Ecosystem-bedrock interaction changes nutrient compartmentalization during early oxidative weathering

Ecosystem-bedrock interactions power the biogeochemical cycles of Earth's shallow crust, supporting life, stimulating substrate transformation, and spurring evolutionary innovation. While oxidative processes have dominated half of terrestrial history, the relative contribution of the biosphere and its chemical fingerprints on Earth's developing regolith are still poorly constrained. Here, we report results from a two-year incipient weathering experiment. We found that the mass release and compartmentalization of major elements during weathering of granite, rhyolite, schist and basalt was rock-specific and regulated by ecosystem components. A tight interplay between physiological needs of different biota, mineral dissolution rates, and substrate nutrient availability resulted in intricate elemental distribution patterns. Biota accelerated CO2 mineralization over abiotic controls as ecosystem complexity increased, and significantly modified stoichiometry of mobilized elements. Microbial and fungal components inhibited element leaching (23.4% and 7%), while plants increased leaching and biomass retention by 63.4%. All biota left comparable biosignatures in the dissolved weathering products. Nevertheless, the magnitude and allocation of weathered fractions under abiotic and biotic treatments provide quantitative evidence for the role of major biosphere components in the evolution of upper continental crust, presenting critical information for large-scale biogeochemical models and for the search for stable in situ biosignatures beyond Earth.Comment: 41 pages (MS, SI and Data), 16 figures (MS and SI), 6 tables (SI and Data). Journal article manuscrip

Specific features of telomerase RNA from Hansenula polymorpha.

Telomerase, a ribonucleoprotein, is responsible for the maintenance of eukaryotic genome integrity by replicating the ends of chromosomes. The core enzyme comprises the conserved protein TERT and an RNA subunit (TER) that, in contrast, displays large variations in size and structure. Here, we report the identification of the telomerase RNA from thermotolerant yeast Hansenula polymorpha (HpTER) and describe its structural features. We show further that the H. polymorpha telomerase reverse transcribes the template beyond the predicted boundary and adds a nontelomeric dT in vitro. Sequencing of the chromosomal ends revealed that this nucleotide is specifically present as a terminal nucleotide at the 3' end of telomeres. Mutational analysis of HpTER confirmed that the incorporation of dT functions to limit telomere length in this species

Sedimentary Ways

This paper is a thought experiment to attune to the geo-physical and geo-political materialities of sediment, a terra-aqueous substance produced when the earth's continental surfaces intra-act with the atmosphere and are chemically transformed by it. The paper is framed by questions of how to engage more closely with the dynamics of earth systems and of how social and political agency emerges alongside earth forces. Sediment is important to such questions because it is the mechanism by which the earth recycles itself and is thick with the climatological and geological histories that have conditioned the possibility of life on the planet. While acknowledging the import of Deleuze and Guattari's metaphysics to such questions, the paper takes a material approach to them. It is based on field work in Bangladesh, but also traverses a range of scientific, historical and theoretical literature. It is arranged in four sections that loosely correspond to the sedimentary cycle. It follows sediment from chemical processes on rock surfaces in the Himalayas, to its lively travels in monsoonal rivers across flood plains to its eventual deposition and subterranean diagenesis. In each section, the paper discusses the material processes at work, their socio-political enmeshments and the theoretical implications of these intra-actions. The paper concludes that sediment serves as a reminder not only of close entanglements of geo-physical and geo-political becomings, but also of the profound indifference of earth systems to human affairs, and asks what this might mean for the re-imagination of politics

Active Site Conformational Dynamics in Human Uridine Phosphorylase 1

Uridine phosphorylase (UPP) is a central enzyme in the pyrimidine salvage pathway, catalyzing the reversible phosphorolysis of uridine to uracil and ribose-1-phosphate. Human UPP activity has been a focus of cancer research due to its role in activating fluoropyrimidine nucleoside chemotherapeutic agents such as 5-fluorouracil (5-FU) and capecitabine. Additionally, specific molecular inhibitors of this enzyme have been found to raise endogenous uridine concentrations, which can produce a cytoprotective effect on normal tissues exposed to these drugs. Here we report the structure of hUPP1 bound to 5-FU at 2.3 Å resolution. Analysis of this structure reveals new insights as to the conformational motions the enzyme undergoes in the course of substrate binding and catalysis. The dimeric enzyme is capable of a large hinge motion between its two domains, facilitating ligand exchange and explaining observed cooperativity between the two active sites in binding phosphate-bearing substrates. Further, a loop toward the back end of the uracil binding pocket is shown to flexibly adjust to the varying chemistry of different compounds through an “induced-fit” association mechanism that was not observed in earlier hUPP1 structures. The details surrounding these dynamic aspects of hUPP1 structure and function provide unexplored avenues to develop novel inhibitors of this protein with improved specificity and increased affinity. Given the recent emergence of new roles for uridine as a neuron protective compound in ischemia and degenerative diseases, such as Alzheimer's and Parkinson's, inhibitors of hUPP1 with greater efficacy, which are able to boost cellular uridine levels without adverse side-effects, may have a wide range of therapeutic applications

Controlled Experiments of Hillslope Coevolution at the Biosphere 2 Landscape Evolution Observatory: Toward Prediction of Coupled Hydrological, Biogeochemical, and Ecological Change

Understanding the process interactions and feedbacks among water, porous geological media, microbes, and vascular plants is crucial for improving predictions of the response of Earth’s critical zone to future climatic conditions. However, the integrated coevolution of landscapes under change is notoriously difficult to investigate. Laboratory studies are limited in spatial and temporal scale, while field studies lack observational density and control. To bridge the gap between controlled laboratory and uncontrollable field studies, the University of Arizona built a macrocosm experiment of unprecedented scale: the Landscape Evolution Observatory (LEO). LEO comprises three replicated, heavily instrumented, hillslope-scale model landscapes within the environmentally controlled Biosphere 2 facility. The model landscapes were designed to initially be simple and purely abiotic, enabling scientists to observe each step in the landscapes’ evolution as they undergo physical, chemical, and biological changes over many years. This chapter describes the model systems and associated research facilities and illustrates how LEO allows for tracking of multiscale matter and energy fluxes at a level of detail impossible in field experiments. Initial sensor, sampler, and soil coring data are already providing insights into the tight linkages between water flow, weathering, and microbial community development. These interacting processes are anticipated to drive the model systems to increasingly complex states and will be impacted by the introduction of vascular plants and changes in climatic regimes over the years to come. By intensively monitoring the evolutionary trajectory, integrating data with mathematical models, and fostering community-wide collaborations, we envision that emergent landscape structures and functions can be linked, and significant progress can be made toward predicting the coupled hydro-biogeochemical and ecological responses to global change

Розрахунок та 3D модель фотокаталітичного панельного реактору для деградації барвників і фенолу

Стаття присвячена розрахунку та 3D моделюванню фотокаталітичного панельного реактору для деградації барвників та фенолу. Для цього було теоретично розглянуто фотокаталітичні реактори різних типів для фотодеструкції органічних полютантів у водних розчинах. Серед наведених фотореактори панельного типу, на наш погляд, є найбільш раціональними. Також зазначена перспективність фотокаталітичного очищення стічних вод від органічних полютантів так званими методами Advanced Oxidation Processes, серед яких гетерогенний фотокаталіз за участі такого фотокаталізатору як титану (IV) оксид є найбільш ефективним. Для проведення фотодеструкції забруднюючих речовин у водних розчинах розглянуто різні типи фотореакторів, що розглядаються у сучасних літературних джерелах, з метою визначення найбільш оптимальної його конструкції. Показано, що відділення порошкоподібного фотокаталізатору від водного розчину після завершення фотокаталітичного процесу успішно можна реалізовувати як за допомогою ультрафільтрації, так й мембранних модулів. На підставі проведеного теоретичного аналізу обґрунтовано вибір фотореактору панельного типу та проведено розрахунок його конструкційних параметрів. Показано, що для однакової молярної концентрації таких полютантів як фенол та катіонний й аніонний барвники (конго червоний та метиленовий голубий) необхідна різна кількість ламп та панелів у фотореактору, а отже й різний об’єм фотореактору. В результаті розроблено більш універсальну конструкцію – панельний фотокаталітичний реактор, який можна у разі необхідності нарощувати з метою збільшення як об’єму фотореактору, так й для досягнення необхідного ступеня очищення від полютантів, і який здатний забезпечити високоефективну фотодеструкцію полютантів різного генезису у стічних водах різноманітного походження. Згідно розробленої конструкції фотокаталітичного реактору проведено його 3D моделювання, що дозволяє наочно уявити всі конструкційні елементи такого нетипового спеціального обладнання.The article is devoted to the calculation and 3D modeling of the photocatalytic panel reactor for the degradation of dyes and phenol. To do this, the photocatalytic reactors of various types for the photodegradation of organic pollutants in aqueous solutions were theoretically examined. In our opinion the panel type photoreactors are the most rational. The prospect of photocatalytic treatment of wastewater from organic pollutants by the so-called methods of Advanced Oxidation Processes, among which the heterogeneous photocatalysis with the participation of such a catalyst as titanium (IV) oxide is most effective, is also noted. In order to determine the optimal design of such equipment various available in the literature types of photoreactors are considered. It is shown that the separation of powdered photo-catalysts can be successfully implemented using membrane modules. Based on theoretical analysis, the choice of the panel type photoreactor was substantiated and its calculation was carried out. It has been shown that for the uniform molar concentration of such pollutants as phenol and dyes (Congo red and Methylene blue), the different number of lamps and sections of the photoreactor are required. As a result, the more versatile design, the panel photoreactor is developed. The number of sections in it can be increased if necessary, and such reactor is capable of providing highly effective photo-destruction of pollutants of different genesis in sewage of various origins. According to the developed design of the photoreactor, its 3D modeling is carried out, which allows to visualize all the structural elements of such unusual type of special equipment

Merging Single-Atom-Dispersed Silver and Carbon Nitride to a Joint Electronic System via Copolymerization with Silver Tricyanomethanide

Herein, we present an approach to create a hybrid between single-atom-dispersed silver and a carbon nitride polymer. Silver tricyanomethanide (AgTCM) is used as a reactive comonomer during templated carbon nitride synthesis to introduce both negative charges and silver atoms/ions to the system. The successful introduction of the extra electron density under the formation of a delocalized joint electronic system is proven by photoluminescence measurements, X-ray photoelectron spectroscopy investigations, and measurements of surface ζ-potential. At the same time, the principal structure of the carbon nitride network is not disturbed, as shown by solid-state nuclear magnetic resonance spectroscopy and electrochemical impedance spectroscopy analysis. The synthesis also results in an improvement of the visible light absorption and the development of higher surface area in the final products. The atom-dispersed AgTCM-doped carbon nitride shows an enhanced performance in the selective hydrogenation of alkynes in comparison with the performance of other conventional Ag-based materials prepared by spray deposition and impregnation-reduction methods, here exemplified with 1-hexyne

How does tmRNA move through the ribosome?

To test the structure of tmRNA in solution, cross-linking experiments were performed which showed two sets of cross-links in two different domains of tmRNA. Site-directed mutagenesis was used to search for tmRNA nucleotide bases that might form a functional analogue of a codon–anticodon duplex to be recognized by the ribosomal A-site. We demonstrate that nucleotide residues U85 and A86 from tmRNA are significant for tmRNA function and propose that they are involved in formation of a tmRNA element playing a central role in A-site recognition. These data are discussed in the frame of a hypothetical model that suggests a general scheme for the interaction of tmRNA with the ribosome and explains how it moves through the ribosome