Wiki: A Tool for Active and Collaborative Learning

In this session the presenter will discuss: What a Wiki is? Why wikis have gained popularity in education? How can a wiki be used as a web authoring tool for students to achieve active and collaborative learning in an online/hybrid learning setting. We\u27ll also introduce programs for creating wikis, show the process of creating a wiki, and share some tips about how to use this tool effectively to achieve your course\u27s learning objectives. Some wiki sites created by students for class work will be demonstrated

Enhanced killing of antibiotic-resistant bacteria enabled by massively parallel combinatorial genetics

New therapeutic strategies are needed to treat infections caused by drug-resistant bacteria, which constitute a major growing threat to human health. Here, we use a high-throughput technology to identify combinatorial genetic perturbations that can enhance the killing of drug-resistant bacteria with antibiotic treatment. This strategy, Combinatorial Genetics En Masse (CombiGEM), enables the rapid generation of high-order barcoded combinations of genetic elements for high-throughput multiplexed characterization based on next-generation sequencing. We created ~34,000 pairwise combinations of Escherichia coli transcription factor (TF) overexpression constructs. Using Illumina sequencing, we identified diverse perturbations in antibiotic-resistance phenotypes against carbapenem-resistant Enterobacteriaceae. Specifically, we found multiple TF combinations that potentiated antibiotic killing by up to 10[superscript 6]-fold and delivered these combinations via phagemids to increase the killing of highly drug-resistant E. coli harboring New Delhi metallo-beta-lactamase-1. Moreover, we constructed libraries of three-wise combinations of transcription factors with >4 million unique members and demonstrated that these could be tracked via next-generation sequencing. We envision that CombiGEM could be extended to other model organisms, disease models, and phenotypes, where it could accelerate massively parallel combinatorial genetics studies for a broad range of biomedical and biotechnology applications, including the treatment of antibiotic-resistant infections.National Institutes of Health (U.S.) (New Innovator Award DP2 OD008435)United States. Office of Naval ResearchEllison Medical Foundation (New Scholar in Aging Award)Henry L. and Grace Doherty Charitable Foundatio

Tree-ring-based precipitation reconstruction in the source region of Weihe River, northwest China since AD 1810

A tree-ring width chronology of Picea purpurea Mast from Mt. Shouyang in the source region of Weihe River (SWR), northwest China, was developed in this study. Correlation analysis showed that the precipitation from previous August to current July was the limiting climate factor of tree growth. Using a reliable and stable linear regression model, which explained 42.6% of the variance of the actual precipitation during the calibration period from 1958 to 2014, a 205-year long precipitation series was reconstructed for the SWR. The dry years in the reconstruction were well supported by historical documents, and famous historical droughts were also recorded in the dry periods of a low-frequency scale of the reconstructed precipitation. As demonstrated by the spatial correlation patterns, the reconstructed series compared well with other hydroclimate records for northwest China, indicating that it could represent large-scale hydroclimate changes. The 2-8-year interannual cycles and the interdecadal quasiperiods of 15.9 years and 18.6 years revealed that the precipitation in this region was probably affected by the El Nino-Southern Oscillation and North Atlantic Oscillation. The dry/wet years corresponded well with the El Nino/La Nina events and the SWR commonly experienced droughts during the low periods of North Atlantic Oscillation

Sunshine duration reconstruction in the southeastern Tibetan Plateau based on tree-ring width and its relationship to volcanic eruptions

Sunshine is as essential as temperature and precipitation for tree growth, but sunshine duration reconstructions based on tree rings have not yet been conducted in China. In this study, we presented a 497-year sunshine duration reconstruction for the southeastern Tibetan Plateau using a width chronology of Abies forrestii from the central Hengduan Mountains. The reconstruction accounted for 53.5% of the variance in the observed sunshine during the period of 1961-2013 based on a stable and reliable linear regression. This reconstructed sunshine duration contained six sunny periods (1630-1656, 1665-1697, 1731-1781, 1793-1836, 1862-1895 and 1910-1992) and seven cloudy periods (1522-1629, 1657-1664, 1698-1730, 1782-1792, 1837-1861, 1896-1909 and 1993-2008) at a low-frequency scale. There was an increasing trend from the 16th century to the late 18th and early 19th centuries and a decreasing trend from the mid-19th to the early 21st centuries. Sunshine displayed inverse patterns to the local Palmer drought severity index on a multidecadal scale, indicating that this region likely experienced droughts under more sunshine conditions. The decrease in sunshine particularly in recent decades was mainly due to increasing atmospheric anthropogenic aerosols. In terms of the interannual variations in sunshine, weak sunshine years matched well with years of major volcanic eruptions. The significant cycles of the 2- to 7-year, 20.0-year and 35.2-year durations as well as the 60.2-year and 78.7-year durations related to the El-Nino Southern Oscillation, the Pacific Decadal Oscillation and the Atlantic Multidecadal Oscillation suggested that the variation in sunshine duration in the southeastern Tibetan Plateau was possibly affected by large-scale ocean-atmosphere circulations. (C) 2018 Elsevier B.V. All rights reserved

Small RNA zippers lock miRNA molecules and block miRNA function in mammalian cells.

MicroRNAs (miRNAs) loss-of-function phenotypes are mainly induced by chemically modified antisense oligonucleotides. Here we develop an alternative inhibitor for miRNAs, termed \u27small RNA zipper\u27. It is designed to connect miRNA molecules end to end, forming a DNA-RNA duplex through a complementary interaction with high affinity, high specificity and high stability. Two miRNAs, miR-221 and miR-17, are tested in human breast cancer cell lines, demonstrating the 70∼90% knockdown of miRNA levels by 30-50 nM small RNA zippers. The miR-221 zipper shows capability in rescuing the expression of target genes of miR-221 and reversing the oncogenic function of miR-221 in breast cancer cells. In addition, we demonstrate that the miR-221 zipper attenuates doxorubicin resistance with higher efficiency than anti-miR-221 in human breast cancer cells. Taken together, small RNA zippers are a miRNA inhibitor, which can be used to induce miRNA loss-of-function phenotypes and validate miRNA target genes

DNA methylation/hydroxymethylation in melanoma

Melanoma is a malignant tumor of melanocytes and is considered to be the most aggressive cancer among all skin diseases. The pathogenesis of melanoma has not been well documented, which may restrict the research and development of biomarkers and therapies. To date, several genetic and epigenetic factors have been identified as contributing to the development and progression of melanoma. Besides the findings on genetic susceptibilities, the recent progress in epigenetic studies has revealed that loss of the DNA hydroxymethylation mark, 5-hydroxymethylcytosine (5-hmC), along with high levels of DNA methylation at promoter regions of several tumor suppressor genes in melanoma, may serve as biomarkers for melanoma. Moreover, 5-Aza-2′-deoxycytidine, an epigenetic modifier causing DNA demethylation, and ten-eleven translocation family dioxygenase (TET), which catalyzes the generation of 5-hmC, demonstrate therapeutic potential in melanoma treatment. In this review, we will summarize the latest progress in research on DNA methylation/hydroxymethylation in melanoma, and we will discuss and provide insight for epigenetic biomarkers and therapies for melanoma. Particularly, we will discuss the role of DNA hydroxymethylation in melanoma infiltrating immune cells, which may also serve as a potential target for melanoma treatment

Tree-ring stable carbon isotope-based April-June relative humidity reconstruction since AD 1648 in Mt. Tianmu, China

Based on accurate dating, we have determined the stable carbon isotope ratios (delta C-13) of five Cryptomeria fortunei specimens from Mt. Tianmu, a subtropical area in southern China. The five delta C-13 time series records are combined into a single representative delta C-13 time series using a "numerical mix method." These are normalized to remove temporal variations of delta(13) C in atmospheric CO2 to obtain a carbon isotopic discrimination (Delta C-13) time series, in which we observe a distinct correlation between Delta C-13 and local April to June mean relative humidity (RH (AMJ) ) (n = 64, r = 0.858, p < 0.0001). We use this relationship to reconstruct RH (AMJ) variations from ad 1648 to 2014 at Mt. Tianmu. The reconstructed sequence show that over the past 367 years, Mt. Tianmu area was relatively wet, but in the latter part of the twentieth century, under the influence of increasing global warming, it has experienced a sharp reduction in relative humidity. Spatial correlation analysis reveals a significant negative correlation between RH (AMJ) at Mt. Tianmu and Sea Surface Temperature (SSTs) in the western equatorial Pacific and Indian Ocean. In other words, there is a positive correlation between tree-ring delta C-13 in Mt. Tianmu and SSTs. Both observed and reconstructed RH (AMJ) show significant positive correlations with East Asian and South Asian monsoons from 1951 to 2014, which indicate that RH (AMJ) from Mt. Tianmu reflects the variability of the Asian summer monsoon intensity to a great extent. The summer monsoon has weakened since 1960. However, an increase in relative humidity since 2003 implies a recent enhancement in the summer monsoon

Pathophysiology and transcriptomic analysis of Picea koraiensis inoculated by bark beetle-vectored fungus Ophiostoma bicolor

Ophiostomatoid fungi exhibit a complex relationship with bark beetles; exhausting of host tree defenses is traditionally regarded as one of the key benefits provided to beetle vectors. Ophiostoma bicolor is one of the dominant species of the mycobiota associated with Ips genus bark beetles which infect the spruce trees across the Eurasian continent. Host spruce trees resist fungal invasion through structural and inducible defenses, but the underlying mechanisms at the molecular level, particularly with respect to the interaction between bark beetle-associated fungi and host trees, remain unclear. The aim of this study was to observe the pathological physiology and molecular changes in Picea koraiensis seedlings after artificial inoculation with O. bicolor strains (TS, BH, QH, MX, and LWQ). This study showed that O. bicolor was a weakly virulent pathogen of spruce, and that the virulent of the five O. bicolor strains showed differentiation. All O. bicolor strains could induce monoterpenoid release. A positive correlation between fungal virulence and release of monoterpenoids was observed. Furthermore, the release rate of monoterpenoids peaked at 4 days post-inoculation (dpi) and then decreased from 4 to 90 dpi. Transcriptomic analysis at 4 dpi showed that many plant-pathogen interaction processes and mitogen-activated protein kinase (MAPK) metabolic processes were activated. The expression of monoterpenoid precursor synthesis genes and diterpenoid synthesis genes was upregulated, indicating that gene expression regulated the release rate of monoterpenoids at 4 dpi. The enriched pathways may reveal the immune response mechanism of spruce to ophiostomatoid fungi. The dominant O. bicolor possibly induces the host defense rather than defense depletion, which is likely the pattern conducted by the pioneers of beetle-associated mycobiota, such as Endoconidiophora spp.. Overall, these results facilitate a better understanding of the interaction mechanism between the dominant association of beetles and the host at the molecular level