Genome-wide transcriptome and proteome profiles indicate an active role of alternative splicing during de-etiolation of maize seedlings.

MAIN CONCLUSION: AS events affect genes encoding protein domain composition and make the single gene produce more proteins with a certain number of genes to satisfy the establishment of photosynthesis during de-etiolation. The drastic switch from skotomorphogenic to photomorphogenic development is an excellent system to elucidate rapid developmental responses to environmental stimuli in plants. To decipher the effects of different light wavelengths on de-etiolation, we illuminated etiolated maize seedlings with blue, red, blue-red mixed and white light, respectively. We found that blue light alone has the strongest effect on photomorphogenesis and that this effect can be attributed to the higher number and expression levels of photosynthesis and chlorosynthesis proteins. Deep sequencing-based transcriptome analysis revealed gene expression changes under different light treatments and a genome-wide alteration in alternative splicing (AS) profiles. We discovered 41,188 novel transcript isoforms for annotated genes, which increases the percentage of multi-exon genes with AS to 63% in maize. We provide peptide support for all defined types of AS, especially retained introns. Further in silico prediction revealed that 58.2% of retained introns have changes in domains compared with their most similar annotated protein isoform. This suggests that AS acts as a protein function switch allowing rapid light response through the addition or removal of functional domains. The richness of novel transcripts and protein isoforms also demonstrates the potential and importance of integrating proteomics into genome annotation in maize.

Lamprey: an important animal model of evolution and disease research.

Lamprey is one representative of the extant jawless vertebrates, known as "living fossils", with a history of more than 500 million years. The ancient lamprey has attracted the attention of many scholars due to its unique functional characteristics and evolutionary status. In terms of immune system, the lamprey has adaptive immune system and immune molecules different from those of jawed vertebrates. Based on the evolutionary status, lamprey is an important developmental and evolutionary animal model for analyses of evolutionary conservation and derivative characteristics of vertebrates. Lamprey pallium provides an evolutionary blueprint for mammalian cerebral cortex. In disease research, lamprey has provided various results as a pathological model of spinal cord injury and biliary atresia. In this review, the life cycle, immune molecules, developmental evolution and physiological structure of lamprey are presented in details in reference with relevant reports from China and abroad. We believe that in-depth studies of lamprey could promote an effective outcome(s) in the research on genetics of animal development and biomedicine.

Identification, recombinant expression and immunological study of Lja-SHP2 in Lampetra japonica.

The protein tyrosine phosphatase SHP2 of higher vertebrates, encoded by ptpn11 gene, catalyzes the dephosphorylation of tyrosine phosphorylation site, and plays regulatory roles in various signaling pathways by cooperating with other protein tyrosine kinase. Previous studies have shown that SHP2 plays an important role in the activation and signal transduction of T and B cells in higher vertebrates. To study the role of a SHP2 homologous molecule of lampreys (Lja-SHP2) in immune response, we cloned and expressed the open reading frame sequence of Lja-SHP2 gene in prokaryotic expression vector pET-32a. The recombinant protein was successfully expressed in E. coli and the rabbit-derived polyclonal antibody was prepared. Lampetra japonica were immunized with mixed bacteria, and the mRNA and protein of Lja-SHP2 in immune-related cells and tissues were detected by real-time quantitative PCR and Western blotting after immunization. The Lja-SHP2 mRNA and protein were not significantly affected in leukocytes and supraneural myeloid bodies, but up-regulated significantly in gill tissues (P<0.05) after challenged by mixed bacteria, which indicated that Lja-SHP2 mainly participates in the immune response of gill tissues after mixed bacteria stimulation. To further investigate whether Lja-SHP2 level was affected in three lymphocyte subsets, the B-cell mitogen lipopolysaccharide (LPS) and T-cell mitogen phytohaemagglutinin (PHA) were employed to boost the immune response in L. japonica. LPS immune stimulation increased Lja-SHP2 in leucocytes significantly compared with the control group, and but had a marginal effect on Lja-SHP2 expression in gills and supraneural myeloid bodies. PHA immune stimulation could up-regulate Lja-SHP2 level in leukocytes, gill tissues and supraneural myeloid bodies. The change of Lja-SHP2 was especially dramatical in leukocytes, which was about 2.5 times higher than that in the control group, suggesting that Lja-SHP2 is involved in the lamprey immune response mediated by PHA. Consistent with the previous finding that PHA could induce the activation of VLRA+ lymphocytes, our results showed that Lja-SHP2 might be included in the immune response of VLRA+ lymphocytes mediated by PHA in gills. This research will benefit exploring the functions of Lja-SHP2 in the immune response of lamprey and will provide clues for understanding the phylogenesis of SHP2 molecular family, and its roles in the early occurrence and evolution of adaptive immune system in higher vertebrates.

IL-18 induced IL-23/IL-17 expression impairs Aß clearance in cultured THP-1 and BV2 cells.

Recent studies have provided overwhelming evidence of the involvement of microglia-related molecular networks in the pathogenesis of Alzheimer's diseases (AD). The potential involvement of pro-inflammatory cytokines interleukin (IL)-18, IL-23 and IL-17 on amyloid (Aß) clearance is still unclear. In this study, we addressed that there might be a net relationship among IL-18, IL-23, and IL-17 and they can affect Aß clearance in cultured macrophage/microglia cells. In human macrophage cell line THP-1, Aß42 incubation could increase the expression of IL-18, IL-23 and IL-17 in a concentration dependent manner. THP-1 cell could clear Aß42 in the culture medium time-dependently, but its capacity of Aß clearance was impaired by IL-18, IL-23 or IL-17 treatment. Similarly, the capacity of the microglia cell line BV2 to clear Aß42 was impaired by IL-18, IL-23 or IL-17 treatment. In co-cultures of BV2 with APP/PS1 neuron, Aß was efficiently cleared by BV2 cell, but Aß clearance was impaired by IL-18, IL-23 or IL-17 treatment. The effects of IL-18, IL-23 and IL-17 could be blocked by their corresponding neutralizing antibodies. In addition, the inhibitory effects of IL-18 were blocked by IL-23 or IL-17 neutralizing antibodies while the inhibitory effects of IL-23 were blocked by IL-17 neutralizing antibodies. Our study provides evidences showing that amyloid induced IL-18/IL-23/IL-17 axis could impair macrophage and microglia-mediated Aß clearance. Thus, IL-18/IL-23/IL-17 axis might be a therapeutic target in AD.

Innate Lymphoid Cells: A Link between the Nervous System and Microbiota in Intestinal Networks.

Innate lymphoid cells (ILCs) are a novel family of innate immune cells that act as key coordinators of intestinal mucosal surface immune defense and are essential for maintaining intestinal homeostasis and barrier integrity by responding to locally produced effector cytokines or direct recognition of exogenous or endogenous danger patterns. ILCs are also involved in the pathogenesis of inflammatory bowel disease (IBD). Many studies have demonstrated the occurrence of crosstalk between ILCs and intestinal microbiota, and ILCs have recently been shown to be connected to the enteric nervous system (ENS). Thus, ILCs may act as a key link between the nervous system and microbiota in intestinal networks. In this review, we briefly summarize the role of the ILCs in the intestinal tract (particularly in the context of IBD) and discuss the relationship between ILCs and the microbiota/ENS.

Different intervention strategies for preventing type 2 diabetes mellitus in China: A systematic review and network meta-analysis of randomized controlled trials.

Different strategies are increasingly used for early intervention in prediabetes in China, but the effects of these strategies on incident diabetes have not yet been confirmed. The aim of the present study was to assess systematically the effects of different strategies for preventing diabetes, aimed at Chinese people with prediabetes. Seven electronic databases were searched to identify eligible trials published from inception to September 20, 2016. Randomized controlled trials with a minimum follow-up duration of 6 months were included. Standard pairwise meta-analysis with a random-effects model and network meta-analysis with a frequentist framework were performed. A total of 63 studies, including 11 intervention strategies, were included. Compared with placebo, all strategies, except for lipid-affecting drugs and sitagliptin, reduced the rate of incident diabetes with different levels of effectiveness, ranging from 0.18 (95% confidence interval [CI] 0.12, 0.27) to 0.39 (95% CI 0.20, 0.75). Ranking probability analysis indicated that metformin and ß-cell-stimulating drugs reduced the risk of diabetes most, with probabilities of 87.4% and 81%, respectively. Ethnicity and cultural factors should be considered for diabetes prevention. Most of the included trials were of poor methodological quality, however, and the results should be interpreted with caution.

[Application progress of CRISPR/Cas9 genome editing technology in the treatment of HIV-1 infection].

The goal of gene therapy is to introduce foreign genes into human target cells in a certain way to correct or compensate diseases caused by defective or abnormal genes. Therefore, gene therapy has great practical significance in studying the treatment of persistent or latent HIV-1 infection. At present, the existing methods of gene therapy have some major defects such as limited target site recognition and high frequency of off-targets. The latest research showed that the clustered regularly interspaced short palindromic repeats (CRISPR) /CRISPR-associated nuclease 9 (Cas9) system from bacteria and archaea has been successfully reformed to a targeted genome editing tool. Thus, how to achieve the goal of treating HIV-1 infection by modifying targeted HIV-1 virus genome effectively using the CRISPR/Cas9 system has become a current research focus. Here we review the latest achievements worldwide and briefly introduce applications of the CRISPR/Cas9 genome editing technology in the treatment of HIV-1 infection, including CCR5 gene editing, removal of HIV-1 virus and activation of HIV-1 virus, in order to provide reference for the prevention and treatment of HIV-1 infection.

[The anti-tumor mechanisms in long-lived rodents].

Rodents, including the nude mice with congenital aplasia of the thymus, cancer-resistant naked mole rat (Heterocephalus glaber) and blind mole rat (Spalax galili), are important model organisms that are widely used in biomedical research. The aging process is closely related to cancer incidence in mammals and the aging degree is positively correlated with the risk of cancer. Since rodents account for 40% of mammals, study of the unique antitumor mechanism in long-lived rodents is very important. Replicative senescence is anti-tumor mechanism that prevalently exist in rodents, however, unique anti-tumor mechanisms have been found in naked mole-rats and blind mole-rats. The cancer resistance of Spalax galili is mediated by cell-released IFN-ß which activates p53 and Rb signaling pathway and the cells undergoes concerted cell death while that of Heterocephalus glaber is mediated by high molecular weight hyaluronan (HMW-HA) which causes contact inhibition. In addition, highly expressed pro-cell-death and anti-inflammation related genes are found in the genome of both naked mole-rats and blind mole-rats. In this review, we summarize the anti-tumor mechanisms in both Heterocephalus glaber and Spalax galili, which may provide information for related research.

Research progress of the structure and function of NF-κB and IκB in different animal groups.

The mammalian nuclear transcription factors NF-κB (Nuclear factor of kappa B) family plays a central role in the immune system, and participates in immune response, tumorigenesis and apoptosis by regulating the genes involved in the development and survival of lymphocytes. Inhibitor of kappa B (IκB) is an inhibitor of NF-κB, which keeps NF-κB in inactive state. When cells are stimulated by external signals, activated IκB is phosphated after a series of signal transmission, and then releases the NF-κB heterodimers that migrate into the nucleus and regulate gene expression. As an important functional protein, they exist in both higher animals and lower animals, and exhibit conserved functions. In this review, we summarize the investigation about NF-κB and IκB in several representative animals from invertebrates to vertebrates, in order to approach a more comprehensive and provide references for related researches.

[Voltage-gated sodium channels are involved in regulating the biological functions of microglial cells].

Microglial cells are widely distributed in the brain and spinal cord, and usually act as resident immune cells which could provide continuous monitoring roles within the central nervous system. When the cells in the central nervous system are injured, microglial cells are activated and induce a series of biological effects. Recently, several voltage-gated sodium channel subtypes were found to be expressed on the surface of the microglial cells which are able to participate in the regulation of the activation, phagocytosis, secretion of multiple cytokines/chemokines, migration, invasion of microglial cells, and etc. In the present study, the latest progresses on the regulation of voltage-gated sodium channel isoforms on microglial cells were summarized and analyzed. In addition, the mechanism and future research of the relationship between voltage-gated sodium channels and microglial cells were also discussed.

[Molecular regulations of phosphatidylserine eversion in plasma membrane].

Phosphatidylserine (PS), one important phospholipid of cell membranes, has crucial biological functions. Under special pathological circumstances such as cell apoptosis, cells cannot generate enough ATP for energy and the concentration of cytoplasmic Ca²âº increases, resulting in PS eversion. PS eversion has different biological functions in different cell types. In addition, the degree of eversion is closely associated with the progress of diseases. Therefore, it can be therapeutic targets of cancer and many other diseases. In this review, we summarize the fundamental biological functions of PS, molecular mechanisms of PS eversion, as well as its potential in translational medicine.

[Genetic basis of immune response of lymphocyte-like cells in the mucosal immune system of Lampetra japonica].

In recent years, the antigen recognition mechanism based on variable lymphocyte receptors (VLRs) was found in agnathan lamprey. To illuminate the genetic basis of immune response of lymphocyte-like cells in the mucosal immune system of lamprey and explore the evolutionary relationship of adaptive immune responses between the jawless and jawed vertebrates, we constructed cDNA libraries of lamprey (Lampetra japonica) gills before and after stimulation, and then performed high-throughput transcriptome sequencing and analysis. Through functional annotation of 88 525 assembled unigenes, 21 704 and 9769 unigenes were annotated in Gene Ontology (GO) and Kyto Encyclopedia of Genes and Genomes (KEGG) databases, respectively. Among 999 unigenes involved in multiple pathways of immune system, 184 unigenes were highly homologous to 51 TCR (T cell receptor) and BCR (B cell receptor) signalling molecules in higher vertebrates, indicating that molecules involved in adaptive immune signalling pathways in higher vertebrates also exist in lampreys. In addition, identification of five VLRA, seven VLRB and four VLRC molecules suggest that at least three types of lymphocyte subsets are distributed in lamprey gill mucosal immune tissues. The results of real-time fluorescence quantitative PCR showed that the expression levels of Lck, Fyn and Zap70 were up-regulated after immune stimulation while those of Syk, Btk and Blnk were not changed significantly, indicating the activation of TCR-like signal transduction pathway after antigen stimulation in lamprey gill tissues. Our studies preliminaryly proved that two parallel adaptive immune systems in jawless and jawed vertebrates have common genetic basis, and also provided valuable clues to the exploration of signalling processes of VLRA⁺, VLRB⁺, and VLRC⁺ lymphocyte-like cells in response to antigens.

[The identification and verification of species-specific microRNAs and their precursors in Lampetra japonica].

MicroRNAs (miRNAs) negatively regulate genes which are involved in various biological processes of metabolism at both transcriptional and post-transcriptional levels. In recent years, the existence and function of miRNAs have been extensively studied in plants and animals with the application of deep sequencing and microarray technology. In this study, small RNAs from leucocytes of Lampetra japonica (L. japonica) were sequenced using the second generation high-throughput sequencing technology. A total of 5 207 787 small RNA sequences were identified, and 4 739 346 of them assembled into 10 989 variants. Based on sequence similarity analysis, the sequences of these variants matched known miRNAs of 306 conserved families, among which 6 conserved miRNA family members expressed at an extremely high level which reflected the conservatism of miRNAs among species. In addition, 70 unannotated sequences were predicted to be new miRNAs, and 34 of them were further verified expressing in antigen-treated L. japonica leucocytes by miRNA microarray assay. Moreover, the minimal folding free energy indexes for 16 of the 34 miRNA precursors exceed 0.85, indicating the existence of species-specific miRNAs in L. japonica which may play important roles in regulating, growth, development and disease response of L. japonica leukocytes.

Increased serum levels of interleukin-18, -23 and -17 in Chinese patients with Alzheimer's disease.

AIMS: To evaluate the serum levels of interleukin (IL)-18, IL-23 and IL-17 in Chinese patients with Alzheimer's disease (AD), and explore correlations between the three cytokines and relevant parameters. METHODS: Serum concentrations of IL-18, IL-23 and IL-17 were measured by ELISA for 53 AD patients and 53 sex- and age-matched healthy controls in a community of elderly individuals in a Shanghai suburb. RESULTS: Serum concentrations of IL-18, IL-23 and IL-17 were significantly higher in AD patients than controls. The serum level of IL-23 was observed to be significantly higher (p = 0.049) in female AD patients than male AD patients. In addition, a significantly inverse correlation was found between IL-18 and MMSE score (rs = -0.356, p = 0.011) for all AD patients. CONCLUSION: Elevated IL-18, IL-23 and IL-17 levels are observed in AD patients and differences may exist between males and females. Besides, IL-18 may correlate with the severity of AD.

Cloning and expression analysis of a novel high-mobility group box 2 homologue from Lampetra japonica.

High-mobility group box 2 (HMGB2) is a nonhistone architectural protein that plays important roles in many biological processes. In this study, we cloned a homologue of the HMGB2 from the lymphocyte-like cells of Lampetra japonica (L. japonica). Sequence analysis reveals that L. japonica HMGB2 contains two highly conserved motifs and shares more than 70 % identity with the homologues from other vertebrate species. Subsequently, Lj-HMGB2 was subcloned into the pET-28a(+) and pIRES2 AcGFP1-Nuc vector and expressed in Rosetta blue (DE3) and Hela cell lines, respectively. The recombinant L. japonica HMGB2 (rLj-HMGB2) with apparent molecular mass of 22 kDa was further purified by His-Bind affinity chromatography. Real-time quantitative PCR indicates that the expression level of Lj-HMGB2 was particularly up-regulated in intestines after challenged with lipopolysaccharide, while up-regulated in lymphocyte-like cells and heart after challenged with concanavalin A in vivo. In addition, rLj-HMGB2 could induce the generation of proinflammatory mediators in the activated human acute monocytic leukemia cell line (THP1), which suggested that Lj-HMGB2 may participate in the immune response of the lampreys.

Effects of exogenous melatonin on the osmotic regulation and antioxidant capacity of Ginkgo biloba seedlings under salt stress.

We investigated the effects of exogenous melatonin on the osmotic regulation and antioxidant capacity of 4-year-old Ginkgo biloba seedlings under salt stress. There were three treatments, with low (50 mmol·L-1), medium (100 mmol·L-1), and high (200 mmol·L-1) NaCl stress. Leaves were sprayed and the soil was watered with melatonin solution (0, 0.02, 0.1, 0.5 mmol·L-1). The results showed that saline stress significantly inhibited the osmoregulation and antioxidant capacities of G. biloba seedlings. Application of exogenous melatonin at appropriate concentrations (0.02, 0.1 mmol·L-1) under salt stress could promote plant growth, reduce the rate of electrolyte leakage, decrease the content of flavonoids and malonic dialdehyde, and enhance peroxidase and superoxide dismutase activities in leaves. High concentration (0.5 mmol·L-1) of exogenous melatonin would aggravate the oxidative and osmotic stresses. The 0.02 and 0.1 mmol·L-1 exogenous melatonin alleviated osmotic stress and oxidative stress in G. biloba seedlings under salt stress, while the 0.02 mmol·L-1 exogenous melatonin treatment had the best effect on NaCl stress alleviation. Ground diameter, branch width, branch length, electrolyte leakage rate, superoxide dismutase activity, and flavonoids content could be used as the key indices for rapid identification of the degree of salt stress in G. biloba seedlings.

Salinity influence correction for zinc ion seawater quality criteria and ecological risk assessment in Chinese seas.

The increasing prevalence of zinc pollution in marine ecosystems, primarily from industrial sources, has become a global environmental concern. This study addresses zinc toxicity in Chinese coastal waters, emphasizing the importance of considering environmental factors like salinity and temperature in establishing water quality criteria (WQC). Data collected from various marine regions underwent meticulous analysis, incorporating salinity corrections to derive more precise criteria values. The short-term criteria for the Bohai Sea, Yellow Sea, East China Sea, and South China Sea were 94.0, 77.6, 84.2, and 118 µg/L under the salinity correction, respectively, and the long-term criteria was 4.10 µg/L. Ecological risk assessments employing diverse methodologies revealed varying levels of risk across sea areas, underscoring the nuanced nature of zinc pollution's impact on marine ecosystems. Greater acute and chronic risk of zinc ions observed in the Yellow Sea region. These findings underscore the imperative need for tailored management strategies to protect local marine life from the environmental threats posed by zinc.

[Structure, distribution, classification, and function of C1q protein family: a review].

The C1q protein family consists of many proteins containing a Clq domain, which exists widely within organisms from bacteria to mammals. The domain organization of these proteins mainly includes a leading signal peptide, a collagen-like region, and a globular Clq domain. According to their structural characteristics, the C1q protein family can be divided into three subgroups: C1q, C1q-like and ghC1q. C1q, as the first subcomponent of classical pathway in the complement system, has the ability to bind immune complexes and triggers activation of the classical complement pathway. In addition, it can be a pattern recognition receptor with the unique ability to sense an amazing variety of ligands. C1q-like protein contains a collagen-like region and a globular Clq domain which is similar to Clq molecule. It involves in leech central nervous system repair. However, in vertebrates, its function converts from a lectin to an immunoglobulin binding molecule and it involves in the activation of complement system. The structure of ghC1q protein is composed of a globular Clq domain and a short N-terminal sequence. This protein contains secreted globular head C1q proteins and cellular globular head C1q proteins. The sghClq protein plays an important role in the innate immune system of invertebrates. The sghC1q proteins that belong to vertebrates may serve as a new class of transneuronal regulators of synapse development and synaptic plasticity in various brain regions. The earliest cghC1q gene can be traced back to bacteria of the genus Bacillus. Its stereotypical gC1q jelly roll topology substantiates that the gC1q domain has an ancient evolutionary history and a highly conserved structure. This review focuses on the structure, distribution, classification, and function of C1q family proteins, providing valuable clues for the future research in this field.

[Variable lymphocyte receptors: the novel tool for clinical diagnosis and therapy].

Monoclonal antibodies, which are widely applied to the diagnosis and therapy of cancers as well as autoimmune diseases, have been made significant progresses. Currently, the monoclonal antibodies for clinical applications are mostly based on the modified immunoglobulins. However, the variable lymphocyte receptors (VLRs), which are recently discovered as specific antigen receptors of jawless vertebrates, provide a new perspective for the development of antibody reagents and drugs. Compared with immunoglobulins, the antigen-binding specificity, affinity and stability of VLRs-based antibodies are better. In addition, the production technology of antigen-specific monoclonal VLRs has become more and more mature. Therefore, the VLRs have a higher clinical value and may become the next-generation antibody drug. This review focuses on the basic feature, production method and application prospect of VLRs, which provides valuable clues for the applications of VLRs in the field of clinical diagnosis and therapy.

Comparative proteomic analysis suggests that mitochondria are involved in autosomal recessive polycystic kidney disease.

Autosomal recessive polycystic kidney disease (ARPKD), characterized by ectatic collecting duct, is an infantile form of PKD occurring in 1 in 20 000 births. Despite having been studied for many years, little is known about the underlying mechanisms. In the current study, we employed, for the first time, a MS-based comparative proteomics approach to investigate the differently expressed proteins between kidney tissue samples of four ARPKD and five control individuals. Thirty two differently expressed proteins were identified and six of the identified protein encoding genes performed on an independent group (three ARPKD subjects, four control subjects) were verified by semi-quantitative RT-PCR, and part of them were further validated by Western blot and immunohistochemistry. Moreover, similar alteration tendency was detected after downregulation of PKHD1 by small interfering RNA in HEK293T cell. Interestingly, most of the identified proteins are associated with mitochondria. This implies that mitochondria may be implicated in ARPKD. Furthermore, the String software was utilized to investigate the biological association network, which is based on known and predicted protein interactions. In conclusion, our findings depicted a global understanding of ARPKD progression and provided a promising resource of targeting protein, and shed some light further investigation of ARPKD.