Identification of a 4-lncRNA signature predicting prognosis of patients with non-small cell lung cancer: a multicenter study in China.

BACKGROUND: Previous findings have indicated that the tumor, nodes, and metastases (TNM) staging system is not sufficient to accurately predict survival outcomes in patients with non-small lung carcinoma (NSCLC). Thus, this study aims to identify a long non-coding RNA (lncRNA) signature for predicting survival in patients with NSCLC and to provide additional prognostic information to TNM staging system. METHODS: Patients with NSCLC were recruited from a hospital and divided into a discovery cohort (n = 194) and validation cohort (n = 172), and detected using a custom lncRNA microarray. Another 73 NSCLC cases obtained from a different hospital (an independent validation cohort) were examined with qRT-PCR. Differentially expressed lncRNAs were determined with the Significance Analysis of Microarrays program, from which lncRNAs associated with survival were identified using Cox regression in the discovery cohort. These prognostic lncRNAs were employed to construct a prognostic signature with a risk-score method. Then, the utility of the prognostic signature was confirmed using the validation cohort and the independent cohort. RESULTS: In the discovery cohort, we identified 305 lncRNAs that were differentially expressed between the NSCLC tissues and matched, adjacent normal lung tissues, of which 15 are associated with survival; a 4-lncRNA prognostic signature was identified from the 15 survival lncRNAs, which was significantly correlated with survivals of NSCLC patients. This signature was further validated in the validation cohort and independent validation cohort. Moreover, multivariate Cox analysis demonstrates that the 4-lncRNA signature is an independent survival predictor. Then we established a new risk-score model by combining 4-lncRNA signature and TNM staging stage. The receiver operating characteristics (ROC) curve indicates that the prognostic value of the combined model is significantly higher than that of the TNM stage alone, in all the cohorts. CONCLUSIONS: In this study, we identified a 4-lncRNA signature that may be a powerful prognosis biomarker and can provide additional survival information to the TNM staging system.

Rare Deleterious PARD3 Variants in the aPKC-Binding Region are Implicated in the Pathogenesis of Human Cranial Neural Tube Defects Via Disrupting Apical Tight Junction Formation.

Increasing evidence that mutation of planar cell polarity (PCP) genes contributes to human cranial neural tube defect (NTD) susceptibility prompted us to hypothesize that rare variants of genes in the core apical-basal polarity (ABP) pathway are risk factors for cranial NTDs. In this study, we screened for rare genomic variation of PARD3 in 138 cranial NTD cases and 274 controls. Overall, the rare deleterious variants of PARD3 were significantly associated with increased risk for cranial NTDs (11/138 vs.7/274, P < 0.05, OR = 3.3). These NTD-specific variants were significantly enriched in the aPKC-binding region (6/138 vs. 0/274, P < 0.01). The East Asian cohort in the ExAC database and another Chinese normal cohort further supported this association. Over-expression analysis in HEK293T and MDCK cells confirmed abnormal aPKC binding or interaction for two PARD3 variants (p.P913Q and p.D783G), resulting in defective tight junction formation via disrupted aPKC binding. Functional analysis in human neural progenitor cells and chick embryos revealed that PARD3 knockdown gave rise to abnormal cell polarity and compromised the polarization process of neuroepithelial tissue. Our studies suggest that rare deleterious variants of PARD3 in the aPKC-binding region contribute to human cranial NTDs, possibly by disrupting apical tight junction formation and subsequent polarization process of the neuroepithelium.

Immunomodulatory and Anti-IBDV Activities of the Polysaccharide AEX from Coccomyxa gloeobotrydiformis.

A number of polysaccharides have been reported to show immunomodulatory and antiviral activities against various animal viruses. AEX is a polysaccharide extracted from the green algae, Coccomyxa gloeobotrydiformis. The aim of this study was to examine the function of AEX in regulating the immune response in chickens and its capacity to inhibit the infectious bursal disease virus (IBDV), to gain an understanding of its immunomodulatory and antiviral ability. Here, preliminary immunological tests in vitro showed that the polysaccharide AEX can activate the chicken peripheral blood molecular cells' (PBMCs) response by inducing the production of cytokines and NO, promote extracellular antigen presentation but negatively regulate intracellular antigen presentation in chicken splenic lymphocytes, and promote the proliferation of splenic lymphocytes and DT40 cells. An antiviral analysis showed that AEX repressed IBDV replication by the deactivation of viral particles or by interfering with adsorption in vitro and reduced the IBDV viral titer in the chicken bursa of Fabricius. Finally, in this study, when AEX was used as an adjuvant for the IBDV vaccine, specific anti-IBDV antibody (IgY, IgM, and IgA) titers were significantly decreased. These results indicate that the polysaccharide AEX may be a potential alternative approach for anti-IBDV therapy and an immunomodulator for the poultry industry. However, more experimentation is needed to find suitable conditions for it to be used as an adjuvant for the IBDV vaccine.

Gene Expression Profiling Reveals Potential Players of Left-Right Asymmetry in Female Chicken Gonads.

Most female birds develop only a left ovary, whereas males develop bilateral testes. The mechanism underlying this process is still not completely understood. Here, we provide a comprehensive transcriptional analysis of female chicken gonads and identify novel candidate side-biased genes. RNA-Seq analysis was carried out on total RNA harvested from the left and right gonads on embryonic day 6 (E6), E12, and post-hatching day 1 (D1). By comparing the gene expression profiles between the left and right gonads, 347 differentially expressed genes (DEGs) were obtained on E6, 3730 were obtained on E12, and 2787 were obtained on D1. Side-specific genes were primarily derived from the autosome rather than the sex chromosome. Gene ontology and pathway analysis showed that the DEGs were most enriched in the Piwi-interactiing RNA (piRNA) metabolic process, germ plasm, chromatoid body, P granule, neuroactive ligand-receptor interaction, microbial metabolism in diverse environments, and methane metabolism. A total of 111 DEGs, five gene ontology (GO) terms, and three pathways were significantly different between the left and right gonads among all the development stages. We also present the gene number and the percentage within eight development-dependent expression patterns of DEGs in the left and right gonads of female chicken.

RIG-I from waterfowl and mammals differ in their abilities to induce antiviral responses against influenza A viruses.

The retinoic acid-induced gene I (RIG-I) plays a crucial role in sensing viral RNA and IFN-ß production. RIG-I varies in length and sequence between different species. We assessed the functional differences between RIG-I proteins derived from mammals and birds. The transfection of duck caspase recruitment domains (CARDs) and duck RIG-I (dCARDs and dRIG-I) and goose CARDs and goose RIG-I (gCARDs and gRIG-I) into chicken DF-1 cells increased the production of IFN-ß mRNA and IFN-stimulated genes and decreased influenza A virus (IAV) replication; whereas human CARDs and RIG-I (hCARDs and hRIG-I) and mouse CARDs and RIG-I (mCARDs and mRIG-I) had no effect. In human 293T and A549 cells, hCARDs had the strongest IFN-inducing activity, followed by mCARDs, dCARDs and gCARDs. The IFN-inducing activity of hRIG-I was stronger than that of mRIG-I, dRIG-I and gRIG-I, in that order. The results showed that, although the ability of dCARDs to activate IFN was stronger than that of gCARDs in DF-1, 293T and A549 cells, dRIG-I had a weaker ability to activate IFN than gRIG-I in DF-1 cells with or without IAV infection. These data suggest that RIG-I proteins from different species have different amino acid sequences and functions. This genetic and functional diversity renders RIG-I flexible, adaptable and capable of recognizing many viruses in different species.

Tumor suppressor miR-145 reverses drug resistance by directly targeting DNA damage-related gene RAD18 in colorectal cancer.

Colorectal cancer (CRC) is one of the most common cancers worldwide. Although chemotherapy is used as a palliative treatment, ultimately, nearly all patients develop drug resistance. Therefore, the cell-inherent DNA repair pathway must reverse the DNA-damaging effect of cytotoxic drugs that mediates therapeutic resistance to chemotherapy. RAD18, a DNA damage-activated E3 ubiquitin ligase, is known to play a critical role in DNA damage repair in cancer cells. Here, we show that RAD18 is highly expressed in human 5-fluorouracil (5-FU)-resistant cancer cells after 5-FU treatment. In addition, RAD18 increases in CRC cells could induce DNA damage repair, suggesting that RAD18 might be a possible target for overcoming drug resistance. Moreover, the expression of tumor suppressor microRNA-145 (miR-145) was negatively correlated with RAD18 expression in CRC tissues of 140 patients. Using luciferase reporters carrying the 3'-untranslated region of RAD18 combined with Western blotting, we identified RAD18 as a direct target of miR-145. Also of interest, suppression of RAD18 by miR-145 enhanced DNA damage in CRC cells after 5-FU treatment. Finally, the 5-FU-resistant cancer cells could be selectively ablated by treatment with miR-145. Taken together, these results suggest that miR-145 can act as an RAD18 inhibitor and contribute as an important factor in reversing drug resistance after chemotherapy.

Expression patterns of prdm1 during chicken embryonic and germline development.

PRDM1 (PR domain containing 1) is a transcriptional repressor that has been identified in various species and is crucial for cell growth, differentiation and development. However, the expression pattern and role of PRDM1 in development has not been sufficiently established in birds. We therefore investigate the spatio-temporal expression of PRDM1 in various tissues, especially in the germline, during chicken development, providing the basis for functional study. Our results show that prdm1 mRNA was expressed in blastodermal cells (BCs) at stage X and in various tissues including the liver, skin, lung, kidney, eye, bursa of fabricius, spleen, proventriculus, gizzard, intestine, testis, ovary, tongue, feathers and thymus but was not or was only sparcely present in the heart, brain and skeletal muscle. The level of prdm1 mRNA was highest in the BCs among all tissues tested and significantly changed during development in many tissues, such as the blastoderm, bursa of fabricius, spleen, feathers and germline. Furthermore, the expression of the PRDM1 protein generally paralleled the mRNA results, except for in the gizzard. Immunohistochemistry also revealed that PRDM1 was localized in the smooth muscle. In addition, during germline development, PRDM1 was found to be continuously expressed in the presumptive primordial germ cells (PGCs) at stage X, the circulating PGCs in blood and the germ cells in the gonads from embryonic day 6 to adult in both males and females. The expression pattern of PRDM1 in chicken thus suggests that this protein plays an important role during chicken development, such as in BC differentiation, feather formation and germ cell specification.

Production of chimeras between the Chinese soft-shelled turtle and Peking duck through transfer of early blastoderm cells.

Chimeras are useful models for studies of developmental biology and cell differentiation. Intraspecies and interspecies germline chimeras have been produced in previous studies, but the feasibility of producing chimeras between animals of two different classes remains unclear. To address this issue, we attempted to produce chimeras between the Chinese soft-shelled turtle and the Peking duck by transferring stage X blastoderm cells to recipient embryos. We then examined the survival and development of the PKH26-labeled donor cells in the heterologous embryos. At early embryonic stages, both turtle and duck donor cells that were labeled with PKH26 were readily observed in the brain, neural tube, heart and gonads of the respective recipient embryos. Movement of turtle donor-derived cells was observed in the duck host embryos after 48 h of incubation. Although none of the hatchlings presented a chimeric phenotype, duck donor-derived cells were detected in a variety of organs in the hatchling turtles, particularly in the gonads. Moreover, in the hatched turtles, mRNA expression of tissue-specific duck genes MEF2a and MEF2c was detected in many tissues, including the muscle, heart, small and large intestines, stomach and kidney. Similarly, SPAG6 mRNA was detected in a subset of turtle tissues, including the gonad and the small and large intestines. These results suggest that duck donor-derived cells can survive and differentiate in recipient turtles; however, no turtle-derived cells were detected in the hatched ducks. Our findings indicate that chimeras can be produced between animals of two different classes.

CD4+CD25+ Cells Are Essential for Maintaining Immune Tolerance in Chickens Inoculated with Bovine Serum Albumin at the Late Stage of Embryonic Development.

In this study, the role of chicken CD4+CD25+ cells during induced immunotolerance was tested. Properties of chicken CD4+CD25+ cells sorted by flow cytometry were analyzed. Results showed that chicken CD4+CD25+ cells express IL-10, TGF-ß highly and suppress proliferation of CD4+CD25- cells in vitro. To induce immunotolerance, embryos were inoculated with bovine serum albumin (BSA) via an intravascular route on embryo incubation day 20 (EID20), and after hatching chicks experienced BSA immunization four times at 7-day intervals. Serum anti-BSA antibodies and CD4+CD25+ cell ratio was analyzed. Results showed that humoral tolerance was obtained and the CD4+CD25+ cell percentage in peripheral blood lymphocytes increased along with this progress. Injection of anti-chicken CD25 antibody via an intravascular route on EID16 is applied to block CD4+CD25+ cells, and the CD4+CD25+ cell ratio decreased significantly up to 35 d post-hatch. Based on the above, injections of anti-chicken CD25 antibody on EID16 and BSA on EID20 were carried out sequentially, and tolerance level was contrasted to the BSA-injection group. Data revealed the anti-BSA antibodies increased significantly in the CD4+CD25+ cell-blocked groups indicating that immune tolerance level was weakened. In conclusion, chicken CD4+CD25+ cells are essential in maintaining induced immune tolerance.

Species delimitation and life stage association of Propsilocerus Kieffer, 1923 (Diptera, Chironomidae) using DNA barcodes.

The utility of COI DNA barcodes in species delimitation is explored as well as life stage associations of five closely related Propsilocerus species: Propsilocerus akamusi (Tokunaga, 1938), Propsilocerus paradoxus (Lundström, 1915), Propsilocerus saetheri Wang, Liu et Paasivirta, 2007, Propsilocerus sinicus Sæther et Wang, 1996, and Propsilocerus taihuensis (Wen, Zhou et Rong, 1994). Results revealed distinctly larger interspecific than intraspecific divergences and indicated a clear "barcode gap". In total, 42 COI barcode sequences including 16 newly generated DNA barcodes were applied to seven Barcode Index Numbers (BINs). A neighbor-joining (NJ) tree comprises five well-separated clusters representing five morphospecies. Comments on how to distinguish the larvae of P. akamusi and P. taihuensis are provided.

Improved Photoreduction of CO2 with Water by Tuning the Valence Band of Covalent Organic Frameworks.

Porous covalent organic frameworks (COFs), as an emerging material, have the characteristics of high stability, large series of components, easy synthesis, modification, and adjustable amplitude. They have the potential to become good catalysts. Bromine, as a halogen, has attracted intensive interest for the modification of photocatalysts for photocatalytic reactions. It is feasible to enhance the activity and selectivity of the material by facile functionalization of the reticular parent structure's electron-withdrawing groups. In addition, the conjugation effect of bromine, further delocalizing the electrons of the COF, is beneficial to the progress of many photocatalytic reactions. Reports on the modification of COFs by bromine functional groups to improve the catalytic performance have not been found so far. Here, TAPP [5,10,15,20-tetrakis(4-aminophenyl)porphyrin] and 2,5-dibromo-1,4-benzenedialdehyde instead of terephthalaldehyde were chosen to synthesize a porphyrin-based COF (TAPBB-COF) by the solvothermal method. As expected, the valence band (VB) of TAPBB-COF is thus adjusted to a more suitable position. Additionally, the CO production when using TAPBB-COF under full-wavelength light for 12 h was 295.2 µmol g-1 , which was three times that of COF-366, and the new material has good recycling stability and selectivity (95.6 %). Theoretical calculations indicate that the nitrogen of the porphyrin ring and the Schiff base, and the bromine in TAPBB-COF contribute greatly to the activation of H2 O and the conversion of CO2 in the photoreaction.

Polypedilum (Cerobregma) heberti sp. n. (Diptera: Chironomidae) from Gaoligong Mountains, Yunnan, China.

DNA barcodes and morphology recognize a new non-biting midge within the genus Polypedilum (Diptera: Chironomidae). Polypedilum (Cerobregma) heberti Lin et Wang sp. n. is described and illustrated based on an adult male from Gaoligong Mountains, Yunnan, China. Key to adult males of the subgenus Cerobregma is given.

[Utilization and growth response of Chrysosporum ovalisporum to different phosphorus compounds]. / 卵孢金孢藻对不同磷化合物的利用及生长响应.

To explore the ability of bloom-forming cyanobacterium Chrysosporum ovalisporum to utilize different kinds of phosphorus compounds in the water column, we examined the growth response of C. ovalisporum in the laboratory by taking dipotassium hydrogen phosphate as the control and set different treatments of phosphorus substrates. The results showed that C. ovalisporum could utilize sodium tripolyphosphate and terasodium pyrophosphate decahydrate, with better utilization of sodium tripolyphosphate. After 15 days, it had the highest biomass and chlorophyll a concentrations under the treatment of sodium tripolyphosphate, with a value of (426.96±47.42) mg·L-1 and (1852.34±116.60) µg·L-1, respectively. Compared with the control, there was no significant difference in biomass of C. ovalisporum under both the (2-aminoethyl)-phosphonic acid and disodium ß-glycerol phosphate pentahydrate treatments. The change characteristics of dissolved inorganic phosphate were related to the alkaline phosphatase activity, indicating that C. ovalisporum was able to utilize these two organophosphorus compounds via enzyme hydrolysis. The concentration of dissolved inorganic phosphate reached 0 mg·L-1 during the whole experiment when the C. ovalisporum were fed with glyphosate. Biomass, specific growth rate, chlorophyll a concentration and photosynthetic activity of algal cells were significantly lower than those of the control, indicating that C. ova-lisporum could not uptake phosphorus compounds in the glyphosate substrate and thus their growth being inhibited. Our results present new insights to understand the diffusion mechanism of C. ovalisporum into different aquatic ecosystems and had theoretical reference value for the prevention and control of new cyanobacterial blooms.

The preparation of new covalent organic framework embedded with silver nanoparticles and its applications in degradation of organic pollutants from waste water.

A covalent organic framework (COF) featuring a unique light porous structure and silver nanoparticles shows high efficiency in the degradation of environmental pollutants. However, the combination of a COF with silver nanoparticles has never been reported until now. Toward this end, 2,4,6-tris-(4-formylphenoxy)-1,3,5-triazine (TPT-CHO) and hydrazine hydrate were selected as the construction units of the COF material (TPHH-COF), which possesses rich nitrogen and oxygen sites. Then a new type of composite catalyst (Ag@TPHH-COF) was successfully obtained by solution infiltration. The obtained materials were also fully characterized by standard methods. The results showed that the silver nanoparticles (with diameters of 5 ± 3 nm) were uniformly dispersed on the surface and in the interlayer gaps of the TPHH-COF substrate. Catalytic studies showed that Ag@TPHH-COF could catalyze the reduction of the various nitroaromatic compounds (NACs) with high efficiency, such as 4-nitrophenol, 2-nitrophenol, 4-nitroaniline, nitrobenzene, 4-nitrotoluene and 1-butyl-4-nitrobenzene. Ag@TPHH-COF could also catalyze the reduction of organic dyes such as Rhodamine B (RhB), Methylene Blue (MB), Methyl Orange (MO) and Congo Red (CR). Moreover, Ag@TPHH-COF has good reusability and high recovery.

Hypoxia-inducible factor-1α activates transforming growth factor-ß1/Smad signaling and increases collagen deposition in dermal fibroblasts.

Hypoxia of local tissue occurs during the scar formation; however, the degree of ischemia and hypoxia in the central areas of keloids is more serious than those in normal scars. Hypoxia-induced factor (HIF), is one of the main cellular responses to hypoxia, allowing cells to adapt to low-oxygen conditions. We investigated the correlation among hypoxia, transforming growth factor-ß1/Smad signaling and collagen deposition. Hypoxia up-regulated TGF-ß1, Smad2/3, p-Smad2/3, Smad4, and total collagen in both normal and keloid fibroblasts via HIF-1α, which was attenuated by HIF-1α inhibition, but TßRII levels were not significantly altered. Silencing Smad4 under hypoxia decreased the mRNA and protein levels of HIF-1α, suggesting up-regulated Smad4 may also plays a role in promoting HIF-1α. Finally, we examined the role of the TGF-ß1/Smad pathway in collagen deposition. When TßRII was inhibited by ITD-1 under hypoxic conditions, p-Smad2/3 levels and collagen deposition decreased. When inhibited TßRII by siRNA under normoxia, the levels of p-Smad2/3, Smad4 and collagen deposition also decreased. This result demonstrated that hypoxia promoted TGF-ß1/Smad signaling via HIF-1α and that both HIF-1α and the TGF-ß1/Smad signaling promotes collagen deposition in hypoxia, which is an important mechanism of keloid formation.

Cultural diffusion of Indo-Aryan languages into Bangladesh: A perspective from mitochondrial DNA.

Although both linguistic and historical studies indicated only a small group of Aryans had been involved into the diffusion of Indo-Aryan languages into Bangladesh, no genetic studies had been carried out to prove this notion. By studying mitochondrial DNA variants of 240 Bengali speakers in Bangladesh, among which 23 mitogenomes are completely sequenced, we found a high proportion of South Asian components in this group. By contrast, only a small proportion of lineages can be traced back to western Eurasia, which could be attributed to recent gene flow. Our results implied a cultural diffusion of the Indo-Aryan languages into Bangladesh.

[Community structure of Chironomid larvae and their indicative significance for water quality in streams of Xianju National Park, China]. / ä»™å± å›½å®¶å ¬å›­æºªæµæ‘‡èšŠå¹¼è™«ç¾¤è½ç»“æž„åŠå ¶å¯¹æ°´è´¨çš„æŒ‡ç¤ºä½œç”¨.

In August 2016, 59 sites of 13 streams in Xianju National Park were surveyed to explore the community structure of Chironomid larvae and their indicative significance for water quality. Water quality of the streams was evaluated based on Hilsenhoff biological index. The results showed that there were 37 clean sites, 19 mild polluted sites and three moderated polluted sites in Xianju National Park. We identified a total of 86 species of Chironomid larvae, belonging to 51 genera and four subfamilies, including 37 species in 19 genera of Chironominae; 35 species in 21 genera of Orthcladiinae; 12 species in 9 genera of Tanypodinae, two species in two genera of Diamesinae. Chironominae accounted for 40.3% of Chironomid larval density. Tanypodinae and Orthcladiinae were almost similar in Chironomid larval density, respectively accounted for 30% and 29.4% of the total. Diamesinae accounted for 0.3% of total Chironomid larval density. Conchapelopia sp. was the overwhelming dominant species and Polypedilum flavum, Rheocricotopus sp., Cricotupus vierriensis, Rheotanytarsus muscicola and Corynoneura carriana were the dominant species of Chironomid larvae. The result of indicator species analysis showed that Cricotupus vierriensis, Nanocladius dichromus, Tanytarsus formosanus, Tanytarsus mendex were indicator species of moderated pollution water, and that Rheocricotopus sp. was the indicator species of clean state water.

A new triazine-based covalent organic polymer for efficient photodegradation of both acidic and basic dyes under visible light.

A new triazine-based covalent organic polymer (named COP-NT), which showed high catalytic activities for the degradation of acidic and basic dyes, is synthesized. Its structure characteristics were fully investigated, which featured large specific surface area, homogeneous porosity, strong visible light absorption, excellent thermal stability and semiconductor performance. The as-prepared COP-NT exhibits good chemical stability both in acidic and alkaline aqueous solutions, which could be used as an efficient photocatalyst for the degradation of methyl orange (MO), rhodamine B (RhB) and methylene blue (MB). The Ea values for the degradation of MO, RhB or MB are 9.40 kJ mol-1, 30.94 kJ mol-1 or 17.54 kJ mol-1, respectively. Furthermore, COP-NT showed excellent reusability in degrading all the above dyes without obvious performance decay.

A new method of subtotal thyroidectomy for Graves' disease leaving a unilateral remnant based on the upper pole.

BACKGROUND: The aim of this prospective randomized study was to evaluate the feasibility of subtotal thyroidectomy with leaving a unilateral remnant based on the upper pole. METHODS: Patients who underwent the subtotal thyroidectomy and isthmusectomy leaving either a unilateral remnant based on the upper pole (Group I, 79 patients) or the bilateral dorsal thyroid tissue remained (Group II, 89 patients) were compared in operation time, blood loss, recurrence, and postoperative complications. RESULTS: Among 168 patients analyzed, the operation time remained similar, but the blood loss, the reoperation time, and recurrence in Group I were much less than Group II. In addition, no postoperative hemorrhage occurred in Group I. Two patients (2.28%) in Group II underwent recurrent laryngeal nerve damages. Four patients (5.06%) in Group I and 3 patients (3.37%) in Group II experienced transient hypocalcemia. Recurrence only occurred in Group II. CONCLUSION: In terms of blood loss, reoperation time, postoperative complication, and the recurrence, subtotal thyroidectomy with recurrent laryngeal nerves identification and the unilateral superior pole remnant of the gland provides a better outcome than subtotal thyroidectomy with bilateral dorsal thyroid tissue remnant.