vesicular stomatitis virus glycoprotein (VSV-G), have been proven safe and efficient as vaccine candidates. However, previous studies showed that VLVs containing rabies virus glycoprotein (RABV-G) grew at relatively low titers in cells, impeding their potential use as a rabies vaccine. In this study, we constructed novel VLVs by transfection of a mutant SFV RNA replicon encoding RABV-G. We found that these VLVs could self-propagate efficiently in cell culture and could evolve to high titers (approximately 10(8) focus-forming units [FFU]/ml) by extensive passaging 25 times in BHK-21 cells. Furthermore, we found that the evolved amino acid changes in SFV nonstructural protein 1 (nsP1) at positions 470 and 482 was critical for this high-titer phenotype. Remarkably, VLVs could induce robust type I interferon (IFN) expression in BV2 cells and were highly sensitive to IFN-α. We found that direct inoculation of VLVs into the mouse brain caused reduced body weight loss, mortality, and neuroinflammation compared with the RABV vaccine strain. Finally, it could induce increased generation of germinal center (GC) B cells, plasma cells (PCs), and virus-neutralizing antibodies (VNAs), as well as provide protection against virulent RABV challenge in immunized mice. This study demonstrated that VLVs containing RABV-G could proliferate in cells and were highly evolvable, revealing the feasibility of developing an economic, safe, and efficacious rabies vaccine. IMPORTANCE VLVs have been shown to represent a more versatile and superior vaccine platform. In previous studies, VLVs containing the Semliki Forest virus replicase (SFV nsP1 to nsP4) and rabies virus glycoprotein (RABV-G) grew to relatively low titers in cells. In our study, we not only succeeded in generating VLVs that proliferate in cells and stably express RABV-G, but the VLVs that evolved grew to higher titers, reaching 10(8) FFU/ml. We also found that nucleic acid changes at positions 470 and 482 in nsP1 were vital for this high-titer phenotype. Moreover, the VLVs that evolved in our studies were highly attenuated in mice, induced potent immunity, and protected mice from lethal RABV infection. Collectively, our study showed that high titers of VLVs containing RABV-G were achieved, demonstrating that these VLVs could be an economical, safe, and efficacious rabies vaccine candidate.

Rabies, caused by rabies virus (RABV), remains a serious threat to public health in most countries worldwide. At present, the administration of rabies vaccines has been the most effective strategy to control rabies. Herein, we evaluate the effect of colloidal manganese salt (Mn jelly [MnJ]) as an adjuvant of rabies vaccine in mice, cats, and dogs. The results showed that MnJ promoted type I interferon (IFN-I) and cytokine production in vitro and the maturation of dendritic cells (DCs) in vitro and in vivo. Besides, MnJ serving as an adjuvant for rabies vaccines could significantly facilitate the generation of T follicular helper (Tfh) cells, germinal center (GC) B cells, plasma cells (PCs), and RABV-specific antibody-secreting cells (ASCs), consequently improve the immunogenicity of rabies vaccines, and provide better protection against virulent RABV challenge. Similarly, MnJ enhanced the humoral immune response in cats and dogs as well. Collectively, our results suggest that MnJ can facilitate the maturation of DCs during rabies vaccination, which can be a promising adjuvant candidate for rabies vaccines. IMPORTANCE Extending the humoral immune response by using adjuvants is an important strategy for vaccine development. In this study, a novel adjuvant, MnJ, supplemented in rabies vaccines was evaluated in mice, cats, and dogs. Our results in the mouse model revealed that MnJ increased the numbers of mature DCs, Tfh cells, GC B cells, PCs, and RABV-specific ASCs, resulting in enhanced immunogenicity and protection rate of rabies vaccines. We further found that MnJ had the same stimulative effect in cats and dogs. Our study provides the first evidence that MnJ serving as a novel adjuvant of rabies vaccines can boost the immune response in both a mouse and pet model.

Because of its portability, the non-cable seismograph has become the future development trend of geophysical instruments. A new wireless data transmission device of 433 M module was proposed; a wireless network was built using the EL1663B_PA module of the SI4463 core, and through the SPI interface to modify the internal parameters. Data transmission used dual antenna mode, the main station as the center of the wireless network coverage up to 550 m or more. The wireless time synchronization system was designed to realize the wireless connection communication between the shallow seismograph and the sensor of each observation point. This program aimed to eliminate the necessary connecting cable and batteries between the conventional shallow seismograph and the detector, greatly reducing the weight of the equipment, and making the shallow seismograph truly low cost, lightweight, flexible and easy to operate and so on.

In recent years, methods based on deep learning have become a hot spot and trend in the field of remote sensing object detection, and a series of encouraging results have been achieved. With the development of science and technology, people's technology and ability to acquire remote sensing data have been comprehensively improved, and high-resolution large-scale remote sensing image data has increased dramatically. However, the current mainstream object detection models cannot directly input large-scale high-resolution images for prediction. This paper proposes a remote sensing object parallel detection algorithm, which uses the mpi4py module to realize multi-CPU+GPU distributed parallel processing. Based on the yolov4 object detection model, it can detect remote sensing images of any scale without reducing the prediction accuracy. And shorten the object detection time according to the number of distributed nodes. The experimental results show that the parallel algorithm has a high speedup ratio, and the parallel detection technology has a good development prospect in the field of remote sensing image object detection.

The laser-matter interaction and bur phenomena associated with lase processing remain unclear, slowing its process development and optimization. Here, through in situ CCD imaging and mathematical model, we revealed the underlying physical mechanism of bur formation during millisecond pulsed laser processing metallic material. The result shows that the laser-induced gas/vapour jet promotes the flow of melt, and the dynamic behavior of up flow melt along the hole wall is responsible for bur formation; another more, the oxidation phenomena of metallic material have positively influence in bur diminution.

Background The central nervous system (CNS) is vulnerable to viral infection, yet few host factors in the CNS are known to defend against invasion by neurotropic viruses. Long noncoding RNAs (lncRNAs) have been revealed to play critical roles in a wide variety of biological processes and are highly abundant in the mammalian brain, but their roles in defending against invasion of pathogens into the CNS remain unclear. Results We report here that multiple neurotropic viruses, including rabies virus, vesicular stomatitis virus, Semliki Forest virus, and herpes simplex virus 1, elicit the neuronal expression of a host-encoded lncRNA EDAL. EDAL inhibits the replication of these neurotropic viruses in neuronal cells and rabies virus infection in mouse brains. EDAL binds to the conserved histone methyltransferase enhancer of zest homolog 2 (EZH2) and specifically causes EZH2 degradation via lysosomes, reducing the cellular H3K27me3 level. The antiviral function of EDAL resides in a 56-nt antiviral substructure through which its 18-nt helix-loop intimately contacts multiple EZH2 sites surrounding T309, a known O-GlcNAcylation site. EDAL positively regulates the transcription of Pcp4l1 encoding a 10-kDa peptide, which inhibits the replication of multiple neurotropic viruses. Conclusions Our findings show that a neuronal lncRNA can exert an effective antiviral function via blocking a specific O-GlcNAcylation that determines EZH2 lysosomal degradation, rather than the traditional interferon-dependent pathway.

Additional file 5. Review history.

Additional file 3. Supplemental Table S2. Sequencing and mapping information of ChIP-seq experiments. Each sample was tested in duplicates. Table S3. The primer sets used in this study. Table S4. The sequence of lncRNA EDAL expressed in this study.

Additional file 4. Complete western blot images of all figures in the manuscript are provided in additional file 4.

Additional file 1: Supplemental Figure S1. Sample correlation analysis. Hierarchical clustering heatmap shows global transcriptional changes after RABV infection. The Pearson correlation coefficients (PCCs) for each sample pair are represented using the colors in the color bar to indicate coefficient magnitude. Figure S2. EDAL transcriptome analysis. (Related to Fig. 1). a Read density of EDAL. The read density is based on normalized RNA-seq signals (TPM) for each sample after RABV infection. The nine tracks show RNA-seq read density at three time points after RABV infection, with three replicates per time point. Density is shown on the y-axis. b The RACE track shows the genomic location of long sequences ends detected by 5′ RACE (blue) and 3′ RACE (orange). The black rectangle indicates the predicted genomic location of EDAL by RNA-seq. The locus of 5′-RACE, 3′-RACE, and RT-qPCR primers were shown in EDAL. c The PhyloCSF score track shows negative protein-coding scores calculated by PhyloCSF. Scores below zero indicate non-coding features. The repeated masker track shows predicted repeat sequences. d The basal level of the target RNAs in RNA-seq (left). Ribosome-RNA complex was isolated from N2a cells, and the RNA copy numbers were quantified by qPCR (right). Malat1 was included as a noncoding RNA control, while Dennd1b and Crebrf were selected as the coding mRNA controls. (n = 3). e Conserved sequences in EDAL. Sequence analyses were performed using the UCSC genome browser. f RNA fluorescent in situ hybridization (FISH) assay were performed in N2a cell. 18S ribosomal RNA (18S) was included as a cytoplasmic control. Figure S3. EDAL is not up-regulated by RABV proteins, dsRNA, or interferons. (Related to Fig. 1). a N2a cells were infected with VSV at different MOIs for 12 h and EDAL level was analyzed by qPCR. b N2a cells were infected with SFV at different MOIs for 18 h and EDAL level was analyzed by qPCR. c N2a cells were infected with HSV-1 at different MOIs for 18 h and EDAL level was analyzed by qPCR. d N2a cells were transfected with plasmids expressing different RABV proteins. EDAL levels were analyzed by qPCR at 24 h post transfection. e N2a cells were transfected with poly(I:C) (a mimic of dsRNA) at indicated doses. EDAL levels were measured by qPCR at 24 h post transfection. f,g N2a cells were treated with IFN-β (f) or IFN-γ (g) for 24 h. EDAL levels were analyzed by qPCR. Statistical analysis of grouped comparisons was carried out by student’s t test (**P

The modeling efficiency, matching, and biocompatibility are key factors affecting the surgical success of a personalized thyroid cartilage prosthesis. We performed three-dimensional reconstruction of a thyroid cartilage prosthesis by combining reverse and forward methods, and then completed the prosthesis design with total or partial resection using a parametric modeling method. Direct manufacturing was performed using selective laser melting (SLM) molding equipment and TC4 material. The structure of the completed implant unit was optimized. The results show good modeling effects for the thyroid cartilage prosthesis with either total or partial resection by the parametric modeling method. Good matching performance was achieved, with overlap suspension between the pillars that meets the requirements of SLM manufacturing. Additionally, the use of SLM molding to produce the thyroid cartilage prosthesis resulted in less powder adhesion on the surface and no obvious nodulation between the porous pillars, allowing the direct use of the prothesis after simple post-treatment. Overall, these results should facilitate the direct application of personalized implants.

This paper presents an antenna of loaded with metamaterial to enhance the gain and directivity of antenna to improve the performance of the ground-penetrating radar system (GPR). By adjusting the parameters of the antenna to change the antenna equivalent capacitance, inductance, and designed the operating frequency of 0.5GHz-1.2GHz ultra-wideband antenna. On the basis of this operating frequency, we also designed the corresponding negative permittivity and permeability materials, and realized the design and simulation of patch antenna and material working in the 1GHz frequency band. The high gain and directivity of the antenna loaded with single negative material are verified by simulation. Compared to the original antenna increased the maximum gain of 7dB, the direction has also been greatly improved.

By filling high refractive thermal liquid (toluene) into the total internal reflection dual-core photonic crystal fiber (DC-PCF), the coupling behaviors of the DC-PCF for different temperature is analyzed by using finite element method, and then a tunable wavelength division multiplexer realized for 980/1550 nm and 1310/1550 nm is obtained at a fixed DC-PCF length of 2475 μm.

To solve the problem of poor fracture identifying effect on electrical logging in oil-based mud, the application of acoustic logging to the quantitative characterisation of fractures is expanded from three aspects, namely, Stoneley waves, longitudinal and transverse waves and cross dipole acoustic waves, and a fracture logging evaluation model closely related to production capacity is established considering the radial extension characteristics of fractures. The Stoneley reflection coefficient is used to determine fractures locations to help detect fractures during normal micro-resistivity imaging logging. Based on the experiment on the relationship between fracture width and acoustic attenuation coefficient, empirical formulae for calculating fracture width have been established by primary wave and shear wave energy information considering the effect of porosity. The new parameters, including spectrum correlation coefficient and energy difference from cross dipole array acoustic logging data, can be used for fractures evaluation. The more developed the fractures are, the greater the energy difference becomes, and the smaller the spectrum correlation coefficient is, the higher the production is. The fracture effective evaluation parameters can be separated into two components, specified as the degree of fracture vertical opening and radial extension. Combining the conventional logging and array acoustic logging (including cross dipole array acoustic logging), a fracture radial extension evaluation model is presented closely related to productivity. Key words: tight sandstone reservoir, fracture evaluation, acoustic logging, oil-based mud, radial extension, Kuqa, Tarim Basin

Rabies, as one of the most threatening zoonoses in the world, causes a fatal central nervous system (CNS) disease. So far, vaccination with rabies vaccines has been the most effective measure to prevent and control this disease. At present, inactivated rabies vaccines are widely used in humans and domestic animals. However, humoral immune responses induced by inactivated rabies vaccines are relatively low and multiple shots are required to achieve protective immunity. Supplementation with an adjuvant is a practical way to improve the immunogenicity of inactivated rabies vaccines. In this study, we found that monophosphoryl-lipid A (MPLA), a well-known TLR4 agonist, could significantly promote the maturation of bone marrow-derived dendritic cells (BMDC) through a TLR4-dependent pathway in vitro and the maturation of conventional DCs (cDCs) in vivo. We also found that MPLA, serving as an adjuvant for inactivated rabies vaccines, could significantly facilitate the generation of T follicular helper (Tfh) cells, germinal center (GC) B cells, and plasma cells (PCs), consequently enhancing the production of RABV-specific total-IgG, IgG2a, IgG2b, and the virus-neutralizing antibodies (VNAs). Furthermore, MPLA could increase the survival ratio of mice challenged with virulent RABV. In conclusion, our results demonstrate that MPLA serving as an adjuvant enhances the intensity of humoral immune responses by activating the cDC&ndash, Tfh&ndash, GC B axis. Our findings will contribute to the improvement of the efficiency of traditional rabies vaccines.

During laser manufacturing, the inevitably generated thermal stress may lead to cracks and defects, thus resulting in work-piece damages. In order to optimize laser manufacturing to inhibit the stress, detailed analysis on the time-varying stress field is necessary. Compared to experimental stress measurement requiring expensive setups and complicated procedures, numerical stress calculation techniques attract much attentions because of their simple and cost-effective requirements as well as multi-parameter analysis capability. However, most of them can only numerically calculate the residual strain in steady state, ignoring the time-varying stress analysis during the laser fabrication. Besides, they did not consider the thermal softening effect with stress release, thus decreasing the accuracy in laser fabrication analysis. In order to realize real time stress analysis inside the work-piece with high accuracy, in this paper, we designed an online monitoring method composing of level set method for free surface monitoring, thermal transfer theory for temperature field calculating and thermo-elasticity theory for stress field retrieving. Proved by the comparisons between the numerical simulations and practical measurements, it is believed that the proposed model can provide quantitative stress with high precision for future stress analyze and laser manufacturing optimization.

Understanding spatter and melt pool dynamics during laser drilling remains a topic of considerable importance to determine the quality of processed materials. Due to metallic materials’ opacity to visible radiation, we studied the spatter dynamics outside of holes during laser drilling using shadow mapping. A 2D transient model for simulating laser material processing was implemented using COMSOL commercial Multiphysics software and the spatter phenomena and melt pool dynamics were assessed. The results can be used as a basis to explain the different processes involved in the material properties during laser processing, which is a powerful tool to understand spatter’ formation mechanism and provide theoretical references for optimizing processing parameters.

Directional wells and cluster wells have become a conventional drilling technique now, which is widely used in various types of oil and gas reservoirs. Each year, more than half of the total drilling are directional wells in China. The main work is not to aim the target area, but to track the reservoirs now. Geosteering drilling is an important technical approach to improve single-well production and recovery ratio, to achieve the “less wells more production” idea. China Geosteering Drilling System (CGDS), integrated the technology of drilling with logging and reservoir engineering, applies the near-bit geological and engineering parameters as well as controlling method to ensure that the wellhole trajectory can pass through reservoir and get best location while drilling. The wellhole trajectory can be adjusted and controlled timely according to the formation features measured by CGDS. The drilling bit is equipped with “eyes”, which can identify oil/gas layer during drilling. Since 2011, we have provided CGDS geosteering services in 29 horizontal wells in Songliao Basin. The total footage reached 18255m, and the longest footage in horizontal section was 1325m in single well, while the average sand penetration rate is above 85%. Comparing with the horizontal wells operated by conventional LWD tools in the same block, the results of the field application shows that the CGDS geosteering system can significantly improve sand penetration rate and substantially reduce the drilling duration. On the basis of introduction to the system, this paper focuses on comparative analysis of significant application effect of CGDS geosteering system for the heterogeneous reservoir in Putaohua Area of Songliao Basin, as well as the lessons learned. Helpful case histories will also be presented.

Adipose triglyceride lipase (ATGL) is a triglyceride hydrolysis lipase and is generally related to lipid metabolism in animals. The ATGL gene was well studied in mammals, however very less was known in birds that differed significantly with mammals for lipid metabolism. In this study, cloning, mRNA real time and association analysis was performed to characterize the ATGL gene in birds. Results showed that the obtained ATGL gene cDNA of parrot, quail, duck were 1,651 bp (NCBI accession number: GQ221784), 1,557 bp (NCBI accession number: GQ221783) and 1,440 bp each, encoded 481-, 482- and 279-amino acid (AA) peptide, respectively. The parrot ATGL (pATGL) gene was found to predominantly express in breast muscle and leg muscle, and very higher ATGL mRNA level was also found in heart, abdominal fat and subcutaneous fat. The quail ATGL (qATGL) gene was also predominantly expressed in breast muscle and leg muscle, and then to a much lesser degree in heart. The duck ATGL (dATGL) gene was found to predominantly express in subcutaneous fat and abdominal fat, quite higher ATGL mRNA was also found in heart, spleen, breast muscle and leg muscle. Blast analyses indicated the high homology of ATGL and its patatin region, and moreover, and the active serine hydrolase motif ("GASAG" for "GXSXG") and the glycine rich motif ("GCGFLG" for "GXGXXG") were completely conservative among 14 species. Association analyses showed that c.950+24CA, c.950+45CG, c.950+73GA, c.950+83CT and c.950+128delA of chicken ATGL gene (cATGL) were all significantly or highly significantly with cingulated fat width (CFW) (P0.05 or P0.01), and c.777-26CA, c.950+45CG, c.950+73GA and c.950+118CT were all significantly or highly significantly with pH value of breast muscle (BMPH) (P0.05).

Background Sugarcane smut can cause losses in cane yield and sugar content that range from 30% to total crop failure. Losses tend to increase with the passage of years. Sporisorium scitamineum is the fungus that causes sugarcane smut. This fungus has the potential to infect all sugarcane species unless a species is resistant to biotrophic fungal pathogens. However, it remains unclear how the fungus breaks through the cell walls of sugarcane and causes the formation of black or gray whip-like structures on the sugarcane plants. Results Here, we report the first high-quality genome sequence of S. scitamineum assembled de novo with a contig N50 of 41 kb, a scaffold N50 of 884 kb and genome size 19.8 Mb, containing an estimated 6,636 genes. This phytopathogen can utilize a wide range of carbon and nitrogen sources. A reduced set of genes encoding plant cell wall hydrolytic enzymes leads to its biotrophic lifestyle, in which damage to the host should be minimized. As a bipolar mating fungus, a and b loci are linked and the mating-type locus segregates as a single locus. The S. scitamineum genome has only 6 G protein-coupled receptors (GPCRs) grouped into five classes, which are responsible for transducing extracellular signals into intracellular responses, however, the genome is without any PTH11-like GPCR. There are 192 virulence associated genes in the genome of S. scitamineum, among which 31 expressed in all the stages, which mainly encode for energy metabolism and redox of short-chain compound related enzymes. Sixty-eight candidates for secreted effector proteins (CSEPs) were found in the genome of S. scitamineum, and 32 of them expressed in the different stages of sugarcane infection, which are probably involved in infection and/or triggering defense responses. There are two non-ribosomal peptide synthetase (NRPS) gene clusters that are involved in the generation of ferrichrome and ferrichrome A, while the terpenes gene cluster is composed of three unknown function genes and seven biosynthesis related genes. Conclusions As a destructive pathogen to sugar industry, the S. scitamineum genome will facilitate future research on the genomic basis and the pathogenic mechanisms of sugarcane smut. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-996) contains supplementary material, which is available to authorized users.