ATD: a comprehensive bioinformatics resource for deciphering the association of autophagy and diseases

Autophagy is the natural, regulated, destructive mechanism of the eukaryotes cell that disassembles unnecessary or dysfunctional components. In recent years, the association between autophagy and diseases has attracted more and more attention, but our understanding of the molecular mechanism about the association in the system perspective is limited and ambiguous. Hence, we developed the comprehensive bioinformatics resource Autophagy To Disease (ATD, http://auto2disease.nwsuaflmz.com) to archive autophagy-associated diseases. This resource provides bioinformatics annotation system about genes and chemicals about autophagy and human diseases by extracting results from previous studies with text mining technology. Based on the big data from ATD, we found that some classes of disease tend to be related with autophagy, including respiratory disease, cancer, urogenital disease and digestive system disease. We also found that some classes of autophagy-related diseases have a strong association among each other and constitute modules. Furthermore, we extracted the autophagy-disease-related genes (ADGs) from ATD and provided a novel algorithm Optimized Random Forest with Label model to predict potential ADGs. This bioinformatics annotation system about autophagy and human diseases may provide a basic resource for the further detection of the molecular mechanisms of autophagy pathway to disease.

Dynamic and modular gene regulatory networks drive the development of gametogenesis

Gametogenesis is a complex process, which includes mitosis and meiosis and results in the production of ovum and sperm. The development of gametogenesis is dynamic and needs many different genes to work synergistically, but it is lack of global perspective research about this process. In this study, we detected the dynamic process of gametogenesis from the perspective of systems biology based on protein-protein interaction networks (PPINs) and functional analysis. Results showed that gametogenesis genes have strong synergistic effects in PPINs within and between different phases during the development. Addition to the synergistic effects on molecular networks, gametogenesis genes showed functional consistency within and between different phases, which provides the further evidence about the dynamic process during the development of gametogenesis. At last, we detected and provided the core molecular modules of different phases about gametogenesis. The gametogenesis genes and related modules can be obtained from our Web site Gametogenesis Molecule Online (GMO, http://gametsonline.nwsuaflmz.com/index.php), which is freely accessible. GMO may be helpful for the reference and application of these genes and modules in the future identification of key genes about gametogenesis. Summary, this work provided a computational perspective and frame to the analysis of the gametogenesis dynamics and modularity in both human and mouse.

Genetic analysis of a hybrid sterility gene that causes both pollen and embryo sac sterility in hybrids between Oryza sativa L. and Oryza longistaminata

Oryza longistaminata originates from African wild rice and contains valuable traits conferring tolerance to biotic and abiotic stress. However, interspecific crosses between O. longistaminata and Oryza sativa cultivars are hindered by reproductive barriers. To dissect the mechanism of interspecific hybrid sterility, we developed a near-isogenic line (NIL) using indica variety RD23 as the recipient parent and O. longistaminata as the donor parent. Both pollen and embryo sac semi-sterility were observed in F₁ hybrids between RD23 and NIL. Cytological analysis demonstrated that pollen abortion in F₁ hybrids occurred at the early bi-nucleate stage due to a failure of the first mitosis in microspores. Partial embryo sacs in the F₁ hybrids were defective during the functional megaspore formation stage. Most notably, nearly half of the male or female gametes were aborted in heterozygotes S40ⁱS40^l, regardless of their genotypes. Thus, S40 was indicated as a one-locus sporophytic sterility gene controlling both male and female fertility in hybrids between RD23 and O. longistaminata. A population of 16 802 plants derived from the hybrid RD23/NIL-S40 was developed to fine-map S40. Finally, the S40 locus was delimited to an 80-kb region on the short arm of chromosome 1 in terms with reference sequences of cv. 93-11. Eight open reading frames (ORFs) were localized in this region. On the basis of gene expression and genomic sequence analysis, ORF5 and ORF8 were identified as candidate genes for the S40 locus. These results are helpful in cloning the S40 gene and marker-assisted transferring of the corresponding neutral allele in rice breeding programs.

Adenosine A2A receptor inactivation alleviates early-onset cognitive dysfunction after traumatic brain injury involving an inhibition of tau hyperphosphorylation

Tau is a microtubule-associated protein, and the oligomeric and hyperphosphorylated forms of tau are increased significantly after neurotrauma and considered important factors in mediating cognitive dysfunction. Blockade of adenosine A_2A receptors, either by caffeine or gene knockout (KO), alleviates cognitive dysfunction after traumatic brain injury (TBI). We postulated that A_2AR activation exacerbates cognitive impairment via promoting tau hyperphosphorylation. Using a mouse model of moderate controlled cortical impact, we showed that TBI induced hyperphosphorylated tau (p-tau) in the hippocampal dentate gyrus and spatial memory deficiency in the Morris water maze test at 7 days and 4 weeks after TBI. Importantly, pharmacological blockade (A_2AR antagonist ZM241385 or non-selective adenosine receptor antagonist caffeine) or genetic inactivation of A_2ARs reduced the level of tau phosphorylation at Ser404 and alleviated spatial memory dysfunction. The A_2AR control of p-tau is further supported by the observations that a KO of A_2AR decreased the activity of the tau phosphorylation kinases, glycogen synthase kinase-3β (GSK-3β) and protein kinase A (PKA) after TBI, and by that CGS21680 (A_2AR agonist) exacerbated okadaic acid-induced tau hyperphosphorylation in cultured primary hippocampal neurons. Lastly, CGS21680-induced neuronal tau hyperphosphorylation and axonal injury were effectively alleviated by individual treatments with ZM241385 (A_2AR antagonist), H89 (PKA antagonist) and SB216763 (GSK-3β antagonist), or by the combined treatment with H89 and SB216763. Our findings suggest a novel mechanism whereby A_2AR activation triggers cognitive dysfunction by increasing the phosphorylation level of tau protein after TBI and suggest a promising therapeutic and prophylactic strategy by targeting aberrant A_2AR signaling via tau phosphorylation.

[Impact of apical preparation diameter on fracture resistance of mandibular premolar roots]

OBJECTIVE

To compare the fracture resistance of roots of mandibular premolar with different apical preparation diameters.

METHODS

Sixty single-rooted single canal permanent mandibular premolar teeth extracted newly for orthodontic reason without immatureness, fracture or cracks were selected, with a curvature less than 10°, and internal length: short diameter of less than 2 at a level 5 mm from the apex. All the teeth were decoronated, leaving roots 13 mm in length. The initial apical file size for the teeth was ≤15#. The roots were assigned to 6 groups based on weights with random block design. Group A: blank control group, no instrumentation was performed. Groups B-F: the master apical file (MAF) was 40#, 45#, 50#, 55# and 60#, respectively. In the five experimental groups the roots were instrumented using hand files with step-back technique at 1 mm increments, resulting in a taper of 0.05. The irrigant used was distilled water. After mounted in acrylic resin, all the teeth were subject to vertical loading using an Instron testing machine until fractured. The occurrence of fractures was detected when the applied load suddenly decreased. The fracture load values and fracture modes were recorded. One-way ANOVA and post-hoc Tukey test were used to determine the difference of fracture load values between the groups (P<0.05). Chi-square tests were used to compare the modes of root fracture.

RESULTS

Five experimental groups exhibited lower fracture load values than that of control group [(1 444±155) N]. The mean fracture load values for roots instrumented to an apical diameter of 50# [(1 027±128) N], 55# [(994±150) N] and 60# [(983±166) N] were significantly lower than that of control group and 40# group [(1 339±131) N] and 45# [(1 287±144) N] (P<0.05). Buccal-lingual fracture, mesio-distal fracture and compound fracture occurred 55%, 13% and 32%, respectively. No difference of fracture mode was detected in the six groups.

CONCLUSION

The fracture resistance reduced significantly when the roots were instrumented to an apical diameter of 50# or larger.

Effect of health education combining diet and exercise supervision in Chinese women with perimenopausal symptoms: a randomized controlled trial

OBJECTIVE

This study aimed to evaluate the effect of health education combining diet and exercise supervision on menopausal symptoms and diet/exercise habits.

METHODS

The randomized controlled study enrolled 60 patients with perimenopausal syndrome (Kupperman Menopause Index (KMI) score ≥15). The participants were randomized into either an intervention group (n = 30) or a control group (n = 30). Women were interviewed with questionnaires about perimenopausal symptoms, diet pattern and exercise habit. Their height and weight were measured. Women in the intervention group received health education, diet supervision and exercise supervision twice a week while those in the control group continued as normal. The total KMI score, scores of individual symptoms, diet pattern and exercise habit were measured after intervention.

RESULTS

The total KMI score, the individual KMI scores for paresthesia, irritability, depression/suspicious, fatigue, arthralgia/myalgia, and palpitations of the intervention group were significantly lower compared with the control group after intervention. The intake of cereal, meat, fats and oils of the intervention group were significantly lower at week 12 compared with baseline. The percentage of women with a regular exercise habit was significantly higher in the intervention group than in the control group after intervention.

CONCLUSIONS

Twelve weeks intervention of health education combining diet and exercise supervision could improve perimenopausal symptoms and help the patients establish good living habits.

GAB2 rs2373115 variant contributes to Alzheimer's disease risk specifically in European population

A genome-wide association study identified GAB2 rs2373115 to be associated with Alzheimer's disease (AD) risk in European population. However, inconsistent results are reported in East Asian population. Here, we performed an updated analysis using 65,704 samples including 20,982 AD cases and 44,722 controls. First, we investigated the GAB2 rs2373115 variant in Asian population using 3974 AD cases and 7568 controls. To further evaluate the effect of rs2373115 in different populations, we selected 17,008 AD cases and 37,154 controls in European population. We used three genetic models, and found no significant heterogeneity in Asian population. A fixed effect model analysis showed no significant association between rs2373115 and AD in Asian population. There was no significant heterogeneity in the pooled East Asian and European populations. The fixed effect model analysis again showed no significant association between rs2373115 and AD in these pooled populations. Taken together, these findings suggest that GAB2 rs2373115 may contribute to AD susceptibility only in European population but not in East Asian population.

Hydronephrosis caused by intrauterine contraceptive device migration: three case reports with literature review

Translocation of intrauterine contraceptive device (IUD) from the uterus rarely occurs, which can lead to serious complications. Here the authors reported three cases of IUD migration from into the ureter, bladder, and peritoneal cavity that caused hydronephrosis, respectively. All the three patients received minimally invasive surgeries and recovered.

Use of photoacoustic excitation and laser vibrometry to remotely detect trace explosives

In this paper, we examine a laser-based approach to remotely initiate, measure, and differentiate acoustic and vibrational emissions from trace quantities of explosive materials against their environment. Using a pulsed ultraviolet laser (266 nm), we induce a significant (>100  Pa) photoacoustic response from small quantities of military-grade explosives. The photoacoustic signal, with frequencies predominantly between 100 and 500 kHz, is detected remotely via a wideband laser Doppler vibrometer. This two-laser system can be used to rapidly detect and discriminate explosives from ordinary background materials, which have significantly weaker photoacoustic response. A 100  ng/cm² limit of detection is estimated. Photoablation is proposed as the dominant mechanism for the large photoacoustic signals generated by explosives.

Impact of Food Restriction on the Expression of the Adiponectin System and Genes in the Hypothalamic-Pituitary-Ovarian Axis of Pre-Pubertal Ewes

Adiponectin, a cytokine secreted typically by adipocytes, has been implicated as a molecular switch between female reproduction and energy balance. The present study was undertaken to investigate the expression of adiponectin system and patterns of genes in the hypothalamic-pituitary-ovary (HPO) axis of food-restricted pre-pubertal ewes. Eighteen 2-month-old female ewes were assigned to 3 groups after a pre-feeding ad libitum for 10 days (six in each group): the control group (C), the low-food-restricted group (LR) and the high-food-restricted group (HR), which were fed with 100%, 70% and 50% of ad libitum food intake, respectively. The hypothalamus, pituitary, ovary and serum were collected after food restriction for 2 months. Results by ELISA showed that food restriction increased serum adiponectin concentrations. Quantitative real-time PCR showed that the gene transcriptions for adiponectin receptor 1 (AdipoR1) and 2 (AdipoR2) were enhanced in the hypothalamic-pituitary-ovarian (HPO) axis, while KISS-1/GPR-54 and gonadotropin-releasing hormone (GnRH) in the hypothalamus and luteinizing hormone β-subunit (LHβ) and follicle-stimulating hormone β-subunit (FSHβ) in the pituitary were reduced after food restriction. Immunohistochemistry results demonstrated that AdipoR1 localized in the oocytes of follicles in the ovary. These results suggest that the alterations in the expression of adiponectin and its receptors in response to food restriction might negatively influence the HPO axis.

Chinese SLE Treatment and Research group (CSTAR) registry VII: prevalence and clinical significance of serositis in Chinese patients with systemic lupus erythematosus

Objectives

To investigate both the prevalence and clinical characteristics of serositis in Chinese patients with systemic lupus erythematosus (SLE) in a large cohort in the Chinese SLE Treatment and Research group (CSTAR) database.

Methods

A prospective cross-sectional study of patients with SLE was conducted based on the data from the CSTAR registry. Serositis was defined according to the 1999 revised American College of Rheumatology (ACR) criteria for SLE – that is, pleuritis/pleural effusion and/or pericarditis/pericardial effusion detected by echocardiography, chest X-ray or chest computerized tomography (CT) scan. Peritonitis/peritoneal effusion were confirmed by abdominal ultrasonography. We analysed the prevalence and clinical associations of serositis with demographic data, organ involvements, laboratory findings and SLE disease activity.

Results

Of 2104 patients with SLE, 345 were diagnosed with serositis. The prevalence of lupus nephritis (LN), interstitial lung disease and pulmonary arterial hypertension, as well as the presence of leukocytopenia, thrombocytopenia, hypocomplementemia and anti-dsDNA antibodies was significantly higher in patients with serositis ( P < 0.05). Significantly higher SLE disease activity scores were found in patients with serositis compared to those patients without serositis ( P < 0.05). Lupus-related peritonitis had similar clinical manifestations and laboratory profiles as serositis caused by SLE.

Conclusions

There is a significant association of nephropathy, interstitial lung disease, pulmonary arterial hypertension, hypocomplementemia, leukocytopenia, thrombocytopenia and elevated anti-dsDNA antibodies with serositis. The results suggest that higher SLE disease activity contributes to serositis development, and should be treated aggressively.