Isolation and analysis of a very virulent Marek’s disease virus strain in China

BACKGROUND: A severe MD was broken out at a farm in Shandong, China, despite FC126 vaccination of the chickens at 1-day-old. The mortality of the flocks reached up to 38.3%. The infected chickens were found to have MD pathological changes, including enlargement of spleens, livers and kidneys, and tumors occured on organs later. Samples were collected from the chickens for diagnosis. METHODS: The collected samples were inoculated into primary duck embryo fibroblast (DEF) cells, and the MDV strain named SD2012-1 was isolated. In order to identify the isolate, amplification by PCR and sequencing of oncogenic Meq and vIL-8 gene were processed, the obtained sequences were compared with the sequences of reference strains, and SD2012-1 was used to challenge immunized SPF chickens. RESULTS: A very virulent MDV isolate strain, SD2012-1, was isolated from a chicken flock in Shandong Province, China, the isolate had the characteristics of very virulent MDV-1, nucleotide and deduced amino acid sequence comparisons of Meq and vIL-8 gene of SD2012-1 with those of reference strains showed SD2012-1 had high homology with MDV strains isolated from China, SD2012-1 could break through the protection provided by HVT vaccine and HVT + SB-1 vaccine immunization and caused the mortality of SPF chickens over 60%. The immune failure occured at the farm could be due to the improper selection of vaccines. SD2012-1 produced death later and the gross postmortem lesions of chickens died early and later were different. CONCLUSIONS: MDV strain SD2012-1 isolated from Shandong Province, China was found to have the characteristics of very virulent MDV-1, which could break through the protection provided by HVT vaccine and HVT + SB-1 vaccine, the virus seemed to have a long latent period, and cause different gross postmortem lesions of chickens between chickens died early and later. A better immunization way should be chosen to prevent infection of this MDV strain in field

Broadband and continuous wave pumped second-harmonic generation from microfiber coated with layered GaSe crystal

The conversion-efficiency for second-harmonic (SH) in optical fibers is significantly limited by extremely weak second-order nonlinearity of fused silica, and pulse pump lasers with high peak power are widely employed. Here, we propose a simple strategy to efficiently realize the broadband and continuous wave (CW) pumped SH, by transferring a crystalline GaSe coating onto a microfiber with phase-matching diameter. In the experiment, high efficiency up to 0.08 %W-1mm-1 is reached for a C-band pump laser. The high enough efficiency not only guarantees SH at a single frequency pumped by a CW laser, but also multi-frequencies mixing supported by three CW light sources. Moreover, broadband SH spectrum is also achieved under the pump of a superluminescent light-emitting diode source with a 79.3 nm bandwidth. The proposed scheme provides a beneficial method to the enhancement of various nonlinear parameter processes, development of quasi-monochromatic or broadband CW light sources at new wavelength regions

DeepSF: deep convolutional neural network for mapping protein sequences to folds

Motivation Protein fold recognition is an important problem in structural bioinformatics. Almost all traditional fold recognition methods use sequence (homology) comparison to indirectly predict the fold of a tar get protein based on the fold of a template protein with known structure, which cannot explain the relationship between sequence and fold. Only a few methods had been developed to classify protein sequences into a small number of folds due to methodological limitations, which are not generally useful in practice. Results We develop a deep 1D-convolution neural network (DeepSF) to directly classify any protein se quence into one of 1195 known folds, which is useful for both fold recognition and the study of se quence-structure relationship. Different from traditional sequence alignment (comparison) based methods, our method automatically extracts fold-related features from a protein sequence of any length and map it to the fold space. We train and test our method on the datasets curated from SCOP1.75, yielding a classification accuracy of 80.4%. On the independent testing dataset curated from SCOP2.06, the classification accuracy is 77.0%. We compare our method with a top profile profile alignment method - HHSearch on hard template-based and template-free modeling targets of CASP9-12 in terms of fold recognition accuracy. The accuracy of our method is 14.5%-29.1% higher than HHSearch on template-free modeling targets and 4.5%-16.7% higher on hard template-based modeling targets for top 1, 5, and 10 predicted folds. The hidden features extracted from sequence by our method is robust against sequence mutation, insertion, deletion and truncation, and can be used for other protein pattern recognition problems such as protein clustering, comparison and ranking.Comment: 28 pages, 13 figure

Genome divergence and dynamics in the thin-tailed desert sheep from Sudan

With climate change bound to affect food and feed production, emphasis will shift to resilient and adapted indigenous livestock to sustain animal production. However, indigenous livestock comprise several varieties, strains and ecotypes whose genomes are poorly characterized. Here, we investigated genomic variation in an African thin-tailed Desert Sheep sampled in Sudan, using 600K genotype data generated from 92 individuals representing five ecotypes. We included data from 18 fat-tailed and 45 thin-tailed sheep from China, to investigate shared ancestry and perform comparative genomic analysis. We observed a clear genomic differentiation between the African thin-tailed Desert Sheep and the Chinese thin-tailed and fat-tailed sheep, suggesting a broad genetic structure between the fat-tailed and thin-tailed sheep in general, and that at least two autosomal gene pools comprise the genome profile of the thin-tailed sheep. Further analysis detected two distinct genetic clusters in both the African thin-tailed Desert Sheep and the Chinese thin-tailed sheep, suggesting a fine-scale and complex genome architecture in thin-tailed sheep. Selection signature analysis suggested differences in adaptation, production, reproduction and morphology likely underly the fine-scale genetic structure in the African thin-tailed Desert Sheep. This may need to be considered in designing breeding programs and genome-wide association studies

The Importance of Learning Islamic History and Civilization of Malaysia in the Building of Human Capital and Identity of the Muslim Society in Malaysia

AbstractThe purpose of this research is to study the importance of learning Islamic History and Civilization in Malaysia for human capital building and identification of the muslim society in Malaysia. Its aim is to clarify the importance of this course, specifically at the Department of Arabic Studies and Islamic Civilization, and the need to produce graduates who are conversant in this field in order that they may utilise it in their lives regardless of whichever field they venture into. This study uses the library research method by analysis and evaluation with an argumentative as well as narrative approach. The results of study finds that knowledge and conversance in this field is integral in the formation of human capital and identity of the muslim society in Malaysia. Knowledge and conversance in this field would enable Malays to know the ‘true’ history of the muslim ummah in Malaysia. This knowledge is crucial to help them form and build a Malay-muslim generation in Malaysia, strongly attached to Malay traditions which have once brought the muslims to the pinnacle of success

Multi-scale integrative analyses identify THBS2+ cancer-associated fibroblasts as a key orchestrator promoting aggressiveness in early-stage lung adenocarcinoma.

Rationale: Subsets of patients with early-stage lung adenocarcinoma (LUAD) have a poor post-surgical course after curative surgery. However, biomarkers stratifying this high-risk subset and molecular underpinnings underlying the aggressive phenotype remain unclear. Methods: We integrated bulk and single-cell transcriptomics, proteomics, secretome and spatial profiling of clinical early-stage LUAD samples to identify molecular underpinnings that promote the aggressive phenotype. Results: We identified and validated THBS2, at multi-omic levels, as a tumor size-independent biomarker that robustly predicted post-surgical survival in multiple independent clinical cohorts of early-stage LUAD. Furthermore, scRNA-seq data revealed that THBS2 is exclusively derived from a specific cancer-associated fibroblast (CAF) subset that is distinct from CAFs defined by classical markers. Interestingly, our data demonstrated that THBS2 was preferentially secreted via exosomes in early-stage LUAD tumors with high aggressiveness, and its levels in the peripheral plasma associated with short recurrence-free survival. Further characterization showed that THBS2-high early-stage LUAD was characterized by suppressed antitumor immunity. Specifically, beyond tumor cells, THBS2+ CAFs mainly interact with B and CD8+ T lymphocytes as well as macrophages within tumor microenvironment of early-stage LUAD, and THBS2-high LUAD was associated with decreased immune cell infiltrates but increased immune exhaustion marker. Clinically, high THBS2 expression predicted poor response to immunotherapies and short post-treatment survival of patients. Finally, THBS2 recombinant protein suppressed ex vivo T cells proliferation and promoted in vivo LUAD tumor growth and distant micro-metastasis. Conclusions: Our multi-level analyses uncovered tumor-specific THBS2+ CAFs as a key orchestrator promoting aggressiveness in early-stage LUAD

Managing nitrogen for sustainable crop production with reduced hydrological nitrogen losses under a winter wheat–summer maize rotation system: an eight-season field study

Excessive nitrogen (N) application in wheat–maize cropping systems was adjusted towards more sustainable practices to reduce hydrological N losses while maintaining crop yield. In comprehensive quantification of N management effects on crop yield, N use efficiency (NUE), hydrological N losses, and soil nitrate residual across eight seasons, we have added to growing evidence of strategies beneficial for sustainable crop production with lower hydrological N losses. The results show that adjusted N practices enhanced crop yield and NUE, as compared to farmer’s practices, but benefits varied with N rates and types. Optimized N treatment (OPT, 180 kg N ha-1 in both maize and wheat seasons) with or without straw returning produced the most crop yield. They increased maize yield by 5.5% and 7.3% and wheat yield by 6.2% and 3.2% on average, as compared to farmer’s practice with huge N application (FP, 345 kg N ha−1 and 240 kg N ha−1 in maize and wheat). Regulation of N release through amendment with controlled release urea at a rate of 144 kg N ha−1 crop−1 (CRU treatment) obtained 4.4% greater maize yield than FP, and sustained a similar wheat yield with less N input, resulting in the highest crop NUE. Additionally, CRU was most effective in mitigating hydrological N loss, with 39.5% and 45.5% less leachate N and 31.9% and 35.9% less runoff N loss than FP in maize and wheat seasons. Synthetic N input correlated significantly and positively with runoff and leachate N losses, indicating it was one of the dominant factors driving hydrological N losses. Moreover, compared to OPT, additional straw returning (STR) or substituting 20% of the nutrients by duck manure (DMS) further reduced runoff N discharges due to the fact that organic matter incorporation increased resilience to rainfall. N over-application in FP caused considerable nitrate accumulation in the 0–90-cm soil profile, while the adjusted N practices, i.e., OPT, STR, CRU, and DMS treatments effectively controlled it to a range of 79.6–92.9 kg N ha−1. This study suggests that efforts using optimized N treatment integrated with CRU or straw returning should be encouraged for sustainable crop production in this region

High-temperature modification of steel slag using composite modifier containing silicon calcium slag, fly ash, and reservoir sediment

Steel slag (SS) is a kind of industrial solid waste, and its accumulation brings certain harm to the ecological environment. In order to promote the building material utilization of SS, high-temperature modification (HTM) of SS is performed using a composite modifier (CMSFR) containing silicon calcium slag (SCS), fly ash (FA), and reservoir sediment (RS). Then, the authors investigated the effect of CMSFR on the cementitious properties and volume soundness of SS mixture after HTM (SMHTM). After that, the mineral composition and microstructure of SMHTM were investigated through X-ray fluorescence analysis (XRF), X-ray diffraction (XRD), scanning electronic microscopy (SEM), energy dispersive spectrometry (EDS), and particle size analysis. It was found that the free CaO (f-CaO) content obviously decreased, and the cementitious properties improved in SMHTM. When the CMSFR content was 20% (SCS: FA: RS = 9:7:4), and the modification temperature (MT) was 1,250°C, the mass fraction of f-CaO in SMHTM dropped from 4.81% to 1.90%, down by 60.5%; the 28-day activity index of SMHTM increased to 85.4%, 14.3% higher than that of raw SS, which meets the technical requirement of Steel slag powder used for cement and concrete (GB/T 20491-2017): the activity index of grade I SS powder must be greater than or equal to 80%. As the mass fraction of CMSFR grew from 10% to 30%, new mineral phases formed in SMHTM, including diopside (CMS2), ceylonite (MgFe2O4), gehlenite (C2AS), tricalcium aluminate (C3A), and magnetite (Fe3O4). The HTM with CMSFR promotes the decomposition of RO phase (a continuous solid solution composed of divalent metal oxides like FeO, MgO, MnO, and CaO) in raw SS, turning the FeO in that phase into Fe3O4. The above results indicate that the SMHTM mixed with CMSFR can be applied harmless in cement and concrete, making low-energy fine grinding of SS a possibility