An integrated genetic linkage map for silkworms with three parental combinations and its application to the mapping of single genes and QTL

<p>Abstract</p> <p>Background</p> <p><it>Bombyx mori</it>, the domesticated silkworm, is a well-studied model insect with great economic and scientific significance. Although more than 400 mutations have been described in silkworms, most have not been identified, especially those affecting economically-important traits. Simple sequence repeats (SSRs) are effective and economical tools for mapping traits and genetic improvement. The current SSR linkage map is of low density and contains few polymorphisms. The purpose of this work was to develop a dense and informative linkage map that would assist in the preliminary mapping and dissection of quantitative trait loci (QTL) in a variety of silkworm strains.</p> <p>Results</p> <p>Through an analysis of > 50,000 genotypes across new mapping populations, we constructed two new linkage maps covering 27 assigned chromosomes and merged the data with previously reported data sets. The integrated consensus map contains 692 unique SSR sites, improving the density from 6.3 cM in the previous map to 4.8 cM. We also developed 497 confirmed neighboring markers for corresponding low-polymorphism sites, with 244 having polymorphisms. Large-scale statistics on the SSR type were suggestive of highly efficient markers, based upon which we searched 16,462 available genomic scaffolds for SSR loci. With the newly constructed map, we mapped single-gene traits, the QTL of filaments, and a number of ribosomal protein genes.</p> <p>Conclusion</p> <p>The integrated map produced in this study is a highly efficient genetic tool for the high-throughput mapping of single genes and QTL. Compared to previous maps, the current map offers a greater number of markers and polymorphisms; thus, it may be used as a resource for marker-assisted breeding.</p

A 13-Gene Metabolic Prognostic Signature Is Associated With Clinical and Immune Features in Stomach Adenocarcinoma

Patients with advanced stomach adenocarcinoma (STAD) commonly show high mortality and poor prognosis. Increasing evidence has suggested that basic metabolic changes may promote the growth and aggressiveness of STAD; therefore, identification of metabolic prognostic signatures in STAD would be meaningful. An integrative analysis was performed with 407 samples from The Cancer Genome Atlas (TCGA) and 433 samples from Gene Expression Omnibus (GEO) to develop a metabolic prognostic signature associated with clinical and immune features in STAD using Cox regression analysis and least absolute shrinkage and selection operator (LASSO). The different proportions of immune cells and differentially expressed immune-related genes (DEIRGs) between high- and low-risk score groups based on the metabolic prognostic signature were evaluated to describe the association of cancer metabolism and immune response in STAD. A total of 883 metabolism-related genes in both TCGA and GEO databases were analyzed to obtain 184 differentially expressed metabolism-related genes (DEMRGs) between tumor and normal tissues. A 13-gene metabolic signature (GSTA2, POLD3, GLA, GGT5, DCK, CKMT2, ASAH1, OPLAH, ME1, ACYP1, NNMT, POLR1A, and RDH12) was constructed for prognostic prediction of STAD. Sixteen survival-related DEMRGs were significantly related to the overall survival of STAD and the immune landscape in the tumor microenvironment. Univariate and multiple Cox regression analyses and the nomogram proved that a metabolism-based prognostic risk score (MPRS) could be an independent risk factor. More importantly, the results were mutually verified using TCGA and GEO data. This study provided a metabolism-related gene signature for prognostic prediction of STAD and explored the association between metabolism and the immune microenvironment for future research, thereby furthering the understanding of the crosstalk between different molecular mechanisms in human STAD. Some prognosis-related metabolic pathways have been revealed, and the survival of STAD patients could be predicted by a risk model based on these pathways, which could serve as prognostic markers in clinical practice

Contrasting responses of soil microbial biomass and extracellular enzyme activity along an elevation gradient on the eastern Qinghai-Tibetan Plateau

Soil microbial community composition and extracellular enzyme activity are two main drivers of biogeochemical cycling. Knowledge about their elevational patterns is of great importance for predicting ecosystem functioning in response to climate change. Nevertheless, there is no consensus on how soil microbial community composition and extracellular enzyme activity vary with elevation, and little is known about their elevational variations on the eastern Qinghai-Tibetan Plateau, a region sensitive to global change. We therefore investigated the soil microbial community composition using phospholipid fatty acids (PLFAs) analysis, and enzyme activities at 2,820 m (coniferous and broadleaved mixed forest), 3,160 m (dark coniferous forest), 3,420 m (alpine dwarf forest), and 4,280 m (alpine shrubland) above sea level. Our results showed that soil microbial community composition and extracellular enzyme activities changed significantly along the elevational gradient. Biomass of total microbes, bacteria, and arbuscular mycorrhizal fungi at the highest elevation were the significantly lowest among the four elevations. In contrast, extracellular enzyme activities involved in carbon (C)-, nitrogen (N)-, and phosphorus (P)- acquiring exhibited the maximum values at the highest elevation. Total nutrients and available nutrients, especially P availability jointly explained the elevational pattern of soil microbial community, while the elevational variation of extracellular enzyme activities was dependent on total nutrients. Microbial metabolism was mainly C- and P-limited with an increasing C limitation but a decreasing P limitation along the elevational gradient, which was related significantly to mean annual temperature and total P. These results indicated a vital role of soil P in driving the elevational patterns of soil microbial community and metabolism. Overall, the study highlighted the contrasting responses of soil microbial biomass and extracellular enzyme activities to elevation, possibly suggesting the differences in adaption strategy between population growth and resource acquisition responding to elevation. The results provide essential information for understanding and predicting the response of belowground community and function to climate change on the eastern Qinghai-Tibetan Plateau

Emerging animal viruses in China, from discovery to control measures

Frequent outbreaks of emerging animal viruses cause great economic losses and pose potential risks for human health. In this thesis, emerging animal viruses that affect the veterinary industry and have a significant economic burden in China and beyond was focused, including Peste des Petits ruminants virus (PPRV), Rabbit hemorrhagic disease virus (RHDV2), and Getah virus (GETV). By studying different aspects of virus infection in relation to innate immunity and a focus on virus-like particle (VLP) vaccine development, important knowledge for future control of emerging animal viruses will be generated. This thesis aimed to understand how to control emerging animal viruses, thereby focusing on several aspects of virus-induced innate immunity in PPRV infection in goats, including the function of caprine MAVS and the ISG, BST2/tetherin, and how PPRV counteracted these factors. In addition, promising vaccine candidates were developed against RHDV1 and RHDV2 in rabbits, and against GETV. Over all, the research presented in this thesis contributed to the understanding of virus-host interactions and provided candidates for veterinary vaccine development

The complete chloroplast genome of Scutellaria scordifolia (Labiatae)

Scutellaria scordifolia Fisch. ex Schrank Li is a traditional Chinese medicinal plant of genus Scutellaria from the Labiatae family. The complete chloroplast genome of was 152,336 bp in length, which contained 133 complete genes including 87 protein-coding genes (87 PCGs), 8 ribosomal RNA genes (8 rRNAs), and 37 transfer RNA genes (37 tRNAs). The GC content of chloroplast DNA was 38.3%. The corresponding values of the LSC, SSC, and IR regions were 36.3%, 32.5%, and 43.6%, respectively. Phylogenetic tree showed that the species from genus Scutellaria were divided into two monophyletic clades, and the divergence time of S. scordifolia was earlier than that of the other species

A novel predictor for the use of concurrent chemotherapy in early-stage cervical cancer with intermediate-risk factors

Objective: For early-stage cervical cancer patients experiencing radical surgery, postoperative radiotherapy was recommended for patients with a combination of intermediate-risk factors. However, there was no consensus on whether to administer concurrent chemotherapy. The aim of the study was to confirm the clinical value of the controlling nutritional status (CONUT) score in guiding the use of concurrent chemotherapy during postoperative radiotherapy. Methods: A total of 969 patients with FIGO stage IB-IIA cervical cancer were retrospectively analyzed. Kaplan-Meier survival analysis was performed to compare disease-free survival (DFS) and cancer-specific survival (CSS) rates between different group. A Cox proportional hazards regression test was used to conduct multivariate analyses. Results: For the patients in the high CONUT group (≥3), the addition of concurrent chemotherapy had better 5-year DFS (91.2 % vs. 72.8 %, P = 0.005) and CSS (93.8 % vs. 77.4 %, P = 0.013) than those without it. Meanwhile, the patients with concurrent chemotherapy had less rate of locoregional recurrence (8.5 % vs 16.7 %, P = 0.034) and distant metastases (11.7 % vs 30.4 %, P = 0.015). The multivariate analysis showed that concurrent chemotherapy was detected to be a factor significantly associated with DFS (P = 0.011), local control (P = 0.041), distant metastasis (P = 0.005) and CSS (P = 0.023). For the patients in low CONUT group (<3), there was no difference in prognosis between patients. Conclusion: Pretreatment CONUT score may be a predictive factor for the use of concurrent chemotherapy in early-stage cervical cancer with intermediate-risk factors during postoperative radiotherapy, and it can be helpful to determine the adjuvant treatment scheme

Characterization of the complete chloroplast genome of Salix maizhokunggarensis (Salicaceae)

The complete chloroplast genome sequence of Salix maizhokunggarensis, a native shrub willow species in the south of China, has been characterized using Illumina pair-end sequencing. The plastome is 155,093 bp in length, with one large single copy region of 83,956 bp, one small single copy region of 16,221 bp, and two inverted repeat (IR) regions of 27,458 bp. It contains 116 genes, including 79 protein-coding genes, 8 ribosomal RNA, and 36 transfer RNA. Phylogenetic tree shows that this species is a sister species to S. suchowensis. The plastome of Salix can provide significant insight for elucidating the phylogenetic relationship of taxa within Salicaceae

Viral Genome-Linked Protein (VPg) Is Essential for Translation Initiation of Rabbit Hemorrhagic Disease Virus (RHDV).

Rabbit hemorrhagic disease virus (RHDV), the causative agent of rabbit hemorrhagic disease, is an important member of the caliciviridae family. Currently, no suitable tissue culture system is available for proliferating RHDV, limiting the study of the pathogenesis of RHDV. In addition, the mechanisms underlying RHDV translation and replication are largely unknown compared with other caliciviridae viruses. The RHDV replicon recently constructed in our laboratory provides an appropriate model to study the pathogenesis of RHDV without in vitro RHDV propagation and culture. Using this RHDV replicon, we demonstrated that the viral genome-linked protein (VPg) is essential for RHDV translation in RK-13 cells for the first time. In addition, we showed that VPg interacts with eukaryotic initiation factor 4E (eIF4E) in vivo and in vitro and that eIF4E silencing inhibits RHDV translation, suggesting the interaction between VPg and eIF4E is involved in RHDV translation. Our results support the hypothesis that VPg serves as a novel cap substitute during the initiation of RHDV translation

Corrigendum to “Nucleolin interacts with the rabbit hemorrhagic disease virus replicase RdRp, nonstructural proteins p16 and p23, playing a role in virus replication”<[Virologica Sinica 37 (2022) 48–59]>, (S1995820X22000049), (10.1016/j.virs.2022.01.004)

Due to our negligence, the original version of this article, published online on 12 January 2022, contained a mistake in Fig. 4A. The lane of β-actin in Western blotting was misused. The correct Fig. 4 is given below. We apologize for our oversight when preparing the figure and state that this does not change the scientific conclusions of the article in any way.[Formula presented] Fig. 4. Identification of interactions between RHDV nonstructural proteins and host factors of RCs. A NCL siRNA inhibited the formation of the RHDV RC. After HA tag affinity purification, the eluted proteins were resolved by SDS-PAGE. The protein bands were visualized with silver staining. PBS acted as a negative control; β-actin acted as an internal control and was detected by IB with mAb against β-actin. B Identification of these interactions by M2H assays. Bait and prey plasmids were co-transfected with pG5luc plasmids into subconfluent HEK-293T cells at a molar ratio of 1:1:1 for the pACT:pBIND:pG5luc vector. At 48 h post-transfection (hpt), the HEK-293T cells were lysed, and Rluc and Fluc activities were evaluated using the Promega Dual-Luciferase Reporter Assay System. All experimental groups were compared with the negative control group (ACT-Bind). Statistical analysis was performed by Student t-tests. ∗P < 0.05 and ∗∗P < 0.01. Data are shown as mean with SD. Replicate 1, 2, 3 means three independent experiments, and each experiment contains three technical replicate values. The number of cells used in all replicate experiments was similar. C These interactions were verified using Co-IP assays. RK-13 cells were co-transfected with bait and prey plasmids. Cell lysates were prepared 48 hpt and the proteins were subjected to IP followed by IB analysis. Myc fusion proteins acted as bait proteins and Flag fusion proteins acted as prey proteins. RHDV, rabbit hemorrhagic disease virus; RC, replication complex; IP, immunoprecipitation; IB, immunoblotting; mAb, monoclonal antibody; SD, standard deviation

Nucleolin mediates the internalization of rabbit hemorrhagic disease virus through clathrin-dependent endocytosis

Rabbit hemorrhagic disease virus (RHDV) is an important member of the Caliciviridae family and a highly lethal pathogen in rabbits. Although the cell receptor of RHDV has been identified, the mechanism underlying RHDV internalization remains unknown. In this study, the entry and post-internalization of RHDV into host cells were investigated using several biochemical inhibitors and RNA interference. Our data demonstrate that rabbit nucleolin (NCL) plays a key role in RHDV internalization. Further study revealed that NCL specifically interacts with the RHDV capsid protein (VP60) through its N-terminal residues (aa 285-318), and the exact position of the VP60 protein for the interaction with NCL is located in a highly conserved region (472Asp-Val-Asn474; DVN motif). Following competitive blocking of the interaction between NCL and VP60 with an artificial DVN peptide (RRTGDVNAAAGSTNGTQ), the internalization efficiency of the virus was markedly reduced. Moreover, NCL also interacts with the C-terminal residues of clathrin light chain A, which is an important component in clathrin-dependent endocytosis. In addition, the results of animal experiments also demonstrated that artificial DVN peptides protected most rabbits from RHDV infection. These findings demonstrate that NCL is involved in RHDV internalization through clathrin-dependent endocytosis.</p