SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data

Quality control (QC) and preprocessing are essential steps for sequencing data analysis to ensure the accuracy of results. However, existing tools cannot provide a satisfying solution with integrated comprehensive functions, proper architectures, and highly scalable acceleration. In this article, we demonstrate SOAPnuke as a tool with abundant functions for a “QC-Preprocess-QC” workflow and MapReduce acceleration framework. Four modules with different preprocessing functions are designed for processing datasets from genomic, small RNA, Digital Gene Expression, and metagenomic experiments, respectively. As a workflow-like tool, SOAPnuke centralizes processing functions into 1 executable and predefines their order to avoid the necessity of reformatting different files when switching tools. Furthermore, the MapReduce framework enables large scalability to distribute all the processing works to an entire compute cluster.

We conducted a benchmarking where SOAPnuke and other tools are used to preprocess a ∼30× NA12878 dataset published by GIAB. The standalone operation of SOAPnuke struck a balance between resource occupancy and performance. When accelerated on 16 working nodes with MapReduce, SOAPnuke achieved ∼5.7 times the fastest speed of other tools.

Synthesis and characterization of two-dimensional Nb4C3 (MXene)

By etching Nb₄AlC₃ powders in hydrofluoric acid, a phase-pure, highly conductive, Nb₄C₃ MXene – the second with formula M₄X₃ – was produced. The latter's structure was investigated using pair distribution function analysis.

WEGO 2.0: a web tool for analyzing and plotting GO annotations, 2018 update

WEGO (Web Gene Ontology Annotation Plot), created in 2006, is a simple but useful tool for visualizing, comparing and plotting GO (Gene Ontology) annotation results. Owing largely to the rapid development of high-throughput sequencing and the increasing acceptance of GO, WEGO has benefitted from outstanding performance regarding the number of users and citations in recent years, which motivated us to update to version 2.0. WEGO uses the GO annotation results as input. Based on GO's standardized DAG (Directed Acyclic Graph) structured vocabulary system, the number of genes corresponding to each GO ID is calculated and shown in a graphical format. WEGO 2.0 updates have targeted four aspects, aiming to provide a more efficient and up-to-date approach for comparative genomic analyses. First, the number of input files, previously limited to three, is now unlimited, allowing WEGO to analyze multiple datasets. Also added in this version are the reference datasets of nine model species that can be adopted as baselines in genomic comparative analyses. Furthermore, in the analyzing processes each Chi-square test is carried out for multiple datasets instead of every two samples. At last, WEGO 2.0 provides an additional output graph along with the traditional WEGO histogram, displaying the sorted P-values of GO terms and indicating their significant differences. At the same time, WEGO 2.0 features an entirely new user interface. WEGO is available for free at http://wego.genomics.org.cn.

Oscillations in extracellular pH and reactive oxygen species modulate tip growth of Arabidopsis root hairs

Root hairs show highly localized cell expansion focused to their growing tips. This growth pattern is accomplished through restriction of secretion to the elongating apex and modulation of cell wall properties, with the wall just behind the tip becoming rigidified to resist the lateral expansive forces of turgor. In this report we show that root hairs exhibit oscillating growth that is associated with oscillating increases in extracellular pH and reactive oxygen species (ROS), which lag growth by approximately 7 s. Consistent with a role for these changes in growth control, artificially increasing extracellular pH arrested root hair elongation, whereas decreasing pH elicited bursting at the tip. Similarly, application of exogenous ROS arrested elongation, whereas scavenging of ROS led to root hair bursting. Roots hairs of the root hair-defective rhd2-1 mutant, which lack a functional version of the NADPH oxidase ATRBOH C, burst at the transition to tip growth. This phenotype could be rescued by elevating the pH of the growth medium to >/=6.0. Such rescued root hairs showed reduced cytoplasmic ROS levels and a lack of the oscillatory production of ROS at the tip. However, they exhibited apparently normal tip growth, including generation of the tip-focused Ca(2+) gradient thought to drive apical growth, indicating that ATRBOH C is not absolutely required to sustain tip growth. These observations indicate that root hair elongation is coupled to spatially distinct regulation of extracellular pH and ROS production that likely affect wall properties associated with the polarized expansion of the cell.

The extended amygdala: are the central nucleus of the amygdala and the bed nucleus of the stria terminalis differentially involved in fear versus anxiety?

Although there is a close correspondence between fear and anxiety, and the study of fear in animals has been extremely valuable for understanding the neural basis of anxiety, it is also clear that a richer animal model of human anxiety disorders would include measures of both stimulus-specific fear and something less stimulus specific, more akin to anxiety. Patients with posttraumatic stress syndrome seem to show normal fear reactions but abnormal anxiety measured with the acoustic startle reflex. Studies in rats, also using the startle reflex, indicate that highly processed explicit cue information (lights, tones) activates the central nucleus of the amygdala, which projects to and modulates the acoustic startle pathway in the brain stem. Less explicit information, such as that produced by exposure to a threatening environment or by intraventricular administration of corticotropin-releasing hormone, may activate another part of the extended amygdala, the bed nucleus of the stria terminalis, which also projects to the startle pathway. Because this information may be less specific and of long duration, activation of the bed nucleus of the stria terminalis may mediate anxiety, whereas activation of the central nucleus of the amygdala may mediate stimulus-specific fear.

Characterization of a novel ranavirus isolated from grouper Epinephelus tauvina

A large icosahedral virus was isolated from diseased grouper Epinephelus tauvina. The virus grew well in several cultured fish cell lines, with stable and high infectivity after serial passages in grouper cell line (GP). The virus was sensitive to both acid and heat treatments. Virus replication was inhibited by 5-iodo-2-deoxyuridine (IUDR), indicative of a DNA-containing genome. The virus infectivity was reduced with ether treatment, suggesting that the virus was lipid-enveloped. Electron micrographs showed abundant cytoplasmic icosahedral virons in the virus-infected GP cells. The size of the intracellular nucleocapsid was 154 nm between the opposite sides, or 176 nm between the opposite vertices with an inner electron-dense core of 93 nm. Virus particles were released through budding from plasma membranes with a size of 200 nm in diameter. SDS-PAGE of purified virus revealed 20 structural protein bands and a major capsid protein (MCP) of 49 kDa. A DNA fragment of approximately 500 nucleotides was successfully amplified by polymerase chain reaction (PCR) using the primers from conserved regions of the MCP gene of frog virus 3 (FV3), the type species of Ranavirus. Subsequent multiple alignment and phylogenetic analysis showed that the newly isolated grouper virus was closely related to largemouth bass virus (LMBV), FV3 and Regina ranavirus (RRV). Our data suggests that the virus isolate is a novel member of genus Ranavirus, family Iridoviridae. We tentatively name the virus as Singapore grouper iridovirus (SGIV). SGIV was able to cause serious systemic disease capable of killing 96% of grouper fry.

The intrinsic organization of the central extended amygdala

The central component of the extended amygdala (CEA) comprises the central amygdaloid nucleus (Ce), the dorsal substantia innominata (SI), and the bed nucleus of the stria terminalis (BNST). Anatomical studies have suggested the presence of an intrinsic system of GABAergic neurons that not only connects homologous subareas of the Ce, SI, and BNST but that also acts as an interface between sensory afferents and brain stem-projecting neurons. CEA outputs, with a few exceptions, arise from separate populations of neurons, but all, including GABAergic neurons themselves, are heavily innervated by GABAergic terminals. GABAergic neurons may serve to integrate output activity of the CEA, though GABAergic neurons form a heterogeneous population whose differential intrinsic connections appear related to their peptide content. Afferents from the dysgranular insular cortex and lateral parabrachial complex preferentially innervate GABAergic neurons, suggesting these neurons may also integrate afferent activity. Afferents from the basolateral amygdala (BL) appear to innervate both output neurons and intrinsic GABAergic neurons. Evidence will be presented to show that BL afferents form synaptic complexes with cortical, GABAergic, and TH-immunoreactive terminal boutons on GABAergic dendritic spines. These complexes may be a key element in control of CEA output activity.

Cortical afferents to the extended amygdala

The projections of the cerebral cortex to the extended amygdala were studied in the rat using anterograde and retrograde tract-tracing techniques. Most cortical areas with strong projections to the extended amygdala preferentially targeted either the medial extended amygdala (including the medial amygdalar nucleus, ventromedial substantia innominata, and the medial part of the bed nucleus the stria terminalis) or the central extended amygdala (including the central amygdalar nucleus, dorsolateral substantia innominata, and the lateral part of the bed nucleus of the stria terminalis). Some cortical areas, however, had equal projections to both medial and central portions. The main areas projecting preferentially to the medial extended amygdala were the ventral subiculum, infralimbic cortex, ventral agranular insular area, and the rostral part of the ventrolateral entorhinal area. The main areas projecting preferentially to the central extended amygdala were the prefrontal cortex, viscerosensory and somatosensory portions of the insular cortex, and the amygdalopiriform transitional area. It is suggested that these cortical inputs may be important for cognitive, mnemonic, and affective aspects of emotional and motivated behavior.

Immunologic basis of transplant-associated arteriosclerosis

Although immunosuppressive therapy minimizes the risk of graft failure due to acute rejection, transplant-associated arteriosclerosis of the coronary arteries remains a significant obstacle to the long-term survival of heart transplant recipients. The participation of specific inflammatory cell types in the genesis of this lesion was examined in a mouse model in which carotid arteries were transplanted across multiple histocompatibility barriers into seven mutant strains with immunologic defects. An acquired immune response--with the participation of CD4+ (helper) T cells, humoral antibody, and macrophages--was essential to the development of the concentric neointimal proliferation and luminal narrowing characteristic of transplant arteriosclerosis. CD8+ (cytotoxic) T cells and natural killer cells were not involved in the process. Arteries allografted into mice deficient in both T-cell receptors and humoral antibody showed almost no neointimal proliferation, whereas those grafted into mice deficient only in helper T cells, humoral antibody, or macrophages developed small neointimas. These small neointimas and the large neointimas of arteries grafted into control animals contained a similar number of inflammatory cells; however, smooth muscle cell number and collagen deposition were diminished in the small neointimas. Also, the degree of inflammatory reaction in the adventitia did not correlate with the size of the neointima. Thus, the reduction in neointimal size in arteries allografted into mice deficient in helper T cells, humoral antibody, or macrophages may be accounted for by a decrease in smooth muscle cell migration or proliferation.

Treatment of Benign Thyroid Nodules: Comparison of Surgery with Radiofrequency Ablation

BACKGROUND AND PURPOSE

Nodular goiter is one of the most common benign lesions in thyroid nodule. The main treatment of the disease is still the traditional surgical resection, however there are many problems such as general anesthesia, surgical scar, postoperative thyroid or parathyroid function abnormalities, and high nodules recurrence rate in residual gland. The purpose of this study was to compare the efficacy, safety, and cost-effectiveness of 2 treatment methods, surgery and radiofrequency ablation, for the treatment of benign thyroid nodules.

MATERIALS AND METHODS

From May 2012 to September 2013, 200 patients with nodular goiters who underwent surgery (group A) and 200 patients treated by radiofrequency ablation (group B) were enrolled in this study. Inclusion criteria were the following: 1) cosmetic problem, 2) nodule-related symptoms, 3) hyperfunctioning nodules related to thyrotoxicosis, and 4) refusal of surgery (for group B). An internally cooled radiofrequency ablation system and an 18-ga internally cooled electrode were used. We compared the 2 groups in terms of efficacy, safety, and cost-effectiveness during a 1-year follow-up.

RESULTS

After radiofrequency ablation, the nodule volume decreased significantly from 5.4 to 0.4 mL (P = .002) at the 12-month follow-up. The incidence of complications was significantly higher from surgery than from radiofrequency ablation (6.0% versus 1.0%, P = .002). Hypothyroidism was detected in 71.5% of patients after surgery but in none following radiofrequency ablation. The rate of residual nodules (11.9% versus 2.9%, P = .004) and hospitalization days was significantly greater after surgery (6.6 versus 2.1 days, P < .001), but the cost difference was not significant.

CONCLUSIONS

Surgical resection and radiofrequency ablation are both effective treatments of nodular goiter. Compared with surgery, the advantages of radiofrequency ablation include fewer complications, preservation of thyroid function, and fewer hospitalization days. Therefore, radiofrequency ablation should be considered a first-line treatment for benign thyroid nodules.

miR-148a is Associated with Obesity and Modulates Adipocyte Differentiation of Mesenchymal Stem Cells through Wnt Signaling

Obesity results from numerous, interacting genetic, behavioral, and physiological factors. Adipogenesis is partially regulated by several adipocyte-selective microRNAs (miRNAs) and transcription factors that regulate proliferation and differentiation of human adipose-derived mesenchymal stem cells (hMSCs-Ad). In this study, we examined the roles of adipocyte-selective miRNAs in the differentiation of hMSCs-Ad to adipocytes. Results showed that the levels of miR-148a, miR-26b, miR-30, and miR-199a increased in differentiating hMSCs-Ad. Among these miRNAs, miR-148a exhibited significant effects on increasing PPRE luciferase activity (it represents PPAR-dependent transcription, a major factor in adipogenesis) than others. Furthermore, miR-148a expression levels increased in adipose tissues from obese people and mice fed high-fat diet. miR-148a acted by suppressing its target gene, Wnt1, an endogenous inhibitor of adipogenesis. Ectopic expression of miR-148a accelerated differentiation and partially rescued Wnt1-mediated inhibition of adipogenesis. Knockdown of miR-148a also inhibited adipogenesis. Analysis of the upstream region of miR-148a locus identified a 3 kb region containing a functional cAMP-response element-binding protein (CREB) required for miR-148a expression in hMSCs-Ad. The results suggest that miR-148a is a biomarker of obesity in human subjects and mouse model, which represents a CREB-modulated miRNA that acts to repress Wnt1, thereby promoting adipocyte differentiation.

The Gelation of CO(2): A Sustainable Route to the Creation of Microcellular Materials

Compounds with strong thermodynamic affinity for carbon dioxide (CO(2)) have been designed and synthesized that dissolve in CO(2), then associate to form gels. Upon removal of the CO(2), these gels produced free-standing foams with cells with an average diameter smaller than 1 micrometer and a bulk density reduction of 97 percent relative to the parent material.

Results of a Randomized, Double-Blind, Placebo-Controlled, Phase III Trial of Trifluridine/Tipiracil (TAS-102) Monotherapy in Asian Patients With Previously Treated Metastatic Colorectal Cancer: The TERRA Study

Purpose

Trifluridine/tipiracil (TAS-102) was effective in patients with metastatic colorectal cancer (mCRC) in a phase II Japanese trial. This regional trial evaluated the efficacy and safety of trifluridine/tipiracil in Asian patients with mCRC with or without exposure to biologic therapy.

Patients and Methods

This randomized, double-blind, placebo-controlled, phase III trial was conducted at 30 sites in China, the Republic of Korea, and Thailand. Patients ≥ 18 years old with histologically or cytologically confirmed adenocarcinoma of the colon or rectum and known KRAS status who were refractory or intolerant to two or more prior chemotherapy regimens were enrolled. Eligible patients were randomly assigned (2:1 ratio; minimization method) to receive trifluridine/tipiracil (twice per day orally; 5 days on and 2 days off for 2 weeks, followed by 14 days off per cycle) or placebo. The primary end point was overall survival (intent-to-treat population).

Results

Between October 16, 2013, and June 15, 2015, 406 patients were randomly assigned to receive trifluridine/tipiracil (n = 271) or placebo (n = 135). Risk of death was significantly lower in the trifluridine/tipiracil arm than in the placebo arm (hazard ratio for death, 0.79; 95% CI, 0.62 to 0.99; log-rank P = .035). Median overall survival was significantly longer in the trifluridine/tipiracil than in the placebo arm (7.8 months [95% CI, 7.1 to 8.8 months] v 7.1 months [95% CI, 5.9 to 8.2 months], respectively), for a median survival follow-up time of 13.8 months (95% CI, 13.1 to 15.3 months) compared with 13.4 months (95% CI, 11.6 to 17.3 months), respectively. The incidence of serious adverse events was similar between the arms (trifluridine/tipiracil, n = 63 [23.2%]; placebo, n = 32 [23.7%]). No treatment-related deaths were reported.

Conclusion

Trifluridine/tipiracil has a statistically significant survival benefit compared with placebo in Asian patients with mCRC refractory or intolerant to standard chemotherapies, regardless of exposure to biologic therapy. The safety profile is similar to previous reports.

Bifunctional alloys for the electroreduction of CO2and CO

We use density functional theory to study the reduction of CO₂and CO to hydrocarbons through a formyl pathway on (111) and (211) facets of L1₂alloys with an A₃B composition.

A novel polymorphism at codon 333 of human immunodeficiency virus type 1 reverse transcriptase can facilitate dual resistance to zidovudine and L-2',3'-dideoxy-3'-thiacytidine

Recent clinical trials examining 3'-azido-3'-deoxythymidine (AZT, zidovudine, or Retrovir) combined with L-2', 3'-dideoxy-3'-thiacytidine (3TC or lamivudine) have shown that combination therapy with these nucleoside analogs affords significant virological and clinical benefits. The addition of 3TC to AZT delays AZT resistance in therapy-naive patients and can restore viral AZT susceptibility in patients who previously received AZT alone. In some AZT-experienced patients, the virological response to AZT-3TC therapy is not sustained and virus resistant to both drugs can be identified. To gain insight into the possible mechanism of dual resistance, we studied a recently described variant resistant to both AZT and 3TC and obtained by simultaneous passage of an AZT-resistant clinical isolate in cell culture with AZT and 3TC. Genetic mapping and site-directed mutagenesis experiments demonstrated that a polymorphism at codon 333 (Gly to Glu) of human immunodeficiency virus type 1 reverse transcriptase (RT) was critical in facilitating dual resistance in a complex background of AZT and 3TC resistance mutations. To assess the potential clinical relevance of RT codon 333 changes, we studied dually resistant viruses from patients taking AZT and 3TC. Genetic mapping of RT molecular clones derived from patients' plasma samples demonstrated that in some cases polymorphism at codon 333 was responsible for facilitating dual resistance.

Biometry of the fetal heart between 10 and 17 weeks of gestation

OBJECTIVES

Assessment of the dimensions of the cardiac chambers and the great arteries in the human fetus may be helpful in the prenatal diagnosis of congenital heart disease. The purpose of this prospective cross-sectional study was to compile normative data in fetal cardiac measurements in early pregnancy. The structure of the fetal heart was examined in 136 normal singleton fetuses between 10 and 17 weeks of gestation.

METHODS

The transversal heart diameter, both ventricular dimensions, interventricular septal thickness, heart area, heart circumference, thoracic diameter, thoracic circumference and thoracic area were measured in the four-chamber view during diastole. Diameters of the pulmonary trunk and ascending aorta were obtained in the short axis and long axis view during systole. Ultrasound examinations were performed with a 5.0-MHz transvaginal and/or transabdominal phased-array sector scanner.

RESULTS

The four-chamber view and the cross-over of the pulmonary artery and the aorta were adequately visualized in 44% of the fetuses at 10 weeks of gestation, in 75% at 11 weeks of gestation, in 93% at 12 weeks of gestation and in 100% of the fetuses at 13-17 weeks of gestation. Before 14 weeks of gestation transvaginal sonography was superior to the transabdominal sonography in visualization of the fetal heart and great arteries. After 14 weeks of gestation transabdominal sonography accurately demonstrated the structure of the fetal heart. The ratio of right and left ventricle (RV/LV) and the ratio of the pulmonary trunk and aorta (PT/AO) were constant during this period of gestation (approximately 1.00 and 1. 10, respectively). The ratio of the cardiac and thoracic area showed only a slight increase with advancing gestational age, but with significant correlation. The fetal heart rate showed a slow decrease from 167 to 150 bpm in this period of gestation. The transversal heart diameter, both ventricular dimensions, interventricular septal thickness, heart area, cardiothoracic diameter ratio, aortic diameter and the pulmonary trunk diameter showed a highly significant linear correlation to the gestational age and the biparietal diameter.

CONCLUSION

The advancing quality of ultrasound images allows fetal echocardiography in the first and early second trimester. Our normative data could be the basis of studying the development of cardiac structures in congenital heart disease and it might be helpful in the detection of some congenital heart defects in early pregnancy.

Direct targeting of SUZ12/ROCK2 by miR-200b/c inhibits cholangiocarcinoma tumourigenesis and metastasis

Background:

The multidrug resistance and distant metastasis of cholangiocarcinoma result in high postoperative recurrence and low long-term survival rates. It has been demonstrated that the ectopic expression of miR-200 suppresses the multidrug resistance and metastasis of cancer. However, the expression and function of miR-200 in cholangiocarcinoma has not yet been described.

Methods:

In this study, we identified dysregulated microRNAs (miRNAs, miR) in cholangiocarcinoma tissue by microarray analysis, and subsequent real-time PCR and northern blot analyses validated the expression of candidate miR. We performed functional analyses and investigated the relationship between miR-200b/c expression and the properties of cholangiocarcinoma cells. A dual luciferase assay was applied to examine the effect of miRNAs on the 3′-UTR of target genes, and we demonstrated the function of the target gene by siRNA transfection identifying the downstream pathway via western blotting.

Results:

We found significantly downregulated expression of four miR-200 family members (miR-200a/b/c/429) and then confirmed that ectopic miR-200b/200c inhibits the migration and invasion of cholangiocarcinoma cells both in vitro and in vivo. We found that miR-200b/c influenced the tumourigenesis of cholangiocarcinoma cells including their tumour-initiating capacity, sphere formation, and drug resistance. We further found that miR-200b/c regulated migration and invasion capacities by directly targeting rho-kinase 2 and regulated tumorigenic properties by directly targeting SUZ12 (a subunit of a polycomb repressor complex).

Conclusion:

Our study shows that miR-200b/c has a critical role in the regulation of the tumorigenic and metastatic capacity of cholangiocarcinoma and reveals the probable underlying mechanisms.

Emergence of a new GII.17 norovirus variant in patients with acute gastroenteritis in Jiangsu, China, September 2014 to March 2015

From September 2014 to March 2015, 23 outbreaks of norovirus (NoV) acute gastroenteritis occurred in Jiangsu, China. Partial sequencing of the NoV capsid gene suggested that 16 of the 23 outbreaks were related to a new GII.17 variant. This variant was first detected in sporadic specimens in October 2014, and became predominant in February 2015. Analysis of the RNA-dependent RNA polymerase (RdRp), and complete capsid including the protruding domain P2 sequences confirmed this GII.17 variant as distinct from previously identified GII variants.

Prolonged circulating lives of single-chain Fv proteins conjugated with polyethylene glycol: a comparison of conjugation chemistries and compounds

The utility of single-chain Fv proteins as therapeutic agents would be substantially broadened if the circulating lives of these minimal antigen-binding polypeptides were both prolonged and adjustable. Poly(ethylene glycol) (PEG) bioconjugate derivatives of the model single-chain Fv, CC49/218 sFv, were constructed using six different linker chemistries that selectively conjugate either primary amines or carboxylic acid groups. Activated PEG polymers with molecular weights of 2000, 5000, 10 000, 12 000, and 20 000 were included in the sFv bioconjugate evaluation. Additionally, the influence of PEG conjugate geometry in branched PEG strands (U-PEG) and the effect of multimeric PEG-sFv bioconjugates on circulating life and affinity were examined. Although random and extensive PEG polymer conjugations have been achievable in highly active derivatives of the prototypical PEG-enzymes, PEGylation of CC49/218 sFv required stringent adjustment of reaction conditions in order to preserve antigen-binding affinity as measured in either mucin-specific or whole cell immunoassays. Purified bioconjugates with PEG:sFv ratios of 1:1 through 2:1 were identified as promising candidates which exhibit sFv affinity (K(d)) values within 2-fold of the unmodified sFv protein. Interestingly, PEG conjugation to carboxylic acid moieties, using a PEG-hydrazide chemistry, achieved significant activity retention in bioconjugates at a higher PEG:sFv ratio (5:1) than with any of the amine-reactive activated PEG polymers. Prolonged circulating life in mice was demonstrated for each of the PEG conjugates. An increase in PEG polymer length was found to be more effective for serum half-life extension than a corresponding increase in total PEG mass. For example, CC49/218 sFv conjugated to either one strand of PEG-20000, or four strands of PEG-5000, displayed about 20- or 14-fold increased serum half-life, respectively, relative to the unmodified sFv. The demonstrated suitability of established random conjugation chemistries for PEGylation of sFv proteins, in conjunction with innovative site-specific conjugation methods, indicates that production of a panoply of sFv proteins with both engineered affinity and tailored circulating life may now be achievable.

Erythropoietin promotes bone formation through EphrinB2/EphB4 signaling

Recent studies have demonstrated that erythropoietin (EPO) has extensive nonhematopoietic biological functions. However, little is known about how EPO regulates bone formation, although several studies suggested that EPO can affect bone homeostasis. In this study, we investigated the effects of EPO on the communication between osteoclasts and osteoblasts through the ephrinB2/EphB4 signaling pathway. We found that EPO slightly promotes osteoblastic differentiation with the increased expression of EphB4 in ST2 cells. However, EPO increased the expression of Nfatc1 and ephrinB2 but decreased the expression of Mmp9 in RAW264.7 cells, resulting in an increase of ephrinB2-expressing osteoclasts and a decrease in resorption activity. The stimulation of ephrinB2/EphB4 signaling via ephrinB2-Fc significantly promoted EPO-mediated osteoblastic differentiation in ST2 cells. EphB4 knockdown through EphB4 shRNA inhibited EPO-mediated osteoblastic phenotypes. Furthermore, in vivo assays clearly demonstrated that EPO efficiently induces new bone formation in the alveolar bone regeneration model. Taken together, these results suggest that ephrinB2/EphB4 signaling may play an important role in EPO-mediated bone formation.

Adipogenic miRNA and meta-signature miRNAs involved in human adipocyte differentiation and obesity

MicroRNAs (miRNAs) have been identified as a new class of regulatory molecules that influence many biological functions, including metabolism, adipocyte differentiation. To determine the role of adipogenic miRNAs in the adipocyte differentiation process, we used microarray technology to monitor miRNA levels in human adipose-derived mesenchymal stem cells (hMSCs-Ad), human stromal vascular cells (SVCs) and differentiated adipocytes. 79 miRNAs were found to be differentially expressed, most of which are located in obesity related chromosomal regions but have not been previously linked to adipocyte differentiation process. A systematic search was made for relevant studies in academic data bases, involving the Gene Expression Omnibus (GEO) ArrayExpress, Pubmed and Embase database. Eight studies on human adipocyte differentiation or obesity were included in the final analysis. After combining our microarray data with meta-analysis of published microarray data, we detected 42 differently expressed miRNAs (meta-signature miRNAs) in mature adipocytes compared to SVCs or hMSCs-Ad. Our study shows meta-signature miRNAs specific for adipogenesis, several of which are correlated with key gene targets demonstrating functional relationships to pathways in BMP signaling pathway, Cell differentiation, Wnt signaling, insulin receptor signaling pathway, MAPK signaling, Cell cycle and lipid metabolic process. Our study shows that the first evidence of hsa-let-7 family, hsa-miR-15a-5p, hsa-miR-27a-3p, hsa-miR-106b-5p, hsa-miR-148a-3p and hsa-miR-26b-5p got a great weight in adipogenesis. We concluded that meta-signature miRNAs involved in adipocyte differentiation and provided pathophysiological roles and novel insight into obesity and its related metabolic diseases.

A clock network for geodesy and fundamental science

Leveraging the unrivalled performance of optical clocks as key tools for geo-science, for astronomy and for fundamental physics beyond the standard model requires comparing the frequency of distant optical clocks faithfully. Here, we report on the comparison and agreement of two strontium optical clocks at an uncertainty of 5 × 10⁻¹⁷ via a newly established phase-coherent frequency link connecting Paris and Braunschweig using 1,415 km of telecom fibre. The remote comparison is limited only by the instability and uncertainty of the strontium lattice clocks themselves, with negligible contributions from the optical frequency transfer. A fractional precision of 3 × 10⁻¹⁷ is reached after only 1,000 s averaging time, which is already 10 times better and more than four orders of magnitude faster than any previous long-distance clock comparison. The capability of performing high resolution international clock comparisons paves the way for a redefinition of the unit of time and an all-optical dissemination of the SI-second.

Comparing the frequency of two distant optical clocks will enable sensitive tests of fundamental physics. Here, the authors compare two strontium optical-lattice clocks 690 kilometres apart to a degree of accuracy that is limited only by the uncertainty of the individual clocks themselves.

Synthesis of 6H-indolo[2,3-b][1,6]naphthyridines and related compounds as the 5-Aza analogues of ellipticine alkaloids

Treatment of 2-(1-alkynyl)phenyl isocyanates 6 with the iminophosphorane 14 produced in situ the benzoenynyl carbodiimides 15. Thermolysis of 15 under refluxing p-xylene furnished the 6H-indolo[2,3-b][1,6]naphthyridines 5, which could be regarded as the 5-aza analogues of ellipticine alkaloids. Similarly, condensation of 6 with the iminophosphorane 20 led to the formation of the 6H-indolo[2,3-b][1,5]naphthyridines 25 as the major isomer and the 10H- indolo[2,3-b][1,7]naphthyridines 26 as the minor isomer. The indolonaphthyridines 32, 33, and 34 having a methoxyl substituent were likewise synthesized. Treatment of the diisocyanate 43 with 2 equiv of the iminophosphorane 7 furnished 45 having two indoloquinoline units incorporated in a seven-fused-ring system.

Reduced transplant arteriosclerosis in plasminogen-deficient mice

Recent gene targeting studies indicate that the plasminogen system is implicated in cell migration and matrix degradation during arterial neointima formation and atherosclerotic aneurysm formation. This study examined whether plasmin proteolysis is involved in accelerated posttransplant arteriosclerosis (graft arterial disease). Donor carotid arteries from wild-type B10.A2R mice were transplanted into either plasminogen wild-type (Plg+/+) or homozygous plasminogen-deficient (Plg-/-) recipient mice with a genetic background of 75% C57BL/6 and 25% 129. Within 15 d after allograft transplantation, leukocytes and macrophages infiltrated the graft intima in Plg+/+ and Plg-/- recipient mice to a similar extent. In Plg+/+ recipients, the elastic laminae in the transplant media exhibited breaks through which macrophages infiltrated before smooth muscle cell proliferation, whereas in Plg-/- recipients, macrophages failed to infiltrate the transplant media which remained structurally more intact. After 45 d of transplantation, a multilayered smooth muscle cell-rich transplant neointima developed in Plg+/+ hosts, in contrast to Plg-/- recipients, in which the transplants contained a smaller intima, predominantly consisting of leukocytes, macrophages, and thrombus. Media necrosis, fragmentation of the elastic laminae, and adventitial remodeling were more pronounced in Plg+/+ than in Plg-/- recipient mice. Expression of the plasminogen activators (PA), urokinase-type PA (u-PA) and tissue-type PA (t-PA), and expression of the matrix metalloproteinases (MMPs), MMP-3, MMP-9, MMP-12, and MMP-13, were significantly increased within 15 d of transplantation when cells actively migrate. These data indicate that plasmin proteolysis plays a major role in allograft arteriosclerosis by mediating elastin degradation, macrophage infiltration, media remodeling, medial smooth muscle cell migration, and formation of a neointima.