Pliocene decoupling of equatorial Pacific temperature and pH gradients.

Ocean dynamics in the equatorial Pacific drive tropical climate patterns that affect marine and terrestrial ecosystems worldwide. How this region will respond to global warming has profound implications for global climate, economic stability and ecosystem health. As a result, numerous studies have investigated equatorial Pacific dynamics during the Pliocene (5.3-2.6 million years ago) and late Miocene (around 6 million years ago) as an analogue for the future behaviour of the region under global warming1-12. Palaeoceanographic records from this time present an apparent paradox with proxy evidence of a reduced east-west sea surface temperature gradient along the equatorial Pacific1,3,7,8-indicative of reduced wind-driven upwelling-conflicting with evidence of enhanced biological productivity in the east Pacific13-15 that typically results from stronger upwelling. Here we reconcile these observations by providing new evidence for a radically different-from-modern circulation regime in the early Pliocene/late Miocene16 that results in older, more acidic and more nutrient-rich water reaching the equatorial Pacific. These results provide a mechanism for enhanced productivity in the early Pliocene/late Miocene east Pacific even in the presence of weaker wind-driven upwelling. Our findings shed new light on equatorial Pacific dynamics and help to constrain the potential changes they will undergo in the near future, given that the Earth is expected to reach Pliocene-like levels of warming in the next century.

Coupled dynamics of the North Equatorial Countercurrent and Intertropical Convergence Zone with relevance to the double-ITCZ problem.

The Intertropical Convergence Zone (ITCZ) is a salient feature of tropical atmospheric circulation characterized by intense convective clouds and rainfall north of the equator. Climate models, however, commonly experience the double-ITCZ problem-the tendency to produce another strong precipitation band but south of the equator. Here, we describe coupled interaction between the ITCZ and the North Equatorial Countercurrent (NECC) that is relevant to this problem. This current is a major component of the tropical Pacific upper-ocean circulation, which flows against easterly trade winds and transports warm water from the western Pacific eastward. Its core follows the latitudinal position of the ITCZ. Trade winds converge toward the ITCZ, creating a local minimum in zonal winds and generating positive wind stress curl that maintains an eastward current despite westward winds. We show that interaction between the ITCZ and the NECC involves positive feedback: a stronger NECC advects warm water from the western Pacific to the colder east thus increasing sea surface temperature (SST) along its path, intensifying convection within the ITCZ and hence strengthening wind stress curl, further strengthening the NECC. To demonstrate this wind stress curl-advection-SST-precipitation (WASP) feedback, we conduct climate model experiments in which we progressively strengthen the surface Ekman component of the NECC and observe the intensification of the ITCZ and the entire NECC. Consequently, a weak NECC leads to a weak ITCZ, which can contribute to the double-ITCZ problem in climate models, since weak wind convergence north of the equator enables stronger convergence in the south.

Implications for the Hydrogenation of Propyne and Propene with Parahydrogen due to the in situ Transformation of Rh2C to Rh0/C.

NMR spectroscopy studies using parahydrogen-induced polarization have previously established the existence of the pairwise hydrogen addition route in the hydrogenation of unsaturated hydrocarbons over heterogeneous catalysts, including those based on rhodium (Rh0). This pathway requires the incorporation of both hydrogen atoms from one hydrogen molecule to the same product molecule. However, the underlying mechanism for such pairwise hydrogen addition must be better understood. The involvement of carbon, either in the form of carbonaceous deposits on the surface of a catalyst or as a metal carbide phase, is known to modify catalytic properties significantly and thus could also affect the pairwise hydrogen addition route. Here, we explored carbon's role by studying the hydrogenation of propene and propyne with parahydrogen on a Rh2C catalyst and comparing the results with those for a Rh0/C catalyst obtained from Rh2C via H2 pretreatment. While the catalysts Rh2C and Rh0/C differ notably in the rate of conversion of parahydrogen to normal hydrogen as well as in terms of hydrogenation activity, our findings suggest that the carbide phase does not play a significant role in the pairwise H2 addition route on rhodium catalysts.

Design of an aryne-platform for the synthesis of non-racemic heterocyclic allocolchicinoids.

A four-step semisynthetic approach towards a highly versatile allocolchicine-related chiral aryne intermediate starting from naturally occurring colchicine was developed, and some of its synthetic transformations were studied. The in situ generated benzyne intermediate afforded a number of non-racemic heterocyclic allocolchicinoids, which were shown to exhibit potent cytotoxicity towards COLO 357, OSA and Raji cells. The proposed methodology is attractive for the synthesis of libraries of new cytotoxic tubulin inhibitors.

Design and preparation of pH-sensitive cytotoxic liposomal formulations containing antitumor colchicine analogues for target release.

Herein, we describe the synthesis of pH-sensitive lipophilic colchicine prodrugs for liposomal bilayer inclusion, as well as preparation and characterization of presumably stealth PEGylated liposomes with above-mentioned prodrugs. These formulations liberate strongly cytotoxic colchicinoid derivatives selectively under slightly acidic tumor-associated conditions, ensuring tumor-targeted delivery of the compounds. The design of the prodrugs is addressed to pH-triggered release of active compounds in the slight acidic media, that corresponds to tumor microenvironment, while keeping sufficient stability of the whole formulation at physiological pH. Correlations between the structure of the conjugates, their hydrolytic stability, colloidal stability, ability of the prodrug retention in the lipid bilayer are described. Several formulations were found promising for further development and in vivo investigations.

Classification of Promoter Sequences from Human Genome.

We have developed a new method for promoter sequence classification based on a genetic algorithm and the MAHDS sequence alignment method. We have created four classes of human promoters, combining 17,310 sequences out of the 29,598 present in the EPD database. We searched the human genome for potential promoter sequences (PPSs) using dynamic programming and position weight matrices representing each of the promoter sequence classes. A total of 3,065,317 potential promoter sequences were found. Only 1,241,206 of them were located in unannotated parts of the human genome. Every other PPS found intersected with either true promoters, transposable elements, or interspersed repeats. We found a strong intersection between PPSs and Alu elements as well as transcript start sites. The number of false positive PPSs is estimated to be 3 × 10-8 per nucleotide, which is several orders of magnitude lower than for any other promoter prediction method. The developed method can be used to search for PPSs in various eukaryotic genomes.

A Split-Marker System for CRISPR-Cas9 Genome Editing in Methylotrophic Yeasts.

Methylotrophic yeasts such as Ogataea polymorpha and Komagataella phaffii (sin. Hansenula polymorpha and Pichia pastoris, respectively) are commonly used in basic research and biotechnological applications, frequently those requiring genome modifications. However, the CRISPR-Cas9 genome editing approaches reported for these species so far are relatively complex and laborious. In this work we present an improved plasmid vector set for CRISPR-Cas9 genome editing in methylotrophic yeasts. This includes a plasmid encoding Cas9 with a nuclear localization signal and plasmids with a scaffold for the single guide RNA (sgRNA). Construction of a sgRNA gene for a particular target sequence requires only the insertion of a 24 bp oligonucleotide duplex into the scaffold. Prior to yeast transformation, each plasmid is cleaved at two sites, one of which is located within the selectable marker, so that the functional marker can be restored only via recombination of the Cas9-containing fragment with the sgRNA gene-containing fragment. This recombination leads to the formation of an autonomously replicating plasmid, which can be lost from yeast clones after acquisition of the required genome modification. The vector set allows the use of G418-resistance and LEU2 auxotrophic selectable markers. The functionality of this setup has been demonstrated in O. polymorpha, O. parapolymorpha, O. haglerorum and Komagataella phaffii.

Understanding the Synergy between Fe and Mo Sites in the Nitrate Reduction Reaction on a Bio-Inspired Bimetallic MXene Electrocatalyst.

Mo- and Fe-containing enzymes catalyze the reduction of nitrate and nitrite ions in nature. Inspired by this activity, we study here the nitrate reduction reaction (NO3 RR) catalyzed by an Fe-substituted two-dimensional molybdenum carbide of the MXene family, viz., Mo2 CTx : Fe (Tx are oxo, hydroxy and fluoro surface termination groups). Mo2 CTx : Fe contains isolated Fe sites in Mo positions of the host MXene (Mo2 CTx ) and features a Faradaic efficiency (FE) and an NH3 yield rate of 41 % and 3.2 µmol h-1 mg-1 , respectively, for the reduction of NO3 - to NH4 + in acidic media and 70 % and 12.9 µmol h-1 mg-1 in neutral media. Regardless of the media, Mo2 CTx : Fe outperforms monometallic Mo2 CTx owing to a more facile reductive defunctionalization of Tx groups, as evidenced by in situ X-ray absorption spectroscopy (Mo K-edge). After surface reduction, a Tx vacancy site binds a nitrate ion that subsequently fills the vacancy site with O* via oxygen transfer. Density function theory calculations provide further evidence that Fe sites promote the formation of surface O vacancies, which are identified as active sites and that function in NO3 RR in close analogy to the prevailing mechanism of the natural Mo-based nitrate reductase enzymes.

Carbon-Supported Potassium Hydride for Efficient Low-Temperature Desulfurization.

The industrial removal of organosulfur impurities from fossil fuels relies on transition-metal-based catalysts in harsh conditions (ca. 400 °C, up to 100 bar H2 ), yet desulfurization (DS) of refractory alkyl dibenzothiophenes (DBTs) remains challenging. Here, we report that carbon-supported potassium hydride (KH/C) enables efficient DS of DBTs in mild conditions, viz. >97 % conversion of DBTs is achieved at 165 °C in 3-6 h while the yields of respective biphenyls are 84-95 % by using only 15 % excess of KH per a C-S bond. In addition, KH/C allows to lower the concentration of 4,6-Me2 DBT in the mesitylene solution from 1000 ppm to <3 ppm (165 °C, 20 h) and provides deoxygenation, denitrogenation and catalytic aromatic hydrogenation reactions. DS of various sulfur heterocycles by using KH/C, a transition-metal-free material based on earth abundant elements, is viable at low temperature and has prospects for the further development towards decentralized removal of organosulfur species from fossil fuels.

Biosynthetic Protein Folding and Molecular Chaperons.

The problem of linear polypeptide chain folding into a unique tertiary structure is one of the fundamental scientific challenges. The process of folding cannot be fully understood without its biological context, especially for big multidomain and multisubunit proteins. The principal features of biosynthetic folding are co-translational folding of growing nascent polypeptide chains and involvement of molecular chaperones in the process. The review summarizes available data on the early events of nascent chain folding, as well as on later advanced steps, including formation of elements of native structure. The relationship between the non-uniformity of translation rate and folding of the growing polypeptide is discussed. The results of studies on the effect of biosynthetic folding features on the parameters of folding as a physical process, its kinetics and mechanisms, are presented. Current understanding and hypotheses on the relationship of biosynthetic folding with the fundamental physical parameters and current views on polypeptide folding in the context of energy landscapes are discussed.

Liposomal Formulation of a PLA2-Sensitive Phospholipid-Allocolchicinoid Conjugate: Stability and Activity Studies In Vitro.

To assess the stability and efficiency of liposomes carrying a phospholipase A2-sensitive phospholipid-allocolchicinoid conjugate (aC-PC) in the bilayer, egg phosphatidylcholine and 1-palmitoyl-2-oleoylphosphatidylglycerol-based formulations were tested in plasma protein binding, tubulin polymerization inhibition, and cytotoxicity assays. Liposomes L-aC-PC10 containing 10 mol. % aC-PC in the bilayer bound less plasma proteins and were more stable in 50% plasma within 4 h incubation, according to calcein release and FRET-based assays. Liposomes with 25 mol. % of the prodrug (L-aC-PC25) were characterized by higher storage stability judged by their hydrodynamic radius evolution yet enhanced deposition of blood plasma opsonins on their surface according to SDS-PAGE and immunoblotting. Notably, inhibition of tubulin polymerization was found to require that the prodrug should be hydrolyzed to the parent allocolchicinoid. The L-aC-PC10 and L-aC-PC25 formulations demonstrated similar tubulin polymerization inhibition and cytotoxic activities. The L-aC-PC10 formulation should be beneficial for applications requiring liposome accumulation at tumor or inflammation sites.

Synthesis, Molecular Docking, In Vitro and In Vivo Studies of Novel Dimorpholinoquinazoline-Based Potential Inhibitors of PI3K/Akt/mTOR Pathway.

A (series) range of potential dimorpholinoquinazoline-based inhibitors of the PI3K/Akt/mTOR cascade was synthesized. Several compounds exhibited cytotoxicity towards a panel of cancer cell lines in the low and sub-micromolar range. Compound 7c with the highest activity and moderate selectivity towards MCF7 cells which express the mutant type of PI3K was also tested for the ability to inhibit PI3K-(signaling pathway) downstream effectors and associated proteins. Compound 7c inhibited the phosphorylation of Akt, mTOR, and S6K at 125-250 nM. It also triggered PARP1 cleavage, ROS production, and cell death via several mechanisms. Inhibition of PI3Kα was observed at a concentration of 7b 50 µM and of 7c 500 µM and higher, that can indicate minority PI3Kα as a target among other kinases in the titled cascade for 7c. In vivo studies demonstrated an inhibition of tumor growth in the colorectal tumor model. According to the docking studies, the replacement of the triazine core in gedatolisib (8) by a quinazoline fragment, and incorporation of a (hetero)aromatic unit connected with the carbamide group via a flexible spacer, can result in more selective inhibition of the PI3Kα isoform.

Use of 6 Nucleotide Length Words to Study the Complexity of Gene Sequences from Different Organisms.

In this paper, we attempted to find a relation between bacteria living conditions and their genome algorithmic complexity. We developed a probabilistic mathematical method for the evaluation of k-words (6 bases length) occurrence irregularity in bacterial gene coding sequences. For this, the coding sequences from different bacterial genomes were analyzed and as an index of k-words occurrence irregularity, we used W, which has a distribution similar to normal. The research results for bacterial genomes show that they can be divided into two uneven groups. First, the smaller one has W in the interval from 170 to 475, while for the second it is from 475 to 875. Plants, metazoan and virus genomes also have W in the same interval as the first bacterial group. We suggested that second bacterial group coding sequences are much less susceptible to evolutionary changes than the first group ones. It is also discussed to use the W index as a biological stress value.

Single-Atom-Substituted Mo2CTx:Fe-Layered Carbide for Selective Oxygen Reduction to Hydrogen Peroxide: Tracking the Evolution of the MXene Phase.

This work critically assesses the electrocatalytic activity, stability, and nature of the active phase of a two-dimensional molybdenum carbide (MXene) with single-atomic iron sites, Mo2CTx:Fe (Tx are surface terminating groups O, OH, and F), in the catalysis of the oxygen reduction reaction (ORR). X-ray absorption spectroscopy unequivocally confirmed that the iron single sites were incorporated into the Mo2CTx structure by substituting Mo atoms in the molybdenum carbide lattice with no other detectable Fe-containing phases. Mo2CTx:Fe, the first two-dimensional carbide with isolated iron sites, demonstrates a high catalytic activity and selectivity in the oxygen reduction to hydrogen peroxide. However, an analysis of the electrode material after the catalytic tests revealed that Mo2CTx:Fe transformed in situ into a graphitic carbon framework with dispersed iron oxyhydroxide (ferrihydrite, Fh) species (Fh/C), which are the actual active species. This experimental observation and the results obtained for the titanium and vanadium 2D carbides challenge previous studies that discuss the activity of the native MXene phases in oxygen electrocatalysis. Our work showcases the role of 2D metal carbides as precursors for active carbon-based (electro)catalysts and, more fundamentally, highlights the intrinsic evolution pathways of MXenes in electrocatalysis.

Engineering of the spin on dopant process on silicon on insulator substrate.

We report on a systematic analysis of phosphorus diffusion in silicon on insulator thin film via spin-on-dopant process (SOD). This method is used to provide an impurity source for semiconductor junction fabrication. The dopant is first spread into the substrate via SOD and then diffused by a rapid thermal annealing process. The dopant concentration and electron mobility were characterized at room and low temperature by four-probe and Hall bar electrical measurements. Time-of-flight-secondary ion mass spectroscopy was performed to estimate the diffusion profile of phosphorus for different annealing treatments. We find that a high phosphorous concentration (greater than 1020 atoms cm-3) with a limited diffusion of other chemical species and allowing to tune the electrical properties via annealing at high temperature for short time. The ease of implementation of the process, the low cost of the technique, the possibility to dope selectively and the uniform doping manufactured with statistical process control show that the methodology applied is very promising as an alternative to the conventional doping methods for the implementation of optoelectronic devices.

Silylation of C-H bonds in aromatic heterocycles by an Earth-abundant metal catalyst.

Heteroaromatic compounds containing carbon-silicon (C-Si) bonds are of great interest in the fields of organic electronics and photonics, drug discovery, nuclear medicine and complex molecule synthesis, because these compounds have very useful physicochemical properties. Many of the methods now used to construct heteroaromatic C-Si bonds involve stoichiometric reactions between heteroaryl organometallic species and silicon electrophiles or direct, transition-metal-catalysed intermolecular carbon-hydrogen (C-H) silylation using rhodium or iridium complexes in the presence of excess hydrogen acceptors. Both approaches are useful, but their limitations include functional group incompatibility, narrow scope of application, high cost and low availability of the catalysts, and unproven scalability. For this reason, a new and general catalytic approach to heteroaromatic C-Si bond construction that avoids such limitations is highly desirable. Here we report an example of cross-dehydrogenative heteroaromatic C-H functionalization catalysed by an Earth-abundant alkali metal species. We found that readily available and inexpensive potassium tert-butoxide catalyses the direct silylation of aromatic heterocycles with hydrosilanes, furnishing heteroarylsilanes in a single step. The silylation proceeds under mild conditions, in the absence of hydrogen acceptors, ligands or additives, and is scalable to greater than 100 grams under optionally solvent-free conditions. Substrate classes that are difficult to activate with precious metal catalysts are silylated in good yield and with excellent regioselectivity. The derived heteroarylsilane products readily engage in versatile transformations enabling new synthetic strategies for heteroaromatic elaboration, and are useful in their own right in pharmaceutical and materials science applications.

Tailoring Lattice Oxygen Binding in Ruthenium Pyrochlores to Enhance Oxygen Evolution Activity.

Ruthenium pyrochlores, that is, oxides of composition A2Ru2O7-δ, have emerged recently as state-of-the-art catalysts for the oxygen evolution reaction (OER) in acidic conditions. Here, we demonstrate that the A-site substituent in yttrium ruthenium pyrochlores Y1.8M0.2Ru2O7-δ (M = Cu, Co, Ni, Fe, Y) controls the concentration of surface oxygen vacancies (VO) in these materials whereby an increased concentration of VO sites correlates with a superior OER activity. DFT calculations rationalize these experimental trends demonstrating that the higher OER activity and VO surface density originate from a weakened strength of the M-O bond, scaling with the formation enthalpy of the respective MOx phases and the coupling between the M d states and O 2p states. Our work introduces a novel catalyst with improved OER performance, Y1.8Cu0.2Ru2O7-δ, and provides general guidelines for the design of active electrocatalysts.

Droplet epitaxy quantum dot based infrared photodetectors.

The fabrication and characterization of an infrared photodetector based on GaAs droplet epitaxy quantum dots embedded in Al0.3Ga0.7As barrier is reported. The high control over dot electronic properties and the high achievable number density allowed by droplet epitaxy technique permitted us to realize a device using a single dot layer in the active region. Moreover, thanks to the independent control over dot height and width, we were able to obtain a very sharp absorption peak in the thermal infrared region (3-8 µm). Low temperature photocurrent spectrum was measured by Fourier spectroscopy, showing a narrow peak at 198 meV (∼6.3 µm) with a full width at half maximum of 25 meV. The observed absorption is in agreement with theoretical prediction based on effective mass approximation of the dot electronic transition.

Wetter subtropics in a warmer world: Contrasting past and future hydrological cycles.

During the warm Miocene and Pliocene Epochs, vast subtropical regions had enough precipitation to support rich vegetation and fauna. Only with global cooling and the onset of glacial cycles some 3 Mya, toward the end of the Pliocene, did the broad patterns of arid and semiarid subtropical regions become fully developed. However, current projections of future global warming caused by CO2 rise generally suggest the intensification of dry conditions over these subtropical regions, rather than the return to a wetter state. What makes future projections different from these past warm climates? Here, we investigate this question by comparing a typical quadrupling-of-CO2 experiment with a simulation driven by sea-surface temperatures closely resembling available reconstructions for the early Pliocene. Based on these two experiments and a suite of other perturbed climate simulations, we argue that this puzzle is explained by weaker atmospheric circulation in response to the different ocean surface temperature patterns of the Pliocene, specifically reduced meridional and zonal temperature gradients. Thus, our results highlight that accurately predicting the response of the hydrological cycle to global warming requires predicting not only how global mean temperature responds to elevated CO2 forcing (climate sensitivity) but also accurately quantifying how meridional sea-surface temperature patterns will change (structural climate sensitivity).

Structural Evolution and Dynamics of an In2O3 Catalyst for CO2 Hydrogenation to Methanol: An Operando XAS-XRD and In Situ TEM Study.

We report an operando examination of a model nanocrystalline In2O3 catalyst for methanol synthesis via CO2 hydrogenation (300 °C, 20 bar) by combining X-ray absorption spectroscopy (XAS), X-ray powder diffraction (XRD), and in situ transmission electron microscopy (TEM). Three distinct catalytic regimes are identified during CO2 hydrogenation: activation, stable performance, and deactivation. The structural evolution of In2O3 nanoparticles (NPs) with time on stream (TOS) followed by XANES-EXAFS-XRD associates the activation stage with a minor decrease of the In-O coordination number and a partial reduction of In2O3 due to the formation of oxygen vacancy sites (i.e., In2O3-x). As the reaction proceeds, a reductive amorphization of In2O3 NPs takes place, characterized by decreasing In-O and In-In coordination numbers and intensities of the In2O3 Bragg peaks. A multivariate analysis of the XANES data confirms the formation of In2O3-x and, with TOS, metallic In. Notably, the appearance of molten In0 coincides with the onset of catalyst deactivation. This phase transition is also visualized by in situ TEM, acquired under reactive conditions at 800 mbar pressure. In situ TEM revealed an electron beam assisted transformation of In2O3 nanoparticles into a dynamic structure in which crystalline and amorphous phases coexist and continuously interconvert. The regeneration of the deactivated In0/In2O3-x catalyst by reoxidation was critically assessed revealing that the spent catalyst can be reoxidized only partially in a CO2 atmosphere or air yielding an average crystallite size of the resultant In2O3 that is approximately an order of magnitude larger than the initial one.