Dominant Cleavage Research Articles

Highly efficient catalytic hydrocracking of East Inner Mongolia lignite and lignite-related model compounds through selective cleavage of aryl C-O bonds

Highly efficient catalytic hydrocracking of lignite through selective cleavage of aryl C-O bonds to produce valuable fuels and chemicals is a prospective but challenging approach. Catalytic hydrocracking reactions of lignite and lignite-related model compounds were performed over a Ni-based catalyst. The results demonstrated that the aryl C-O bonds in benzyl phenyl ether and dinaphthyl ether were preferentially cleaved and the resulting aromatic monomers were subsequently hydrogenated with continuous optimization of reaction conditions. Moreover, a complete conversion of model compounds and 100 % selectivity of monomeric products were achieved. The density functional theory calculations unraveled that the stable horizontal adsorption of both benzene rings in benzyl phenyl ether at Ni sites can reduce the electron cloud density around ether-oxygen bonds and weaken their dissociation energy, facilitating the dominant cleavage of aryl C-O bonds. Component analyses and structural characterizations indicated that aromatic hydrocarbons were mainly produced (50.02 %) after catalytic hydrocracking of lignite through the selective cleavage of C-O bonds, effective removal of oxygen-containing structure and cracking of side chain groups on aromatic rings. Most significantly, this study proposed the probable mechanism that H+ species originating from the heterolytic cleavage of H2 and H···H were the main active hydrogen species, committing to cracking C-O bonds, while H···H species were tendentious for subsequent hydrogenation of aromatic rings.

Arabidopsis and maize terminator strength is determined by GC content, polyadenylation motifs and cleavage probability

The 3’ end of a gene, often called a terminator, modulates mRNA stability, localization, translation, and polyadenylation. Here, we adapted Plant STARR-seq, a massively parallel reporter assay, to measure the activity of over 50,000 terminators from the plants Arabidopsis thaliana and Zea mays. We characterize thousands of plant terminators, including many that outperform bacterial terminators commonly used in plants. Terminator activity is species-specific, differing in tobacco leaf and maize protoplast assays. While recapitulating known biology, our results reveal the relative contributions of polyadenylation motifs to terminator strength. We built a computational model to predict terminator strength and used it to conduct in silico evolution that generated optimized synthetic terminators. Additionally, we discover alternative polyadenylation sites across tens of thousands of terminators; however, the strongest terminators tend to have a dominant cleavage site. Our results establish features of plant terminator function and identify strong naturally occurring and synthetic terminators.

Effect of strain rates on mechanical behavior, microstructure evolution and failure mechanism of extruded-annealed AZ91 magnesium alloy under room-temperature tension

Loading rate is usually considered as a significant factor affecting formability of AZ91 magnesium alloy structural components. Herein, uniaxial tensile tests are conducted on extruded-annealed AZ91 alloy under room temperature with strain rates ranging from 1 × 10−4 s−1 to 1 × 10−2 s−1. Mechanical properties, microstructure characteristics, and fracture morphologies tensioned at these different strain rates are investigated. Extruded-annealed AZ91 alloy exhibits a positive strain-rate dependence of strength and a negative strain-rate dependence of elongation. With strain rate increasing, strain rate sensitivity basically decreases while strain-hardening rate increases. At higher strain rate, the larger strength is mainly attributed to the more rapid accumulation of dislocation and the larger dislocation density, and the lower elongation is mostly owing to the more elevated level of inhomogeneous deformation related with dislocations accumulation. As strain rate increases, the area fraction of basal texture increases while that of prismatic and pyramid texture decreases in tensioned samples, which is associated with the dominant room-temperature deformation mode of basal-slip and twinning co-induced lattice rotation. With tension strain rate increasing, there are three kinds of fracture modes including ductile facture with more and deeper dimples at low strain rate, ductile-brittle facture with some dimples and cleavage planes at mediate strain rate and brittle facture with dominant cleavage planes at high strain rate.

Differentiation in Protest Politics: Participation by Political Insiders and Outsiders

The political participation literature has documented a long-term trend of the normalization of noninstitutional participation that is often equated with the conventionalization of engagement in protest politics. Less is known on the extent to which noninstitutional forms are differentiated by their mobilization context. Population surveys find it difficult to contextualize individual engagement, and on-site surveys point to effects that are hard to generalize. This study fills this gap by emphasizing differentiation and distinguishing participation according to the issue of engagement. It introduces a conceptual distinction between political insiders and outsiders, defined based on the extent to which they are embedded in the organizational landscape of the dominant cleavage dimension. Using an original survey conducted in Germany during the Covid-19 crisis, the analysis demonstrates that general-population surveys are fit to examine issue-specific participation patterns. The results expose an insider and outsider divide, captured by the effect of attitudinal and behavioral indicators, and demonstrates that the two groups are equally likely to participate in noninstitutional forms. However, insiders engage on the established issues of climate and anti-racism, whereas outsiders engage on the new issues of Covid-19 related economic assistance and civil liberties restrictions. In addition, dynamic models reveal that noninstitutional participation is rooted in volatile issue preferences. Overall, the paper argues that participation during the Covid-19 crisis has furthered the trend towards a differentiated protest arena.

Proteolytic Activity against the Distal Polybasic Tract of the Gamma Subunit of the Epithelial Sodium Channel ENaC in Nephrotic Urine.

Experimental nephrotic syndrome in mice leads to proteolytic activation of the epithelial sodium channel ENaC, possibly involving the distal polybasic tract of its γ-subunit (183RKRK). We sought to determine if urine samples from both nephrotic mice and a cohort of patients with acute nephrotic syndrome contain a specific proteolytic activity against this region of γ-ENaC. A peptide substrate consisting of amino acids 180-194 of murine γ-ENaC was N-terminally coupled to a fluorophore, yielding AMCA-FTGRKRKISGKIIHK. The substrate was incubated with nephrotic urine samples from mice as well as patients with or without the serine protease inhibitor, aprotinin. The digested peptides were separated on a reverse phase HPLC and detected with a fluorescence detector (350/450 nm). Peptide masses of the peaks were determined with a MALDI-TOF mass spectrometer. In addition, urinary proteolytic activity was quantitated using AMC-coupled substrates reflecting different cleavage sites within the polybasic tract. No significant proteolytic activity against the substrate was found in the urine of healthy humans or mice. Incubation with urine samples of nephrotic patients (n = 8) or mice subjected to three different models of experimental nephrotic syndrome (n = 4 each) led to cleavage of the substrate within the polybasic tract prevented by the serine protease inhibitor aprotinin. The most dominant cleavage product was FTGRKR in both species, which was confirmed using quantitative measurements with FTGRKR- AMC. Nephrotic urine from both humans and mice contains aprotinin-sensitive proteolytic activity against the distal polybasic tract of γ-ENaC, reflecting excretion of active proteases in the urine or proteasuria.

A reinterpretation of the Snow Lake gold camp, Trans-Hudson Orogen, Canada: the use of cleavages as markers to correlate structures across deformed terranes

The Snow Lake gold camp is located within amphibolite facies volcanic rocks of the ca. 1.88–1.87 Ga Flin Flon – Glennie Complex (FFGC) in the Trans-Hudson Orogen, Manitoba. During thrusting and collision with the Archean Sask craton, volcanic rocks were interleaved with turbidites of the ca. 1.855–1.84 Ga Burntwood Group and sandstone and conglomerate of the ca. 1.845–1.835 Ga Missi Group. The main cleavage in the turbidites was previously attributed to thrusting and used as a marker for correlating structures across the camp. A re-examination of this cleavage suggests that it overprints the thrust faults and formed during later collision between the FFGC and the Archean Superior craton. This has important implications as it further suggests that (1) previously unrecognized, early brittle thrust faults repeat volcanic stratigraphy and may have created the boundary conditions that enabled the formation of ductile thrust faults, fold nappes, and mega sheath folds; (2) shear sense indicators along ductile thrust faults formed during their reactivation as sinistral shear zones rather than during thrusting; and (3) peak metamorphic conditions were caused by thrusting and stacking during collision with the Sask craton but were attained later during collision with the Superior craton due to the time lag between orogenesis and the re-equilibration of regional isotherms. Results from this study may be applicable to other complexly deformed terranes where the dominant regional cleavage differs in expression in mixed volcanic and sedimentary successions and has been used as a marker for correlating structures.

Geochemistry and provenance of the Turquoise Bluff Slate, northeastern Tasmania: tectonic significance

The Ordovician Turquoise Bluff Slate in northeastern Tasmania is a 2 km-thick sequence of deep-marine siliceous black slates. It is dominated by meta-siltstones with bimodal grainsize distributions typical of turbidite TE-1 and TE-2 facies. The slates have high SiO2 indicating they are hemipelagites. The high Ba and V indicate they were deposited in an anoxic environment associated with high oceanic productivity. All these features are common in muddy turbidites. U–Th–Pb dating of detrital monazite and authigenic xenotime in the slates supports previous evidence that the dominant cleavage, in this unit, formed during the Benambran Orogeny. The whole-rock composition of the slates is similar to black slates in the Adaminaby Group, NSW. A review of Paleozoic whole-rock compositions from the Lachlan Orogen confirms they all have trace element contents similar to average Australian shale. However, there are subtle differences in composition. The Turquoise Bluff Slate and other Mathinna Supergroup rocks from the Eastern Tasmania Terrane have higher average Cr content than similar age turbidites from Victoria and NSW. This probably reflects a small contribution from Tasmania Cambrian ultramafic rocks in the provenance. If this were correct, northeastern Tasmania was closer to western Tasmania in the Paleozoic than other provinces of the Lachlan Orogen, southeastern Australia. Other subtle features of the whole-rock composition of Paleozoic sedimentary rocks from the Lachlan Orogen indicate it may be possible to recognise provincial variations in composition that will provide new constraints on tectonic models of southeastern Australia.

Multilevel conflict over policy application–detecting changing cleavage patterns

ABSTRACTThis paper presents actions for annulment as indicator for conflict over policy application in the EU and argues that it is a valuable complement to the indicator of infringement proceedings. This is because annulment actions shed light on conflicts in areas that remain undetected by infringement proceedings and because annulment actions are able to uncover potential multilevel characters of these conflicts. On this basis, the paper identifies four different types of multilevel application conflicts. Based on an original dataset on all actions for annulment initiated against the European Commission between 1957 and 2009, the paper explores the dominant cleavage structure in application conflicts over time. This cleavage structure has changed: national governments have started to become more and more reluctant to use their access to annulment proceedings to influence legal developments in many policy sectors as they no longer try to actively influence the legal dialogue in court.

United in revolt and discourse: urban and noble perceptions of ‘bad government’ in fifteenth-century Brabant (1420–1)

ABSTRACTThis case study on the Brabantine uprising of 1420–1 reveals common ground between noble and urban political values, calling into question the dominant historiographical cleavage between noble and urban ideologies. In 1420, one of the most severe political conflicts in Brabantine history caused a coalition of members of the upper nobility and Leuven city councillors to remove Duke John IV from the throne and convict his councillors. Preceding these drastic events, both parties had written texts together to legitimise their political position and attract supporters. By analysing the writings of the insurgents, this article illustrates how these noblemen and urban councillors combined their political ideas in practice to create a coherent discourse that supported their claims to power. The analysis also emphasises the insurgents’ appropriation, interpretation and use of key notions, such as the ‘common good’, to criticise Duke John’s government and promote their cause.

Ideology or National Interest? External Relations Votes in the European Parliament

Studies of roll-call votes in the European Parliament show that most party groups are very cohesive, the left-right dimension is the dominant cleavage in the chamber, and that most votes are adopted with broad majorities. This paper asks whether these findings extend to external relations, issue areas characterized by intergovernmentalism and entrenched national interests. The ‘politics stops at the water’s edge’ idiom suggests that national interests trump party politics. In contrast, recent studies of politicization in international relations find evidence for party political cleavages as regards external relations. Examining the positions of party groups and national delegations throughout the 1979-2014 period, the paper compares voting behaviour in external relations with overall patterns of party unity and coalitions whilst also differentiating between various types of foreign and security policy matters.

Investigation of Overall Pyrolysis Stages for Liulin Bituminous Coal by Large-Scale ReaxFF Molecular Dynamics

Deep understanding of the detailed coal pyrolysis process is very important for clean coal utilization. The overall stages in coal pyrolysis were investigated by ReaxFF MD simulations of large-scale coal models combined with reaction analysis of a cheminformatics approach. Analysis of slow heat-up ReaxFF molecular dynamics (MD) simulations shows that the Liulin coal pyrolysis process can be divided into four stages based on the thermal cleavage of bridge bonds: the activation stage of the coal structure (Stage-I), the primary pyrolysis stage (Stage-IIA), the secondary pyrolysis stage (Stage-IIB), and the recombination dominated stage (Stage-III). The transition from the dominant cleavage of the ether bridged bond into breaking of the aliphatic bridged bonds corresponds to the transition of Stage-IIA to Stage-IIB in Liulin bituminous coal pyrolysis. Further investigation of the relationship between radicals and gas production suggests that temperatures for the transition of gas generation rates can be used...

Proteolytic processing of the cilium adhesin MHJ_0194 (P123J ) in Mycoplasma hyopneumoniae generates a functionally diverse array of cleavage fragments that bind multiple host molecules.

Mycoplasma hyopneumoniae, the aetiological agent of porcine enzootic pneumonia, regulates the presentation of proteins on its cell surface via endoproteolysis, including those of the cilial adhesin P123 (MHJ_0194). These proteolytic cleavage events create functional adhesins that bind to proteoglycans and glycoproteins on the surface of ciliated and non-ciliated epithelial cells and to the circulatory host molecule plasminogen. Two dominant cleavage events of the P123 preprotein have been previously characterized; however, immunoblotting studies suggest that more complex processing events occur. These extensive processing events are characterized here. The functional significance of the P97 cleavage fragments is also poorly understood. Affinity chromatography using heparin, fibronectin and plasminogen as bait and peptide arrays were used to expand our knowledge of the adhesive capabilities of P123 cleavage fragments and characterize a novel binding motif in the C-terminus of P123. Further, we use immunohistochemistry to examine in vivo, the biological significance of interactions between M. hyopneumoniae and fibronectin and show that M. hyopneumoniae induces fibronectin deposition at the site of infection on the ciliated epithelium. Our data supports the hypothesis that M. hyopneumoniae possesses the molecular machinery to influence key molecular communication pathways in host cells.

P159 from Mycoplasma hyopneumoniae Binds Porcine Cilia and Heparin and Is Cleaved in a Manner Akin to Ectodomain Shedding

Mycoplasma hyopneumoniae colonizes the ciliated epithelial lining of the upper respiratory tract of swine and results in chronic infection. Previously, we have observed that members of P97 and P102 paralog families of cilium adhesins undergo endoproteolytic processing on the surface of M. hyopneumoniae. We show that P159 (MHJ_0494), an epithelial cell adhesin unrelated to P97 and P102 paralog families, is a cilium adhesin that undergoes dominant cleavage events at S/T-X-F↓X-D/E-like motifs located at positions (233)F↓Q(234) and (981)F↓Q(982), generating P27, P110, and P52. An unrelated cleavage site (738)L-K-V↓G-A-A(743) in P110 shows sequence identity with a cleavage site (L-N-V↓A-V-S) identified in the P97 paralog, Mhp385, and generates 76 (P76) and 35 kDa (P35) fragments. LC-MS/MS analysis of biotinylated surface proteins identified six peptides with a biotin moiety on their N-terminus indicating novel, low abundance neo-N-termini. LC-MS/MS of proteins separated by 2D-PAGE, 2D immunoblotting using monospecific antiserum raised against recombinant fragments spanning P159 (F1(P159)-F4(P159)), and proteins that bound to heparin-agarose were all used to map P159 cleavage fragments. P159 is the first cilium adhesin not belonging to the P97/P102 paralog families and is extensively processed in a manner akin to ectodomain shedding in eukaryotes.

Length‐dependent proteolytic cleavage of short oligopeptides catalyzed by matrix metalloprotease‐9

Matrix metalloproteinases (MMPs), as the enzymes to degrade extracellular matrix proteins, play a major role on cell behaviors. Among them, MMP-9 usually catalyzes the degradation of proteins with the dominant cleavage at G/L site. Recent high-throughput screening suggests that S/L is a new major site for the cleavage when the substrates of MMP-9 are oligopeptides. Here we examine the cleavage sites of the N-terminal substituted short oligopeptides as the substrates of MMP-9. As the first example of such study of N-substituted small peptides, our results suggest that the substitute group at the N-terminal and the length of peptides significantly affect the position of the cleavage site on the oligopeptides, which provides a useful insight for the design of small peptide derivatives as the substrates of MMP-9.

Catholic Politics in the United States: Challenges in the Past, Present, and Future

AbstractThroughout the history of the US, the Catholic Church has occupied a variety of political roles. This essay identifies three distinctive periods of Catholic politics: An era in which US Catholicism represented a primarily “immigrant” church (approximately from the mid-19th century to World War II), a period of assimilation and acculturation (roughly 1945–1980), and a period of integration into the dominant partisan and ideological cleavages of American politics (approximately 1980 to the present). Each of these eras was characterized by a distinctive pattern of interaction among the American Catholic laity, the organized Roman Catholic hierarchy in the US, and the Vatican.

Selective cleavage enhanced by acetylating the side chain of lysine

Selective cleavage is of great interest in mass spectrometry studies as it can help sequence identification by promoting simple fragmentation pattern of peptides and proteins. In this work, the collision-induced dissociation of peptides containing internal lysine and acetylated lysine residues were studied. The experimental and computational results revealed that multiple fragmentation pathways coexisted when the lysine residue was two amino acid residues away from N-terminal of the peptide. After acetylation of the lysine side-chain, b(n)+ ions were the most abundant primary fragment products and the Lys(Ac)-Gly amide bond became the dominant cleavage site via an oxazolone pathway. Acetylating the side-chain of lysine promoted the selective cleavage of Lys-Xxx amide bond and generated much more information of the peptide backbone sequence. The results re-evaluate the selective cleavage due to the lysine basic side-chain and provide information for studying the post-translational modification of proteins and other bio-molecules containing Lys residues.

Genome-wide Analysis of Pre-mRNA 3′ End Processing Reveals a Decisive Role of Human Cleavage Factor I in the Regulation of 3′ UTR Length

Through alternative polyadenylation, human mRNAs acquire longer or shorter 3' untranslated regions, the latter typically associated with higher transcript stability and increased protein production. To understand the dynamics of polyadenylation site usage, we performed transcriptome-wide mapping of both binding sites of 3' end processing factors CPSF-160, CPSF-100, CPSF-73, CPSF-30, Fip1, CstF-64, CstF-64τ, CF I(m)25, CF I(m)59, and CF I(m)68 and 3' end processing sites in HEK293 cells. We found that although binding sites of these factors generally cluster around the poly(A) sites most frequently used in cleavage, CstF-64/CstF-64τ and CFI(m) proteins have much higher positional specificity compared to CPSF components. Knockdown of CF I(m)68 induced a systematic use of proximal polyadenylation sites, indicating that changes in relative abundance of a single 3' end processing factor can modulate the length of 3' untranslated regions across the transcriptome and suggesting a mechanism behind the previously observed increase in tumor cell invasiveness upon CF I(m)68 knockdown.

Characterization of Cleavage Events in the Multifunctional Cilium Adhesin Mhp684 (P146) Reveals a Mechanism by Which Mycoplasma hyopneumoniae Regulates Surface Topography

ABSTRACT Mycoplasma hyopneumoniae causes enormous economic losses to swine production worldwide by colonizing the ciliated epithelium in the porcine respiratory tract, resulting in widespread damage to the mucociliary escalator, prolonged inflammation, reduced weight gain, and secondary infections. Protein Mhp684 (P146) comprises 1,317 amino acids, and while the N-terminal 400 residues display significant sequence identity to the archetype cilium adhesin P97, the remainder of the molecule is novel and displays unusual motifs. Proteome analysis shows that P146 preprotein is endogenously cleaved into three major fragments identified here as P50P146, P40P146, and P85P146 that reside on the cell surface. Liquid chromatography with tandem mass spectrometry (LC-MS/MS) identified a semitryptic peptide that delineated a major cleavage site in Mhp684. Cleavage occurred at the phenylalanine residue within sequence 672ATEF↓QQ677, consistent with a cleavage motif resembling S/T-X-F↓X-D/E recently identified in Mhp683 and other P97/P102 family members. Biotinylated surface proteins recovered by avidin chromatography and separated by two-dimensional gel electrophoresis (2-D GE) showed that more-extensive endoproteolytic cleavage of P146 occurs. Recombinant fragments F1P146-F3P146 that mimic P50P146, P40P146, and P85P146 were constructed and shown to bind porcine epithelial cilia and biotinylated heparin with physiologically relevant affinity. Recombinant versions of F3P146 generated from M. hyopneumoniae strain J and 232 sequences strongly bind porcine plasminogen, and the removal of their respective C-terminal lysine and arginine residues significantly reduces this interaction. These data reveal that P146 is an extensively processed, multifunctional adhesin of M. hyopneumoniae. Extensive cleavage coupled with variable cleavage efficiency provides a mechanism by which M. hyopneumoniae regulates protein topography.

Metabolism of peptide reporters in cell lysates and single cells.

The stability of an Abl kinase substrate peptide in a cytosolic lysate and in single cells was characterized. In the cytosolic lysate, the starting peptide was metabolized at an average initial rate of 1.7 ± 0.3 zmol pg(-1) s(-1) with a t(1/2) of 1.3 min. Five different fragments formed over time; however, a dominant cleavage site was identified. Multiple rational design cycles were utilized to develop a lead peptide with a phenylalanine and alanine replaced by an (N-methyl)phenylalanine and isoleucine, respectively, to attain cytosolic peptidase resistance while maintaining Abl substrate efficacy. This lead peptide possessed a 15-fold greater lifetime in the cytosolic lysate while attaining a 7-fold improvement in k(cat) as an Abl kinase substrate compared to the starting peptide. However, when loaded into single cells, the starting peptide and lead peptide possessed nearly identical degradation rates and an altered pattern of fragmentation relative to that in cell lysates. Preferential accumulation of a fragment with cleavage at an Ala-Ala bond in single cells suggested that dissimilar peptidases act on the peptides in the lysate versus single cells. A design strategy for peptide stabilization, analogous to that demonstrated for the lysate, should be effective for stabilization in single cells.

The use of strong anion‐exchange (SAX) magnetic particles for the extraction of therapeutic siRNA and their analysis by liquid chromatography/mass spectrometry

Traditional methods for extracting oligonucleotides from serum and other biological fluids are often time-consuming and require multiple steps. Magnetic particle based separation of oligonucleotides has gained importance recently due to the advantages of simplicity and high efficiency. Here we report the development and optimization of commercially available strong anion-exchange (SAX) magnetic beads for the extraction of siRNA from human serum. The beads allowed for rapid extraction of siRNA from human serum in 100-200 μL of liquid chromatography/mass spectrometry (LC/MS)-compatible buffer in less than 1 h for a 96-well plate with no further drying steps. Due to the strong cation-binding properties of oligonucleotides, volatile ammonium salts such as triethylammonium bicarbonate (TEAB), ammonium bicarbonate, and NH(4) Cl were used to elute the siRNA from the beads. For more hydrophobic siRNA sequences, the addition of 5-10% organic solvent was required for elution. The recovery of chemically modified siRNA from human serum was around 80% for two types of beads examined; however, the recovery for highly modified sequences differed greatly between the two types of beads. In addition to extracting highly modified oligonucleotides, the SAX beads were also able to extract liposomal formulated siRNAs from serum with no interference from the lipid formulation. The extraction of siRNA from human serum was linear over the tested range of 50 ng/mL to 10 µg/mL. Using this extraction methodology, we have created a workflow to monitor siRNA serum stability by LC/MS. Initial observations confirm that RNase A type degradation with strand cleavage on the 3' side of uridine or cytosine is the dominant cleavage pattern in serum. This finding has implications for the selection and modification of therapeutic siRNAs and demonstrates the utility of magnetic beads as a simple and rapid extraction technique for siRNA.