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Numerous different species of LAB are used in different fields due to their unique characteristics. However, Lacticaseibacillus chiayiensis, a newly established species in 2018, has limited microorganism resources, and lacks comprehensive evaluations of its properties. In this study, L. chiayiensis AACE3, isolated from fermented blueberry, was evaluated by genomic analysis and in vitro assays of the properties. The genome identified genes associated with biofilm formation (luxS, ccpA, brpA), resistance to oxidative stress (tpx, trxA, trxB, hslO), tolerance to acidic conditions (dltA, dltC), resistance to unfavorable osmotic pressure (opuBB, gbuA, gbuB, gbuC), and adhesion (luxS, dltA, dltC). The AACE3 showed 112 unique genes, relative to the other three L. chiayiensis strains. Among them, the presence of genes such as clpP, pepO, and feoA suggests a possible advantage of AACE3 over other L. chiayiensis in terms of environmental adaptation. In vitro evaluation of the properties revealed that AACE3 had robust antibacterial activity against eight common pathogens: Streptococcus agalactiae, Staphylococcus aureus, Escherichia coli, Salmonella enteritidis, Salmonella choleraesuis, Shigella flexneri, Pseudomonas aeruginosa, and Klebsiella pneumoniae. In addition, AACE3 showed more than 80% survival rate in all tests simulating gastrointestinal fluid, and it exhibited high antioxidant capacity. Interestingly, the cell culture supernatant was superior to intact organisms and ultrasonically crushed bacterial extracts in all tests of antioxidant capacity. These results suggested that the antioxidant capacity may originate from certain metabolites and extracellular enzymes produced by AACE3. Moreover, AACE3 was a moderate biofilm producer due to the self-agglomeration effect. Taken together, L. chiayiensis AACE3 appears to be a candidate strain for combating the growing incidence of pathogen infections and antioxidant production.

Lactic acid bacteria are generally regarded as alternatives to antibiotics in livestock and poultry farming, especially Lactobacillus strains, which are safe and have probiotic potential. Although Lactobacillus salivarius has long been proposed to be a probiotic, the understanding of the roles of this species is still in its infancy. Here, a strain of L. salivarius CGMCC20700 isolated from the intestinal mucosa of Yunnan black-bone chicken broilers was investigated in the context of its safety and probiotic characteristics by whole-genome sequencing in parallel with phenotypic analysis. Whole-genome sequencing results showed that L. salivarius CGMCC20700 has a single scaffold of 1,737,577 bp with an average guanine-to-cytosine (GC) ratio of 33.51% and 1,757 protein-coding genes. The annotation of Clusters of Orthologous Groups (COG) classified the predicted proteins from the assembled genome as possessing cellular, metabolic, and information-related functions. Sequences related to risk assessment, such as antibiotic resistance and virulence genes, were identified, and the strain was further confirmed as safe according to the results of antibiotic resistance, hemolytic, and acute oral toxicology tests. Two gene clusters of antibacterial compounds and broad-spectrum antimicrobial activity were identified using genome mining tools and antibacterial spectrum tests. Stress resistance genes, active stressor removal genes, and adhesion related genes that were identified and examined with various phenotypic assays (such as stress tolerance tests in acids and bile salts and auto aggregation and hydrophobicity assays). The strain showed a high survival rate in the presence of bile salts and under acidic conditions and exhibited significant auto aggregation capacity and hydrophobicity. Overall, L. salivarius CGMCC20700 demonstrated excellent safety and probiotic potential at both the genomic and physiological levels and can be considered an appropriate candidate probiotic for livestock and poultry farming.

Grassland caterpillars (Lepidoptera: Lymantriinae:Gynaephora) are the most damaging pests to alpine meadows in the Qinghai-Tibetan Plateau (QTP). Here, we conducted extensive sampling from 39 geographic populations covering almost the entire distribution of the eightGynaephoraspecies in the QTP to investigate phylogeographic patterns and speciation based on two mitochondrial genes (cox1andnad5). A total of 40 haplotypes were detected in the 39 populations, with >70% of haplotypes specific to single population. The monophyletic QTPGynaephoramigrated from non-QTP regions during the Pliocene, corresponding to the uplift of the QTP, suggesting a mode of transport into the QTP. Among the eight QTPGynaephoraspecies described by morphological characteristics, two species (G. alpherakiiandG. menyuanensis) were recovered as monophyletic groups (Clades B and C), while the remaining six species formed two monophyletic clades: Clade A (G. qinghaiensis,G. jiuzhiensis, andG. qumalaiensis) and Clade D (G. aureate,G. rouergensis, andG. minora). These results suggested that the number of the QTPGynaephoraspecies may be overestimated and further studies based on both morphological and nuclear gene data are needed. Genetic differentiation and speciation were driven by intensive uplifts of the QTP and associated climate fluctuations during the Pleistocene, suggesting that isolation and subsequent divergence was the dominant mode of speciation. The Sanjiangyuan region (i.e., Clade A, characterized by high genetic diversity) may have been a glacial refugium of the QTPGynaephora, as supported by analyses of gene flow and biogeography. High levels of genetic diversity were found in QTPGynaephora,without population expansion, which may explain the high-altitude adaptation and outbreaks of grassland caterpillars in alpine meadows of the QTP. This study provides the largest phylogeographic analysis of QTPGynaephoraand improves our understanding of the diversity and speciation of QTP insects.

Staphylococcus aureus and its biofilm have emerged as a significant threat to the safety of dairy products. In recent years, lactic acid bacteria (LAB) bacteriocins have been widely acknowledged as the potential natural antibacterial substance in food biopreservation due to their excellent antibacterial effects. However, few LAB bacteriocins with antibacterial and antibiofilm activity against S. aureus have been reported in dairy products. In the present study, a novel bacteriocin LSX01 of Lactobacillus paracasei LS-6 isolated from a traditional fermented yogurt produced in Yunnan, China, was purified and characterized extensively. The LSX01 possessed a molecular weight of 967.49 Da and an AA sequence of LDQAGISYT. The minimum inhibitory concentration of LSX01 against S. aureus_45 was 16.90 μg/mL, which was close to or lower than the previously reported bacteriocins. The LSX01 exhibited an extensive antimicrobial spectrum against both gram-positive and gram-negative bacteria. Moreover, LSX01 exhibited excellent tolerance to heat and acid-base treatments, and sensitivity to the proteolytic enzymes, such as pepsin and proteinase K. Furthermore, the treatment of S. aureus_45 planktonic cells with LSX01 significantly reduced their metabolic activity and disrupted the cell membrane integrity. Scan electron microscopy results demonstrated that LSX01 induced cytoplasmic content leakage and cell deformation. Additionally, biofilm formation of S. aureus_45 was also significantly inhibited by LSX01. Overall, the results suggested that the novel LAB bacteriocin LSX01 possessed antibacterial activity and antibiofilm activity against S. aureus and, hence, could have potential for improving safety of dairy products.

Multidrug-resistant (MDR) Staphylococcus aureus biofilms have emerged as a serious threat to human health. Recently, the development of antibiotic replacement therapy has gained much attention due to the potential application of bacteriocin. The present study sought to evaluate the antibacterial effect of bacteriocin XJS01 against MDR S. aureus, a previously reported bacteriocin against S. aureus strain 2612:1606BL1486 (S. aureus_26, an MDR strain demonstrated here), and its potential application as an antibiofilm agent. The minimum bactericide concentration of XJS01 against MDR S. aureus_26 was 33.18 μg/mL. XJS01 exhibited excellent storage stability and resistance against acid and reduced the density of established MDR S. aureus_26 biofilm. The hemolytic and HEK293T cytotoxicity activities of XJS01 and the histological analyses in mice confirmed its safety. Moreover, XJS01 effectively disrupted the MDR S. aureus_26 biofilm established on the skin wound surface and reduced the biofilm-isolated bacteria, thereby decreasing the release of pro-inflammatory cytokines and the proliferation of alternatively activated macrophages. Compared to mupirocin, XJS01 exhibited an excellent therapeutic effect on mice skin wounds, confirming it to be a potential alternative to antibiotics.

As a fish unique to Yunnan Province in China, Sinocyclocheilus grahami hosts abundant potential probiotic resources in its intestinal tract. However, the genomic characteristics of the probiotic potential bacteria in its intestine and their effects on S. grahami have not yet been established. In this study, we investigated the functional genomics and host response of a strain, Lactobacillus salivarius S01, isolated from the intestine of S. grahami (bred in captivity). The results revealed that the total length of the genome was 1,737,623 bp (GC content, 33.09%), comprised of 1895 genes, including 22 rRNA operons and 78 transfer RNA genes. Three clusters of antibacterial substances related genes were identified using antiSMASH and BAGEL4 database predictions. In addition, manual examination confirmed the presence of functional genes related to stress resistance, adhesion, immunity, and other genes responsible for probiotic potential in the genome of L. salivarius S01. Subsequently, the probiotic effect of L. salivarius S01 was investigated in vivo by feeding S. grahami a diet with bacterial supplementation. The results showed that potential probiotic supplementation increased the activity of antioxidant enzymes (SOD, CAT, and POD) in the hepar and reduced oxidative damage (MDA). Furthermore, the gut microbial community and diversity of S. grahami from different treatment groups were compared using high-throughput sequencing. The diversity index of the gut microbial community in the group supplemented with potential probiotics was higher than that in the control group, indicating that supplementation with potential probiotics increased gut microbial diversity. At the phylum level, the abundance of Proteobacteria decreased with potential probiotic supplementation, while the abundance of Firmicutes, Actinobacteriota, and Bacteroidota increased. At the genus level, there was a decrease in the abundance of the pathogenic bacterium Aeromonas and an increase in the abundance of the potential probiotic bacterium Bifidobacterium. The results of this study suggest that L. salivarius S01 is a promising potential probiotic candidate that provides multiple benefits for the microbiome of S. grahami.

Distinct expression of the miRNAs has rarely been explored in basal cell carcinoma (BCC) of skin, and the regulatory role of miRNAs in BCC development remains quite opaque. Here, we collected control tissues from adjacent noncancerous skin ( n = 15 ; control group) and tissues at tumor centers from patients with cheek BCC ( n = 15 ; BCC group) using punch biopsies. After six small RNA sequencing- (sRNA-seq-) based miRNA expression profiles were generated for both BCC and controls, including three biological replicates, we conducted comparative analysis on the sRNA-seq dataset, discovering 181 differentially expressed miRNAs (DEMs) out of the 1,873 miRNAs in BCCs. In order to validate the sRNA-seq data, expression of 15 randomly selected DEMs was measured using the TaqMan probe-based quantitative real-time PCR. Functional analysis of predicted target genes of DEMs in BCCs shows that these miRNAs are primarily involved in various types of cancers, immune response, epithelial growth, and morphogenesis, as well as energy production and metabolism, indicating that BCC development is caused, at least in part, by changes in miRNA regulation for biological and disease processes. In particular, the “basal cell carcinoma pathways” were found to be enriched by predicted DEM targets, and regulatory relationships between DEMs and their targeted genes in this pathway were further uncovered. These results revealed the association between BCCs and abundant miRNA molecules that regulate target genes, functional modules, and signaling pathways in carcinogenesis.

Mitochondria are the leading organelle for energy metabolism. The toxic effects of environmental toxicants on mitochondrial morphology, energy metabolism, and their determination of cell fate have already been broadly studied. However, minimal research exists on effects of environmental toxicants such as pesticides on mitochondrial energy metabolism at in vitro subcellular level, particularly from an omics perspectives (e.g., metabolomics). Here, German cockroach (Blattella germanica) was fed diets with (0.01 and 0.001 mg/mL) and without abamectin, and highly purified fat body mitochondria were isolated. Swelling measurement confirmed abnormal mitochondrial swelling caused by abamectin stress. The activity of two key mitochondrial energy metabolism-related enzymes, namely succinic dehydrogenase and isocitrate dehydrogenase, was significantly affected. The metabolomic responses of the isolated mitochondria to abamectin were analyzed via untargeted liquid chromatography/mass spectrometry metabolomics technology. Fifty-two differential metabolites (DMs) were identified in the mitochondria between the 0.001 mg/mL abamectin-fed and the control groups. Many of these DMs were significantly enriched in pathways involved in ATP production and energy consumption (e.g., oxidative phosphorylation, TCA cycle, and pentose phosphate pathway). Nineteen of the DMs were typically related to energy metabolism. This study is valuable for further understanding mitochondrial toxicology under environmental toxicants, particularly its subcellular level.

As a fish unique to Yunnan Province in China

Spiders are among the most varied terrestrial predators, with highly diverse morphology, ecology, and behavior. Morphological and molecular data have greatly contributed to advances in the phylogeny and evolutionary dynamics of spiders. Here, we performed comprehensive mitochondrial phylogenomics analysis on 78 mitochondrial genomes (mitogenomes) representing 29 families; of these, 23 species from eight families were newly generated. Mesothelae retained the same gene arrangement as the arthropod ancestor (蜘蛛是陆地生态系统中物种数量最丰富的捕食类群之一，其形态、生态和行为极具多样性。利用形态学和分子生物学数据，对蜘蛛系统发育及进化历史的已有研究取得了较大进展。该研究新测了8科23种蜘蛛的线粒体基因组，并基于29科78种蜘蛛的线粒体基因组数据对蜘蛛进行了线粒体谱系基因组学分析。中纺亚目保留了节肢动物祖先美洲鲎的基因排序，而后纺亚目（Opisthothelae）表现出频繁的线粒体基因重排，共发现12种基因重排模式。蜘蛛线粒体基因重排，仅涉及线粒体tRNA基因和控制区。蜘蛛线粒体tRNA基因长度极度缩短，导致缺失DHU臂或TΨC臂，使得tRNA基因表现出高度的结构多样性。特别是，

Antibacterial activity and mechanism of action of bacteriocins against bacteria that cause pork contamination remain unclear. Here, antibacterial activity of bacteriocin LFX01 against two important indicator strains (i.e., Staphylococcus aureus and Escherichia coli) and its mechanism of action were investigated. The results showed antibacterial activity of LFX01 against growth and biofilm formation of S. aureus_26 (strain 2612:1606BL1486) and E. coli_02 (strain CMCC(B)44102). Additionally, the results demonstrated that LFX01 could decrease cell metabolic activity, disrupt cell membrane permeability and integrity, and trigger leakage of intracellular contents (e.g., K

Phenyllactic acid (PLA) has been demonstrated to possess antibacterial activity and capacity to prolong food shelf life. However, studies on the performance of PLA in inhibiting Staphylococcus aureus and its effectiveness when applied to dairy products are largely lacking. Here, antibacterial activity (planktonic and biofilm states) of PLA against S. aureus CICC10145 (S. aureus_45) were investigated. The results showed that PLA inhibited growth of S. aureus_45 and formation of S. aureus_45 biofilm. Next, the antibacterial action target of PLA was uncovered from both physiological and phenotypic perspectives. The results showed that PLA decreased cell metabolic activity and cell viability, damaged cell membrane integrity, triggered leakage of intracellular contents (DNA, proteins, and ATP), and caused oxidative stress damage and morphological deformation of S. aureus_45. In practical application, the antibacterial activity of PLA against S. aureus_45 cells was further confirmed in skim milk and cheese as dairy food models, and the antibacterial effects can be adequately maintained during storage for 21 d, at least at 4°C. These findings suggested that PLA could be a potential candidate for controlling S. aureus outgrowth in dairy foods.

Cucujiformia, the largest taxon in the order Coleoptera, exhibits extraordinary morphological, ecological, and behavioral diversity. This infraorder is currently divided into seven superfamilies, but considerably incongruent relationships among superfamilies have been reported by recent phylogenomic studies. Here, we combined the 21 newly sequenced transcriptomes representing six superfamilies with nine previously published cucujiform genomes/transcriptomes to elucidate the phylogeny and evolution of Cucujiformia. The monophyly of each of five superfamilies were consistently supported by all phylogenetic analyses based on the twelve datasets (matrix occupancy, amino acid and nucleotide data) and the two analytical methods (maximum likelihood method and Bayesian inference). Both the amino acid datasets and the RY recoded nucleotide datasets recovered the monophyly of Cucujoidea. Topology test results statistically supported the following robust superfamily-level phylogeny in Cucujiformia: (Coccinelloidea, (Cleroidea, (Tenebrionoidea, (Cucujoidea, (Chrysomeloidea, Curculionoidea))))). Our divergence time analyses recovered a Permian origin of Cucujiformia and a Jurassic-Cretaceous origin of most superfamilies. The diversification of phytophagous beetles that occurred in the Cretaceous can be attributed to its co-evolution with angiosperms, supporting the hypothesis of a Cretaceous Terrestrial Revolution.

To evaluate the diagnostic value of serum Brain-derived neurotrophic factor (BDNF) levels for discriminating PD with depression from without depression, and to investigate whether serum BDNF levels were associated with motor severity and gender in depressed PD patients. Demographic and clinical data were collected from 122 PD patients with depression, 137 without depression and 110 healthy controls. All participants’ serum BDNF concentrations were measured. Their motor abilities and activity were assessed by the Unified PD Rating Scale Part III (UPDRS III) score and the Hoehn and Yahr (H–Y) stage. Depression was scored using the 17-item Hamilton Rating Scale for Depression (HAMD-17). Associations were analyzed with multivariate regression. The serum BDNF levels were lower in depressed PD patients compared to non-depressed PD patients and controls (p

Bacteriocins inhibit various foodborne bacteria in planktonic and biofilm forms. However, bacteriocins with antibacterial and antibiofilm activity against Staphylococcus argenteus, a pathogen that can cause food poisoning, are still poorly known. Here, the novel bacteriocin LSB1 derived from Lactobacillus plantarum CGMCC 1.12934 was purified and characterized extensively. LSB1 had a molecular weight of 1425.78 Da and an amino acid sequence of YIFVTGGVVSSLGK. Moreover, LSB1 exhibited excellent stability under heat and acid-base stress and presented sensitivity to pepsin and proteinase K. LSB1 exhibited an extensive antimicrobial spectrum against both Gram-positive and Gram-negative bacteria. Minimum inhibitory concentration of LSB1 against S. argenteus_70917 was 10.36 µg/ml, which was lower than that of most of the previously found bacteriocins against Staphylococcus strains. Furthermore, LSB1 significantly inhibited S. argenteus_70917 planktonic cells (p 0.01) and decreased their viability. Scanning electron microscopy analysis revealed that cell membrane permeability of S. argenteus_70917 upon exposure to LSB1 showed leakage of cytoplasmic contents and rupture, leading to cell death. In addition, biofilm formation ability of S. argenteus_70917 was significantly (p 0.01) impaired by LSB1, with the percent inhibition of 35% at 10 µg/ml and 80% at 20 µg/ml. Overall, this study indicates that LSB1 can be considered a potential antibacterial agent in the control of S. argenteus in both planktonic and biofilm states. PRACTICAL APPLICATION: Foodborne pathogenic bacteria, such as Staphylococcus argenteus, and their biofilms represent potential risks for food safety. In recent years, customers' demand for "natural" products has increased food control. This study describes the novel bacteriocin LSB1 produced by the lactic acid bacterium species Lactobacillus plantarum. LSB1 showed strong antibacterial and antibiofilm activity against S. argenteus as well as thermal and acid-alkaline stability. Furthermore, the mechanisms of action of LSB1 on S. argenteus were preliminarily explored. These results indicate that LSB1 might be potentially used as an effective and natural food preservative.

Phages are considered the most abundant and diverse biological entities on Earth. Although many phages have been isolated, most of this diversity remains completely unexplored. Recent advances in genome sequencing, however, have provided unprecedented glimpses into the virosphere. The lytic cold-active Siphoviridae bacteriophage VW6S, infecting the host Pseudomonas fluorescens W-6, was isolated from the Napahai plateau wetland in China. The newly sequenced phage VW6S contained double-stranded DNA with a genome size of 37,917 bp, an overall GC content of 56.90% and 52 open reading frames (ORFs). The genome was organized into several modules containing genes for packaging, structural proteins, replication/transcription, and cell lysis. The sequence contained 16 transcription terminators, no tRNAs. The lysis cassette of VW6S consisted of 4 proteins (holin protein, lysin protein and 2 putative spanins). This is the first report on cold-active SiphoviridaePseudomonas fluorescens bacteriophage genome sequencing.

The genome sequence of a novel Meiothermus bacteriophage, named MMP7, which was isolated from Tengchong hot spring in Yunnan Province of China and belongs to the family Myoviridae, was sequenced in this study. To the best of our knowledge, this is the first reported genome sequence of a Meiothermus phage, which has a circular DNA genome of 32,864 bp and a GC content of 64%. The MMP7 genome contains 53 putative protein-encoding genes but no rRNA or tRNA genes, and it exhibits low overall sequence similarity and no significant homology to phage genomes whose sequences are publicly available, suggesting that MMP7 is a novel phage. Consistent with current taxonomic results, whole-genome-based phylogenetic analysis revealed that Meiothermus phage MMP7 has close evolutionary relationship to Thermus phages. Together, our results could be helpful for discovering new thermostable antimicrobial agents and understanding the evolution and genetic diversity of Meiothermus phages in extreme environments.

Pemetrexed plus platinum doublet chemotherapy regimen remains to be the standard first-line treatment for lung adenocarcinoma patients. However, few biomarkers can be used to identify potential beneficiaries with maximal efficacy and minimal toxicity. This study aimed to explore potential biomarker models predictive of efficacy and toxicity after pemetrexed plus platinum chemotherapy based on metabolomics profiling.A total of 144 patients who received at least two cycles of pemetrexed plus platinum chemotherapy were enroled in the study. Serum samples were collected before initial treatment to perform metabolomics profiling analysis. Logistic regression analysis was performed to establish prediction models.157 metabolites were found to be differentially expressed between the response group and the nonresponse group. A panel of Phosphatidylserine 20:4/20:1, Sphingomyelin d18:1/18:0, and Phosphatidic Acid 18:1/20:0 could predict pemetrexed and platinum chemotherapy response with an Area Under the Receiver Operating Characteristic curve (AUROC) of 0.7968. 76 metabolites were associated with hematological toxicity of pemetrexed plus platinum chemotherapy. A panel incorporating triglyceride 14:0/22:3/22:5, 3-(3-Hydroxyphenyl) Propionate Acid, and Carnitine C18:0 was the best predictive ability of hematological toxicity with an AUROC of 0.7954. 54 differential expressed metabolites were found to be associated with hepatotoxicity of pemetrexed plus platinum chemotherapy. A model incorporating stearidonic acid, Thromboxane B3, l-Homocitrulline, and phosphoinositide 20:3/18:0 showed the best predictive ability of hepatotoxicity with an AUROC of 0.8186.This study established effective and convenient models that can predict the efficacy and toxicity of pemetrexed plus platinum chemotherapy in lung adenocarcinoma patients before treatment delivery.

Objective: To objective of the study was to investigate whether serum brain-derived neurotrophic factor (BDNF) levels are associated with the severity of restless legs syndrome (RLS) in Parkinson's disease (PD).Methods: A total of 249 PD patients with (n = 53) and without RLS (n = 196) and 326 age-matched controls were included in this study. All the serum BDNF levels of the participants were measured. The International Restless Legs Syndrome Study Group Rating Scale (IRLSSG-RS) was administered for the severity of RLS. The severity of PD patients were assessed by the Unified PD Rating Scale (UPDRS) and the Hoehn and Yahr (H-Y) stage.Results: The prevalence of RLS was significantly higher in PD patients (21.3%) than in the controls group (7.4%) (p < 0.05). The IRLSSG-RS score in PD patients with RLS (16.25 ± 5.24) was significantly increased than in controls with RLS (12.08 ± 3.99) (p < 0.01). The serum BDNF levels were significantly decreased in PD patients with RLS than in PD patients without RLS, controls without RLS, and controls with RLS (p < 0.001). BDNF levels were negatively associated with IRLSSG-RS in both PD patients with RLS and controls with RLS group (both p < 0.01). Multiple regression analysis confirmed that in either PD with RLS or controls with RLS group, BDNF was an independent contributor to IRLSSG-RS (both p < 0.01).Conclusions: Decreased serum BDNF levels may be involved in the pathophysiology of RLS in PD, suggesting that it may serve as a potential blood biomarker of diagnostic value for RLS in PD.

Few bacteriocins with antibacterial activity against Shigella flexneri have been reported. Here, a novel bacteriocin (LFX01) produced by Lactiplantibacillus plantarum strain LF-8 from the intestine of tilapia was purified and extensively characterized. LFX01 possesses a molecular weight of 1049.56 Da and an amino acid sequence of I-T-G-G-P-A-V-V-H-Q-A. LFX01 significantly inhibited S. flexneri strain 14 (S. flexneri_14) growth. Moreover, it exhibited excellent stability under heat and acid-base stress, and presented sensitivity to a variety of proteases, such as proteinase K, pepsin, and trypsin. The minimum inhibitory concentration (MIC) of LFX01 against S. flexneri_14 was 12.65 μg/mL, which was smaller than that of most of the previously found bacteriocins. Furthermore, LFX01 significantly inhibited (p < 0.05) S. flexneri_14 cells and decreased their cell viability. In addition, LFX01 could significantly (p < 0.05) inhibit biofilm formation of S. flexneri_14. Scanning electron microscopy analysis presented that the cell membrane permeability of S. flexneri_14 was demolished by LFX01, leading to cytoplasmic contents leakage and cell rupture death. In summary, a novel bacteriocin of lactic acid bacteria (LAB) was found, which could effectively control S. flexneri in both planktonic and biofilm states.

Bupleuri Radix, serving as the sovereign medicinal in many antidepressant compound preparations, has been proved effective in treating depression in mice, but its effect on the intestinal flora remains unclear. The present study aimed to investigate the effects of Bupleurum chinense(one of the original materials of Bupleuri Radix) on the behaviors and the diversity of intestinal flora of depressed mice. A depression mouse model was induced by repeated social defeat stress. Specifically, C57 BL/6 J male mice were exposed to the attack from the CD-1 mice. Then, C57 BL/6 J male mice were divided into a depression group and a B. chinense group, with normal saline and B. chinense administered(ig) respectively. Sucrose preference test and tail suspension test were conducted during and after the experiment respectively, to analyze the effects of B. chinense on the behaviors of the depressed mice. The feces were collected after the experiment. The V3-V4 16 S rDNA regions of intestinal flora of mice in each group were sequenced by Ion S5 TMXL for the analysis of the number of operational taxonomic units(OTUs), richness, alpha and beta diversity indexes, and differential phyla and genera. The results indicated that B. chinense could decrease depressive-like behaviors of mice, increase sucrose preference, and shorten the time of immobility in tail suspension test. After B. chinense intervention, the relative abundance of Firmicutes was significantly decreased, while that of Bacteroidetes was increased at the phylum level. At the genus level, the relative abundance of Lactobacillus and Lachnoclostridium decreased(Plt;0.05), while that of Bacteroides, Alistopes, etc. was elevated(Plt;0.05). The findings demonstrate that B. chinense can regulate the intestinal flora and improve the depressive-like behaviors of mice with depression.

So far, methods that yield the high purity and activity of the isolated mitochondria from insects have not been reported and determined. Here, we develop methods that combine differential centrifugation and discontinuous Nycodenz density gradient centrifugation to isolate highly purified mitochondria from the thorax muscle of insects, and the methods were widely validated across three orders (Coleoptera, Hymenoptera, and Blattaria) covering four insect species using Western blot and transmission electron microscopy (TEM) analysis. The results showed the removal of the residual contamination with nonmitochondrial components such as nucleus, sarcolemma, cytosol, and endoplasmic reticulum. Furthermore, TEM, mitochondria staining, fluorescence detection, and flow cytometry analyses were employed to assess membrane integrity and activity of the isolated mitochondria. The results showed no loss of mitochondria activity/integrity after isolation. In addition, temporal dynamics in activity of the isolated mitochondria under commonly used laboratory temperature (-20 °C, 4 °C, and 25 °C) were respectively detected using a fluorescence microplate reader. The results showed that it should be avoided to store the isolated mitochondria at room temperature, and the mitochondria can meet the requirements of the most downstream experiments when they were stored at -20 °C. Overall, the study presented a method for isolating highly purified and active mitochondria from insects. This study firstly described a high-speed discontinuous density gradient centrifugation-based method that could be widely applied for mitochondria isolation in insects. The present study also provided an example to assess purity and integrity/activity of the isolated mitochondria.

Rhodosporidium kratochvilovae strain YM25235 is a cold-adapted oleaginous yeast strain that can grow at 15°C. It is capable of producing polyunsaturated fatty acids. Here, we used the Nanopore Platform to first assemble the R. kratochvilovae strain YM25235 genome into a 23.71 Mb size containing 46 scaffolds and 8,472 predicted genes. To explore the molecular mechanism behind the low temperature response of R. kratochvilovae strain YM25235, we analyzed the RNA transcriptomic data from low temperature (15°C) and normal temperature (30°C) groups using the next-generation deep sequencing technology (RNA-seq). We identified 1,300 differentially expressed genes (DEGs) by comparing the cultures grown at low temperature (15°C) and normal temperature (30°C) transcriptome libraries, including 553 significantly upregulated and 747 significantly downregulated DEGs. Gene ontology and pathway enrichment analysis revealed that DEGs were primarily related to metabolic processes, cellular processes, cellular organelles, and catalytic activity, whereas the overrepresented pathways included the MAPK signaling pathway, metabolic pathways, and amino sugar and nucleotide sugar metabolism. We validated the RNA-seq results by detecting the expression of 15 DEGs using qPCR. This study provides valuable information on the low temperature response of R. kratochvilovae strain YM25235 for further research and broadens our understanding for the response of R. kratochvilovae strain YM25235 to low temperature.

To study the characteristics of two malate dehydrogenases (MDHs), their coding genes MIMDH1 and MIMDH2 were cloned and expressed in Escherichiacoli BL21 cells. The molecular weights of both recombinant enzymes partially purified using Ni-NTA affinity chromatography were 32 kDa, and the specific activities of purified MIMDH1 and MIMDH2 were 329.3 and 241.3 U/mg protein, respectively. The optimal temperatures for MIMDH1 and MIMDH2 activities were 55 and 30oC, respectively, with 70% MIMDH1 activity and ≥70% MIMDH2 activity remaining after 30 min incubation at 45oC. Addition of 2 mM Zn2+ enhanced MIMDH1 activity, whereas the addition of other metal ions resulted in different degrees of inhibition. The inhibitory effect of Co2+ was most pronounced on MIMDH1, reaching 82.8% inhibition. Addition of 2 mM Ba2+ or Mn2+ increased MIMDH2 activity, the addition of other metal ions resulted in different degrees of inhibition. Furthermore, MIMDH1 was stable at pH range of 7.5–8.5, with optimal activity observed at pH of 8.0. MIMDH2 showed similar stability at the same pH range, but was optimal at pH of 7.5. The Vmax and KM values for recombinant MIMDH1 and MIMDH2 catalyzing the reduction of oxaloacetate to malate were 17.66 µmol mg–1min–1 and 0.541 mM, 15.59 µmol mg–1min–1 and 0.683 mM, respectively.

Amphioxus has been widely used as a model for the comparative immunology of vertebrates. Studies have reported that gene expression changes in the amphioxus gill in response to biotic stress, such as microbial and their mimic challenge, but little is known about how gene expression is affected by abiotic stress in the marine environment, such as nitrite. A lack of information regarding gene expression response to abiotic stress hinders a comprehensive understanding of gill defense response in amphioxus. Here, RNA sequencing was used to carry out gene expression profiling analyses of Branchiostoma belcheri gills under nitrite stress. Six libraries were created for the control and treatment groups, including three biological replicates. In total, 2416 differently expressed genes (DEGs) were detected in response to nitrite stress, of which 1522 DEGs were up-regulated in the treatment group in comparison to the control, while the remaining 894 DEGs were down-regulated genes. Functional enrichment revealed that these DEGs are primarily involved in disease, innate immunity, xenobiotic biodegradation and metabolism, and biomolecular processes and apoptosis. We screened 11 key nitrite-responsive DEGs to detect their expression responses to nitrite stress at different time points, and validate the sequencing data using real time quantitative PCR. The results indicated that the expression of gene encoding CYP3A, POD, CASPR1, GST, MAO, DDH, and XDH/XO were induced, while those encoding MRC, GT, DNASE1L, and RIPK5 were reduced, to participate in the anti-nitrite response. This study provides a useful resource for research of molecular toxicology in amphioxus under environmental stress.

The influential factors of chemotherapy-induced myelosuppression in esophageal cancer in central China are unclear. This study aimed to investigate the effect of commonly used chemotherapy regimens on the incidence of myelosuppression in clinical treatment of esophageal cancer.In this retrospective study, 624 patients with esophageal cancer who received six different chemotherapy regimens between 2013 and 2020 at our institute were included. Chemotherapy consisted of lobaplatin, 5-fluorouracil (5-F), lobaplatin and 5-F, nedaplatin, nedaplatin and paclitaxel (PTX), cisplatin and PTX. Multivariable logistic regression analysis was used to explore the risk of myelosuppression among the six different chemotherapy regimens.Compared with lobaplatin group, the incidence of myelosuppression in patients treated with chemotherapy regimens of lobaplatin and 5-F, nedaplatin, nedaplatin and PTX and cisplatin and PTX were significantly ameliorated. The dose of lobaplatin was significantly reduced (P=0.007) when lobaplatin was combined with 5-F, and the combination could significantly reduce the risk of myelosuppression (P=0.022). Furthermore, chemotherapeutic regimens, the dose of platinum, hemoglobin and uric acid levels, age, sex, total bilirubin and immune-enhancing drugs were found to be strong predictors of developing myelosuppression.Targeted preventive interventions that enhance immune function, reduce uric acid levels and choose combined medication during chemotherapy should be implemented for high-risk patients to reduce the occurrence of myelosuppression. In addition, the dose of lobaplatin should be adjusted when combined with other chemotherapy drugs to reduce the incidence of myelosuppression.

The egg-pathogenic fungus Purpureocillium lilacinum parasitizes on nematode eggs, and thus, it is used as a good biocontrol agent against plant root-knot nematodes. However, little is known about the transcriptional response of P. lilacinum while infecting nematode eggs. This study presents the whole transcriptome sequencing of P. lilacinum and transcriptome-wide gene expression analysis of P. lilacinum upon infecting the eggs of Meloidogyne incognita compared to non-infecting controls. A transcriptomic library of P. lilacinum was used as reference gene set and six transcriptomic libraries of the non-infecting control and P. lilacinum infecting M. incognita eggs were constructed, respectively, comprising three biological replicates of each. A total of 1,011 differently expressed genes (DEGs) were identified in the infecting samples, including 553 up-regulated and 458 down-regulated genes compared to the non-infecting control samples. Furthermore, functional enrichment analysis exhibited that these DEGs were primarily involved in oxidative phosphorylation, oxidoreductase activity, and metabolic processes. Fifteen DEGs were randomly selected to verify the RNA sequencing results through quantitative real-time polymerase chain reaction (qPCR). The study focused on P. lilacinum genes that were strongly expressed upon infecting M. incognita eggs. These DEGs were primarily involved in detoxification, parasitic behavior, and nutritional utilization. This study contributes significantly to the understanding of the molecular mechanisms underlying the parasitic action of P. lilacinum on nematode eggs and provides a valuable genetic resource for further research on parasitic behavior of P. lilacinum. Notably, this study examined the transcriptomics of P. lilacinum infecting M. incognita eggs at only one time point. Since there were fungi at different stages of the infection process at that time point, the transcriptional profiles are not precisely examining one specific stage in this process.

Given mitochondrion is the 'energy and oxygen usage factories', adaptive signatures of mitochondrial genes have been extensively investigated in vertebrates from different altitudes, but few studies focus on insects. Here, we sequenced the complete mitochondrial genome (mitogenome) of Dolycoris. baccarum living in the Tibetan Plateau (DBHC, ∼3200 m above sea level (asl)) and conducted a detailed comparative analysis with another D. baccarum mitogenome (DBQY) from relatively low altitude (∼1300 m asl). All the 37 mitochondrial genes were highly conserved and under purifying selection, except for two mitochondrial protein-coding genes (MPCGs) (atp6 and nad5) that showed positively selected signatures. We therefore further examined non-synonymous substitutions in atp6 and nad5, by sequencing more individuals from three populations with different altitudes. We found that these non-synonymous substitutions were polymorphic in these populations, likely due to relaxed selection constraints in different altitudes. Purifying selection in all mitochondrial genes may be due to their functional importance for the precision of ATP production usually. Length difference in mitochondrial control regions between DBHC and DBQY was also conversed at the population level, indicating that sequence size adjustments in control region may be associated with adaptation to divergent altitudes. Quantitatively real-time PCR analysis for 12 MPCGs showed that gene expression patterns had a significant change between the two populations, suggesting that expression levels of MPCGs could be modulated by divergent environmental pressures (e.g. oxygen content and ambient temperature). These results provided an important guide for further uncovering genetic mechanisms of ecological adaptation in insects.

The dipole distributions of water molecules across the channel of single-walled carbon nanotubes (SWCNTs) under high pressure gradient P are studied using molecular dynamics (MD) simulations. It is found that the profiles of the dipole distributions are highly symmetrical with two peak values around 30° and 150° at zero or low pressure gradient (P ≤ 6MPa), and remarkably asymmetric with the main peak around 30° under high pressure gradient (P ≥ 12MPa). The reason is mainly that molecules can enter into the SWCNTs from two ends under low pressure water, whereas the water molecules can only enter into the tube from one end under high pressure. Further, it also implies that water molecules prefer to retain the hydrogens forward when entering into and passing through the nanotube. Our observations may be instructive for future applications in nanometer scale fluid devices and biological channels.

Amphioxus, a cephalochordate, is a key model animal for studying the evolution of vertebrate immunity. Recently, studies have revealed that microRNA (miRNA) expression profiles change significantly in the amphioxus gill after immune stimulation, but it remains largely unknown how gene expression responds to immune stress. Elucidating gene expression changes in the amphioxus gill will provide a deeper understanding of the evolution of gill immunity in vertebrates. Here, we used high-throughput RNA sequencing technology (RNA-seq) to conduct tag-based digital gene expression profiling (DGE) analyses of the gills of control Branchiostoma belcheri and of those exposed to the viral mimic, poly(I:C) (pIC). Six libraries were created for the control and treatment groups including three biological replicates per group. A total of 1999 differently expressed genes (DEGs) were obtained, with 571 and 1428 DEGs showing up- or down-regulation, respectively, in the treatment group. Enrichment analysis of gene ontology (GO) terms and pathways revealed that the DEGs were primarily related to immune and defense response, apoptosis, human disease, cancer, protein metabolism, enzyme activity, and regulatory processes. In addition, eight DEGs were randomly selected to validate the RNA-seq data using real-time quantitative PCR (qRT-PCR), and the results confirmed the accuracy of the RNA-seq approach. Next, we screened eight key responding genes to examine the dynamic changes in expression levels at different time points in more detail. The results indicated that expressions of TRADD, MARCH, RNF31, NF-κb, CYP450, TNFRSF6B, IFI and LECT1 were induced to participate in the antiviral response against pIC. This study provides a valuable resource for understanding the role of the amphioxus gill in antiviral immunity and the evolution of gill immunity in vertebrates.

Planktonic Salmonella Enteritidis and their biofilm threaten human health through the food chain. However, the resources of bacteriocins with activity against this threat are still limited. This study purified and characterized a novel bacteriocin (AMYX6) produced by the Bacillus amyloliquefaciens strain JDF-17, isolated from the intestine of the Nile tilapia (Oreochromis niloticus). The analysis results of AKTA Purifier and nano liquid chromatography coupled with tandem mass spectrometry uncovered a molecular mass of 1323.73 Da and an amino acid composition of PVFLSDHIRIQ. AMYX6 inhibited the strain of S. Enteritidis CMCC(B)50335 (S. Enteritidis_35). AMYX6 also showed good resistance to heat and acid-base treatments, and was found to be sensitive to proteases such as trypsin, protease K, papain, and pepsin. The minimum inhibitory concentration of AMYX6 against S. Enteritidis_35 was 12.17 μg/mL, which is lower than the levels reported for most bacteriocins. Furthermore, exposure to AMYX6 significantly inhibited (p

Molecular dynamics simulations are carried out to study the transport properties of water molecules across 1.34 nm long single-walled carbon nanotubes (SWCNTs) under hydrostatic pressure with different directions. It is found that when the deflection angle φ between the hydrostatic pressure and the tube-axis direction changes from 0 ° to 90 °, the net flux shows significant differences. It is interesting to note that the maximum flux is counter-intuitively obtained at φ=45°, which is about three times that of at φ=0°. This enhancement is mainly attributed to the excellent intermolecular structure, the orientation distribution, and the filling rate of in-tube water at φ=45°. Yet, it is worth noting that with the increase of the length of the SWCNT, the anomalous effect will gradually weaken until it almost disappears. Our work is of great significance for the practical application of high-efficiency nanofiltration membranes under pressure gradients.

The novel bacteriocin JS17 was obtained from Bacillus subtilis JSX-5, isolated from blueberry (Vaccinium uliginosum) ferments. JS17 was purified by AKTA Purifier, semi-preparative reversed-phase high performance liquid chromatography, and nano liquid chromatography coupled with tandem mass spectrometry, in succession. Its molecular mass was 652.37 Da and its amino acid sequence was identified as L-F-R-A-F. A homology BLAST search confirmed JS17 as a novel bacteriocin. JS17 was found to have an extensive antibacterial activity spectrum against both Gram-positive and Gram-negative bacteria. JS17 showed heat tolerance, and it was highly stable over pH 2–10 and was sensitive to proteinase K and pepsin. This indicates that JS17 exhibits protein properties and has application potential under high temperature and acid-base conditions. The minimum inhibitory concentration and minimum bactericide concentration of JS17 against Escherichia coli were 10.56 μg/mL and 22.03 μg/mL, respectively, which is lower than that of most previously described bacteriocins. Furthermore, scanning electron microscopy showed that JS17 bactericidally destroyed the cell membrane integrity of E. coli, resulting in cell dissolution and impaired membrane permeability. This study first purified B. subtilis bacteriocin from fruit ferments, suggesting the potential for using JS17 as a food bio-preservative.

Bacteriocins are known to inhibit various foodborne bacteria and their biofilms; however, few bacteriocins with activity against food-derived Staphylococcus aureus have been reported. Here, a novel bacteriocin (XJS01) from the Lactobacillus salivarius strain CGMCC2070 was obtained, purified, and extensively characterized. Molecular mass and amino acid composition of XJS01 were 666.31 Da and F–S-G-L-A-G-D, respectively. XJS01 inhibited the S. aureus strain 2612:1606BL1486 (S. aureus_26), which was originally isolated from chicken meat. Also, XJS01 showed good resistance to heat treatment, and was only susceptible to pepsin treatment. The minimum inhibitory concentration of XJS01 against S. aureus_26 was 9.85 μg/mL, which is lower than previously reported levels for most described bacteriocins. Furthermore, exposure to XJS01 also decreased viability and significantly inhibited (p

// Qi-Lin Zhang 1,2,* , Qian-Hua Zhu 3,* , Feng Zhang 1,2 , Bin Xu 1,2 , Xiu-Qiang Wang 1,2 and Jun-Yuan Chen 1,2 1 State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing, China 2 LPS, Nanjing Institute of Geology and Paleontology, Nanjing, China 3 Beijing Genomics Institute, Shenzhen, China * These authors contributed equally to this work Correspondence to: Jun-Yuan Chen, email: // Qi-Lin Zhang, email: // Keywords : Branchiostoma belcheri, miRNA, poly (I:C), deep sequencing, Immunology and Microbiology Section, Immune response, Immunity Received : July 13, 2017 Accepted : August 04, 2017 Published : August 28, 2017 Abstract Amphioxus is a key experimental animal for studying the evolution of vertebrate immune system. However, we still do not know about the roles of microRNAs (miRNAs) under viral stress in amphioxus. In this study, we sequenced six small RNA libraries (three biological replicates were included in the treatments challenged by the viral mimic, poly (I:C) (pIC) and control groups, respectively) from Branchiostoma belcheri . A total of 151 known miRNAs, 197 new miRNAs (named novel_mir, including nine conserved miRNAs) were identified by deep sequencing from the six libraries. We primarily focused on differentially expressed miRNAs (DEMs) after pIC challenge. Next, we screened a total of 77 DEMs, including 27 down- and 50 up-regulated DEMs in response to pIC challenge. Furthermore, we used real-time quantitative PCR (qRT-PCR) to verify the expression levels of 10 randomly selected DEMs. Target genes likely regulated by DEMs were predicted, and functional enrichment analyses of these targets were performed using bioinformatics approach. MiRNA targets of DEMs are primarily involved in immune response, diseases, cancer and regulation process, and could be largely linked to 14 immune-related signaling pathways, including NF-kappa B, NOD-like receptor, RIG-I-like receptor and endocytosis. The present study for the first time explores key regulatory roles of miRNAs in the innate antiviral immune response in amphioxus, and will provide insight into the molecular basis of antiviral immunity and evolution of immune-related miRNAs.

Recently, amphioxus has served as a model for studying the origin and evolution of vertebrate immunity. However, little is known about how microRNAs (miRNAs) are involved in the immune defense in amphioxus. In this article, we identified the amphioxus miRNAs in the acute-phase response to lipopolysaccharide (LPS). We determined the time point for the peak of immune response in amphioxus after LPS challenge by evaluating the expression of Branchiostoma belcheri toll-like receptor 1, NF-κb (c-Rel), and big defensin which react with pathogen-associated molecular patterns(PAMPs). Then we chose 12 h as the point to perform miRNA microarray analysis to select the differentially expressed miRNAs. Furthermore, we used quantitative real-time PCR to detect the expression patterns of selected amphioxus miRNAs under effective LPS challenge during the time course. The microarray data revealed that the miRNA expression file was significantly changed after LPS stimulation. The changes of the 10 most upregulated and 7 most downregualted miRNAs in gills of the amphioxus following challenge with LPS revealed a temporal induction kinetic. Our current study will provide valuable information to take an insight into molecular mechanism of innate immune and the evolution of the miRNA family.

The adaptive evolution of animals to high-elevation environments has been extensively studied in vertebrates, while few studies have focused on insects. Gynaephora species (Lepidoptera: Lymantriinae) are endemic to the Qinghai-Tibetan Plateau (QTP) and represent an important insect pest of alpine meadows. Here, we present a detailed comparative analysis of the mitochondrial genomes (mitogenomes) of two Gynaephora species inhabiting different high-elevation environments: G. alpherakii and G. menyuanensis. The results indicated that the general mitogenomic features (genome size, nucleotide composition, codon usage and secondary structures of tRNAs) were well conserved between the two species. All of mitochondrial protein-coding genes were evolving under purifying selection, suggesting that selection constraints may play a role in ensuring adequate energy production. However, a number of substitutions and indels were identified that altered the protein conformations of ATP8 and NAD1, which may be the result of adaptive evolution of the two Gynaephora species to different high-elevation environments. Levels of gene expression for nine mitochondrial genes in nine different developmental stages were significantly suppressed in G. alpherakii, which lives at the higher elevation (~4800m above sea level), suggesting that gene expression patterns could be modulated by atmospheric oxygen content and environmental temperature. These results enhance our understanding of the genetic bases for the adaptive evolution of insects endemic to the QTP.

NdF3 is an excellent efficient material for infrared fluorescence and solid-state lasers. Herein, we describe the formation processes and a possible formation mechanism for single crystal NdF3 nanoplates with cavities via a simple hydrothermal method. Enhanced infrared fluorescence and decreased upconversion emissions were observed from the NdF3 nanoplates with cavities, which were attributed to the porous structure, and surface defects availed nonradioactive relaxation of the Nd3+. These single-crystalline NdF3 nanoplates with cavities will provide new perspectives and opportunities in fascinating light phosphor powders and advanced devices.

Taiwania cryptomerioides is an endangered relict conifer species native to East Asia with a variety of practical applications. To contribute to its conservation and sustainable utilization, its complete chloroplast genome was assembled from Illumina sequencing reads. The circular genome is 131,427 bp in size with a biased nucleotide composition (33.5% A, 17.5% C, 17.2% G & 31.8% T). It encodes a panel of 114 gene species, including 83 protein-coding genes (PCGs) and 31 tRNAs. Gene duplication was detected for three tRNA gene species (trnI-CAU, trnQ-UUG & trnV-GAC). Besides, 15 gene species (atpF, ndhA, ndhB, petB, petD, rpl16, rpl2, rpoC1, rps16, trnA-UGC, trnG-UCC, trnI-GAU, trnK-UUU, trnL-UAA & trnV-UAC) possess a single intron, and another one (ycf3) has a couple of introns. Phylogenetic analysis suggests that T. cryptomerioides and T. flousiana are closely related to each other within the family Cupressaceae.

Amphioxus is the closest living invertebrate proxy of the vertebrate ancestor. Systematic gene identification and expression profile analysis of amphioxus organs is thus important for clarifying the molecular mechanisms of organ function formation and further understanding the evolutionary origin of organs and genes in vertebrates. The precise regulation of microRNAs (miRNAs) is crucial for the functional specification and differentiation of organs. In particular, those miRNAs that are expressed specifically in organs (OSMs) play key roles in organ identity, differentiation, and function. In this study, the genome-wide miRNA transcriptome was analyzed in eight organs of adult amphioxus Branchiostoma belcheri using deep sequencing. A total of 167 known miRNAs and 23 novel miRNAs (named novel_mir), including 139 conserved miRNAs, were discovered, and 79 of these were identified as OSMs. Additionally, analyses of the expression patterns of eight randomly selected known miRNAs demonstrated the accuracy of the miRNA deep sequencing that was used in this study. Furthermore, potentially OSM-regulated genes were predicted for each organ type. Functional enrichment of these predicted targets, as well as further functional analyses of known OSMs, was conducted. We found that the OSMs were potentially to be involved in organ specific functions, such as epidermis development, gonad development, muscle cell development, proteolysis, lipid metabolism and generation of neurons. Moreover, OSMs with non-organ specific functions were detected, and primarily include those related to innate immunity and response to stimuli. These findings provide insights into the regulatory roles of OSMs in various amphioxus organs.

Animals can remodel their gene expression to compensate for the effects of different ecological factors, which can confer resistance to extreme environment alteration, such as altitude changes. Understanding response of gene expression to divergent-altitude habitats, such as Tibetan Plateau (TP) and lower altitude area, in natural populations remains one of the greatest challenges. Previous studies extensively focused on vertebrates, while the current lack of understanding about transcriptomic gene expression alteration in divergent-altitude adaptation of invertebrates, especially the insects. Here, we downloaded raw data/reads of Dolycoris baccarum distributed in 1,300 m a.s.l (above sea level) and its corresponding TP strain (3,200 m a.s.l), and performed a mixed assembly of these two transcriptomes to construct unigene set of D. baccarum. Subsequently, we analyzed the gene expression changes between two populations, and validate the sequencing data using real time quantitative PCR. A total of 4,816 differentially expressed genes were largely enriched to GO involved in DNA repair, hypoxia response, energy production, suggesting that substantial plasticity in gene expressions was mainly associated with the ability to resist UV radiation, hypoxia, and cold. Our study firstly provides novel insights into gene expression variations of insects in divergent-altitude adaptation.

Adaptation to high-altitude environments has been extensively studied in vertebrates, but studies on invertebrates, especially insects, are very limited. Insects show different characteristics in phenotype, physiology and behavior from vertebrates and thus may have evolved specific mechanisms of high-altitude adaptation. Here, we downloaded clean data/reads of Gynaephora species (alpherakii and menyuanensis) distributed in 3,000 m a.s.l (above sea level) and 4,800 m a.s.l on the Tibetan Plateau (TP), and performed a mixed assembly of these two transcriptomes to construct unigene set of Gynaephora to infer potential genetic mechanisms at gene expression level of high-altitude adaptation in insects. Subsequently, by comparing gene expression of these two Gynaephora species, we obtained 3,238 differentially expressed genes (DEGs), most of which were significantly enriched in mitochondrial function, ATP production and energy metabolism. This study is useful for understanding the adaptation, evolution and speciation of Gynaephora endemic to the TP and provides novel insight into high-altitude adaptation in TP animals.Adaptation to high-altitude environments has been extensively studied in vertebrates, but studies on invertebrates, especially insects, are very limited. Insects show different characteristics in phenotype, physiology and behavior from vertebrates and thus may have evolved specific mechanisms of high-altitude adaptation. Here, we downloaded clean data/reads of Gynaephora species (alpherakii and menyuanensis) distributed in 3,000 m a.s.l (above sea level) and 4,800 m a.s.l on the Tibetan Plateau (TP), and performed a mixed assembly of these two transcriptomes to construct unigene set of Gynaephora to infer potential genetic mechanisms at gene expression level of high-altitude adaptation in insects. Subsequently, by comparing gene expression of these two Gynaephora species, we obtained 3,238 differentially expressed genes (DEGs), most of which were significantly enriched in mitochondrial function, ATP production and energy metabolism. This study is useful for understanding the adaptation, evolution and spec...

Amphioxus, or cephalochordates, are often used as the living invertebrate proxy of vertebrate ancestors and are widely used as evolutionary biology models of chordates. However, their phylogeny, divergence history, and speciation characteristics remain poorly understood, and phylogenomic studies to explore these problems lacking entirely from the literature. Here, we determined a new transcriptome of Branchiostoma japonicum. Combined with mass sequences of all other 18 species, a 19-way phylogeny was constructed via multiple methods (ML, BI, PhyloBayes, and ASTRAL), consistently supporting a phylogeny of [(B. belcheri + B. japonicum) + (B. lanceolatum + B. floridae) + Asymmetron lucayanum] in amphioxus. Congruent phylogenetic signals were found across mitochondrial genes, 12S RNA, and complete mitochondrial genomes according to previous reports, indicating that 12S RNA may have potential as a molecular marker for phylogenetic analysis in amphioxus. Molecular dating analysis indicated a radiation of the cephalochordates during the Cretaceous (∼104-61 million years ago), supporting an association between the diversification and speciation of cephalochordates with continental drift and associated changes in their respective habitats during this time. The identified functional enrichment analysis for species-specific domains indicated that their function mainly involves immune response, apoptosis, and lipid metabolism and utilization, signaling that pathogens and changes of energy requirements are an important driving force for amphioxus speciation. This study represents the first large-scale phylogenomic analysis of most major amphioxus genera based on phylogenomic data, providing a new perspective on both phylogeny and divergence speciation of cephalochordates.