To study how chlorogenic acid affects changes of reactive oxygen species (ROS) and the proteins involved in ROS scavenging of nectarine during storage time, the fruits were treated with chlorogenic acid (CHA) then stored at 25°C for further studies. The CHA-treatment significantly reduced O2-· production rate, H2O2 content, and membrane permeability of nectarine fruit during storage. The key proteins related the nectarine fruit senescence during storage were identified by two-dimensional electrophoresis and MALDI-TOF/TOF. Level and enzymatic activity of peroxidase were reduced, while both the protein levels and the enzymatic activities of superoxide dismutase, glutathione reductase, glutathione-s-transferase and monodehydroascorbate reductase were enhanced in nectarine fruit treated with CHA. In addition, levels of several pathogen-related proteins were also enhanced by CHA-treatment. Taking together, the present study showed that CHA could influence changes in defense related proteins and reduced oxidative damage in nectarine fruit during postharvest ripening.

Mixed lineage kinase-4 (MLK-4) is an important member of the mixed-lineage family of kinases that regulates the extracellular signal-regulated kinases and c-Jun N-terminal kinase (JNK) signaling pathways. The functions and mechanisms of MLK-4 in cancer initiation and progression have not been well understood. The present study investigated the expression, function and regulatory mechanism of MLK-4 in gastric carcinoma cells. Biochemical data indicated that normal MLK-4 was downregulated, which exerted dominant negative effects on gastric carcinoma cell viability, migration and invasion. The experimental data demonstrated that MLK-4 supplement abrogated activity of these mutants and induced inhibitory effects on gastric carcinoma cell viabilty, migration and invasion in vitro and in vivo. In addition, to determine the regulatory mechanism of MLK-4, its signaling pathway was assessed in gastric carcinoma cancer cells by regulating MLK-4. The present observations indicated that restoring MLK-4 activity by supplemental MLK-4 reduced gastric carcinoma cell colony formation in vitro and suppressed tumor viability, migration and invasion in vivo. The results of the present study indicated that MLK-4 may be a potential protein for targeting gastric carcinoma by suppressing kinases, which may lead to reduction of JNK signaling and enhance therapeutic efficacy in gastric carcinoma.

The extracellular vesicles (EVs) of uterine flushing fluids (UFs) mediate intrauterine communication between conceptus and uterus in pigs. The small RNAs of UFs-EVs are widely recognized as important factors that influence embryonic implantation. However, small RNAs expression profiles of porcine UFs-EVs during peri-implantation are still unknown. In this study, cup-shaped EVs of porcine UFs on days 10 (D10), 13 (D13) and 18 (D18) of pregnancy were isolated and characterized. The expression of small RNAs in these EVs was comprehensively profiled through sequencing. A total of 152 known microRNAs (miRNAs), 43 novel miRNAs, 6248 known Piwi-interacting RNAs (piRNAs) and 110 novel piRNAs were identified. Among these small RNAs, RT-qRCR results indicated that ssc-let-7f-5p, ssc-let-7i-5p and ssc-let-7g were differentially expressed during the three stages. Bioinformatics analysis showed that the miRNAs differentially expressed in the three comparisons (D10 vs D13, D13 vs D18 and D10 vs D18) were involved in important processes and pathways related to immunization, endometrial receptivity and embryo development, which play important roles in embryonic implantation. Our results reveal that EVs from porcine UFs contain various small RNAs with potentially vital effects on implantation. This research also provides resources for studies of miRNAs and piRNAs in the cross-talk between embryo and endometrium.

Protein lysine acetylation is a reversible posttranslational modification and plays a pivotal role in a broad array of physiological functions. In our study, a strategy combining immunoaffinity enrichment of acetylated peptides based on anti-acetyllysine antibody with high-resolution tandem mass spectrometry was employed for a systemic survey of acetylation sites in a polyphagous pest insect Thrips tabaci. In total, 597 acetylated proteins containing 995 lysine acetylation sites were identified in T. tabaci. Interestingly, functional enrichment analysis showed that acetylated proteins are implicated in the regulation of diverse KEGG pathways, including carbohydrate metabolism, energy metabolism, amino acid metabolism, and translational process. In particular, a large fraction of metabolic enzymes, including multiple rate-limiting enzymes, was also found to be acetylated. Comparative analysis indicated that a proportion of euNOG entries was shared by three insects. Furthermore, motif analysis showed that the sequence flanking acetylation sites exhibited subcellular compartment-specific patterns. Protein-protein interaction network analysis demonstrated that acetylated proteins formed several densely connected sub-networks tightly associated with ribosome, fatty acid metabolism, oxidative phosphorylation and purine metabolism, thus strengthening the functional enrichment result. Overall, our study provides a comprehensive view of acetylation sites, facilitating an in-depth investigation of functional roles of acetylation in the future. SIGNIFICANCE: Onion thrips is a polyphagous agricultural pest insect. Insecticide resistance has been frequently reported due to the intensive use of chemical pesticides. Lysine acetylation is a ubiquitous posttranslational modification and plays important roles in gene regulation. An in-depth understanding of transcriptional regulation is crucial for designing novel and highly efficient pesticides. With high-resolution mass spectrometry based proteomics method, we systematically explored the acetylome in this insect. In total, 595 proteins containing 995 acetylation sites were identified in this study. Bioinformatic analysis revealed that acetylated proteins are implicated in regulating diverse biological processes, including carbohydrate metabolism, energy metabolism, amino acid metabolism, and translational process. Furthermore, protein-protein interaction network analysis showed that ribosome, fatty acid metabolism, oxidative metabolism and purine metabolism are significantly enriched for acetylated proteins. Our results provide insights into the targets of acetylation in onion thrips and facilitate elucidation of transcriptional regulation and design of novel control strategies against this insect.

Over the past decade, second-generation sequencing (SGS) has been widely used to elucidate the transcriptome across many organisms. However, the full-length (FL) transcripts and alternative splice (AS) isoforms could not be confidently and accurately defined with SGS. Pacific biosciences (PacBio) single-molecule real-time sequencing was conducted to obtain FL transcriptome data in the codling moth. In total, 25,940 high-quality FL isoforms were obtained and clustered to 14,099 nonredundant clusters. Interestingly, nearly 90% of nonredundant PacBio transcripts were novel compared to reference genes. Among them, 3389 transcripts potentially represented novel genes. Additionally, a large number of AS events were discovered, and most of the splice junctions in the PacBio isoforms could be supported by short reads in public datasets. Furthermore, 952 FL lncRNAs and 81 fusion transcripts were identified and validated using RT-PCR analysis. Overall, an atlas of FL transcripts was obtained in the codling moth, which will help provide further insights into the complexity of the transcriptome and facilitate improving genome annotations and functional studies in this insect.

Longan (Dimocarpus longan) is a subtropical fruit best known for its nutritious fruit and regarded as a precious tonic and traditional medicine since ancient times. High-quality chromosome-scale genome assembly is valuable for functional genomic study and genetic improvement of longan. Here, we report a chromosome-level reference genome sequence for longan cultivar JDB with an assembled genome of 455.5 Mb in size anchored to fifteen chromosomes, representing a significant improvement of contiguity (contig N50 = 12.1 Mb, scaffold N50 = 29.5 Mb) over a previous draft assembly. A total of 40 420 protein-coding genes were predicted in D. longan genome. Synteny analysis suggests longan shares the widespread gamma event with core eudicots, but has no other whole genome duplications. Comparative genomics showed that D. longan genome experienced significant expansions of gene families related to phenylpropanoid biosynthesis and UDP-glucosyltransferase. Deep genome sequencing analysis of longan cultivars identified longan biogeography as a major contributing factor for genetic diversity, and revealed a clear population admixture and introgression among cultivars of different geographic origins, postulating a likely migration trajectory of longan overall confirmed by existing historical records. Finally, genome-wide association studies (GWAS) of longan cultivars identified quantitative trait loci (QTL) for six different fruit quality traits and revealed a shared QTL containing three genes for total soluble solid and seed weight. The chromosome-level reference genome assembly, annotation and population genetic resource for D. longan will facilitate the molecular studies and breeding of desirable longan cultivars in the future.

Seashore mallow (Kosteletzkya virginica), as a noninvasive perennial halophytic oilseed-producing dicot, is native from the Gulf to the Atlantic coasts of the U.S. The purpose of our research was to investigate 1-aminocyclopropane-1carboxylic acid deaminase (ACCD) producing endophytic fungi from K.virginica. A total of 59 endophytic fungal strains, isolated from roots in K.virginica of seedlings, were grouped into 12 genera including in Penicillium, Aspergillus, Fusarium, Trichoderma, Rhizopycnis sp., Ceriporia Donk, Trametes sp., Schizophyllum commune sp., Alternaria, Cladosporium, Cylindrocarpon, and Scytalidium according to sequences of ITS. The ACD activity of 10 endophytic fungi isolated was detected. T.asperellum had the highest ACC deaminase activity among all 10 isolated genera of fungal strains, followed by T. viride. Dry weight and fresh weight of plant, plant height, root length, SOD activity, and chlorophyll content of wheat and soybean inoculated with T.asperellum or T. viride was increased compared with non-inoculated control plants under non salt or salt stress. Further analysis showed that T.asperellum or T.viride strains induced downregulation of the expression of ethylene synthesis-related genes such as ACC oxidase (ACO) and ACC synthase (ACS), thereby reducing ethylene synthesis and damage to plants under salt stress. These endophytic fungi can be used as alternative bioinoculants to increase crop yield in saline soil.

The beet armyworm Spodoptera exigua is a polyphagous caterpillar that causes serious damage to many species of crops and vegetables. To gain insight into how this polyphagous insect differs from less harmful oligophagous species, we generated a chromosome-level assembly and compared it to closely related species with the same or different feeding habits.

Non-obstructive azoospermia (NOA) is a disease related to spermatogenic disorders. Currently, the specific etiological mechanism of NOA is unclear. This study aimed to use integrated bioinformatics to screen biomarkers and pathways involved in NOA and reveal their potential molecular mechanisms.

Insect olfaction is vital for foraging, mating, host-seeking, and avoidance of predators/pathogens. In insects, odorant binding proteins (OBPs) are involved in transporting hydrophobic odor molecules from the external environment to receptor neurons. The codling moth, Cydia pomonella, one of the most destructive insect fruit pests, causes enormous economic losses. However, little is known about the number, variety, gains and losses, and evolution of OBP genes in C. pomonella. Here we report the identification of 40 OBPs in C. pomonella, most (75%) of which are classic OBPs, using genomic and transcriptomic analyses. Two OBP genes were lost in C. pomonella relative to possible distant ancestor in Lepidoptera lineage based on an analysis of gene gains and losses. The phylogenetic tree and chromosome location showed that the expansion of OBP genes mainly resulted from tandem duplications, as the CpomGOBP2 gene was duplicated twice along with loss of CpomPBPB. Two positive selection sites of the CpomGOBP1 gene were identified while other OBP genes evolved under purifying selection. Our results provide fundamental knowledge of OBP genes allowing further study of their function in C. pomonella.

Lung metastatic breast cancer (LMBC) leads to a large number of deaths in women with breast cancer, and radiotherapy has been considered the common assay for tumour therapy except for surgery. However, radiotherapy still faces problems of low efficiency due to resistance and easily induced side effects. Here, the authors designed lipid-decorated bismuth-based nanoflowers (DP-BNFs) as both a radiosensitiser and a photothermal therapy agent for LMBC treatment. The BNFs were prepared by oxidation of bismuth nitrate and subsequent reduction using sodium borohydride. The preparation parameters and formulation of DP-BNFs were optimised via a single-factor experiment, with the factors including reaction temperature, a molar ratio of reducing agents, and the types and amount of decorated lipid materials. The result indicated that the BNFs prepared at 170°C with the Bi/NaBH4 ratio of 1:0.7 exhibited the best yield and particle size around 160 nm. After being spray dried with lactose to prepare dry powder inhalation (DP-BNF@Lat-MPs), their effects on improving therapeutic efficiency of the radiotherapy and photothermal therapy combination were measured using the western blot assay to determine the tumour apoptosis. In a word, DP-BNF@Lat-MPs could be a novel inhalable integrated microsphere that provides a new possibility for thermoradiotherapy of LMBC.

Stimulator of interferon genes (STING) pathway activation predicts the effectiveness of targeting the PD-1/PD-L1 axis in lung cancer. Active IFN-γ signaling is a common feature in tumors that respond to PD-1/PD-L1 blockade. The connection between IFN-γ and STING signaling in cancer cells has not been documented. We showed that IFN-γ caused DNA damage and the accumulation of cytosolic dsDNA, leading to the activation of the cGAS- and IFI16-dependent STING pathway in lung adenocarcinoma cells. IFN-γ-induced iNOS expression and nitric oxide production were responsible for DNA damage and STING activation. Additional etoposide treatment enhanced IFN-γ-induced IFN-β and CCL5 expression. Tumor-infiltrating T cells stimulated with a combination of anti-CD3 and anti-PD-1 antibodies caused STING activation and increased IFN-β and CCL5 expression in lung adenocarcinoma. These effects were abrogated by the addition of an IFN-γ neutralizing antibody. Our results suggest that the activation of tumor-infiltrating T cells could alter the tumor microenvironment via the IFN-γ-mediated activation of STING signaling in cancer cells.

Preventative effects of Lactobacillus fermentum and Bacillus coagulans against Clostridium perfringens infection in broilers have been well-demonstrated. The present study was conducted to investigate the modulation of these two probiotics on intestinal immunity and microbiota of C. perfringens-challenged birds. The 336 one-day-old broilers were assigned to four groups with six replicates in each group. Birds in the control were unchallenged and fed a basal diet, and birds in the three challenged groups were dietary supplemented with nothing (Cp group), 1 × 109 CFU/kg of L. fermentum (Lf_Cp group), or 1 × 1010 CFU/kg of B. coagulans (Bc_Cp group). Challenge was performed from days 14 to 20, and samples were collected on days 21 and 28. Challenge upregulated interleukin (IL)-1β and transforming growth factor (TGF)-β4 mRNA expression in jejunum on day 21, which was downregulated by B. coagulans and L. fermentum, respectively (P < 0.05). Both probiotic groups upregulated jejunal IL-1β, interferon (IFN)-γ, IL-17, and TGF-β4 on day 28 as well as IFN-γ on day 21 (P < 0.05). The Bc_Cp group increased CD3+ T cell counts in the jejunal crypt on day 21 (P < 0.05). Challenge decreased the ileal ACE index on day 21 and cecal microbial richness on day 28, which were increased by probiotic treatments, and ileal bacterial richness decreased in the Bc_Cp group on day 28 (P < 0.05). Only ileal microbiota on day 21 was distinctly affected with an R-value at 0.3116 by ANOSIM analysis (P < 0.05). Compared with the control, ileal Firmicutes increased on day 21, and ileal Bacteroidetes and cecal Proteobacteria decreased on day 28 in challenged groups (P < 0.05). Challenge increased Romboutsia spp. in the ileum as well as unclassified f_Lachnospiraceae and Ruminococcus_torques group in the cecum, and decreased Lactobacillus spp. in the ileum on day 21, which were all conversely modulated by L. fermentum (P < 0.05). Challenge increased amino acid metabolism of ileal microbiota and membrane transport of cecal microbiota, and decreased amino acid metabolism of cecal microbiota on day 21, which were conversely regulated by both probiotics (P < 0.05). In conclusion, L. fermentum and B. coagulans attenuated the intestinal inflammation and microbial dysbiosis soon after C. perfringens challenge.

Chronic obstructive pulmonary disease (COPD) is the most burdened chronic respiratory disease in the world, resulting in a reduced quality of life and limited physical activity for patients. Pulmonary rehabilitation (PR) is an effective therapy for COPD. Effective PR relies on an accurate pulmonary rehabilitation program. An adequate pre-rehabilitation assessment helps healthcare professionals to develop an accurate pulmonary rehabilitation program. However, pre-rehabilitation assessment strategies lack specific selection criteria and an assessment of the patient's overall functioning.

FANCD2 protein, a key coordinator and effector of the interstrand crosslink repair pathway, is also required to prevent excessive nascent strand degradation at hydroxyurea-induced stalled forks. The RAD51 recombinase has also been implicated in regulation of resection at stalled replication forks. The mechanistic contributions of these proteins to fork protection are not well understood. Here, we used purified FANCD2 and RAD51 to study how each protein regulates DNA resection at stalled forks. We characterized three mechanisms of FANCD2-mediated fork protection: (1) The N-terminal domain of FANCD2 inhibits the essential DNA2 nuclease activity by directly binding to DNA2 accounting for over-resection in FANCD2 defective cells. (2) Independent of dimerization with FANCI, FANCD2 itself stabilizes RAD51 filaments to inhibit multiple nucleases, including DNA2, MRE11 and EXO1. (3) Unexpectedly, we uncovered a new FANCD2 function: by stabilizing RAD51 filaments, FANCD2 acts to stimulate the strand exchange activity of RAD51. Our work biochemically explains non-canonical mechanisms by which FANCD2 and RAD51 protect stalled forks. We propose a model in which the strand exchange activity of FANCD2 provides a simple molecular explanation for genetic interactions between FANCD2 and BRCA2 in the FA/BRCA fork protection pathway.

The growth and development of skeletal muscle directly impacts the quantity and quality of pork production. Chinese indigenous pig breeds and exotic species vary greatly in terms of muscle production and performance traits. We present transcriptome profiles of 110 skeletal muscle samples from Tongcheng (TC) and Yorkshire (YK) pigs at 11 developmental periods (30, 40, 55, 63, 70, 90, and 105 days of gestation, and 0, 1, 3, and 5 weeks of age) using digital gene expression on Solexa/Illumina's Genome Analyzer platform to investigate the differences in prenatal and postnatal skeletal muscle between the two breeds.

Our previous proteomic analysis revealed that mitogen-activated protein kinase activator with WD40 repeats (MAWD) and MAWD-binding protein (MAWBP) were downregulated in gastric cancer (GC) tissues. These proteins interacted and formed complexes in GC cells. To investigate the role of MAWD and MAWBP in GC differentiation, we analyzed the relationship between MAWD/MAWBP and clinicopathologic characteristics of GC tissues and examined the expression of E-cadherin and pepsinogen C (PGC)-used as gastric mucosa differentiation markers-in MAWD/MAWBP-overexpressing GC cells and xenografts.

Miniature inverted-repeat transposable elements (MITEs) have a broad impact on genome structure and function. Although MITEs are found associated to genes, little is known about their effect on gene regulation. We have identified a novel MITE family, named Triton, whilst analyzing two independent trichosanthin (TCS) gene promoters (TP9 and TP12) cloned from Trichosanthes kirilowii Maximowicz. Triton1 and Triton2 are nested in TP9, and Triton3 (with 93% sequence similarity to Triton2) is in TP12. To assess the effect of MITE insertion on TCS promoters, we excised Triton1 from TP9 and inserted it into TP12. GUS activity analysis revealed that nested Triton1 is required for effective repression of promoter activity. Detailed analyses of a series of 5'-truncated promoters concerning Triton1 showed that a dark-specific repressor and some constitutive elements endow Triton1 with ability to response to light conditions. These results suggest that Triton1 MITE, which contains cis-regulatory elements, could mediate gene expression.

To analyze the level and diagnostic value of plasmacytoma variant translocation 1 (PVT1) in gastric cancer (GC) of Han and Uygur in Xinjiang, China, we collected 42 GC and 47 normal gastric tissues and performed tissue microarray. In situ hybridization was used to detect PVT1, while immunohistochemistry was used to analyze c-myc. The relationship between PVT1, c-myc and clinical pathological features was investigated. We then analyzed the expression of PVT1 in six GC cell lines. RNA interference was used to silence PVT1 in BGC823 and AGS cells. c-myc was detected by western blotting after silencing PVT1, while proliferation, invasion and migration ability were also analyzed. We found that PVT1 and c-myc were highly expressed in both Han and Uygur GC tissues. In Han GC, PVT1 was correlated with lymph node metastasis and primary tumor site. In Uygur GC, both PVT1 and c-myc were correlated with lymph node metastasis and clinical staging. PVT1 was positively correlated with c-myc. BGC823 and AGS cells exhibited high levels of PVT1. When PVT1 expression was silenced, the expression of c-myc decreased, while migration and invasion ability were also decreased in cells. PVT1 could therefore be a potential biomarker to predict the metastatic tendency of GC in both Han and Uygur patients.

For a long time, the Christie-Atkinson-Munch-Peterson (CAMP) test has been a standard test for the identification of Streptococcus agalactiae, and a positive result for S.agalactiae has been considered sensitive enough.