Human endogenous retrovirus K Rec forms a regulatory loop with MITF that opposes the progression of melanoma to an invasive stage

In the human genome, HERV-K(HML2) is the most recently endogenized retrovirus (ERV). While HERV-K(HML2) transcription is observed in healthy tissues, various cancers showed the upregulation of retroviral derived endogenized accessory products (e.g., envelope (Env), Np9 and Rec). Still, it is not clear whether the different HERV-K-derived genes contribute to a disease, or they are mere by-products. Here, we focus on the potential role of Rec in melanoma. Our in vitro model and high throughput data mining, including single-cell transcriptome analyses of patent’s material, reveal that Rec expression marks the proliferative (still controllable) stage of melanoma, and is involved in maintaining a delicate balance between cell proliferation and invasion. Thus, similar to melanocyte-inducing transcription factor (MITF), Rec is a sensitive marker of melanoma progression. Our Rec-knockdown in vitro system can faithfully model a subpopulation (MITF malignancy) of melanoma cells in human patients. Like Env, Rec modulates an endothelial-mesenchymal transition (EMT)-like process of cancer progression; however, they seem to affect the phenotype switch inversely. Rec inhibits the transition to the invasive state by altering the expression level of some key determinants of the EMT-like process, including MITF that directly binds the LTR5 _Hs of HERV-K. The Hominoid-specific HERV-K products might explain certain species-specific features of melanoma progression, and pinpoint to the limitation of using animal models in melanoma studies

Quantification of metabolic niche occupancy dynamics in a Baltic Sea bacterial community

Progress in molecular methods has enabled the monitoring of bacterial populations in time. Nevertheless, understanding community dynamics and its links with ecosystem functioning remains challenging due to the tremendous diversity of microorganisms. Conceptual frameworks that make sense of time series of taxonomically rich bacterial communities, regarding their potential ecological function, are needed. A key concept for organizing ecological functions is the niche, the set of strategies that enable a population to persist and define its impacts on the surroundings. Here we present a framework based on manifold learning to organize genomic information into potentially occupied bacterial metabolic niches over time. Manifold learning tries to uncover low-dimensional data structures in high-dimensional data sets that can be used to describe the data in reduced dimensions. We apply the method to re-construct the dynamics of putatively occupied metabolic niches using a long-term bacterial time series from the Baltic Sea, the Linnaeus Microbial Observatory (LMO). The results reveal a relatively low-dimensional space of occupied metabolic niches comprising groups of taxa with similar functional capabilities. Time patterns of occupied niches were strongly driven by seasonality. Some metabolic niches were dominated by one bacterial taxon, whereas others were occupied by multiple taxa, depending on the season. These results illustrate the power of manifold learning approaches to advance our understanding of the links between community composition and functioning in microbial systems

Implications of Shallower Memory Controller Transaction Queues in Scalable Memory Systems

Scalable memory systems provide scalable bandwidth to the core growth demands in multicores and embedded systems processors. In these systems, as memory controllers (MCs) are scaled, memory traffic per MC is reduced, so transaction queues become shallower. As a consequence, there is an opportunity to explore transaction queue utilization and its impact on energy utilization. In this paper, we propose to evaluate the performance and energy-per-bit impact when reducing transaction queue sizes along with the MCs of these systems. Experimental results show that reducing 50 % on the number of entries, bandwidth and energy-per-bit levels are not affected, whilst reducing aggressively of about 90 %, bandwidth is similarly reduced while causing significantly higher energy-per-bit utilization

Human endogenous retrovirus K rec forms a regulatory loop with MITF that opposes the progression of melanoma to an invasive stage

The HML2 subfamily of HERV-K (henceforth HERV-K) represents the most recently endogenized retrovirus in the human genome. While the products of certain HERV-K genomic copies are expressed in normal tissues, they are upregulated in several pathological conditions, including various tumors. It remains unclear whether HERV-K(HML2)-encoded products overexpressed in cancer contribute to disease progression or are merely by-products of tumorigenesis. Here, we focus on the regulatory activities of the Long Terminal Repeats (LTR5_Hs) of HERV-K and the potential role of the HERV-K-encoded Rec in melanoma. Our regulatory genomics analysis of LTR5_Hs loci indicates that Melanocyte Inducing Transcription Factor (MITF) (also known as binds to a canonical E-box motif (CA(C/T)GTG) within these elements in proliferative type of melanoma, and that depletion of MITF results in reduced HERV-K expression. In turn, experimentally depleting Rec in a proliferative melanoma cell line leads to lower mRNA levels of MITF and its predicted target genes. Furthermore, Rec knockdown leads to an upregulation of epithelial-to-mesenchymal associated genes and an enhanced invasion phenotype of proliferative melanoma cells. Together these results suggest the existence of a regulatory loop between MITF and Rec that may modulate the transition from proliferative to invasive stages of melanoma. Because HERV-K(HML2) elements are restricted to hominoid primates, these findings might explain certain species-specific features of melanoma progression and point to some limitations of animal models in melanoma studies

Unital Quantum Channels - Convex Structure and Revivals of Birkhoff's Theorem

The set of doubly-stochastic quantum channels and its subset of mixtures of unitaries are investigated. We provide a detailed analysis of their structure together with computable criteria for the separation of the two sets. When applied to O(d)-covariant channels this leads to a complete characterization and reveals a remarkable feature: instances of channels which are not in the convex hull of unitaries can return to it when either taking finitely many copies of them or supplementing with a completely depolarizing channel. In these scenarios this implies that a channel whose noise initially resists any environment-assisted attempt of correction can become perfectly correctable.Comment: 31 page

Essential Oils as Multicomponent Mixtures and Their Potential for Human Health and Well-Being

Essential oils (EOs) and their individual volatile organic constituents have been an inherent part of our civilization for thousands of years. They are widely used as fragrances in perfumes and cosmetics and contribute to a healthy diet, but also act as active ingredients of pharmaceutical products. Their antibacterial, antiviral, and anti-inflammatory properties have qualified EOs early on for both, the causal and symptomatic therapy of a number of diseases, but also for prevention. Obtained from natural, mostly plant materials, EOs constitute a typical example of a multicomponent mixture (more than one constituent substances, MOCS) with up to several hundreds of individual compounds, which in a sophisticated composition make up the property of a particular complete EO. The integrative use of EOs as MOCS will play a major role in human and veterinary medicine now and in the future and is already widely used in some cases, e.g. , in aromatherapy for the treatment of psychosomatic complaints, for inhalation in the treatment of respiratory diseases, or topically administered to manage adverse skin diseases. The diversity of molecules with different functionalities exhibits a broad range of multiple physical and chemical properties, which are the base of their multi-target activity as opposed to single isolated compounds. Whether and how such a broad-spectrum effect is reflected in natural mixtures and which kind of pharmacological potential they provide will be considered in the context of ONE Health in more detail in this review

Characterization of two novel antioxidant tetrahydroxyxanthones from Hypericum seeds and scanning electronmicroscopic investigations of their testa

Hypericum-Samen wurden kürzlich als natürliche Quelle für eine Reihe von Xanthon-Derivaten beschrieben. In Methanol-Extrakten von H. perforatum und H. tetrapterum konnten per HPLC(DAD)-MSn zwei Hauptkomponenten, die Tetrahydroxyxanthone THX-1 und -2, identifiziert werden, deren genaue Konfiguration bislang unbekannt war. Beide Substanzen wurden deshalb über chromatographische Auftrennung an Polyamid und Kieselgel aus dem Samenextrakt angereichert und mit Hilfe von 1D- und 2DNMR- Techniken eine Strukturanalyse vorgenommen. Durch Synthese von THX-1 und -2 und Vergleich ihrer chromatographischen sowie spektroskopischen/spektrometrischen Eigenschaften mit den natürlichen THX in H. perforatum wurde die exakte Konfiguration als 1,4,6,7-THX (THX-1) und 1,2,6,7-THX (THX-2) bestimmt. Die beiden neuartigen Verbindungen zeigten eine dreifach stärkere Radikalfängerwirkung im DPPH-Test als das wasserlösliche Vitamin E-Derivat Trolox® und sind somit starke Antioxidantien. Ferner konnte durch rasterelektronenmikroskopische Untersuchungen (SEM) die zweilagige Struktur der Hypericum-Samenschale (Testa) gezeigt werden, wobei die Xanthone wahrscheinlich in der sehr dickwandigen, lignifizierten Skerenchymschicht eingelagert sind.Hypericum seeds have recently been identified as a natural source of different xanthone derivatives. Two main constituents, the tetrahydroxyxanthones THX-1 and -2, were identified in methanolic extracts of H. perforatum and H. tetrapterum by means of HPLC(DAD)-MSn methods. However, the exact configuration of both THX was unknown so far. For this reason, the two compounds were enriched by chromatography on polyamide and silica, and the corresponding fraction was investigated by 1D- and 2D-NMR techniques. Based on a tentative structural assignment a total synthesis of THX-1 and -2 was performed. Comparing the chromatographic and spectroscopic/spectrometric features of synthetic THX-1 and -2 with their natural counterparts their exact configuration was determined as 1,4,6,7-THX (THX-1) and 1,2,6,7-THX (THX-2), respectively. The novel compounds exhibited a threefold higher radical scavenging activity in the DPPH assay than the vitamin E derivative Trolox®. Hence, they are strong antioxidants. Furthermore, scanning electron microscopy (SEM) provided insights into the two-layer structure of the testa (seed coat), with the thick lignified sclerenchyma layer presumably being the depository of the xanthones

Genome-wide profiling reveals remarkable parallels between insertion site selection properties of the MLV retrovirus and the piggyBac transposon in primary human CD4(+) T cells

The inherent risks associated with vector insertion in gene therapy need to be carefully assessed. We analyzed the genome-wide distributions of Sleeping Beauty (SB) and piggyBac (PB) transposon insertions as well as MLV retrovirus and HIV lentivirus insertions in human CD4+ T cells cells with respect to a panel of 40 chromatin states. The distribution of SB transposon insertions displayed the least deviation from random, while the PB transposon and the MLV retrovirus showed unexpected parallels across all chromatin states. Both MLV and PB insertions are enriched at transcriptional start sites (TSSs) and co-localize with BRD4-associated sites. We demonstrate physical interaction between the PB transposase and BET-domain proteins (including BRD4), suggesting convergent evolution of a tethering mechanism that directs integrating genetic elements into TSSs. We detect unequal biases across the four systems with respect to targeting genes whose deregulation has been previously linked to serious adverse events in gene therapy clinical trials. The SB transposon has the highest theoretical chance of targeting a safe harbor locus in the human genome. The data underscore the significance of vector choice to reduce the mutagenic load on cells in clinical applications

Single hadron response measurement and calorimeter jet energy scale uncertainty with the ATLAS detector at the LHC

The uncertainty on the calorimeter energy response to jets of particles is derived for the ATLAS experiment at the Large Hadron Collider (LHC). First, the calorimeter response to single isolated charged hadrons is measured and compared to the Monte Carlo simulation using proton-proton collisions at centre-of-mass energies of sqrt(s) = 900 GeV and 7 TeV collected during 2009 and 2010. Then, using the decay of K_s and Lambda particles, the calorimeter response to specific types of particles (positively and negatively charged pions, protons, and anti-protons) is measured and compared to the Monte Carlo predictions. Finally, the jet energy scale uncertainty is determined by propagating the response uncertainty for single charged and neutral particles to jets. The response uncertainty is 2-5% for central isolated hadrons and 1-3% for the final calorimeter jet energy scale.Comment: 24 pages plus author list (36 pages total), 23 figures, 1 table, submitted to European Physical Journal

Standalone vertex finding in the ATLAS muon spectrometer

A dedicated reconstruction algorithm to find decay vertices in the ATLAS muon spectrometer is presented. The algorithm searches the region just upstream of or inside the muon spectrometer volume for multi-particle vertices that originate from the decay of particles with long decay paths. The performance of the algorithm is evaluated using both a sample of simulated Higgs boson events, in which the Higgs boson decays to long-lived neutral particles that in turn decay to bbar b final states, and pp collision data at √s = 7 TeV collected with the ATLAS detector at the LHC during 2011