Metabolite components and nutritional composition of the endosperm in seven species from Gleditsia.

As an important agricultural product, the endosperm portion of Gleditsia sinensis seeds, called "zào jiǎo mǐ" (ZJM) in Chinese, has gradually gained popularity and has been accepted by the public. However, there is limited information on the nutritional value and metabolic components of endosperm among Gleditsia. This study compared the endosperm composition among seven species. The types of metabolites, content of nutrients and amino acids were determined. A total of 4495 types of metabolites were detected. Galactose metabolism (gmx00052) was enriched in all combinations compared with G. sinensis. The polysaccharides content ranged from 51.49 to 80.37 g/100 g. Based on considerations of growth rate, seed yield, amino acid content, and interspecific differences, G. fera could be an alternative planting option to G. sinensis. These results can provide a reference for growers in selecting Gleditsia varieties and provide insights into the industrial applications of Gleditsia endosperm products.

Transcriptome analysis reveals regulatory mechanisms of different drought-tolerant Gleditsia sinensis seedlings under drought stress.

BACKGROUND: Gleditsia sinensis is a significant tree species from both ecological and economic perspectives. However, its growth is hampered by temporary droughts during the seedling stage, thereby impeding the development of the G. sinensis industry. Drought stress and rehydration of semi-annual potted seedlings using an artificial simulated water control method. RNA sequencing (RNA-seq) analyses were conducted on leaves collected from highly resistant (HR) and highly susceptible (HS) seedling families at five different stages during the process of drought stress and rehydration to investigate their gene expression patterns. RESULTS: The differentially expressed genes (DEGs) were predominantly enriched in pathways related to "chloroplast" (GO:0009507), "photosynthesis" (GO:0015979), "plant hormone signal transduction" (map04075), "flavonoid biosynthesis" (map00941), "stress response", "response to reactive oxygen species (ROS)" (GO:0000302), "signal transduction" (GO:0007165) in G. sinensis HR and HS families exposed to mild and severe drought stress. Additionally, the pathways related to "plant hormone signal transduction" (map04075), and osmoregulation were also enriched. The difference in drought tolerance between the two families of G. sinensis may be associated with "transmembrane transporter activity" (GO:0022857), "stress response", "hormones and signal transduction" (GO:0007165), "cutin, suberine and wax biosynthesis" (map00073), "ribosome" (map03010), "photosynthesis" (map00195), "sugar metabolism", and others. An enrichment analysis of DEGs under severe drought stress suggests that the drought tolerance of both families may be related to "water-soluble vitamin metabolic process" (GO:0006767), "photosynthesis" (map00195), "plant hormone signal transduction" (map04075), "starch and sucrose metabolism" (map00500), and "galactose metabolism" (map00052). Osmoregulation-related genes such as delta-1-pyrroline-5-carboxylate synthase (P5CS), Amino acid permease (AAP), Amino acid permease 2 (AAP2) and Trehalose-phosphate synthase (TPS), as well as the antioxidant enzyme L-ascorbate peroxidase 6 (APX6), may be significant genes involved in drought tolerance in G. sinensis. Five genes were selected randomly to validate the RNA-seq results using quantitative real-time PCR (RT-qPCR) and they indicated that the transcriptome data were reliable. CONCLUSIONS: The study presents information on the molecular regulation of the drought tolerance mechanism in G. sinensis and provides a reference for further research on the molecular mechanisms involved in drought tolerance breeding of G. sinensis.

Physiological response and drought resistance evaluation of Gleditsia sinensis seedlings under drought-rehydration state.

G. sinensis is a crucial tree species in China, possessing important economic and ecological value, and having a wide geographical distribution. G. sinensis seedlings is highly vulnerable to the drought-rehydration-drought cycle during their growth, and there is a lack of quantitative and systematic research on the physiological mechanisms of drought resistance and rehydration in G. sinensis. There is also a lack of good drought-resistant families and reliable methods for evaluating drought resistance, which severely hinders the selection and promotion of drought-resistant G. sinensis families and the industry's development. Therefore, this study selection 58 families seedlings of G. sinensis to drought stress and rehydration using an artificial simulated water control method in potted seedlings. The aim was to compare the effects of different levels of drought and rehydration on the growth and physiological indices of seedlings from different families. Identification of drought-resistant families and dependable drought related indices and techniques, the explanation of divergence in drought stress effects on various drought-resistant seedlings and the mechanisms underpinning growth and physiological responses, and the provision of theoretical reference for G. sinensis drought-resistant variety selection and cultivation. The Drought Resistance Index (DRI) served as the primary indicator, supplemented by growth, leaf morphology, and photosynthetic physiological indicators, to thoroughly assess and identify five distinct drought tolerant taxa while also selecting five representative families. Soluble protein (SP), proline (Pro), and malondialdehyde (MDA) contents, as well as the activities of catalase (CAT), peroxidase (POD) and superoxide dismutase (SOD) in seedlings from the five families, increased as the degree of drought intensified. The highest values were appeared during periods of severe drought, and gradually decreased after subsequent rehydration. Principal component analysis (PCA) revealed MDA and soluble sugars (SS) as the primary predictors of drought and rehydration response in G. sinensis seedlings respectively. Changes in osmoregulatory substance content and increased antioxidant enzyme activity may be crucial for responding to drought tolerance mechanisms. Leaf morphological indicators, seedling height, soil plant analysis development (SPAD) value, photosynthetic indicators, and MDA are dependable parameters for assessing the drought tolerance of G. sinensis seedlings. When assessing the drought-resistance of seedlings using physiological indicators such as photosynthesis, a comprehensive analysis should incorporate multiple indicators and methods. This evaluation approach could serve as a reference for screening exceptional drought-resistant families of G. sinensis.

Influence of seamless nursing model of humanistic care on nursing quality and blood infection risk of neurosurgical ICU patients and its correlation with APACHE II score.

This research aims to explore the influence of seamless nursing mode of humanistic care on nursing quality and blood infection risk of ICU patients in neurosurgery, and the model of correlation with APACHE II score. 110 ICU patients are grouped into control set and study set, which are, respectively, given the previous routine nursing and the seamless management based on humanistic care to compare the two sets in the following aspects: nursing quality, blood infection rate, anxiety and depression extension before and after nursing, nursing satisfaction and APACHE II score, and to figure out the correlation between patient nursing quality score, and to compare blood infection and APACHE II score. Comparison and statistical analysis are used to disclose the influence and the correlation. The results show that there is not only a large negative correlation between nursing quality scores and APACHE II scores, but also a large negative correlation between the risk of blood infection and APACHE II score.

Activation-induced pyroptosis contributes to the loss of MAIT cells in chronic HIV-1 infected patients.

BACKGROUND: Mucosal-associated invariant T (MAIT) cells are systemically depleted in human immunodeficiency virus type 1 (HIV-1) infected patients and are not replenished even after successful combined antiretroviral therapy (cART). This study aimed to identify the mechanism underlying MAIT cell depletion. METHODS: In the present study, we applied flow cytometry, single-cell RNA sequencing and immunohistochemical staining to evaluate the characteristics of pyroptotic MAIT cells in a total of 127 HIV-1 infected individuals, including 69 treatment-naive patients, 28 complete responders, 15 immunological non-responders, and 15 elite controllers, at the Fifth Medical Center of Chinese PLA General Hospital, Beijing, China. RESULTS: Single-cell transcriptomic profiles revealed that circulating MAIT cells from HIV-1 infected subjects were highly activated, with upregulation of pyroptosis-related genes. Further analysis revealed that increased frequencies of pyroptotic MAIT cells correlated with markers of systemic T-cell activation, microbial translocation, and intestinal damage in cART-naive patients and poor CD4+ T-cell recovery in long-term cART patients. Immunohistochemical staining revealed that MAIT cells in the gut mucosa of HIV-1 infected patients exhibited a strong active gasdermin-D (GSDMD, marker of pyroptosis) signal near the cavity side, suggesting that these MAIT cells underwent active pyroptosis in the colorectal mucosa. Increased levels of the proinflammatory cytokines interleukin-12 (IL-12) and IL-18 were observed in HIV-1 infected patients. In addition, activated MAIT cells exhibited an increased pyroptotic phenotype after being triggered by HIV-1 virions, T-cell receptor signals, IL-12 plus IL-18, and combinations of these factors, in vitro. CONCLUSIONS: Activation-induced MAIT cell pyroptosis contributes to the loss of MAIT cells in HIV-1 infected patients, which could potentiate disease progression and poor immune reconstitution.

Global transcriptomic characterization of T cells in individuals with chronic HIV-1 infection.

To obtain a comprehensive scenario of T cell profiles and synergistic immune responses, we performed single-cell RNA sequencing (scRNA-seq) on the peripheral T cells of 14 individuals with chronic human immunodeficiency virus 1 (HIV-1) infection, including nine treatment-naive (TP) and eight antiretroviral therapy (ART) participants (of whom three were paired with TP cases), and compared the results with four healthy donors (HD). Through analyzing the transcriptional profiles of CD4+ and CD8+ T cells, coupled with assembled T cell receptor sequences, we observed the significant loss of naive T cells, prolonged inflammation, and increased response to interferon-α in TP individuals, which could be partially restored by ART. Interestingly, we revealed that CD4+ and CD8+ Effector-GNLY clusters were expanded in TP cases, and persistently increased in ART individuals where they were typically correlated with poor immune restoration. This transcriptional dataset enables a deeper understanding of the pathogenesis of HIV-1 infection and is also a rich resource for developing novel immune targeted therapeutic strategies.

Dynamic Metabolomics Study of the Bile Acid Pathway During Perioperative Primary Hepatic Carcinoma Following Liver Transplantation.

BACKGROUND There are many situations of abnormal metabolism influencing liver graft function. This study aims to provide data for the development of liver function recovery after liver transplantation by dynamically analyzing metabolites of bile acids pathway in serum. MATERIAL AND METHODS A comprehensive metabolomics profiling of serum of 9 liver transplantation patients before transplantation, on the 1st, 3rd, and 7th days after liver transplantation, and healthy individuals were performed by ultra-performance liquid chromatography-mass spectrometry (UPLC-MS). Multivariate data and dynamic analysis were used to search for biomarkers between the metabolomics profiles present in perioperative liver transplantation and normal controls. RESULTS Thirty-three differential endogenous metabolites were screened by the threshold of variable importance in the projection (VIP) from an orthogonal partial least square discriminant analysis (OPLS-DA) greater than 1.0, q-value <0.05, and fold change (FC) ≤0.8 or ≥1.2 between the preoperative group and the normal controls in negative mode. The metabolite intensities of taurocholic acid, taurochenodeoxycholic acid, chenodeoxycholic acid glycine conjugate, and glycocholic acid pre-transplantation were significantly higher than those of normal controls. The average metabolite intensities of taurocholic acid and taurochenodesoxycholic acid on the first day after liver transplantation were lower than those observed pre-transplantation. The average metabolite intensities on day 3 after liver transplantation showed a sudden increase and then decreased after 7 postoperative days. The average metabolite intensities of glycocholic acid and chenodeoxycholic acid glycine conjugate showed an increasing trend on the 1st, 3rd, and 7th days after liver transplantation. CONCLUSIONS Use of taurocholic acid and taurochenodeoxycholic acid-related bile secretion, liver regeneration, and de novo bile acid synthesis may help clinical evaluation and provide data for the development of liver function recovery after liver transplantation.

Microenvironment-Induced In Situ Self-Assembly of Polymer-Peptide Conjugates That Attack Solid Tumors Deeply.

In cancer treatment, the unsatisfactory solid-tumor penetration of nanomaterials limits their therapeutic efficacy. We employed an in vivo self-assembly strategy and designed polymer-peptide conjugates (PPCs) that underwent an acid-induced hydrophobicity increase with a narrow pH-response range (from 7.4 to 6.5). In situ self-assembly in the tumor microenvironment at appropriate molecular concentrations (around the IC50 values of PPCs) enabled drug delivery deeper into the tumor. A cytotoxic peptide KLAK, decorated with the pH-sensitive moiety cis-aconitic anhydride (CAA), and a cell-penetrating peptide TAT were conjugated onto poly(ß-thioester) backbones to produce PT-K-CAA, which can penetrate deeply into solid tumors owing to its small size as a single chain. During penetration in vivo, CAA responds to the weak acid, leading to the self-assembly of PPCs and the recovery of therapeutic activity. Therefore, a deep-penetration ability for enhanced cancer therapy is provided by this in vivo assembly strategy.

Near-Infrared Laser-Driven in Situ Self-Assembly as a General Strategy for Deep Tumor Therapy.

Nanotherapeutics have encountered some bottleneck problems in cancer therapy, such as poor penetration and inefficient accumulation in tumor site. We herein developed a novel strategy for deep tissue penetration in molecular level and near-infrared (NIR) laser guided in situ self-assembly to solve these challenges. For the proof-of-concept study, we synthesized the polymer-peptide conjugates (PPCs) composed of (i) poly(ß-thioester) as thermoresponsive backbone, (ii) functional peptides (cytotoxic peptide and cell-penetrating peptide), and (iii) the NIR molecule with photothermal property. The PPCs in the molecular level with small size (<10 nm) can penetrate deeply into the interior of the tumor at body temperature. Under the irradiation of NIR laser, the temperature rise induced by photothermal molecules led to the intratumoral self-assembly of thermoresponsive PPCs. The resultant spherical nanoparticles can accumulate in tumor and enter cells effectively, inducing cell apoptosis by destroying mitochondria membrane. Through the site-specific size control, a variety of merits of PPCs are realized including deep tumor penetration, enhanced accumulation, and cellular internalization in vivo. Taking advantage of the NIR guided in situ assembly strategy, numerous polymeric or nanoscaled therapeutics with high anticancer activity can be exploited.

The differentially expressed circular ribonucleic acids of primary hepatic carcinoma following liver transplantation as new diagnostic biomarkers for primary hepatic carcinoma.

Recent studies have shown that circular ribonucleic acids have differential expression in some diseases. This study compared the expression levels of five circular ribonucleic acids between patients of primary hepatic carcinoma following liver transplantation and healthy individuals for searching a new diagnostic biomarker about primary hepatic carcinoma. We chose differentially expressed targeted circular ribonucleic acids according to fold change ≥2.0 or ≤-2.0 between circular ribonucleic acids microarray of perioperative liver transplantation and normal controls. Then we used the Arraystar home-made micro-ribonucleic acid target prediction software based on TargetScan and miRanda to predict circular ribonucleic acid/micro-ribonucleic acid interactions. And we assess the expression levels of hsa_circ_100571, hsa_circ_400031, hsa_circ_102032, hsa_circ_103096, and hsa_circ_102347 in the peripheral blood of normal controls and liver transplantation patients before transplantation and on the first, third, and seventh days after transplantation by real-time quantitative polymerase chain reaction. We chose five circular ribonucleic acids, two of which have been correlated with micro-ribonucleic acid-related carcinoma recurrence after liver transplantation, hepatocellular carcinoma and analyzed their expression with 2-△△Ct method. The expression level of hsa_circ_100571 and hsa_circ_400031 on day 1 after liver transplantation was higher than pre-transplantation (p < 0.01), and these levels showed a declining trend on post-transplantation. The expression level of hsa_circ_102032 and hsa_circ_103096 on day 1 after liver transplantation was lower than pre-transplantation (p < 0.01) and decreased on post-transplantation. There were the significantly different expressions between the post-transplantation day 7 and normal control (p < 0.01). The expression level of hsa_circ_102347 on day 1 after liver transplantation was lower than pre-transplantation (p < 0.01). This expression showed a declining trend on post-transplantation, and the postoperative day 7 level was similar to normal control (p > 0.05). Five types of circular ribonucleic acid-related micro-ribonucleic acids had varying degrees of upregulation and downregulation between perioperative transplantation of primary hepatic carcinoma patients and normal controls; the hsa_circ_102347 is most likely to have association with primary hepatic carcinoma.

Enzyme-sensitive cytotoxic peptide-dendrimer conjugates enhance cell apoptosis and deep tumor penetration.

Peptide nanodrugs have been developed as promising antitumor chemotherapeutics because they partially overcome the drawbacks of free peptide drugs, but insufficient tumor penetration and interference of peptide function limit their further application. In this work, we have developed multifunctional peptide conjugated dendrimers for improving tumor penetration, cancer cell-specific peptide delivery and anticancer ability. The cytotoxic peptide KLAK, cell-penetrating peptide TAT and matrix metalloproteinase 2 (MMP2)-sensitive peptide-poly(ethylene glycol) (PEG) were conjugated onto dendrimers by one-pot synthesis to gain PKT-S-PEG. The enzyme-sensitive properties and incubation stability of the dendrimers were investigated by dynamic light scattering (DLS) and transmission electron microscopy (TEM). Moreover, the cell viability, internalization pathway, mitochondria-regulated apoptosis and tumor penetration ability were measured by CCK-8 assay, lysosome colocalization, JC-1 assay and multicellular spheroid (MCS) experiments, respectively, in human primary glioblastoma (U87) cells. PKT-S-PEG showed significantly enhanced intracellular delivery performance, antitumor efficacy and deep tumor penetration capacity compared to a control non-MMP2 sensitive dendrimer PKT-C-PEG. The MMP2-overexpressing tumor microenvironment caused deprotection by removal of PEG, resulting in the decrease of particle size and exposure of KLAK and TAT, which enhanced tumor penetration, the entry of bioactive peptides into cells and subsequently the effective disruption of mitochondria. We believe that the peptide-dendrimer conjugate has potential for specific and effective delivery of peptide-based therapeutics into tumors.

An "On-Site Transformation" Strategy for Treatment of Bacterial Infection.

To date, numerous nanosystems have been developed as antibiotic replacements for bacterial infection treatment. However, these advanced systems are limited owing to their nontargeting accumulation and the consequent side effects. Herein, transformable polymer-peptide biomaterials have been developed that enable specific accumulation in the infectious site and long-term retention, resulting in enhanced binding capability and killing efficacy toward bacteria. The polymer-peptide conjugates are composed of a chitosan backbone and two functional peptides, i.e., an antimicrobial peptide and a poly(ethylene glycol)-tethered enzyme-cleavable peptide (CPC-1). The CPC-1 initially self-assembles into nanoparticles with pegylated coronas. Upon the peptides are cleaved by the gelatinase secreted by a broad spectrum of bacterial species, the resultant compartments of nanoparticles spontaneously transformed into fibrous nanostructures that are stabilized by enhanced chain-chain interaction, leading to exposure of antimicrobial peptide residues for multivalent cooperative electrostatic interactions with bacterial membranes. Intriguingly, the in situ morphological transformation also critically improves the accumulation and retention of CPC-1 in infectious sites in vivo, which exhibits highly efficient antibacterial activity. This proof-of-concept study demonstrates that pathological environment-driven smart self-assemblies may provide a new idea for design of high-performance biomaterials for disease diagnostics and therapeutics.

In Situ Monitoring Intracellular Structural Change of Nanovehicles through Photoacoustic Signals Based on Phenylboronate-Linked RGD-Dextran/Purpurin 18 Conjugates.

The stimuli-responsive polymeric nanocarriers have been studied extensively, and their structural changes in cells are important for the controlled intracellular drug release. The present work reported RGD-dextran/purpurin 18 conjugates with pH-responsive phenylboronate as spacer for monitoring the structural change of nanovehicles through ratiometric photoacoustic (PA) signal. Phenylboronic acid modified purpurin 18 (NPBA-P18) could attach onto the RGD-decorated dextran (RGD-Dex), and the resulting RGD-Dex/NPBA-P18 (RDNP) conjugates with different molar ratios of RGD-Dex and NPBA-P18 were prepared. When the moles of NPBA-P18 were equivalent to more than triple of RGD-Dex, the single-stranded RDNP conjugates could self-assemble into nanoparticles in aqueous solution due to the fairly strong hydrophobicity of NPBA-P18. The pH-responsive aggregations of NPBA-P18 were investigated by UV-vis, fluorescence, and circular dichroism spectra, as well as transmission electron microscope. Based on distinct PA signals between monomeric and aggregated state, ratiometric PA signal of I750/I710 could be presented to trace the structural change progress. Compared with RDNP single chains, the nanoparticles exhibited effective cellular internalization through endocytosis pathway. Furthermore, the nanoparticles could form well-ordered aggregates responding to intracellular acidic environment, and the resulting structural change was also monitored by ratiometric PA signal. Therefore, the noninvasive PA approach could provide a deep insight into monitoring the intracellular structural change process of stimuli-responsive nanocarriers.

Circular RNA and gene expression profiles in gastric cancer based on microarray chip technology.

The aim of the present study was to screen gastric cancer (GC) tissue and adjacent tissue for differences in mRNA and circular (circRNA) expression, to analyze the differences in circRNA and mRNA expression, and to investigate the circRNA expression in gastric carcinoma and its mechanism. circRNA and mRNA differential expression profiles generated using Agilent microarray technology were analyzed in the GC tissues and adjacent tissues. qRT-PCR was used to verify the differential expression of circRNAs and mRNAs according to the interactions between circRNAs and miRNAs as well as the possible existence of miRNA and mRNA interactions. We found that: i) the circRNA expression profile revealed 1,285 significant differences in circRNA expression, with circRNA expression downregulated in 594 samples and upregulated in 691 samples via interactions with miRNAs. The qRT-PCR validation experiments showed that hsa_circRNA_400071, hsa_circRNA_000543 and hsa_circRNA_001959 expression was consistent with the microarray analysis results. ii) 29,112 genes were found in the GC tissues and adjacent tissues, including 5,460 differentially expressed genes. Among them, 2,390 differentially expressed genes were upregulated and 3,070 genes were downregulated. Gene Ontology (GO) analysis of the differentially expressed genes revealed these genes involved in biological process classification, cellular component classification and molecular function classification. Pathway analysis of the differentially expressed genes identified 83 significantly enriched genes, including 28 upregulated genes and 55 downregulated genes. iii) 69 differentially expressed circRNAs were found that might adsorb specific miRNAs to regulate the expression of their target gene mRNAs. The conclusions are: i) differentially expressed circRNAs had corresponding miRNA binding sites. These circRNAs regulated the expression of target genes through interactions with miRNAs and might become new molecular biomarkers for GC in the future. ii) Differentially expressed genes may be involved in the occurrence of GC via a variety of mechanisms. iii) CD44, CXXC5, MYH9, MALAT1 and other genes may have important implications for the occurrence and development of GC through the regulation, interaction, and mutual influence of circRNA-miRNA-mRNA via different mechanisms.

ARHGAP4 mutated in a Chinese intellectually challenged family.

OBJECTIVE: Mental retardation is characterized by lower intelligence compared to the average intelligence of persons the same age. These patients have low adaptive capacity acquired by society. The genetic factors of causing MR include monogenic disease, chromosome structural aberration, and chromosome number aberration and so on. We explored the cause of a Chinese family suffering from mental retardation. METHODS: We used karyotyping technology to determine the karyotype of the proband, and we used FISH to verify the result of the karyotyping. We used whole-exome sequencing to identify the disease-causing gene and used Sanger sequencing to verify the result of whole-exome sequencing to assess the family's gene expression. RESULTS: The G-banding of the karyotype revealed that the patient's karyotype is 46, XY. FISH revealed that the patient does not have a trisomy syndrome. The karyotype of the proband is normal. Using whole-exome sequencing, we identified 108,767 variants in the exome gene of the patient, including 101,787 SNPs and 6980 InDels. Combining clinical information and bioinformatics analysis, including databases filtering and SIFT analysis, we found ARHGAP4 in X chromosome was candidate MR disease-causing gene. PCR and Sanger sequencing results were consistent with whole-exome sequencing. ARHGAP4 (T491M) mutation was present in the genome of the proband and his mother is a carrier, while his father, sister, and brother do not carry this mutation. CONCLUSION: According to clinical information, whole-exome sequencing results and Sanger verification results, ARHGAP4 (T491M) mutation may be disease-causing gene of the MR patient. The relation between ARHGAP4 mutation and MR clinical characteristic is needed to be illuminated with participation of more MR patients.

CCDC40 mutation as a cause of primary ciliary dyskinesia: a case report and review of literature.

BACKGROUND AND AIMS: Primary ciliary dyskinesia (PCD) is a rare, genetically heterogeneous disorder. Genetic defects affecting motility of cilia and flagella cause chronic destructive airway disease, situs inversus and, frequently, male infertility in PCD. To date, although several genes have been implicated in PCD, the genetic bases of most cases of PCD remain elusive. METHODS: By applying a whole-exome sequencing strategy, we reported a case of PCD carrying a novel mutant alleles in CCDC40 gene, and did literature review. RESULTS: A 36-year-old nonsmoking Chinese man suffered from chronic cough since childhood and an 8-year history of primary infertility. Lung biopsy showed respiratory bronchiolitis. Chest images showed bronchiectasis and situs inversus. Semen analysis showed high sperm counts and poor sperm motility. Transmission electron microscopy (TEM) of cilia cross-sections showed ultrastructural defects, including inner dynein arms (IDA) defect and axonemal disorganization. To identify gene mutations that cause PCD, we performed exome sequencing to analyze genome of this patient, and discovered a previously uncharacterized mutant alleles (NM_001243342.1:c.2609G>A; p. R870H) in CCDC40 gene. In addition, we summarize the PCD disease-causing genes and CCDC40 mutant sites based on current literature. CONCLUSIONS: We identified a novel mutant alleles in CCDC40 gene, which altered the protein sequence and resulted in the ultrastructural defects in the microtubule structure of cilia. Thereby, these defects lead to the patient with bronchiectasis, bronchiolitis and infertility.

Study on 3'-UTR length polymorphism in peripheral blood mononuclear cells of uremia patient.

OBJECTIVE: The objective of this study was to measure the 3'-untranslated region (3'-UTR) polymorphism lengths in peripheral blood mononuclear cells (PBMCs) from uremia patients. METHOD: We sequenced the alternative polyadenylation sites in the 3'-UTR of PBMCs from 10 uremic patients and 10 healthy people to detect different gene expression levels between uremia patients and healthy controls. Quantitative reverse transcription polymerase chain reaction was used as validation. RESULT: Compared with the healthy control group, 691 genes in uremic patients had significantly different 3'-UTR lengths. Of these genes, 475 genes showed shortened 3'-UTRs, and the 3'-UTRs of 216 genes were lengthened. The verification results matched the original sequencing results. CONCLUSION: There were significant differences in 3'-UTR lengths between uremic patients and healthy controls, and analysis of the differential genes may contribute to the understanding of uremia pathogenesis.

Composition and variation analysis of the TCR ß-chain CDR3 repertoire in systemic lupus erythematosus using high-throughput sequencing.

The ability of T lymphocytes to mount an immune response against a diverse array of pathogens is primarily conveyed by the amino acid (aa) sequence of the hypervariable complementarity-determining region 3 (CDR3) segments of the T cell receptor (TCR). In this study, we used a combination of multiplex-PCR, Illumina sequencing and IMGT/HighV-QUEST for a standardized analysis of the characteristics and polymorphisms of the T-cell receptor BV complementarity-determining region 3 (TCR BV CDR3) gene in peripheral blood mononuclear cells (PBMCs) from SLE patients and healthy donors (NC). We found the distributions of CDR3, VD indel, and DJ indel lengths to be comparable between the SLE and NC groups. The degree of clonal expansion in the SLE group was significantly greater than in the NC group, and the expression levels of 10 TRßV segments and 6 TRßJ segments were also significantly different in the SLE group. Regarding public T cell responses, 3CDR3 DNA sequences and 4 aa sequences were shared by all SLE patients and may serve as biomarkers for SLE disease risk, diagnosis and/or prognosis.

Evaluating a particular circulating microRNA species from an SLE patient using stem-loop qRT-PCR.

Systemic lupus erythematosus (SLE) is a complex autoimmune disease, and correct judgment of SLE activity is very important in guiding precise clinical treatment. Circulating microRNAs (miRNAs) could serve as potential biomarkers of disease activity or status in SLE, and here we describe a modified qRT-PCR method for detecting them. Stem loop has become one of the most powerful methods for determining miRNA expression because it is highly sensitive and accurate and requires only small amount of sample. In this chapter, we focus on a stem-loop reverse transcription-bound SYBR green qRT-PCR protocol for evaluating a particular circulating miRNA species in SLE patients.

Microarray technology for analysis of microRNA expression in renal biopsies of lupus nephritis patients.

Systemic lupus erythematosus (SLE) is a complex autoimmune disease, which predominantly occurs in females and is characterized by autoantibody production against a host of nuclear self-antigens and deposition of proinflammatory immune complexes in the organs including kidney glomeruli. MicroRNAs are small noncoding intracellular RNAs that modulate gene expression at the posttranslational level. Microarray technology is in widespread use for analysis of microRNA (miRNA) gene expression because of its flexibility and accurate high throughput. RNA microarray technology is based on nucleic acid hybridization between a mixture of labeled RNA targets and their corresponding complementary probes. This article offers a technological overview of microarray technology for analysis of microRNA gene expression in kidney biopsies from SLE patients.