The Transcriptional Mediator Component Med12 Is Required for Hindbrain Boundary Formation

Background: Rhombomere boundaries form during hindbrain segmentation and are critical for maintaining segmental integrity and regulating migration in the hindbrain. Some genetic models affecting hindbrain boundary formation have been described, but involvement of components of the transcriptional mediator complex in boundary formation has not reported so far. Principal Findings: The kto/med12 mutant zebrafish, which affects the Mediator component Med12, causes specific loss of rhombomere boundary cells even though segmentation of the hindbrain takes place at least in part. In ktomutant embryos, cells forming rhombomere boundaries were largely absent as indicated by the use of several marker genes. While no obvious increase in cell death was observed, we found a notable reduction of cell proliferation in the hindbrain of kto mutant zebrafish. Conclusions: The kto/med12 mutation results in specific defects of boundary cell formation in the zebrafish hindbrain

TimeKit: A Time-series Forecasting-based Upgrade Kit for Collaborative Filtering

Recommender systems are a long-standing research problem in data mining and machine learning. They are incremental in nature, as new user-item interaction logs arrive. In real-world applications, we need to periodically train a collaborative filtering algorithm to extract user/item embedding vectors and therefore, a time-series of embedding vectors can be naturally defined. We present a time-series forecasting-based upgrade kit (TimeKit), which works in the following way: it i) first decides a base collaborative filtering algorithm, ii) extracts user/item embedding vectors with the base algorithm from user-item interaction logs incrementally, e.g., every month, iii) trains our time-series forecasting model with the extracted time-series of embedding vectors, and then iv) forecasts the future embedding vectors and recommend with their dot-product scores owing to a recent breakthrough in processing complicated time-series data, i.e., neural controlled differential equations (NCDEs). Our experiments with four real-world benchmark datasets show that the proposed time-series forecasting-based upgrade kit can significantly enhance existing popular collaborative filtering algorithms.Comment: Accepted at IEEE BigData 202

Diosgenin Induces Apoptosis in HepG2 Cells through Generation of Reactive Oxygen Species and Mitochondrial Pathway

Diosgenin, a naturally occurring steroid saponin found abundantly in legumes and yams, is a precursor of various synthetic steroidal drugs. Diosgenin is studied for the mechanism of its action in apoptotic pathway in human hepatocellular carcinoma cells. Based on DAPI staining, diosgenin-treated cells manifested nuclear shrinkage, condensation, and fragmentation. Treatment of HepG2 cells with 40 μM diosgenin resulted in activation of the caspase-3, -8, -9 and cleavage of poly-ADP-ribose polymerase (PARP) and the release of cytochrome c. In the upstream, diosgenin increased the expression of Bax, decreased the expression of Bid and Bcl-2, and augmented the Bax/Bcl-2 ratio. Diosgenin-induced, dose-dependent induction of apoptosis was accompanied by sustained phosphorylation of JNK, p38 MAPK and apoptosis signal-regulating kinase (ASK)-1, as well as generation of the ROS. NAC administration, a scavenger of ROS, reversed diosgene-induced cell death. These results suggest that diosgenin-induced apoptosis in HepG2 cells through Bcl-2 protein family-mediated mitochndria/caspase-3-dependent pathway. Also, diosgenin strongly generated ROS and this oxidative stress might induce apoptosis through activation of ASK1, which are critical upstream signals for JNK/p38 MAPK activation in HepG2 cancer cells

Pre-gastrula expression of zebrafish extraembryonic genes

<p>Abstract</p> <p>Background</p> <p>Many species form extraembryonic tissues during embryogenesis, such as the placenta of humans and other viviparous mammals. Extraembryonic tissues have various roles in protecting, nourishing and patterning embryos. Prior to gastrulation in zebrafish, the yolk syncytial layer - an extraembryonic nuclear syncytium - produces signals that induce mesoderm and endoderm formation. Mesoderm and endoderm precursor cells are situated in the embryonic margin, an external ring of cells along the embryo-yolk interface. The yolk syncytial layer initially forms below the margin, in a domain called the external yolk syncytial layer (E-YSL).</p> <p>Results</p> <p>We hypothesize that key components of the yolk syncytial layer's mesoderm and endoderm inducing activity are expressed as mRNAs in the E-YSL. To identify genes expressed in the E-YSL, we used microarrays to compare the transcription profiles of intact pre-gastrula embryos with pre-gastrula embryonic cells that we had separated from the yolk and yolk syncytial layer. This identified a cohort of genes with enriched expression in intact embryos. Here we describe our whole mount <it>in situ </it>hybridization analysis of sixty-eight of them. This includes ten genes with E-YSL expression (<it>camsap1l1</it>, <it>gata3</it>, <it>znf503</it>, <it>hnf1ba</it>, <it>slc26a1</it>, <it>slc40a1</it>, <it>gata6</it>, <it>gpr137bb</it>, <it>otop1 </it>and <it>cebpa</it>), four genes with expression in the enveloping layer (EVL), a superficial epithelium that protects the embryo (<it>zgc:136817</it>, <it>zgc:152778</it>, <it>slc14a2 </it>and <it>elovl6l</it>), three EVL genes whose expression is transiently confined to the animal pole (<it>elovl6l</it>, <it>zgc:136359 </it>and <it>clica</it>), and six genes with transient maternal expression (<it>mtf1</it>, <it>wu:fj59f04</it>, <it>mospd2</it>, <it>rftn2</it>, <it>arrdc1a </it>and <it>pho</it>). We also assessed the requirement of Nodal signaling for the expression of selected genes in the E-YSL, EVL and margin. Margin expression was Nodal dependent for all genes we tested, including the concentrated margin expression of an EVL gene: <it>zgc:110712</it>. All other instances of EVL and E-YSL expression that we tested were Nodal independent.</p> <p>Conclusion</p> <p>We have devised an effective strategy for enriching and identifying genes expressed in the E-YSL of pre-gastrula embryos. To our surprise, maternal genes and genes expressed in the EVL were also enriched by this strategy. A number of these genes are promising candidates for future functional studies on early embryonic patterning.</p

Lhx1 Is Required for Specification of the Renal Progenitor Cell Field

In the vertebrate embryo, the kidney is derived from the intermediate mesoderm. The LIM-class homeobox transcription factor lhx1 is expressed early in the intermediate mesoderm and is one of the first genes to be expressed in the nephric mesenchyme. In this study, we investigated the role of Lhx1 in specification of the kidney field by either overexpressing or depleting lhx1 in Xenopus embryos or depleting lhx1 in an explant culture system. By overexpressing a constitutively-active form of Lhx1, we established its capacity to expand the kidney field during the specification stage of kidney organogenesis. In addition, the ability of Lhx1 to expand the kidney field diminishes as kidney organogenesis transitions to the morphogenesis stage. In a complimentary set of experiments, we determined that embryos depleted of lhx1, show an almost complete loss of the kidney field. Using an explant culture system to induce kidney tissue, we confirmed that expression of genes from both proximal and distal kidney structures is affected by the absence of lhx1. Taken together our results demonstrate an essential role for Lhx1 in driving specification of the entire kidney field from the intermediate mesoderm

Cardioprotective Effect of the SDF-1α/CXCR4 Axis in Ischemic Postconditioning in Isolated Rat Hearts

Background and Objectives: Information about the role of the stromal cell-derived factor1a (SDF-1 alpha)/chemokine receptor type 4 (CXCR4) axis in ischemic postconditioning (IPOC) is currently limited. We hypothesized that the SDF-1 alpha/CXCR4 signaling pathway is directly involved in the cardioprotective effect of IPOC. Methods: Isolated rat hearts were divided into four groups. The control group was subjected to 30-min of regional ischemia and 2-hour of reperfusion (n=12). The IPOC group was induced with 6 cycles of 10-second reperfusion and 10-second global ischemia (n=8) in each cycle. The CXCR4 antagonist, AMD3100, was applied before reperfusion in the IPOC group (AMD+IPOC group, n=11) and control group (AMD group, n=9). Hemodynamic changes with electrocardiography were monitored and infarct size was measured. The SDF-1 alpha, lactate dehydrogenase (LDH) and creatine kinase (CK) concentrations in perfusate were measured. We also analyzed extracellular signal-regulated kinase 1/2 (ERK1/2) and Akt phosphorylation state expression. Results: IPOC significantly reduced infarct size, but AMD3100 attenuated the infarct reducing effect of IPOC. IPOC significantly decreased LDH and CK, but these effects were reversed by AMD3100. ERK1/2 and Akt phosphorylation increased with IPOC and these effects were blocked by AMD3100. Conclusion: Based on the results of this study, SDF-1 alpha/CXCR4 signaling may be involved in IPOC cardioprotection and this signaling pathway couples to the ERK1/2 and Akt pathways.111Ysciescopuskc

Cardioprotective Effect of the SDF-1α/CXCR4 Axis in Ischemic Postconditioning in Isolated Rat Hearts

Information about the role of the stromal cell-derived factor-1α (SDF-1α)/chemokine receptor type 4 (CXCR4) axis in ischemic postconditioning (IPOC) is currently limited. We hypothesized that the SDF-1α/CXCR4 signaling pathway is directly involved in the cardioprotective effect of IPOC

Source Characteristics of Atmospheric CO(2)and CH(4)in a Northeastern Highland Area of South Korea

This study aims to present the atmospheric CO(2)and CH(4)levels and analyze their source characteristics at an observation station in a northeastern highland area of Korea for the 2012-2014 period. We summarized the measured CO(2)and CH(4)concentrations for the 2012-2014 period. In addition, we characterized the major source of the rise of CO(2)and CH(4)in Ganseong (GS) by employing bivariate polar plots (BPP) and the concentration weighted trajectory (CWT) method together with currently available information on emission sources. For the three years, CO(2)was generally high in the order of winter, spring, autumn and summer and CH(4)high in the order of winter, autumn, spring and summer. The observed positive correlations between the hourly CO(2)and CH(4)in every season suggested the possibility of shared common emission sources, but there is a necessity for elucidation on this in the future. The BPP analysis indicated the local sources that are likely to be associated with the rise of greenhouse gases (GHGs) observed at GS (combustion in the village, plant respirations nearby GS, and mobile emissions on the nearby road for CO(2)and leakages from the gas stations along the road and agricultural activities for CH4). Synthesizing the CWT results together with emission source information from national and global emission inventories, we identified likely major source areas and characterized major emission sources. For example, the identified major sources for the winter CO(2)are coal combustion, coal washing and industrial activities in Inner Mongolia, northern and the northeastern China, fuel burning for the energy for the infrastructure of a northwestern city in South Korea, and the manufacturing industry and fuel combustion in the northern parts of North Korea. Hopefully, these kinds of results will aid environmental researchers and decision-makers in performing more in-depth studies for GHG sources in order to derive effective mitigation strategies