Integration of eQTL and machine learning to dissect causal genes with pleiotropic effects in genetic regulation networks of seed cotton yield.

The dissection of a gene regulatory network (GRN) that complements the genome-wide association study (GWAS) locus and the crosstalk underlying multiple agronomical traits remains a major challenge. In this study, we generate 558 transcriptional profiles of lint-bearing ovules at one day post-anthesis from a selective core cotton germplasm, from which 12,207 expression quantitative trait loci (eQTLs) are identified. Sixty-six known phenotypic GWAS loci are colocalized with 1,090 eQTLs, forming 38 functional GRNs associated predominantly with seed yield. Of the eGenes, 34 exhibit pleiotropic effects. Combining the eQTLs within the seed yield GRNs significantly increases the portion of narrow-sense heritability. The extreme gradient boosting (XGBoost) machine learning approach is applied to predict seed cotton yield phenotypes on the basis of gene expression. Top-ranking eGenes (NF-YB3, FLA2, and GRDP1) derived with pleiotropic effects on yield traits are validated, along with their potential roles by correlation analysis, domestication selection analysis, and transgenic plants.

Predation of Cyclopoid Copepods on the Theronts of Ichthyophthirius multifiliis: Shedding Light on Biocontrol of White Spot Disease.

White spot disease, caused by the parasitic ciliate Ichthyophthirius multifiliis, is a significant threat to the freshwater fish farming industry worldwide, resulting in massive mortality and economic losses. Eliminating the free-swimming theronts from the culture environment is considered crucial for the control of I. multifiliis infection. It is well-documented that planktonic ciliates are valuable food resources for macro-zooplankton in aquatic ecosystems. In this study, we developed a fluorescence labeling method for alive theronts and found that cyclopoid copepods Thermocyclops taihokuensis, Mesocyclops spp., Macrocyclops sp., and Paracyclopina sp. present predation on the theronts in co-culture experiments. Laboratory challenge tests further confirmed that the presence of zooplankton in the culture water body significantly reduced the infection of I. multifiliis in goldfish (p < 0.01). Results from this study revealed that cyclopoid copepods have the potential to be used as biological control agents against white spot disease in aquaculture.

Characterization of the complete mitochondrial genome of Nippotaenia mogurndae Yamaguti and Miyata, 1940 (Cestoda: Nippotaeniidae).

In this study, we report the first complete mitochondrial genome of the tapeworm Nippotaenia mogurndae in the order Nippotaeniidea Yamaguti, 1939. This mitogenome, which is 14,307 base pairs (bp) long with an A + T content of 72.2%, consists of 12 protein-coding genes, 22 transfer RNA (tRNA) genes, two rRNA genes, and two non-coding regions. Most tRNAs have a conventional cloverleaf structure, but trnS1 and trnR lack dihydrouridine arms of tRNA. The two largest non-coding regions, NCR1 (220 bp) and NCR2 (817 bp), are located between trnY and trnS2 and between nad5 and trnG, respectively. Phylogenetic analyses of mitogenomic data indicate that N. mogurndae is closely related to tapeworms in the order Cyclophyllidea.

The lincRNA XH123 is involved in cotton cold-stress regulation.

KEY MESSAGE: We characterize a functional lincRNA, XH123 in cotton seedling in defense of cold stress. The silencing of XH123 leads to increased sensitivity to cold stress and the decay of chloroplast. Cotton, which originated from the arid mid-American region, is one of the most important cash crops worldwide. Cultivated cotton is now widely spread throughout high-altitude regions such as those in the far northwest of Asia. In such areas, spring temperatures below 12 ℃ impose cold stress on cotton seedlings, with concomitant threat of lost yield and productivity. It is documented that cold stress can induce differential expression of long noncoding RNAs (lncRNAs) in cotton; however, it is not yet clear if these cold-responsive lncRNAs are actively involved with tolerance of cold stress at the molecular level. Here, we select ten long intergenic non-coding RNAs as candidate genes and use virus-induced gene silencing and additional cold treatments to examine their roles in the response to cold stress during the cotton seedling stage. One such gene, XH123, was revealed to be involved in tolerance of cold stress. Specifically, XH123-silenced plants demonstrated sensitivity to cold stress, exhibiting chloroplast damage and increased endogenous levels of reactive oxygen species. The transcriptome profile of XH123-silenced seedlings was similar to that of cold-stressed seedlings having the known cold stress gene PIF3 silenced. These results imply that the lincRNA XH123 is actively involved with cold stress regulation in cotton during the seedling stage.

Functional examination of lncRNAs in allotetraploid Gossypium hirsutum.

BACKGROUND: An evolutionary model using diploid and allotetraploid cotton species identified 80 % of non-coding transcripts in allotetraploid cotton as being uniquely activated in comparison with its diploid ancestors. The function of the lncRNAs activated in allotetraploid cotton remain largely unknown. RESULTS: We employed transcriptome analysis to examine the relationship between the lncRNAs and mRNAs of protein coding genes (PCGs) in cotton leaf tissue under abiotic stresses. LncRNA expression was preferentially associated with that of the flanking PCGs. Selected highly-expressed lncRNA candidates (n = 111) were subjected to a functional screening pilot test in which virus-induced gene silencing was integrated with abiotic stress treatment. From this low-throughput screen, we obtained candidate lncRNAs relating to plant height and tolerance to drought and other abiotic stresses. CONCLUSIONS: Low-throughput screen is an effective method to find functional lncRNA for further study. LncRNAs were more active in abiotic stresses than PCG expression, especially temperature stress. LncRNA XLOC107738 may take a cis-regulatory role in response to environmental stimuli. The degree to which lncRNAs are constitutively expressed may impact expression patterns and functions on the individual gene level rather than in genome-wide aggregate.

Absence of CG methylation alters the long noncoding transcriptome landscape in multiple species.

The noncoding regions throughout the genome are in large part comprised of transposable elements (TEs), some of which are functionalized with long intergenic noncoding RNAs (lincRNAs). DNA methylation is predominantly associated with TEs, but little is known about its contribution to the transcription of lincRNAs. Here, we examine the lincRNA profiles of DNA methylation-related mutants of five species, Arabidopsis, rice, tomato, maize, and mouse, to elucidate patterns in lincRNA regulation under altered DNA methylation status. Significant activation of lincRNAs was observed in the absence of CG DNA methylation rather than non-CG. Our study establishes a working model of the contribution of DNA methylation to regulation of the dynamic activity of lincRNA transcription.

Paclitaxel plus nedaplatin vs. paclitaxel plus carboplatin in women with epithelial ovarian cancer: A multi-center, randomized, open-label, phase III trial.

The multi-center, randomized, open-label, phase III trial discussed in the present study was performed to compare the clinical outcomes of nedaplatin (NDP) plus paclitaxel, and carboplatin (CBP) plus paclitaxel for the treatment of epithelial ovarian cancer (EOC). In the current study, 182 patients with International Federation of Gynecology and Obstetrics (FIGO) stage II-IV EOC were randomly assigned to receive NDP plus paclitaxel or CBP plus paclitaxel at 3-week intervals for a total of six courses. The primary endpoints were progression-free survival rate (PFS) and overall survival rate (OS). The secondary endpoints were toxicity profiles. The median follow-up was 44.63 months [95% confidence interval (CI) 33.67-46.47 months] for the NDP group and 47.63 months (95% CI 45.13-49.07 months) for the CBP group. Overall, there was no significant difference in PFS or OS between the two groups (P=0.09 for PFS, and P=0.65 for OS). For the patients with FIGO stage III-IV EOC, the NDP plus paclitaxel regimen significantly prolonged PFS (P=0.02) but did not result in improved OS (P=0.53) when compared with the CBP group. The patients in the NDP plus paclitaxel group also exhibited a lower incidence rate of grade 3 or 4 leucopenia (P=0.03). Other hematological and non-hematological toxicity profiles were similar between the two groups. Compared with CBP plus paclitaxel regimens, NDP plus paclitaxel regimens achieved comparable survival outcomes and similar toxicity profiles. However, patients of FIGO stage III-IV EOC may experience more clinical benefits from NDP plus paclitaxel treatment, including a prolonged PFS and a lower incidence rate of leucopenia. Therefore, an NDP-based regimen may be an alternative choice when using platinum-based agents to treat EOC.

HPV16 early gene E5 specifically reduces miRNA-196a in cervical cancer cells.

High-risk human papillomavirus (HPV) type 16, which is responsible for greater than 50% of cervical cancer cases, is the most prevalent and lethal HPV type. However, the molecular mechanisms of cervical carcinogenesis remain elusive, particularly the early steps of HPV infection that may transform normal cervical epithelium into a pre-neoplastic state. Here, we report that a group of microRNAs (microRNAs) were aberrantly decreased in HPV16-positive normal cervical tissues, and these groups of microRNAs are further reduced in cervical carcinoma. Among these miRNAs, miR196a expression is the most reduced in HPV16-infected tissues. Interestingly, miR196a expression is low in HPV16-positive cervical cancer cell lines but high in HPV16-negative cervical cancer cell lines. Furthermore, we found that only HPV16 early gene E5 specifically down-regulated miRNA196a in the cervical cancer cell lines. In addition, HoxB8, a known miR196a target gene, is up-regulated in the HPV16 cervical carcinoma cell line but not in HPV18 cervical cancer cell lines. Various doses of miR196a affected cervical cancer cell proliferation and apoptosis. Altogether, these results suggested that HPV16 E5 specifically down-regulates miR196a upon infection of the human cervix and initiates the transformation of normal cervix cells to cervical carcinoma.

Asian Society of Gynecologic Oncology International Workshop 2014.

The Asian Society of Gynecologic Oncology International Workshop 2014 on gynecologic oncology was held in Asan Medical Center, Seoul, Korea on the 23rd to 24th August 2014. A total of 179 participants from 17 countries participated in the workshop, and the up-to-date findings on the management of gynecologic cancers were presented and discussed. This meeting focused on the new trends in the management of cervical cancer, fertility-sparing management of gynecologic cancers, surgical management of gynecologic cancers, and recent advances in translational research on gynecologic cancers.

[The effects of progesterone and insulin-like growth factor (IGF- I and IGF-II) on proliferation in human decidual stromal cells of early pregnancy in vitro].

OBJECTIVE: To study the effect of progesterone and Insulin-like growth factor (IGF-I and IGF-II) on proliferation in human decidual stromal cells of early pregnancy in vitro. METHODS: [3H]Thymidine (3H-TdR) uptake was applied to assess cell proliferation in human decidual stromal cells of early pregnancy (gestation of 5 to 7 weeks) in vitro after cultured with progesterone, IGF-I or IGF-II. RESULTS: Progesterone, IGF-I and IGF-II stimulated cell proliferation by 1.6-3.4 folds inhuman decidual stromal cells of early pregnancy in vitro (P<0.01), and those effects were time-dependent (P<0.01). CONCLUSION: Progesterone, IGF-I and IGF-II may play an important role in the regulation of proliferation and decidualization of stromal cells in human decidua of early pregnancy, which is essential for embryo implantation and the maintenance of early pregnancy.

[Expression of peroxiredoxin III in cervical lesions].

OBJECTIVE: To investigate the expression feature of peroxiredoxin III in cervical lesions and to further understand the mechanism for cervical cancer development/progression. METHODS: Expression of peroxiredoxin III was immunohistochemically detected in cervical cancer. In addition, cervical epithelia were transfected with recombinant adeno-associated virus vector containing human papillomavirus 16 E6/E7 and peroxiredoxin III expression was detected by quantitative real time PCR and Western blotting. RESULTS: Peroxiredoxin III was significantly up-regulated in cervical cancer tissues. Nevertheless, expression of peroxiredoxin III remained unchanged in cervical epithelial cells after transfection. CONCLUSION: It seems that Prx III is not related to cervical cancer initiation. Up-regulation of peroxiredoxin III in cervical cancer might be an active response to oxidative stress in malignant cells, which protects against oxidatiton-induced apoptosis.

[The affection of antigen presentation ability, which sources from the spleen macrophage of Balb/c mouse during late gestation, on maternal Th2/Th1 type of immune].

OBJECTIVE: To study the relationship between antigen presentation ability of spleen macrophage and maternal Th2>Th1 immune bias in Balb/c mice during late pregnancy. METHODS: Balb/c mice during late gestation were adopted in our study, and mice of same species in estrus were used as control. With antigen stimulation, the spleen macrophages of Balb/c mice were pulsed as antigen presentation cells (APC). T cells sensitized previously by pulsed macrophage (1 degree APC) were cultured in mixture with macrophage pulsed by same antigen (2 degrees APC). An antigen special lymphocyte transformation test in vitro was used to evaluate the antigen presentation ability of spleen macrophage from mice of late gestation, and a flow cytometry method was used to measured the ration of CD4, CD8, IL-10 and IFN-gamma positive cell in T cells which had being induced to proliferate. RESULTS: When spleen macrophage from mice during late gestation was used as 1 degree APC, the proliferation of sensitized T cell induced by macrophage from late pregnancy mice used as 2 degree APC was no more intense than that from estrous mice (P > 0.05). When spleen macrophage from mice in oestrus was used as 1 degree APC, the proliferation of sensitized T cell induced by macrophage from late pregnancy mice as 2 degrees APC was lower intense than that from estrous mice (P < 0.05). The type of 1 degree APC did not affect the ratio of IL-10 positive T cell, and macrophage from late pregnancy mice could induce more IL-10 positive T cell than that from estrous mice when they were used as 2 degrees APC (P < 0.05). The type of 1 degree or 2 degrees APC did not affect the ratio of IFN-gamma positive T cell. CONCLUSION: The spleen macrophage from mice during late gestation is not an effective APC, but can induce maternal Th2 type of immune and maintain the Th1 type immune at a lower stage during pregnancy, which means it may has some important role in pregnancy.

[P53 codon 72 polymorphism in cervical cancers and its correlation with HPV16,18E6].

OBJECTIVES: To examine p53 codon 72 polymorphism in cervical cancers and its correlation with HPV16/18 E6. METHODS: Cervical specimens were taken from 81 patients with cervical squamous cancer, 18 patients with cervical adenocarcinoma, 88 patients with CIN II - III and 60 patients without cancers. PCR was used to examine the p53 genotypes and the expression of HPV16 and 18 E6. RESULTS: The frequencies of p53 Arg homozygosity in cervical squamous cancer, cervical adenocarcinoma and CIN (II - III) were 58.020%, 55.55% and 59.09% respectively, greater than those of p53 Arg/Pro heterozygosity (30.86%, 27.78%, 21.59%) and those of p53 Pro homozygosity (11.12%, 16.67%, 19.32%). The normal cervical samples also showed less frequency of p53 Arg homozygosity (23.33%) than cervical squamous cancer. There were no significant differences in the frequencies of p53 Arg homozygosity, p53 Arg/Pro heterozygosity and p53 Pro homozygosity (23.33%, 40.00% and 36.67% respectively). The frequency of HPV16,18 E6-positive in cervical cancer and CIN was much higher than that in control group (81.84%, 50.00% and 53.41%) for the normal cervical samples. The expression of HPV16 and 18 E6 in cervical squamous cancers was more frequent than in CIN. The frequency of p53 Arg homozygosity in HRHPV E6-positive cervical squamous cancers (64.06%) was greater than in HRHPV E6-negative cervical squamous cancers (35.29%) and in HRHPV E6-positive normal samples (33.33%). The p53 codon 72 polymorphism showed no differences in samples with different FIGO staging and grades. CONCLUSION: p53 Arg homozygosity could serve as a risk indicator for the tumorigenesis of cervix. In combination with HRHPV E6, it might be able to predict the progression of cervical lesions. p53 codon 72 polymorphism is not associated with FIGO staging and grades of cervical cancers.

[Evaluation of the effect of fertility-saving surgery on young patients with malignant ovarian tumors].

OBJECTIVE: To evaluate the impact of fertility-saving surgery and adjuvant chemotherapy on survival and fertility of young patients with ovarian malignant tumors. METHODS: A retrospective analysis was done on 38 patients with ovarian malignant germ cell tumors, 22 patients with malignant epithelial tumors and 4 patients with sexual cord mesenchymal tumors receiving conservative treatments. Outcomes such as menstruation and reproduction ability were assessed. RESULTS: Fifty-nine among 64 patients have been alive up to now (92%). The overall survival rate for ovarian epithelial malignancies, malignant germ cell tumors and sexual cord mesenchymal tumors were 95% (21/22), 89% (34/38) and 4/4, respectively. Fifteen patients received second operation and recurrence was found in 6 patients. Among the 59 surviving patients, 53 had normal menstruation. Thirteen patients among 20 patients who wanted to get pregnant had 15 pregnancies and 9 successful deliveries. CONCLUSIONS: The management of fertility-saving surgery on patients with ovarian malignant germ cell tumors, whatever the stagings are, is a safe option. For patients with ovarian epithelial carcinomas, fertility-saving surgery is only indicated for low-stage (stage I), high-grade (G1), and patients who hope to maintain fertility function eagerly. Cisplatinum-based combination chemotherapy is necessary. Standardized chemotherapy has no effect on fertility function.

[Comparison of therapeutical effect between arterial interventional chemotherapy and venous chemotherapy on bulky or locally advanced cervical cancer].

OBJECTIVE: To investigate the therapeutical effect of arterial interventional chemotherapy and venous chemotherapy on bulky or locally advanced cervical cancer. METHODS: A retrospective study was carried out on 174 patients with bulky or locally advanced cervical cancers admitted to our hospital from Sept 1997 to Sept 2003. The therapeutical, toxic and adverse effects of either arterial interventional or venous chemotherapy were analyzed and compared. RESULTS: Among those 174 patients, 69 were given arterial interventional chemotherapy. Patients with cervical adenocarcinoma received cisplatin, fluorouracil, mitomycin C, and patients with squamous carcinoma of cervix were treated with bleomycin, cisplatin. The effective rate was 81%, and the rate of surgery after chemotherapy was 67%. While in the venous chemotherapy group, 105 patients were treated with the same chemotherapeutical schemes and doses as in arterial interventional chemotherapy group. The effective rate was 83% and the rate of surgery after chemotherapy was 70%. The differences between these two groups showed no significance (P > 0.05). No intolerable toxic and adverse effects were noticed during neoadjuvant chemotherapy. The 3- and 5-year survival rates of arterial interventional chemotherapy group were 76%, 70% respectively, and those of venous chemotherapy group were 78%, 71% respectively, without significant difference (P > 0.05). CONCLUSIONS: Neoadjuvant chemotherapy is a safe and effective means for treating patients with bulky or locally advanced cervical cancer. The therapeutical effects of venous and arterial interventional chemotherapy are similar. And no intolerable toxic and adverse effects were noticed during neoadjuvant chemotherapy. Venous administration is easy and inexpensive and less demanding for special equipment. It shows promising prospect in clinical application.

[Study of thalidomide on the growth and angiogenesis of ovary cancer SKOV3 transplanted subcutaneously in nude mice].

OBJECTIVE: To study the effect of thalidomide (Thd) used alone and in combination with cytoxan (CTX) on the growth and angiogenesis of human ovarian cancer transplanted subcutaneously in nude mice. METHODS: Human ovarian cancer model transplanted subcutaneously in nude mice was established, and divided into 3 groups: control group, Thd group, and Thd + CTX group. Tumor volume and weight, vascular endothelial growth factor (VEGF) mRNA, VEGF protein, microvascular density (MVD) were detected. The level of VEGF mRNA in tumor tissue was determined by relative quantative reverse transcription polymerase chain reaction. VEGF protein level in serum was determined by enzyme-linked immunosorbent assay (ELISA). MVD was calculated by immunohistochemistry. RESULTS: (1) Tumor volumes in Thd group and Thd + CTX group were smaller than those in control group (P < 0.05). (2) Expression of VEGF mRNA level in Thd group (55 +/- 9) and Thd + CTX group (26 +/- 7) was significantly lower than that in control group (79 +/- 7, P < 0.01). Serum VEGF level in Thd group, [(29 +/- 10) pg/ml] and Thd + CTX group [(12 +/- 6) pg/ml] was significantly lower than that in control group, [(71 +/- 16) pg/ml, P < 0.01]. (3) MVD in Thd group (12.6 +/- 3.3) and Thd + CTX group (10.6 +/- 1.9) was significantly smaller than that in control group (19.3 +/- 2.8, P < 0.01). CONCLUSIONS: Thalidomide can inhibit the growth and angiogenesis of human ovarian cancer transplanted subcutaneously in nude mice. Treatment with thalidomide is a potentially useful antitumor therapy for ovarian cancer.

[Immortalization of human embryonic cervical epithelial cells induced by E6, E7 genes of human papillomavirus 16].

OBJECTIVE: To establish an immortalized cell line derived from the embryonic cervical epithelium by infection with the recombinant adeno-associated virus (rAAV) containing human papillomavirus (HPV)16 E6, E7, and to study the biological features of cervical cancer cell line. METHODS: Human embryonic cervical tissues were cultured in keratinocyte free serum (K-FS) medium and infected with rAAV containing HPV16 E6, E7. Morphological features and growth rate were examined by light, electronic and fluorescence microscopies. The fragments of E6, E7 were detected by polymerase chain reaction (PCR) and laser confocal microscopy. The biological characteristics of human cervical epithelium were observed by soft agar culture, scid mice inoculation and chromosome analysis. Cell proliferative dynamics was plotted by flow cytometry. RESULTS: After a long-term culture, the phenotype kept the characteristics of primary epithelial cells. They showed monolayer, anchorage-dependent and attachment-inhibited growth without forming colonies in soft agar culture. They were non-oncogenic when inoculated into scid mice. The tonofilament expression in the cervical cancer cells was inspected by electronic microscopy, demonstrating that the cells were squamous epithelium in origin. The cell line contained HPV16 E6, E7 genes by PCR and laser confocal detection. Chromosome analysis disclosed that the karyotype was diploid or polyploid. The 11th chromosome was assumed to be the integration site by rAAV containing HPV16 E6, E7. CONCLUSIONS: Establishment of the immortalized cervical epithelial cell line by infection with rAAV containing HPV16 E6, E7, supports that HPV16 E6, E7 may be the primary etiology of cervical cancer. It will facilitate further research on the etiology and pathogenesis of cervical cancer.

[Study on the TIL and NK of IL-2 injected via pelvic retroperitoneal space in gynecological cancer patient].

OBJECTIVE: To verify the feasibility and effect of biotherapy instituted via pelvic retroperitoneal space on gynecological cancer. METHODS: Injecting IL-2 (and/or) 5-Fu through a tube installed in the pelvic retroperitoneal space. Counting the subpopulation of T cell and NK of lymph-nodes of pelvis after the drugs being by FCM. RESULTS: The numbers of CD3+, CD4+, CD8+, CD25+ and NK cells in treatment group were significantly higher than those in the control group. And the numbers of these cells in the IL-2 + 5-Fu group were significantly higher than those in the 5-Fu group. The CD25+ and NK cell numbers in the IL-2 group were significantly higher than those in the 5-Fu group (P < 0.05). CONCLUSION: The IL-2 injected via pelvic retroperitoneal space can promote the activity, development and infiltrating of T cell and NK cell in the tumor tissue.