Novel insights into the Thaumarchaeota in the deepest oceans: their metabolism and potential adaptation mechanisms

Background: Marine Group I (MGI) Thaumarchaeota, which play key roles in the global biogeochemical cycling of nitrogen and carbon (ammonia oxidizers), thrive in the aphotic deep sea with massive populations. Recent studies have revealed that MGI Thaumarchaeota were present in the deepest part of oceans - the hadal zone (depth > 6,000 m, consisting almost entirely of trenches), with the predominant phylotype being distinct from that in the “shallower” deep sea. However, little is known about the metabolism and distribution of these ammonia oxidizers in the hadal water. Results: In this study, metagenomic data were obtained from 0-10,500 m deep seawater samples from the Mariana Trench. The distribution patterns of Thaumarchaeota derived from metagenomics and 16S rRNA gene sequencing were in line with that reported in previous studies: abundance of Thaumarchaeota peaked in bathypelagic zone (depth 1,000 – 4,000 m) and the predominant clade shifted in the hadal zone. Several metagenome-assembled thaumarchaeotal genomes were recovered, including a near-complete one representing the dominant hadal phylotype of MGI. Using comparative genomics we predict that unexpected genes involved in bioenergetics, including two distinct ATP synthase genes (predicted to be coupled with H+ and Na+ respectively), and genes horizontally transferred from other extremophiles, such as those encoding putative di-myo-inositol-phosphate (DIP) synthases, might significantly contribute to the success of this hadal clade under the extreme condition. We also found that hadal MGI have the genetic potential to import a far higher range of organic compounds than their shallower water counterparts. Despite this trait, hadal MDI ammonia oxidation and carbon fixation genes are highly transcribed providing evidence they are likely autotrophic, contributing to the primary production in the aphotic deep sea. Conclusions: Our study reveals potentially novel adaptation mechanisms of deep-sea thaumarchaeotal clades and suggests key functions of deep-sea Thaumarchaeota in carbon and nitrogen cycling

Exosomes promote pre-metastatic niche formation in ovarian cancer.

Ovarian cancer is one of the most common gynecological malignancies. Upon initial diagnosis, the majority of patients present with widespread metastatic growth within the peritoneal cavity. This metastatic growth occurs in stages, with the formation of a pre-metastatic niche occurring prior to macroscopic tumor cell invasion. Exosomes released by the primary ovarian tumor are small extracellular vesicles which prepare the distant tumor microenvironment for accelerated metastatic invasion. They regulate intercellular communication between tumor cells and normal stroma, cancer-associated fibroblasts, and local immune cells within the tumor microenvironment. In this review, we highlight the emerging roles of ovarian cancer exosomes as coordinators of pre-metastatic niche formation, biomarkers amenable to liquid biopsy, and targets of chemotherapy

Direct Observation of Dynamic Symmetry Breaking above Room Temperature in Methylammonium Lead Iodide Perovskite

Lead halide perovskites such as methylammonium lead triiodide (MAPI) have outstanding optical and electronic properties for photovoltaic applications, yet a full understanding of how this solution processable material works so well is currently missing. Previous research has revealed that MAPI possesses multiple forms of static disorder regardless of preparation method, which is surprising in light of its excellent performance. Using high energy resolution inelastic X-ray (HERIX) scattering, we measure phonon dispersions in MAPI and find direct evidence for another form of disorder in single crystals: large amplitude anharmonic zone-edge rotational instabilities of the PbI_6 octahedra that persist to room temperature and above, left over from structural phase transitions that take place tens to hundreds of degrees below. Phonon calculations show that the orientations of the methylammonium couple strongly and cooperatively to these modes. The result is a non-centrosymmetric, instantaneous local structure, which we observe in atomic pair distribution function (PDF) measurements. This local symmetry breaking is unobservable by Bragg diffraction, but can explain key material properties such as the structural phase sequence, ultra low thermal transport, and large minority charge carrier lifetimes despite moderate carrier mobility.Comment: 30 pages, 11 figure

On-shell constrained M2M_2 variables with applications to mass measurements and topology disambiguation

We consider a class of on-shell constrained mass variables that are 3+1 dimensional generalizations of the Cambridge $M_{T2}$ variable and that automatically incorporate various assumptions about the underlying event topology. The presence of additional on-shell constraints causes their kinematic distributions to exhibit sharper endpoints than the usual $M_{T2}$ distribution. We study the mathematical properties of these new variables, e.g., the uniqueness of the solution selected by the minimization over the invisible particle 4-momenta. We then use this solution to reconstruct the masses of various particles along the decay chain. We propose several tests for validating the assumed event topology in missing energy events from new physics. The tests are able to determine: 1) whether the decays in the event are two-body or three-body, 2) if the decay is two-body, whether the intermediate resonances in the two decay chains are the same, and 3) the exact sequence in which the visible particles are emitted from each decay chain.Comment: 44pages, 17 figures. revised version, published in JHEP. Minor addition: a paragraph discussing the effect on the background at the end of section 5.

Compilation of the data on the land withdrawals in Alaska

Major decisions an the use and disposition of land in Alaska are being made by the State and Federal governments. These decisions will affect the utilization of all our land resources including minerals. Since minerals are an essential component of our existance, the availability and access to minerals is an important issue. There are approximately 2600 land orders and acts classifying land in Alaska that restrict the utilization of our minerals resources. As of April 1977, approximately twenty-six percent of Alaska, or 100,875,391 acres was open to mineral entry and location under the Federal Mining Laws and the State Mining and Mineral leasing Laws

The structure of the core NuRD repression complex provides insights into its interaction with chromatin

The NuRD complex is a multi-protein transcriptional corepressor that couples histone deacetylase and ATP-dependent chromatin remodelling activities. The complex regulates the higher-order structure of chromatin, and has important roles in the regulation of gene expression, DNA damage repair and cell differentiation. HDACs 1 and 2 are recruited by the MTA1 corepressor to form the catalytic core of the complex. The histone chaperone protein RBBP4, has previously been shown to bind to the carboxy-terminal tail of MTA1. We show that MTA1 recruits a second copy of RBBP4. The crystal structure reveals an extensive interface between MTA1 and RBBP4. An EM structure, supported by SAXS and crosslinking, reveals the architecture of the dimeric HDAC1:MTA1:RBBP4 assembly which forms the core of the NuRD complex. We find evidence that in this complex RBBP4 mediates interaction with histone H3 tails, but not histone H4, suggesting a mechanism for recruitment of the NuRD complex to chromati