The Symbiotic Green Algae, Oophila (Chlamydomonadales, Chlorophyceae): A Heterotrophic Growth Study and Taxonomic History

The green alga Oophila ambystomatus (Chlamydomonadales, Chlorophyceae) is well known as the symbiotic partner of Ambystoma maculatum, the yellow-spotted salamander. Recent molecular work has revealed phylogenetic diversity within isolates of Oophila from New England. Here I investigate physiological properties and genetic diversity of the algal symbionts representing different evolutionary lineages. In other well-studied symbiotic systems involving algae, e.g., Chlorella and Hydra, algae and lichen, or Symbiodinium and Scleractinian corals, the algal symbiont is capable of multiple trophic modes, thus influencing its capacity as a partner. In this study I investigated whether genetically differentiated strains of Oophila are capable of absorbing organic carbon compounds (heterotrophic growth) and hypothesize how this might play into its symbiotic relationship. A growth study examined each strain’s ability to grow in light (16:8 L:D; 41 μmol/m2) and in dark (0:24 L:D; 0 μmol/m2) in three different media types (BBM, BBM+glu, BBM+gal). I determined there is metabolic variability among the strains that indicates each may provide differential benefits to their partner. I also reviewed the taxonomic history of Oophila to resolve confusion over its validity. After a brief recount of its history, I determined that the name is valid, and suggest a recent collection from the type locality of Middlesex Fells Reservation be designated as an epitype given that the aged type material lacks diagnostic features and its DNA is degraded. An epitype will provide future researchers an unambiguous anchoring specimen and sequence for future taxonomic, molecular and physiological studies

Green Fingers for Climate-Resilient Cities – Connecting Processes of Landscape Planning and Designing with Co-Creation

Taking the transdisciplinary research study “Green fingers for a climate resilient city”, funded by the German Ministry of education and research (BMBF), as an example, this paper follows the hypothesis that processes of landscape planning and designing multifunctional green spaces and processes of co-creation need to be combined to stimulate climate resilient city transformation. The findings are that efforts to combine these processes benefit from making complex climate-resilient city planning accessible for people of different professional backgrounds. The paper showcases how storytelling (Schmidt 2019), mapping (Langner 2009) and guided walks (Schultz 2019) are means to mutually engage with, perceive and understand multifunctional green spaces, inspire ownership, and build capacity for the city’s climate-resilient transformation

Recurrent patterns of DNA copy number alterations in tumors reflect metabolic selection pressures.

Copy number alteration (CNA) profiling of human tumors has revealed recurrent patterns of DNA amplifications and deletions across diverse cancer types. These patterns are suggestive of conserved selection pressures during tumor evolution but cannot be fully explained by known oncogenes and tumor suppressor genes. Using a pan-cancer analysis of CNA data from patient tumors and experimental systems, here we show that principal component analysis-defined CNA signatures are predictive of glycolytic phenotypes, including 18F-fluorodeoxy-glucose (FDG) avidity of patient tumors, and increased proliferation. The primary CNA signature is enriched for p53 mutations and is associated with glycolysis through coordinate amplification of glycolytic genes and other cancer-linked metabolic enzymes. A pan-cancer and cross-species comparison of CNAs highlighted 26 consistently altered DNA regions, containing 11 enzymes in the glycolysis pathway in addition to known cancer-driving genes. Furthermore, exogenous expression of hexokinase and enolase enzymes in an experimental immortalization system altered the subsequent copy number status of the corresponding endogenous loci, supporting the hypothesis that these metabolic genes act as drivers within the conserved CNA amplification regions. Taken together, these results demonstrate that metabolic stress acts as a selective pressure underlying the recurrent CNAs observed in human tumors, and further cast genomic instability as an enabling event in tumorigenesis and metabolic evolution

Ibrutinib Unmasks Critical Role of Bruton Tyrosine Kinase in Primary CNS Lymphoma.

Bruton tyrosine kinase (BTK) links the B-cell antigen receptor (BCR) and Toll-like receptors with NF-κB. The role of BTK in primary central nervous system (CNS) lymphoma (PCNSL) is unknown. We performed a phase I clinical trial with ibrutinib, the first-in-class BTK inhibitor, for patients with relapsed or refractory CNS lymphoma. Clinical responses to ibrutinib occurred in 10 of 13 (77%) patients with PCNSL, including five complete responses. The only PCNSL with complete ibrutinib resistance harbored a mutation within the coiled-coil domain of CARD11, a known ibrutinib resistance mechanism. Incomplete tumor responses were associated with mutations in the B-cell antigen receptor-associated protein CD79B

Pathway Commons, a web resource for biological pathway data

Pathway Commons (http://www.pathwaycommons.org) is a collection of publicly available pathway data from multiple organisms. Pathway Commons provides a web-based interface that enables biologists to browse and search a comprehensive collection of pathways from multiple sources represented in a common language, a download site that provides integrated bulk sets of pathway information in standard or convenient formats and a web service that software developers can use to conveniently query and access all data. Database providers can share their pathway data via a common repository. Pathways include biochemical reactions, complex assembly, transport and catalysis events and physical interactions involving proteins, DNA, RNA, small molecules and complexes. Pathway Commons aims to collect and integrate all public pathway data available in standard formats. Pathway Commons currently contains data from nine databases with over 1400 pathways and 687 000 interactions and will be continually expanded and updated

Verschwörungsglaube, Medienzynismus und Militanz: Einstellungen und Informationsquellen von Menschen mit AfD-Wahlpräferenz - ein Beitrag zur Radikalisierungsforschung

Der Beitrag untersucht medienbezogene Einstellungen und das Ausmaß des Verschwörungsglaubens von Menschen mit AfD-Wahlpräferenz. Er greift die Debatte über Kampfbegriffe wie "Lügenpresse" und "Systemmedien" auf und erweitert die Radikalisierungsforschung um einen kommunikationswissenschaftlichen Zugang. Dafür verwendet er das Konzept des "Medienzynismus". Es bezeichnet ein Einstellungsmuster mit verschwörungsideologischen Zügen: Journalist*innen werden als Lügner und System-Kollaborateure betrachtet. Der Beitrag analysiert auch die Mediennutzung von Menschen mit AfD-Präferenz sowie ihre Einstellungen zu Gewalt. Die Basis bilden vier Bevölkerungsumfragen aus den Jahren 2016 bis 2019. Die Daten wurden in Regressionsanalysen und mit einem Strukturgleichungsmodell ausgewertet. Dabei zeigt sich die Radikalität der AfD-Gruppe: Bei ihr sind Medienzynismus und Verschwörungsglaube stark ausgeprägt. Dies geht mit einer überdurchschnittlichen Nutzung "alternativer" Medien und einem höheren Verständnis für die Anwendung von Gewalt einher. Die Studie findet keine eindeutigen Hinweise für eine sich verschärfende Radikalisierung im Zeitverlauf, aber auch keine Abschwächung. Die Befunde stützen Befürchtungen, dass der Verschwörungsglaube mit einer Affinität zu Gewalt verbunden und die Radikalisierung durch eine spezifische Mediennutzung gefördert werden kann.The article examines the media-related attitudes of people who are likely to vote for the AfD party. It builds on the debate on terms such as „lying press“ (fake news media) and adds a media studies approach to radicalization research. It introduces the concept of "media cynicism", which describes a pattern of attitudes that includes features of conspiracy ideologies: journalists are viewed as liars and system collaborators. The article also examines media use, conspiracy beliefs, and attitudes towards violence. Four surveys from 2016 to 2019 form the basis of the study. The data were analyzed using regression analyses and structural equation modeling. The findings illustrate the radicalism of AfD voters: They tend to show strong media cynicism and beliefs in conspiracies. This goes hand in hand with an above-average use of "alternative" media and an increased support for using violence. The study does not find clear indications of an enhanced radicalization of AfD voters over time, but also finds no signs of a slowdown. The findings support fears that beliefs in conspiracies are connected to an affinity for violence and that radicalization can be fueled by the use of specific news media channels

Off-target effects dominate a large-scale RNAi screen for modulators of the TGF-β pathway and reveal microRNA regulation of TGFBR2

10.1186/1758-907X-2-3Silence21

Clinical multiplexed exome sequencing distinguishes adult oligodendroglial neoplasms from astrocytic and mixed lineage gliomas

Classifying adult gliomas remains largely a histologic diagnosis based on morphology; however astrocytic, oligodendroglial and mixed lineage tumors can display overlapping histologic features. We used multiplexed exome sequencing (OncoPanel) on 108 primary or recurrent adult gliomas, comprising 65 oligodendrogliomas, 28 astrocytomas and 15 mixed oligoastrocytomas to identify lesions that could enhance lineage classification. Mutations in TP53 (20/28, 71%) and ATRX (15/28, 54%) were enriched in astrocytic tumors compared to oligodendroglial tumors of which 4/65 (6%) had mutations in TP53 and 2/65 (3%) had ATRX mutations. We found that oligoastrocytomas harbored mutations in TP53 (80%, 12/15) and ATRX (60%, 9/15) at frequencies similar to pure astrocytic tumors, suggesting that oligoastrocytomas and astrocytomas may represent a single genetic or biological entity. p53 protein expression correlated with mutation status and showed significant increases in astrocytomas and oligoastrocytomas compared to oligodendrogliomas, a finding that also may facilitate accurate classification. Furthermore our OncoPanel analysis revealed that 15% of IDH1/2 mutant gliomas would not be detected by traditional IDH1 (p.R132H) antibody testing, supporting the use of genomic technologies in providing clinically relevant data. In all, our results demonstrate that multiplexed exome sequencing can support evaluation and classification of adult low-grade gliomas with a single clinical test

Rapid Induction of Tumor-specific Type 1 T Helper Cells in Metastatic Melanoma Patients by Vaccination with Mature, Cryopreserved, Peptide-loaded Monocyte-derived Dendritic Cells

There is consensus that an optimized cancer vaccine will have to induce not only CD8+ cytotoxic but also CD4+ T helper (Th) cells, particularly interferon (IFN)-γ–producing, type 1 Th cells. The induction of strong, ex vivo detectable type 1 Th cell responses has not been reported to date. We demonstrate now that the subcutaneous injection of cryopreserved, mature, antigen-loaded, monocyte-derived dendritic cells (DCs) rapidly induces unequivocal Th1 responses (ex vivo detectable IFN-γ–producing effectors as well as proliferating precursors) both to the control antigen KLH and to major histocompatibility complex (MHC) class II–restricted tumor peptides (melanoma-antigen [Mage]-3.DP4 and Mage-3.DR13) in the majority of 16 evaluable patients with metastatic melanoma. These Th1 cells recognized not only peptides, but also DCs loaded with Mage-3 protein, and in case of Mage-3DP4–specific Th1 cells IFN-γ was released even after direct recognition of viable, Mage-3–expressing HLA-DP4+ melanoma cells. The capacity of DCs to rapidly induce Th1 cells should be valuable to evaluate whether Th1 cells are instrumental in targeting human cancer and chronic infections